--- /dev/null
+Server-side components of Arvados contained in the apps/ and services/
+directories, including the API Server, Workbench, and Crunch, are licenced
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+The Arvados client Software Development Kits contained in the sdk/ directory,
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+Aravados documentation are licensed under the Apache License, Version 2.0 (see
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+
+The Arvados Documentation located in the doc/ directory is licensed under the
+Creative Commons Attribution-Share Alike 3.0 United States (see by-sa-3.0.txt)
\ No newline at end of file
--- /dev/null
+
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--- /dev/null
+Welcome to Arvados!
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--- /dev/null
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+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+ You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+ In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+ If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+
+ Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
/config/environments/development.rb
/config/environments/test.rb
/config/environments/production.rb
+/config/application.yml
/config/piwik.yml
# gem 'capistrano'
# To use debugger
-# gem 'debugger'
+#gem 'byebug'
gem 'rvm-capistrano', :group => :test
gem 'piwik_analytics'
gem 'httpclient'
gem 'themes_for_rails'
+gem "deep_merge", :require => 'deep_merge/rails_compat'
\ No newline at end of file
coffee-script-source (1.6.3)
commonjs (0.2.7)
daemon_controller (1.1.7)
+ deep_merge (1.0.1)
erubis (2.7.0)
execjs (2.0.2)
highline (1.6.20)
bootstrap-sass (~> 3.1.0)
bootstrap-x-editable-rails
coffee-rails (~> 3.2.0)
+ deep_merge
httpclient
jquery-rails
less
}
targets.fadeToggle(200);
});
+
$(document).
on('ajax:send', function(e, xhr) {
$('.loading').fadeTo('fast', 1);
fixer.duplicateTheadTr();
fixer.fixThead();
});
-})(jQuery);
+});
$.fn.editable.defaults.ajaxOptions = {type: 'put', dataType: 'json'};
$.fn.editable.defaults.send = 'always';
+
+// Default for editing is popup. I experimented with inline which is a little
+// nicer in that it shows up right under the mouse instead of nearby. However,
+// the inline box is taller than the regular content, which causes the page
+// layout to shift unless we make the table rows tall, which leaves a lot of
+// wasted space when not editing. Also inline can get cut off if the page is
+// too narrow, when the popup box will just move to do the right thing.
+//$.fn.editable.defaults.mode = 'inline';
+
$.fn.editable.defaults.params = function (params) {
var a = {};
var key = params.pk.key;
a[key] = {};
a[key][params.name] = params.value;
return a;
-};
\ No newline at end of file
+};
+
+$.fn.editable.defaults.validate = function (value) {
+ if (value == "***invalid***") {
+ return "Invalid selection";
+ }
+}
--- /dev/null
+
+(function() {
+ var run_pipeline_button_state = function() {
+ var a = $('a.editable.required.editable-empty');
+ if (a.length > 0) {
+ $("#run-pipeline-button").addClass("disabled");
+ }
+ else {
+ $("#run-pipeline-button").removeClass("disabled");
+ }
+ }
+
+ $.fn.editable.defaults.success = function (response, newValue) {
+ var tag = $(this);
+ if (tag.hasClass("required")) {
+ if (newValue && newValue.trim() != "") {
+ tag.removeClass("editable-empty");
+ tag.parent().css("background-color", "");
+ tag.parent().prev().css("background-color", "");
+ }
+ else {
+ tag.addClass("editable-empty");
+ tag.parent().css("background-color", "#ffdddd");
+ tag.parent().prev().css("background-color", "#ffdddd");
+ }
+ }
+ run_pipeline_button_state();
+ }
+
+ $(window).on('load', function() {
+ var a = $('a.editable.required');
+ for (var i = 0; i < a.length; i++) {
+ var tag = $(a[i]);
+ if (tag.hasClass("editable-empty")) {
+ tag.parent().css("background-color", "#ffdddd");
+ tag.parent().prev().css("background-color", "#ffdddd");
+ }
+ else {
+ tag.parent().css("background-color", "");
+ tag.parent().prev().css("background-color", "");
+ }
+ }
+ run_pipeline_button_state();
+ } );
+
+})();
+++ /dev/null
-# Place all the behaviors and hooks related to the matching controller here.
-# All this logic will automatically be available in application.js.
-# You can use CoffeeScript in this file: http://jashkenas.github.com/coffee-script/
--- /dev/null
+//= require jquery
+//= require jquery_ujs
+
+/** Javascript for local persistent selection. */
+
+get_selection_list = null;
+form_selection_sources = {};
+
+jQuery(function($){
+ var storage = localStorage; // sessionStorage
+
+ get_selection_list = function() {
+ if (!storage.persistentSelection) {
+ storage.persistentSelection = JSON.stringify([]);
+ }
+ return JSON.parse(storage.persistentSelection);
+ }
+
+ var put_storage = function(lst) {
+ storage.persistentSelection = JSON.stringify(lst);
+ }
+
+ var add_selection = function(uuid, name, href, type) {
+ var lst = get_selection_list();
+ lst.push({"uuid": uuid, "name": name, "href": href, "type": type});
+ put_storage(lst);
+ update_count();
+ };
+
+ var remove_selection = function(uuid) {
+ var lst = get_selection_list();
+ for (var i = 0; i < lst.length; i++) {
+ if (lst[i].uuid == uuid) {
+ lst.splice(i, 1);
+ i--;
+ }
+ }
+ put_storage(lst);
+ update_count();
+ };
+
+ var remove_selection_click = function(e) {
+ remove_selection($(this).val());
+ };
+
+ var clear_selections = function() {
+ put_storage([]);
+ update_count();
+ }
+
+ var update_count = function(e) {
+ var lst = get_selection_list();
+ $("#persistent-selection-count").text(lst.length);
+ if (lst.length > 0) {
+ $('#selection-form-content').html(
+ '<li><a href="#" id="clear_selections_button">Clear selections</a></li>'
+ + '<li><input type="submit" name="combine_selected_files_into_collection" '
+ + ' id="combine_selected_files_into_collection" '
+ + ' value="Combine selected collections and files into a new collection" /></li>'
+ + '<li class="notification"><table style="width: 100%"></table></li>');
+
+ for (var i = 0; i < lst.length; i++) {
+ $('#selection-form-content > li > table').append("<tr>"
+ + "<td>"
+ + "<input class='remove-selection' name='selection[]' type='checkbox' value='" + lst[i].uuid + "' checked='true' data-stoppropagation='true' />"
+ + "</td>"
+
+ + "<td>"
+ + "<div style='padding-left: 1em'><a href=\"" + lst[i].href + "\">" + lst[i].name + "</a></div>"
+ + "</td>"
+
+ + "<td style=\"vertical-align: top\">"
+ + "<span style=\"padding-right: 1em\">" + lst[i].type + "</span>"
+ + "</td>"
+
+ + "</tr>");
+ }
+ } else {
+ $('#selection-form-content').html("<li class='notification empty'>No selections.</li>");
+ }
+
+ var checkboxes = $('.persistent-selection:checkbox');
+ for (i = 0; i < checkboxes.length; i++) {
+ for (var j = 0; j < lst.length; j++) {
+ if (lst[j].uuid == $(checkboxes[i]).val()) {
+ checkboxes[i].checked = true;
+ break;
+ }
+ }
+ if (j == lst.length) {
+ checkboxes[i].checked = false;
+ }
+ }
+
+ $('.remove-selection').on('click', remove_selection_click);
+ $('#clear_selections_button').on('click', clear_selections);
+ };
+
+ $(document).
+ on('change', '.persistent-selection:checkbox', function(e) {
+ //console.log($(this));
+ //console.log($(this).val());
+
+ var inc = 0;
+ if ($(this).is(":checked")) {
+ add_selection($(this).val(), $(this).attr('friendly_name'), $(this).attr('href'), $(this).attr('friendly_type'));
+ }
+ else {
+ remove_selection($(this).val());
+ }
+ });
+
+
+ $(window).on('load storage', update_count);
+
+ $('#selection-form-content').on("click", function(e) {
+ e.stopPropagation();
+ });
+});
+
+add_form_selection_sources = null;
+select_form_sources = null;
+
+(function() {
+ var form_selection_sources = {};
+ add_form_selection_sources = function (src) {
+ for (var i = 0; i < src.length; i++) {
+ var t = form_selection_sources[src[i].type];
+ if (!t) {
+ t = form_selection_sources[src[i].type] = {};
+ }
+ if (!t[src[i].uuid]) {
+ t[src[i].uuid] = src[i];
+ }
+ }
+ };
+
+ select_form_sources = function(type) {
+ var ret = [];
+
+ if (get_selection_list) {
+ var lst = get_selection_list();
+ if (lst.length > 0) {
+ var text = "― Selections ―";
+ var span = document.createElement('span');
+ span.innerHTML = text;
+ ret.push({text: span.innerHTML, value: "***invalid***"});
+
+ for (var i = 0; i < lst.length; i++) {
+ if (lst[i].type == type) {
+ ret.push({text: lst[i].name, value: lst[i].uuid})
+ }
+ }
+ }
+ }
+
+ var text = "― Recent ―";
+ var span = document.createElement('span');
+ span.innerHTML = text;
+ ret.push({text: span.innerHTML, value: "***invalid***"});
+
+ var t = form_selection_sources[type];
+ for (var key in t) {
+ if (t.hasOwnProperty(key)) {
+ var obj = t[key];
+ ret.push({text: obj.name, value: obj.uuid})
+ }
+ }
+ return ret;
+ };
+})();
+
}
function smart_scroll_fixup(s) {
- console.log(s);
+ //console.log(s);
if (s != null && s.type == 'shown.bs.tab') {
s = [s.target];
}
else {
s = $(".smart-scroll");
}
- console.log(s);
+ //console.log(s);
for (var i = 0; i < s.length; i++) {
a = s[i];
var h = window.innerHeight - a.getBoundingClientRect().top - 20;
}
.inline-progress-container {
- width: 100px;
+ width: 100%;
display:inline-block;
}
position:relative;
top:1.5em;
}
+
+/* Setting the height needs to be fixed with javascript. */
+.dropdown-menu {
+ padding-right: 20px;
+ max-height: 440px;
+ width: 400px;
+ overflow-y: auto;
+}
+
// Place all the styles related to the PipelineTemplates controller here.
// They will automatically be included in application.css.
// You can use Sass (SCSS) here: http://sass-lang.com/
+
+.pipeline_color_legend {
+ padding-left: 1em;
+ padding-right: 1em;
+}
+
+table.pipeline-components-table {
+ width: 100%;
+ table-layout: fixed;
+ overflow: hidden;
+}
+
+table.pipeline-components-table thead th {
+ text-align: bottom;
+}
+table.pipeline-components-table div.progress {
+ margin-bottom: 0;
+}
+
+table.pipeline-components-table td {
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+td.required {
+ background: #ffdddd;
+}
--- /dev/null
+#persistent-selection-list {
+ width: 500px;
+}
+
+#selection-form-content > li > a, #selection-form-content > li > input {
+ display: block;
+ padding: 3px 20px;
+ clear: both;
+ font-weight: normal;
+ line-height: 1.42857;
+ color: rgb(51, 51, 51);
+ white-space: nowrap;
+ border: none;
+ background: transparent;
+ width: 100%;
+ text-align: left;
+}
+
+#selection-form-content li table tr {
+ padding: 3px 20px;
+ line-height: 1.42857;
+ border-top: 1px solid rgb(221, 221, 221);
+}
+
+#selection-form-content a:hover, #selection-form-content a:focus, #selection-form-content input:hover, #selection-form-content input:focus, #selection-form-content tr:hover {
+ text-decoration: none;
+ color: rgb(38, 38, 38);
+ background-color: whitesmoke;
+}
\ No newline at end of file
--- /dev/null
+class ActionsController < ApplicationController
+
+ skip_before_filter :find_object_by_uuid, only: :post
+
+ def combine_selected_files_into_collection
+ lst = []
+ files = []
+ params["selection"].each do |s|
+ m = CollectionsHelper.match(s)
+ if m and m[1] and m[2]
+ lst.append(m[1] + m[2])
+ files.append(m)
+ end
+ end
+
+ collections = Collection.where(uuid: lst)
+
+ chash = {}
+ collections.each do |c|
+ c.reload()
+ chash[c.uuid] = c
+ end
+
+ combined = ""
+ files.each do |m|
+ mt = chash[m[1]+m[2]].manifest_text
+ if m[4]
+ IO.popen(['arv-normalize', '--extract', m[4][1..-1]], 'w+b') do |io|
+ io.write mt
+ io.close_write
+ while buf = io.read(2**20)
+ combined += buf
+ end
+ end
+ else
+ combined += chash[m[1]+m[2]].manifest_text
+ end
+ end
+
+ normalized = ''
+ IO.popen(['arv-normalize'], 'w+b') do |io|
+ io.write combined
+ io.close_write
+ while buf = io.read(2**20)
+ normalized += buf
+ end
+ end
+
+ require 'digest/md5'
+
+ d = Digest::MD5.new()
+ d << normalized
+ newuuid = "#{d.hexdigest}+#{normalized.length}"
+
+ env = Hash[ENV].
+ merge({
+ 'ARVADOS_API_HOST' =>
+ $arvados_api_client.arvados_v1_base.
+ sub(/\/arvados\/v1/, '').
+ sub(/^https?:\/\//, ''),
+ 'ARVADOS_API_TOKEN' => Thread.current[:arvados_api_token],
+ 'ARVADOS_API_HOST_INSECURE' =>
+ Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+ })
+
+ IO.popen([env, 'arv-put', '--raw'], 'w+b') do |io|
+ io.write normalized
+ io.close_write
+ while buf = io.read(2**20)
+
+ end
+ end
+
+ newc = Collection.new({:uuid => newuuid, :manifest_text => normalized})
+ newc.save!
+
+ chash.each do |k,v|
+ l = Link.new({
+ tail_kind: "arvados#collection",
+ tail_uuid: k,
+ head_kind: "arvados#collection",
+ head_uuid: newuuid,
+ link_class: "provenance",
+ name: "provided"
+ })
+ l.save!
+ end
+
+ redirect_to controller: 'collections', action: :show, id: newc.uuid
+ end
+
+ def post
+ if params["combine_selected_files_into_collection"]
+ combine_selected_files_into_collection
+ else
+ redirect_to :back
+ end
+ end
+end
def unprocessable(message=nil)
@errors ||= []
+
@errors << message if message
render_error status: 422
end
def create
@object ||= model_class.new params[model_class.to_s.underscore.singularize]
@object.save!
+
respond_to do |f|
f.json { render json: @object }
f.html {
}
}
- @@notification_tests.push lambda { |controller, current_user|
- Job.limit(1).where(created_by: current_user.uuid).each do
- return nil
- end
- return lambda { |view|
- view.render partial: 'notifications/jobs_notification'
- }
- }
+ #@@notification_tests.push lambda { |controller, current_user|
+ # Job.limit(1).where(created_by: current_user.uuid).each do
+ # return nil
+ # end
+ # return lambda { |view|
+ # view.render partial: 'notifications/jobs_notification'
+ # }
+ #}
@@notification_tests.push lambda { |controller, current_user|
Collection.limit(1).where(created_by: current_user.uuid).each do
end
Collection.where(uuid: @object.uuid).each do |u|
- @prov_svg = ProvenanceHelper::create_provenance_graph u.provenance, "provenance_svg", {:direction => :top_down, :combine_jobs => :script_only} rescue nil
- @used_by_svg = ProvenanceHelper::create_provenance_graph u.used_by, "used_by_svg", {:direction => :top_down, :combine_jobs => :script_only, :pdata_only => true} rescue nil
+ puts request
+ @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :bottom_up,
+ :combine_jobs => :script_only}) rescue nil
+ @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
end
end
nodes << c
end
- @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {:all_script_parameters => true, :script_version_nodes => true}
+ @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {
+ :request => request,
+ :all_script_parameters => true,
+ :script_version_nodes => true}
end
def index
class KeepDisksController < ApplicationController
+ def create
+ defaults = { is_readable: true, is_writable: true }
+ @object = KeepDisk.new defaults.merge(params[:keep_disk] || {})
+ super
+ end
end
end
def show
+ if @object.components.empty? and @object.pipeline_template_uuid
+ template = PipelineTemplate.find(@object.pipeline_template_uuid)
+ pipeline = {}
+ template.components.each do |component_name, component_props|
+ pipeline[component_name] = {}
+ component_props.each do |k, v|
+ if k == :script_parameters
+ pipeline[component_name][:script_parameters] = {}
+ v.each do |param_name, param_value|
+ if param_value.is_a? Hash
+ if param_value[:value]
+ pipeline[component_name][:script_parameters][param_name] = param_value[:value]
+ elsif param_value[:default]
+ pipeline[component_name][:script_parameters][param_name] = param_value[:default]
+ elsif param_value[:optional] != nil or param_value[:required] != nil or param_value[:dataclass] != nil
+ pipeline[component_name][:script_parameters][param_name] = ""
+ else
+ pipeline[component_name][:script_parameters][param_name] = param_value
+ end
+ else
+ pipeline[component_name][:script_parameters][param_name] = param_value
+ end
+ end
+ else
+ pipeline[component_name][k] = v
+ end
+ end
+ end
+ @object.components= pipeline
+ @object.save
+ end
+
@pipelines = [@object]
if params[:compare]
provenance, pips = graph(@pipelines)
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
:script_version_nodes => true,
@pipelines = @objects
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
:script_version_nodes => true,
%w(Compare Graph)
end
+ def update
+ updates = params[@object.class.to_s.underscore.singularize.to_sym]
+ if updates["components"]
+ require 'deep_merge/rails_compat'
+ updates["components"] = updates["components"].deeper_merge(@object.components)
+ end
+ super
+ end
+
+ def index
+ @objects ||= model_class.limit(20).all
+ super
+ end
+
protected
def for_comparison v
if v.is_a? Hash or v.is_a? Array
class PipelineTemplatesController < ApplicationController
+
+ def show
+ @objects = []
+ PipelineInstance.where(pipeline_template_uuid: @object.uuid).each do |pipeline|
+ @objects.push(pipeline)
+ end
+ super
+ end
+
+ def show_pane_list
+ %w(Components Pipelines Attributes Metadata JSON API)
+ end
+
end
class UsersController < ApplicationController
skip_before_filter :find_object_by_uuid, :only => [:welcome, :activity]
skip_around_filter :thread_with_mandatory_api_token, :only => :welcome
+ before_filter :ensure_current_user_is_admin, only: :sudo
def welcome
if current_user
end
end
+ def show_pane_list
+ if current_user.andand.is_admin
+ super | %w(Admin)
+ else
+ super
+ end
+ end
+
+ def sudo
+ resp = $arvados_api_client.api(ApiClientAuthorization, '', {
+ api_client_authorization: {
+ owner_uuid: @object.uuid
+ }
+ })
+ redirect_to root_url(api_token: resp[:api_token])
+ end
+
def home
@showallalerts = false
@my_ssh_keys = AuthorizedKey.where(authorized_user_uuid: current_user.uuid)
controller.current_user
end
+ def self.match_uuid(uuid)
+ /^([0-9a-z]{5})-([0-9a-z]{5})-([0-9a-z]{15})$/.match(uuid.to_s)
+ end
+
def current_api_host
Rails.configuration.arvados_v1_base.gsub /https?:\/\/|\/arvados\/v1/,''
end
end
end
style_opts[:class] = (style_opts[:class] || '') + ' nowrap'
- link_to link_name, { controller: resource_class.to_s.underscore.pluralize, action: 'show', id: link_uuid }, style_opts
+ link_to link_name, { controller: resource_class.to_s.tableize, action: 'show', id: link_uuid }, style_opts
else
attrvalue
end
:class => "editable"
}.merge(htmloptions)
end
+
+ def render_editable_subattribute(object, attr, subattr, template, htmloptions={})
+ if object
+ attrvalue = object.send(attr)
+ subattr.each do |k|
+ if attrvalue and attrvalue.is_a? Hash
+ attrvalue = attrvalue[k]
+ else
+ break
+ end
+ end
+ end
+
+ datatype = nil
+ required = true
+ if template
+ #puts "Template is #{template.class} #{template.is_a? Hash} #{template}"
+ if template.is_a? Hash
+ if template[:output_of]
+ return raw("<span class='label label-default'>#{template[:output_of]}</span>")
+ end
+ if template[:dataclass]
+ dataclass = template[:dataclass]
+ end
+ if template[:optional] != nil
+ required = (template[:optional] != "true")
+ end
+ if template[:required] != nil
+ required = template[:required]
+ end
+ end
+ end
+
+ rsc = template
+ if template.is_a? Hash
+ if template[:value]
+ rsc = template[:value]
+ elsif template[:default]
+ rsc = template[:default]
+ end
+ end
+
+ return link_to_if_arvados_object(rsc) if !object
+ return link_to_if_arvados_object(attrvalue) if !object.attribute_editable? attr
+
+ if dataclass
+ begin
+ dataclass = dataclass.constantize
+ rescue NameError
+ end
+ else
+ dataclass = ArvadosBase.resource_class_for_uuid(rsc)
+ end
+
+ if dataclass && dataclass.is_a?(Class)
+ datatype = 'select'
+ elsif dataclass == 'number'
+ datatype = 'number'
+ else
+ if template.is_a? Array
+ # ?!?
+ elsif template.is_a? String
+ if /^\d+$/.match(template)
+ datatype = 'number'
+ else
+ datatype = 'text'
+ end
+ end
+ end
+
+ id = "#{object.uuid}-#{subattr.join('-')}"
+ dn = "[#{attr}]"
+ subattr.each do |a|
+ dn += "[#{a}]"
+ end
+
+ if attrvalue.is_a? String
+ attrvalue = attrvalue.strip
+ end
+
+ if dataclass and dataclass.is_a? Class
+ items = []
+ if attrvalue and !attrvalue.empty?
+ items.append({name: attrvalue, uuid: attrvalue, type: dataclass.to_s})
+ end
+ #dataclass.where(uuid: attrvalue).each do |item|
+ # items.append({name: item.uuid, uuid: item.uuid, type: dataclass.to_s})
+ #end
+ dataclass.limit(10).each do |item|
+ items.append({name: item.uuid, uuid: item.uuid, type: dataclass.to_s})
+ end
+ end
+
+ lt = link_to attrvalue, '#', {
+ "data-emptytext" => "none",
+ "data-placement" => "bottom",
+ "data-type" => datatype,
+ "data-url" => url_for(action: "update", id: object.uuid, controller: object.class.to_s.pluralize.underscore),
+ "data-title" => "Set value for #{subattr[-1].to_s}",
+ "data-name" => dn,
+ "data-pk" => "{id: \"#{object.uuid}\", key: \"#{object.class.to_s.underscore}\"}",
+ "data-showbuttons" => "false",
+ "data-value" => attrvalue,
+ :class => "editable #{'required' if required}",
+ :id => id
+ }.merge(htmloptions)
+
+ lt += raw("\n<script>")
+
+ if items and items.length > 0
+ lt += raw("add_form_selection_sources(#{items.to_json});\n")
+ end
+
+ lt += raw("$('##{id}').editable({source: function() { return select_form_sources('#{dataclass}'); } });\n")
+
+ lt += raw("</script>")
+
+ lt
+ end
end
{source: x.tail_uuid, target: x.head_uuid, type: x.name}
end
end
+
+ def self.match(uuid)
+ /^([a-f0-9]{32})(\+[0-9]+)?(\+.*?)?(\/.*)?$/.match(uuid.to_s)
+ end
end
module PipelineInstancesHelper
- def pipeline_summary object=nil
- object ||= @object
- ret = {todo:0, running:0, queued:0, done:0, failed:0, total:0}
- object.components.values.each do |c|
- ret[:total] += 1
- case
- when !c[:job]
- ret[:todo] += 1
- when c[:job][:success]
- ret[:done] += 1
- when c[:job][:failed]
- ret[:failed] += 1
- when c[:job][:finished_at]
- ret[:running] += 1 # XXX finished but !success and !failed??
- when c[:job][:started_at]
- ret[:running] += 1
- else
- ret[:queued] += 1
- end
- end
- ret.merge! Hash[ret.collect do |k,v|
- [('percent_' + k.to_s).to_sym,
- ret[:total]<1 ? 0 : (100.0*v/ret[:total]).floor]
- end]
- ret
- end
def pipeline_jobs object=nil
object ||= @object
end
def render_pipeline_job pj
- if pj[:percent_done]
- pj[:progress_bar] = raw("<div class=\"progress\" style=\"width:100px\"><span class=\"progress-bar progress-bar-success\" style=\"width:#{pj[:percent_done]}%\"></span><span class=\"progress-bar\" style=\"width:#{pj[:percent_running]}%\"></span></div>")
- elsif pj[:progress]
- raw("<div class=\"progress\" style=\"width:100px\"><span class=\"progress-bar\" style=\"width:#{pj[:progress]*100}%\"></span></div>")
- end
+ pj[:progress_bar] = render partial: 'job_progress', locals: {:j => pj[:job]}
pj[:output_link] = link_to_if_arvados_object pj[:output]
pj[:job_link] = link_to_if_arvados_object pj[:job][:uuid]
pj
end
+
protected
def pipeline_jobs_newschool object
ret = []
i = -1
- object.components.each do |cname, c|
+
+ comp = []
+
+ template = PipelineTemplate.find(@object.pipeline_template_uuid) rescue nil
+ if template
+ order = PipelineTemplatesHelper::sort_components(template.components)
+ order.each do |k|
+ if object.components[k]
+ comp.push([k, object.components[k]])
+ end
+ end
+ else
+ object.components.each do |k, v|
+ comp.push([k, v])
+ end
+ end
+
+ comp.each do |cname, c|
+ puts cname, c
i += 1
pj = {index: i, name: cname}
pj[:job] = c[:job].is_a?(Hash) ? c[:job] : {}
+require 'tsort'
+
+class Hash
+ include TSort
+ def tsort_each_node(&block)
+ keys.sort.each(&block)
+ end
+
+ def tsort_each_child(node)
+ if self[node]
+ self[node][:script_parameters].sort.map do |k, v|
+ if v.is_a? Hash and v[:output_of]
+ yield v[:output_of].to_sym
+ end
+ end
+ end
+ end
+end
+
module PipelineTemplatesHelper
+ def self.sort_components(components)
+ components.tsort
+ end
end
@visited = {}
@jobs = {}
end
-
+
def self.collection_uuid(uuid)
- m = /^([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?$/.match(uuid.to_s)
+ m = CollectionsHelper.match(uuid)
if m
- #if m[2]
- return m[1]
- #else
+ if m[2]
+ return m[1]+m[2]
+ else
+ return m[1]
+ end
# Collection.where(uuid: ['contains', m[1]]).each do |u|
# puts "fixup #{uuid} to #{u.uuid}"
# return u.uuid
end
end
+ def url_for u
+ p = { :host => @opts[:request].host,
+ :port => @opts[:request].port,
+ :protocol => @opts[:request].protocol }
+ p.merge! u
+ Rails.application.routes.url_helpers.url_for (p)
+ end
+
def determine_fillcolor(n)
fillcolor = %w(aaaaaa aaffaa aaaaff aaaaaa ffaaaa)[n || 0] || 'aaaaaa'
"style=filled,fillcolor=\"##{fillcolor}\""
end
def describe_node(uuid)
+ uuid = uuid.to_sym
bgcolor = determine_fillcolor @opts[:pips][uuid] if @opts[:pips]
rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
if rsc
- href = "/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}"
+ href = url_for ({:controller => rsc.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s })
#"\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{href}\"];\n"
if rsc == Collection
#puts "empty!"
return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
end
+ puts "#{uuid.class} #{@pdata[uuid]}"
if @pdata[uuid]
#puts @pdata[uuid]
if @pdata[uuid][:name]
return "\"#{uuid}\" [label=\"#{@pdata[uuid][:name]}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
- else
+ else
files = nil
if @pdata[uuid].respond_to? :files
files = @pdata[uuid].files
if i < files.length
label += "\\n⋮"
end
+ #puts "#{uuid} #{label} #{files}"
return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
end
end
end
- return "\"#{uuid}\" [label=\"#{rsc}\",href=\"#{href}\",#{bgcolor}];\n"
end
+ return "\"#{uuid}\" [label=\"#{rsc}\",href=\"#{href}\",#{bgcolor}];\n"
end
"\"#{uuid}\" [#{bgcolor}];\n"
end
gr = "\"#{head}\" -> \"#{tail}\""
end
if extra.length > 0
- gr += "["
+ gr += " ["
extra.each do |k, v|
gr += "#{k}=\"#{v}\","
end
gr += edge(job_uuid(job), job[:script_version], {:label => "script_version"})
end
end
+ elsif rsc == Link
+ # do nothing
else
gr += describe_node(uuid)
end
@pdata.each do |k, link|
if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
+ href = url_for ({:controller => Link.to_s.tableize,
+ :action => :show,
+ :id => link[:uuid] })
+
gr += describe_node(link[:tail_uuid])
- gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => "/links/#{link[:uuid]}"})
+ gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => href})
gr += generate_provenance_edges(link[:tail_uuid])
end
end
def describe_jobs
gr = ""
@jobs.each do |k, v|
- gr += "\"#{k}\" [href=\"/jobs?"
+ href = url_for ({:controller => Job.to_s.tableize,
+ :action => :index })
+
+ gr += "\"#{k}\" [href=\"#{href}?"
n = 0
v.each do |u|
gr += "\",label=\""
if @opts[:combine_jobs] == :script_only
- gr += uuid = "#{v[0][:script]}"
+ gr += "#{v[0][:script]}"
elsif @opts[:combine_jobs] == :script_and_version
- gr += uuid = "#{v[0][:script]}"
+ gr += "#{v[0][:script]}" # Just show the name but the nodes will be distinct
else
- gr += uuid = "#{v[0][:script]}\\n#{v[0][:finished_at]}"
+ gr += "#{v[0][:script]}\\n#{v[0][:finished_at]}"
end
gr += "\",#{determine_fillcolor n}];\n"
end
gr += "}"
svg = ""
- #puts gr
-
+ puts gr
+
require 'open3'
Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
attr_reader :kind
@columns
end
+
def self.column(name, sql_type = nil, default = nil, null = true)
ActiveRecord::ConnectionAdapters::Column.new(name.to_s, default, sql_type.to_s, null)
end
+
def self.attribute_info
self.columns
@attribute_info
end
+
def self.find(uuid, opts={})
if uuid.class != String or uuid.length < 27 then
raise 'argument to find() must be a uuid string. Acceptable formats: warehouse locator or string with format xxxxx-xxxxx-xxxxxxxxxxxxxxx'
end
new.private_reload(hash)
end
+
def self.order(*args)
ArvadosResourceList.new(self).order(*args)
end
+
def self.filter(*args)
ArvadosResourceList.new(self).filter(*args)
end
+
def self.where(*args)
ArvadosResourceList.new(self).where(*args)
end
+
def self.limit(*args)
ArvadosResourceList.new(self).limit(*args)
end
+
def self.eager(*args)
ArvadosResourceList.new(self).eager(*args)
end
+
def self.all(*args)
ArvadosResourceList.new(self).all(*args)
end
+
def save
obdata = {}
self.class.columns.each do |col|
end
end
+ @new_record = false
+
self
end
+
def save!
self.save or raise Exception.new("Save failed")
end
@links = $arvados_api_client.api Link, '', { _method: 'GET', where: o, eager: true }
@links = $arvados_api_client.unpack_api_response(@links)
end
+
def all_links
return @all_links if @all_links
res = $arvados_api_client.api Link, '', {
}
@all_links = $arvados_api_client.unpack_api_response(res)
end
+
def reload
private_reload(self.uuid)
end
+
def private_reload(uuid_or_hash)
raise "No such object" if !uuid_or_hash
if uuid_or_hash.is_a? Hash
end
end
@all_links = nil
+ @new_record = false
self
end
+
+ def to_param
+ uuid
+ end
+
def dup
super.forget_uuid!
end
(name if self.respond_to? :name) || uuid
end
+ def selection_label
+ friendly_link_name
+ end
+
protected
def forget_uuid!
class Collection < ArvadosBase
+
def total_bytes
if files
tot = 0
def used_by
$arvados_api_client.api "collections/#{self.uuid}/", "used_by"
end
+
end
end
end
end
-
+
def attribute_editable?(attr)
- attr == 'name'
+ attr.to_sym == :name || (attr.to_sym == :components and self.active == nil)
end
def attributes_for_display
<% end %>
<% content_for :js do %>
- $(window).on('load', function() {
- $('ul.nav-tabs > li > a').on('shown.bs.tab', smart_scroll_fixup);
- });
+ $(window).on('load', smart_scroll_fixup);
+ $(document).on('shown.bs.tab', 'ul.nav-tabs > li > a', smart_scroll_fixup);
<% end %>
--- /dev/null
+<% percent_total_tasks = 100 / (j[:tasks_summary][:done] + j[:tasks_summary][:running] + j[:tasks_summary][:failed] + j[:tasks_summary][:todo]) rescue 0 %>
+
+<% if defined? scaleby %>
+ <% percent_total_tasks *= scaleby %>
+<% end %>
+
+<% if not defined? scaleby %>
+ <div class="progress">
+<% end %>
+
+<span class="progress-bar progress-bar-success" style="width: <%= j[:tasks_summary][:done] * percent_total_tasks rescue 0 %>%;">
+</span>
+<span class="progress-bar progress-bar-danger" style="width: <%= j[:tasks_summary][:failed] * percent_total_tasks rescue 0 %>%;">
+</span>
+<span class="progress-bar" style="width: <%= j[:tasks_summary][:running] * percent_total_tasks rescue 0 %>%;">
+</span>
+
+<% if not defined? scaleby %>
+</div>
+<% end %>
--- /dev/null
+<% if j[:success] %>
+ <span class="label label-success"><%= if defined? title then title else 'success' end %></span>
+<% elsif j[:success] == false %>
+ <span class="label label-danger"><%= if defined? title then title else 'failed' end %></span>
+<% elsif j[:finished_at] %>
+ <span class="label label-default"><%= if defined? title then title else 'finished' end %></span>
+<% elsif j[:started_at] %>
+ <span class="label label-info"><%= if defined? title then title else 'running' end %></span>
+<% else %>
+ <span class="label label-default"><%= if defined? title then title else 'not running' end %></span>
+<% end %>
--- /dev/null
+<% component_frac = 1.0 / p.components.length %>
+<div class="progress">
+ <% p.components.each do |k,c| %>
+ <% if c[:job] %>
+ <%= render partial: "job_progress", locals: {:j => c[:job], :scaleby => component_frac } %>
+ <% end %>
+ <% end %>
+</div>
--- /dev/null
+<% if p.success %>
+ <span class="label label-success">finished</span>
+<% elsif p.success == false %>
+ <span class="label label-danger">failed</span>
+<% elsif p.active %>
+ <span class="label label-info">running</span>
+<% else %>
+ <% if (p.components.select do |k,v| v[:job] end).length == 0 %>
+ <span class="label label-default">not started</span>
+ <% else %>
+ <span class="label label-default">not running</span>
+ <% end %>
+<% end %>
--- /dev/null
+<%if object %>
+<%= check_box_tag 'uuids[]', object.uuid, false, {
+ :class => 'persistent-selection',
+ :friendly_type => object.class.name,
+ :friendly_name => object.selection_label,
+ :href => "#{url_for controller: object.class.name.tableize, action: 'show', id: object.uuid }"
+} %>
+<% end %>
<% attr_blacklist = ' created_at modified_at modified_by_user_uuid modified_by_client_uuid updated_at' %>
+<%= form_tag do |f| %>
+
<table class="table table-condensed arv-index">
<thead>
<tr>
+ <th></th>
<% @objects.first.attributes_for_display.each do |attr, attrvalue| %>
<% next if attr_blacklist.index(" "+attr) %>
<th class="arv-attr-<%= attr %>">
<tbody>
<% @objects.each do |object| %>
<tr data-object-uuid="<%= object.uuid %>">
+ <td>
+ <%= render :partial => "selection_checkbox", :locals => {:object => object} %>
+ </td>
+
<% object.attributes_for_display.each do |attr, attrvalue| %>
<% next if attr_blacklist.index(" "+attr) %>
<td class="arv-object-<%= object.class.to_s %> arv-attr-<%= attr %>">
</table>
<% end %>
+
+<% end %>
<% @collections.each do |c| %>
<tr class="collection" data-object-uuid="<%= c.uuid %>">
+ <td>
+ <%= render :partial => "selection_checkbox", :locals => {:object => c} %>
+ </td>
<td>
<%= link_to_if_arvados_object c.uuid %>
</td>
<table class="table table-condensed table-fixedlayout">
<colgroup>
+ <col width="4%" />
<col width="35%" />
<col width="40%" />
<col width="15%" />
</colgroup>
<thead>
<tr>
+ <th></th>
<th>path</th>
<th>file</th>
<th style="text-align:right">size</th>
</tr>
</thead><tbody>
<% if @object then @object.files.sort_by{|f|[f[0],f[1]]}.each do |file| %>
- <% file_path = "#{file[0]}/#{file[1]}" %>
- <tr>
- <td>
- <%= file[0] %>
- </td>
+ <% f0 = file[0] %>
+ <% f0 = '' if f0 == '.' %>
+ <% f0 = f0[2..-1] if f0[0..1] == './' %>
+ <% f0 += '/' if not f0.empty? %>
+ <% file_path = "#{f0}#{file[1]}" %>
+ <tr>
+ <td>
+ <%= check_box_tag 'uuids[]', @object.uuid+'/'+file_path, false, {
+ :class => 'persistent-selection',
+ :friendly_type => "File",
+ :friendly_name => "#{@object.uuid}/#{file_path}",
+ :href => "#{url_for controller: 'collections', action: 'show', id: @object.uuid }/#{file_path}"
+ } %>
+ </td>
+ <td>
+ <%= file[0] %>
+ </td>
- <td>
- <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %>
- </td>
+ <td>
+ <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %>
+ </td>
- <td style="text-align:right">
- <%= raw(human_readable_bytes_html(file[2])) %>
- </td>
+ <td style="text-align:right">
+ <%= raw(human_readable_bytes_html(file[2])) %>
+ </td>
- <td>
- <div style="display:inline-block">
- <%= link_to raw('<i class="glyphicon glyphicon-download-alt"></i>'), {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'attachment'}, {class: 'btn btn-info btn-sm', title: 'Download'} %>
- </div>
- </td>
- </tr>
+ <td>
+
<div style="display:inline-block">
+ <%= link_to raw('<i class="glyphicon glyphicon-download-alt"></i>'), {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'attachment'}, {class: 'btn btn-info btn-sm', title: 'Download'} %>
+ </div>
+ </td>
+ </tr>
<% end; end %>
</tbody>
</table>
<div style="padding-right: 1em">
+<%= form_tag do |f| %>
+
<table id="collections-index" class="topalign table table-condensed table-fixedlayout table-fixed-header-row">
<colgroup>
+ <col width="4%" />
<col width="10%" />
<col width="36%" />
<col width="15%" />
</colgroup>
<thead>
<tr class="contain-align-left">
+ <th></th>
<th>uuid</th>
<th>contents</th>
<th>owner</th>
<%= render partial: 'index_tbody' %>
</tbody>
</table>
+
+<% end %>
+
</div>
<% content_for :footer_js do %>
<i class="icon-plus-sign expand-collapse-row" data-id="<%= j.uuid %>" style="cursor: pointer"></i>
</td>
<td>
- <% if j.success == false %>
- <span class="badge badge-warning" title="fail">✖</span>
- <% elsif j.success %>
- <span class="badge badge-success" title="success">✔</span>
- <% elsif j.running %>
- <span class="badge badge-info" title="running">✈</span>
- <% else %>
- <span class="badge" title="queued">✉</span>
- <% end %>
+ <%= render partial: 'job_status_label', locals: {:j => j} %>
</td>
<td>
- <% if j.started_at and not j.finished_at %>
- <% percent_total_tasks = 100 / (j.tasks_summary[:running] + j.tasks_summary[:done] + j.tasks_summary[:todo]) rescue 0 %>
- <div class="progress" style="margin-bottom: 0">
- <div class="bar bar-success" style="width: <%= j.tasks_summary[:done] * percent_total_tasks rescue 0 %>%;"></div>
- <div class="bar" style="width: <%= j.tasks_summary[:running] * percent_total_tasks rescue 0 %>%; opacity: 0.3"></div>
+ <div class="inline-progress-container">
+ <%= render partial: 'job_progress', locals: {:j => j} %>
</div>
- <% end %>
</td>
<td>
<%= link_to_if_arvados_object j.uuid %>
padding-top: 1.25em;
}
- /* Setting the height needs to be fixed with javascript. */
- .dropdown-menu {
- padding-right: 20px;
- max-height: 440px;
- width: 400px;
- overflow-y: auto;
- }
-
@media (min-width: 768px) {
.left-nav {
position: fixed;
<span class="glyphicon glyphicon-arrow-right"></span>
</li>
<li>
-<%= link_to controller.breadcrumb_page_name, request.fullpath %>
+ <%= link_to controller.breadcrumb_page_name, request.fullpath %>
+ </li>
+ <li style="padding: 14px 0 14px">
+ <%= form_tag do |f| %>
+ <%= render :partial => "selection_checkbox", :locals => {:object => @object} %>
+ <% end %>
</li>
<% end %>
<% end %>
</li>
-->
- <!-- XXX placeholder for this when persistent selection is implemented
- <li class="dropdown">
+ <li class="dropdown notification-menu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">
<span class="glyphicon glyphicon-paperclip"></span>
- <span class="badge badge-alert"><%= @selection_count %></span>
+ <span class="badge" id="persistent-selection-count"></span>
<span class="caret"></span>
</a>
- <ul class="dropdown-menu" role="menu">
- <li style="padding: 10px">No selections.</li>
+ <ul class="dropdown-menu" role="menu" id="persistent-selection-list">
+ <%= form_tag '/actions' do %>
+ <div id="selection-form-content"></div>
+ <% end %>
</ul>
</li>
- -->
<% if current_user.is_active %>
<li class="dropdown notification-menu">
<p><%= image_tag "dax.png", class: "dax" %>
Hi, I noticed you haven't run a pipeline yet.
<%= link_to "Click here to learn how to run an Arvados Crunch pipeline.",
- "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-new-pipeline.html",
+ "#{Rails.configuration.arvados_docsite}/user/tutorials/tutorial-pipeline-workbench.html",
style: "font-weight: bold",
target: "_blank" %>
</p>
<% content_for :css do %>
- .pipeline_color_legend {
- padding-left: 1em;
- padding-right: 1em;
- }
-table.pipeline-components-table thead th {
- text-align: bottom;
-}
-table.pipeline-components-table div.progress {
- margin-bottom: 0;
-}
+
<% end %>
-<br />
+<% template = PipelineTemplate.find(@object.pipeline_template_uuid) rescue nil %>
+
+<%= content_for :content_top do %>
+ <% if template %>
+ <h2><%= template.name %></h2>
+ <% end %>
+<% end %>
+
+<% if @object.active != nil %>
<table class="table pipeline-components-table">
<colgroup>
- <col width="15%" />
- <col width="15%" />
- <col width="35%" />
- <col width="35%" />
+ <col style="width: 15%" />
+ <col style="width: 20%" />
+ <col style="width: 12%" />
+ <col style="width: 12%" />
+ <col style="width: 45%" />
</colgroup>
<thead>
<tr>
<th>
component
+ </th><th>
+ script, version
</th><th>
progress
<%= link_to '(refresh)', request.fullpath, class: 'refresh', remote: true, method: 'get' %>
</th><th>
- script, version
</th><th>
output
</th>
<% render_pipeline_jobs.each do |pj| %>
<tr>
<td>
+ <% job_status = render(partial: 'job_status_label',
+ locals: { :j => pj[:job], :title => pj[:name] }) %>
<% if pj[:job].andand[:uuid] %>
- <%= link_to pj[:name], job_url(id: pj[:job][:uuid]) %>
+ <%= link_to(job_status, job_url(id: pj[:job][:uuid])) %>
<% else %>
- <%= pj[:name] %>
- <% end %>
- </td><td>
- <%= pj[:progress_bar] %>
- <% if pj[:job].andand[:cancelled_at] %>
- <span class="pull-right label label-warning">cancelled</span>
- <% elsif pj[:failed] %>
- <span class="pull-right label label-warning">failed</span>
- <% elsif pj[:result] == 'queued' %>
- <span class="pull-right label">queued</span>
+ <%= job_status %>
<% end %>
</td><td>
<%= pj[:script] %>
<br /><span class="deemphasize"><%= pj[:script_version] %></span>
+ </td><td>
+ <%= pj[:progress_bar] %>
+ </td><td>
+ <%= render(partial: 'job_status_label',
+ locals: { :j => pj[:job] }) %>
</td><td>
<%= link_to_if_arvados_object pj[:output] %>
</td>
<% end %>
</tbody>
<tfoot>
- <tr><td colspan="4"></td></tr>
+ <tr><td colspan="5"></td></tr>
</tfoot>
</table>
<% if @object.active %>
<% content_for :js do %>
-setInterval(function(){$('a.refresh').click()}, 30000);
+setInterval(function(){$('a.refresh').click()}, 15000);
<% end %>
<% end %>
-<pre><%= JSON.pretty_generate @object.attributes %></pre>
+<% else %>
+
+ <p>Please set the desired input parameters for the components of this pipeline. Parameters highlighted in red are required.</p>
+
+ <% content_for :tab_line_buttons do %>
+ <%= form_tag @object, :method => :put do |f| %>
+
+ <%= hidden_field @object.class.to_s.underscore.singularize.to_sym, :active, :value => true %>
+
+ <%= button_tag "Run pipeline", {class: 'btn btn-primary pull-right', id: "run-pipeline-button"} %>
+ <% end %>
+ <% end %>
+
+ <%= render partial: 'pipeline_templates/show_components_template', locals: {:template => template, :obj => @object} %>
+
+<% end %>
<table class="table table-condensed table-fixedlayout">
<colgroup>
<col width="5%" />
- <col width="10%" />
+ <col width="15%" />
+ <col width="25%" />
<col width="20%" />
- <col width="10%" />
- <col width="30%" />
<col width="15%" />
- <col width="10%" />
+ <col width="20%" />
</colgroup>
<thead>
<tr class="contain-align-left">
Status
</th><th>
Instance
- </th><th colspan="2">
+ </th><th>
Template
</th><th>
Owner
<tr data-object-uuid="<%= ob.uuid %>">
<td>
- <%= check_box_tag 'uuids[]', ob.uuid, false %>
+ <%= check_box_tag 'uuids[]', ob.uuid, false, :class => 'persistent-selection' %>
</td><td>
- <% if ob.success %>
- <span class="label label-success">success</span>
- <% elsif ob.active %>
- <span class="label label-info">active</span>
- <% end %>
- </td><td colspan="2">
+ <%= render partial: 'pipeline_status_label', locals: {:p => ob} %>
+ </td><td colspan="1">
<%= link_to_if_arvados_object ob, friendly_name: true %>
</td><td>
<%= link_to_if_arvados_object ob.pipeline_template_uuid, friendly_name: true %>
</td>
</tr>
<tr>
- <td style="border-top: 0;" colspan="3">
+ <td style="border-top: 0;" colspan="2">
</td>
- <td style="border-top: 0; opacity: 0.5;" colspan="4">
+ <td style="border-top: 0; opacity: 0.5;" colspan="5">
<% ob.components.each do |cname, c| %>
- <% status = if !(c.is_a?(Hash) && c[:job].is_a?(Hash))
- nil
- elsif c[:job][:success]
- 'success'
- elsif c[:job][:running]
- 'info'
- else
- 'warning'
- end %>
- <span class="label label-<%= status || 'default' %>"><%= cname.to_s %></span>
+ <% if c[:job] %>
+ <%= render partial: "job_status_label", locals: {:j => c[:job], :title => cname.to_s } %>
+ <% else %>
+ <span class="label label-default"><%= cname.to_s %></span>
+ <% end %>
<% end %>
</td>
</tr>
var new_content = "<%= escape_javascript(render template: 'pipeline_instances/show') %>";
if ($('div.body-content').html() != new_content)
$('div.body-content').html(new_content);
+$(document).trigger('ajax:complete');
+<%= content_for :content_top do %>
+ <h2>Template '<%= @object.name %>'</h2>
+<% end %>
+
<table class="table topalign">
<thead>
</thead>
<tbody>
<% @object.attributes_for_display.each do |attr, attrvalue| %>
- <% if attr == 'components' and attrvalue.is_a? Hash and attrvalue[:steps].is_a? Array %>
-
- <tr><td>components[steps]</td><td>
- <table class="table">
- <% attrvalue[:steps].each_with_index do |s, i| %>
- <tr>
- <td><%= i %></td>
- <% %w(name function min_revision max_steps_per_node params).each do |key| %>
- <td>
- <% if key == 'params' %>
- <% s[key.to_sym].each do |p| %>
- <%= p[:name] %>
- <% if p[:data_locator] || p[:value] %>
- ← <%= p[:data_locator] || p[:value] %>
- <% end %>
- <%= '(optional)' if p[:optional] %>
- <br />
- <% end %>
- <% else %>
- <%= s[key.to_sym] %>
- <% end %>
- </td>
- <% end %>
- </tr>
- <% end %>
- </table>
- </td></tr>
-
- <% else %>
- <%= render partial: 'application/arvados_object_attr', locals: { attr: attr, attrvalue: attrvalue } %>
- <% end %>
+ <% if attr != 'components' %>
+ <%= render partial: 'application/arvados_object_attr', locals: { attr: attr, attrvalue: attrvalue } %>
+ <% end %>
<% end %>
</tbody>
</table>
--- /dev/null
+<% content_for :tab_line_buttons do %>
+ <%= form_tag '/pipeline_instances' do |f| %>
+ <%= hidden_field :pipeline_instance, :pipeline_template_uuid, :value => @object.uuid %>
+ <%= button_tag "Create pipeline", {class: 'btn btn-primary pull-right', id: "run-pipeline-button"} %>
+<% end %>
+<% end %>
+
+<%= render partial: 'pipeline_templates/show_components_template', locals: {:template => @object, :obj => nil} %>
--- /dev/null
+<table class="table pipeline-components-table" style="margin-top: -.1em">
+ <colgroup>
+ <col style="width: 15%" />
+ <col style="width: 20%" />
+ <col style="width: 20%" />
+ <col style="width: 45%" />
+ </colgroup>
+
+ <thead>
+ <tr>
+ <th>
+ component
+ </th><th>
+ script
+ </th><th>
+ parameter
+ </th><th>
+ value
+ </th>
+ </tr>
+ </thead>
+ <tbody>
+ <% order = PipelineTemplatesHelper::sort_components(template.components) %>
+ <% puts "order is #{order}" %>
+ <% order.each do |k| %>
+ <% template_value = template.components[k] %>
+ <% puts "#{k} #{template_value}" %>
+ <% if not template_value then next end %>
+ <tr>
+ <td><span class="label label-default"><%= k %></span></td>
+
+ <td><%= render_editable_subattribute obj, :components, [k, :script], template_value[:script] %></td>
+
+ <td>script version</td>
+
+ <td>
+ <%= render_editable_subattribute obj, :components, [k, :script_version], template_value[:script_version] %>
+ </td>
+ </tr>
+
+ <% if template_value[:script_parameters].length > 0 %>
+ <% template_value[:script_parameters].each do |p, tv| %>
+ <tr>
+ <td style="border-top: none"></td>
+ <td style="border-top: none"></td>
+
+ <td class="property-edit-row"><%= p %></td>
+ <td class="property-edit-row"><%= render_editable_subattribute obj, :components, [k, :script_parameters, p.to_sym], tv %></td>
+ <% end %>
+ </tr>
+ <% end %>
+ <% end %>
+ </tbody>
+</table>
--- /dev/null
+
+ <%= render partial: 'pipeline_instances/show_recent' %>
+<% content_for :css do %>
+ .playbutton {
+ color: white;
+ background: rgb(91, 192, 222);
+ border: 0px;
+ border-radius: 3px;
+ padding: 0px 3px;
+ }
+ .playbutton:hover {
+ background: rgb(57, 179, 215);
+ }
+<% end %>
+
<table class="table table-hover">
<thead>
<tr class="contain-align-left">
<th>
+ </th><th>
id
</th><th>
name
<% @objects.sort_by { |ob| ob[:created_at] }.reverse.each do |ob| %>
<tr>
+ <td>
+ <%= form_tag '/pipeline_instances' do |f| %>
+ <%= hidden_field :pipeline_instance, :pipeline_template_uuid, :value => ob.uuid %>
+ <%= button_tag nil, {class: 'playbutton', title: "Run #{ob.name}"} do %>
+ <span class="glyphicon glyphicon-play"></span>
+ <% end %>
+ <% end %>
+ </td>
<td>
<%= link_to_if_arvados_object ob %>
</td><td>
--- /dev/null
+<p>As an admin, you can log in as this user. When you’ve
+finished, you will need to log out and log in again with your own
+account.</p>
+
+<blockquote>
+<%= button_to "Log in as #{@object.full_name}", sudo_user_url(id: @object.uuid), class: 'btn btn-primary' %>
+</blockquote>
<col width="20%" />
<col width="20%" />
<col width="13%" />
- <col width="27%" />
+ <col width="13%" />
+ <col width="20%" />
</colgroup>
<tr>
<th>Log</th>
<th>Age</th>
<th>Status</th>
+ <th>Progress</th>
</tr>
<% @my_jobs[0..6].each do |j| %>
<tr>
<td>
<small>
- <%= link_to j.script[0..31], job_path(j.uuid) %>
+ <%= link_to((j.script.andand[0..31] || j.uuid), job_path(j.uuid)) %>
</small>
</td>
</td>
<td>
- <% if j.success %>
- <span class="label label-success">finished</span>
- <% elsif j.success == false %>
- <span class="label label-danger">failed</span>
- <% elsif j.finished_at %>
- <span class="label">finished?</span>
- <% elsif j.started_at %>
- <span class="label label-info">running</span>
- <% else %>
- <span class="label">queued</span>
- <% end %>
- <% percent_total_tasks = 100 / (j.tasks_summary[:running] + j.tasks_summary[:done] + j.tasks_summary[:todo]) rescue 0 %>
- <div class="inline-progress-container pull-right">
- <div class="progress">
- <span class="progress-bar progress-bar-success" style="width: <%= j.tasks_summary[:done] * percent_total_tasks rescue 0 %>%;">
- </span>
- <span class="progress-bar" style="width: <%= j.tasks_summary[:running] * percent_total_tasks rescue 0 %>%;">
- </span>
- <% if j.success == false %>
- <span class="progress-bar progress-bar-danger" style="width: <%= tasks_summary[:failed] * percent_total_tasks rescue 0 %>%;">
- </span>
- <% end %>
- </div>
+ <%= render partial: 'job_status_label', locals: {:j => j} %>
+</td>
+<td>
+ <div class="inline-progress-container">
+ <%= render partial: 'job_progress', locals: {:j => j} %>
</div>
</td>
<col width="30%" />
<col width="30%" />
<col width="13%" />
- <col width="27%" />
+ <col width="13%" />
+ <col width="20%" />
</colgroup>
<tr>
<th>Template</th>
<th>Age</th>
<th>Status</th>
+ <th>Progress</th>
</tr>
<% @my_pipelines[0..6].each do |p| %>
</td>
<td>
- <% if p.success %>
- <span class="label label-success">finished</span>
- <% elsif p.success == false %>
- <span class="label label-danger">failed</span>
- <% elsif p.active and p.modified_at < 30.minutes.ago %>
- <span class="label label-info">stopped</span>
- <% elsif p.active %>
- <span class="label label-info">running</span>
- <% else %>
- <span class="label">queued</span>
- <% end %>
+ <%= render partial: 'pipeline_status_label', locals: {:p => p} %>
+ </td>
- <% summary = pipeline_summary p %>
- <div class="inline-progress-container pull-right">
- <div class="progress">
- <span class="progress-bar progress-bar-success" style="width: <%= summary[:percent_done] %>%;">
- </span>
- <% if p.success == false %>
- <span class="progress-bar progress-bar-danger" style="width: <%= 100.0 - summary[:percent_done] %>%;">
- </span>
- <% else %>
- <span class="progress-bar" style="width: <%= summary[:percent_running] %>%;">
- </span>
- <span class="progress-bar progress-bar-info" style="width: <%= summary[:percent_queued] %>%;">
- </span>
- <span class="progress-bar progress-bar-danger" style="width: <%= summary[:percent_failed] %>%;">
- </span>
- <% end %>
- </div>
+ <td>
+ <div class="inline-progress-container">
+ <%= render partial: 'pipeline_progress', locals: {:p => p} %>
</div>
</td>
-
</tr>
<% end %>
</table>
--- /dev/null
+# Do not use this file for site configuration. Create config.yml
+# instead (see application.yml.example).
+
+development:
+ cache_classes: false
+ whiny_nils: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_mailer.raise_delivery_errors: false
+ active_support.deprecation: :log
+ action_dispatch.best_standards_support: :builtin
+ active_record.mass_assignment_sanitizer: :strict
+ active_record.auto_explain_threshold_in_seconds: 0.5
+ assets.compress: false
+ assets.debug: true
+ profiling_enabled: true
+ site_name: Workbench:dev
+
+production:
+ force_ssl: true
+ cache_classes: true
+ consider_all_requests_local: false
+ action_controller.perform_caching: true
+ serve_static_assets: false
+ assets.compress: true
+ assets.compile: false
+ assets.digest: true
+ i18n.fallbacks: true
+ active_support.deprecation: :notify
+ profiling_enabled: false
+
+ arvados_insecure_https: false
+
+ data_import_dir: /data/arvados-workbench-upload/data
+ data_export_dir: /data/arvados-workbench-download/data
+
+ site_name: Arvados Workbench
+
+test:
+ cache_classes: true
+ serve_static_assets: true
+ static_cache_control: public, max-age=3600
+ whiny_nils: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_dispatch.show_exceptions: false
+ action_controller.allow_forgery_protection: false
+ action_mailer.delivery_method: :test
+ active_record.mass_assignment_sanitizer: :strict
+ active_support.deprecation: :stderr
+ profiling_enabled: false
+ secret_token: <%= rand(2**256).to_s(36) %>
+
+ site_name: Workbench:test
+
+common:
+ data_import_dir: /tmp/arvados-workbench-upload
+ data_export_dir: /tmp/arvados-workbench-download
+ arvados_login_base: https://arvados.local/login
+ arvados_v1_base: https://arvados.local/arvados/v1
+ arvados_insecure_https: true
+ activation_contact_link: mailto:info@arvados.org
+ arvados_docsite: http://doc.arvados.org
+ arvados_theme: default
+ show_user_agreement_inline: false
+ secret_token: ~
--- /dev/null
+# Copy this file to application.yml and edit to suit.
+#
+# Consult application.default.yml for the full list of configuration
+# settings.
+#
+# The order of precedence is:
+# 1. config/environments/{RAILS_ENV}.rb (deprecated)
+# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
+# 3. Section in application.yml called "common"
+# 4. Section in application.default.yml corresponding to RAILS_ENV
+# 5. Section in application.default.yml called "common"
+
+common:
+ # At minimum, you need a nice long randomly generated secret_token here.
+ secret_token: ~
+
+ # You probably also want to point to your API server.
+ arvados_login_base: https://arvados.local:3000/login
+ arvados_v1_base: https://arvados.local:3000/arvados/v1
+ arvados_insecure_https: true
--- /dev/null
+$application_config = {}
+
+%w(application.default application).each do |cfgfile|
+ path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
+ if File.exists? path
+ yaml = ERB.new(IO.read path).result(binding)
+ confs = YAML.load(yaml)
+ $application_config.merge!(confs['common'] || {})
+ $application_config.merge!(confs[::Rails.env.to_s] || {})
+ end
+end
+
+ArvadosWorkbench::Application.configure do
+ nils = []
+ $application_config.each do |k, v|
+ # "foo.bar: baz" --> { config.foo.bar = baz }
+ cfg = config
+ ks = k.split '.'
+ k = ks.pop
+ ks.each do |kk|
+ cfg = cfg.send(kk)
+ end
+ if cfg.respond_to?(k.to_sym) and !cfg.send(k).nil?
+ # Config must have been set already in environments/*.rb.
+ #
+ # After config files have been migrated, this mechanism should
+ # be deprecated, then removed.
+ elsif v.nil?
+ # Config variables are not allowed to be nil. Make a "naughty"
+ # list, and present it below.
+ nils << k
+ else
+ cfg.send "#{k}=", v
+ end
+ end
+ if !nils.empty?
+ raise <<EOS
+Refusing to start in #{::Rails.env.to_s} mode with missing configuration.
+
+The following configuration settings must be specified in
+config/application.yml:
+* #{nils.join "\n* "}
+
+EOS
+ end
+end
themes_for_rails
resources :keep_disks
- resources :user_agreements
- post '/user_agreements/sign' => 'user_agreements#sign'
+ resources :user_agreements do
+ put 'sign', on: :collection
+ get 'signatures', on: :collection
+ end
get '/user_agreements/signatures' => 'user_agreements#signatures'
resources :nodes
resources :humans
get 'home', :on => :member
get 'welcome', :on => :collection
get 'activity', :on => :collection
+ post 'sudo', :on => :member
end
resources :logs
resources :factory_jobs
match '/collections/graph' => 'collections#graph'
resources :collections
get '/collections/:uuid/*file' => 'collections#show_file', :format => false
+
+ post 'actions' => 'actions#post'
+
root :to => 'users#welcome'
# Send unroutable requests to an arbitrary controller
--- /dev/null
+namespace :config do
+ desc 'Ensure site configuration has all required settings'
+ task check: :environment do
+ $application_config.sort.each do |k, v|
+ $stderr.puts "%-32s %s" % [k, eval("Rails.configuration.#{k}")]
+ end
+ end
+end
--- /dev/null
+Creative Commons Legal Code
+
+Attribution-ShareAlike 3.0 United States
+
+License
+
+THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE
+COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY
+COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS
+AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
+
+BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE
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+CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE
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+
+1. Definitions
+
+ a. "Collective Work" means a work, such as a periodical issue, anthology or
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+ with one or more other contributions, constituting separate and independent
+ works in themselves, are assembled into a collective whole. A work that
+ constitutes a Collective Work will not be considered a Derivative Work (as
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+ b. "Creative Commons Compatible License" means a license that is listed at
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+ license with the same License Elements as this License.
+
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+ Work may be recast, transformed, or adapted, except that a work that
+ constitutes a Collective Work will not be considered a Derivative Work for
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+restrict any rights arising from fair use, first sale or other limitations on
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+ Works, and to reproduce the Work as incorporated in the Collective Works;
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+ jurisdictions).
+
+The above rights may be exercised in all media and formats whether now known or
+hereafter devised. The above rights include the right to make such
+modifications as are technically necessary to exercise the rights in other
+media and formats. All rights not expressly granted by Licensor are hereby
+reserved.
+
+4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
+
+ a. You may distribute, publicly display, publicly perform, or publicly
+ digitally perform the Work only under the terms of this License, and You
+ must include a copy of, or the Uniform Resource Identifier for, this
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+ Work as incorporated in a Collective Work, but this does not require the
+ Collective Work apart from the Work itself to be made subject to the terms
+ of this License. If You create a Collective Work, upon notice from any
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+
+ b. You may distribute, publicly display, publicly perform, or publicly
+ digitally perform a Derivative Work only under: (i) the terms of this
+ License; (ii) a later version of this License with the same License
+ Elements as this License; (iii) either the Creative Commons (Unported)
+ license or a Creative Commons jurisdiction license (either this or a later
+ license version) that contains the same License Elements as this License
+ (e.g. Attribution-ShareAlike 3.0 (Unported)); (iv) a Creative Commons
+ Compatible License. If you license the Derivative Work under one of the
+ licenses mentioned in (iv), you must comply with the terms of that
+ license. If you license the Derivative Work under the terms of any of the
+ licenses mentioned in (i), (ii) or (iii) (the "Applicable License"), you
+ must comply with the terms of the Applicable License generally and with the
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+ Applicable License and to the disclaimer of warranties; and, (IV) when You
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+ Derivative Work that restrict the ability of a recipient of the Derivative
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+ Derivative Work as incorporated in a Collective Work, but this does not
+ require the Collective Work apart from the Derivative Work itself to be
+ made subject to the terms of the Applicable License.
+
+ c. If You distribute, publicly display, publicly perform, or publicly
+ digitally perform the Work (as defined in Section 1 above) or any
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+ and provide, reasonable to the medium or means You are utilizing: (i) the
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+7. Termination
+
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+ withdraw this License (or any other license that has been, or is required
+ to be, granted under the terms of this License), and this License will
+ continue in full force and effect unless terminated as stated above.
+
+8. Miscellaneous
+
+ a. Each time You distribute or publicly digitally perform the Work (as defined
+ in Section 1 above) or a Collective Work (as defined in Section 1 above),
+ the Licensor offers to the recipient a license to the Work on the same
+ terms and conditions as the license granted to You under this License.
+
+ b. Each time You distribute or publicly digitally perform a Derivative Work,
+ Licensor offers to the recipient a license to the original Work on the same
+ terms and conditions as the license granted to You under this License.
+
+ c. If any provision of this License is invalid or unenforceable under
+ applicable law, it shall not affect the validity or enforceability of the
+ remainder of the terms of this License, and without further action by the
+ parties to this agreement, such provision shall be reformed to the minimum
+ extent necessary to make such provision valid and enforceable.
+
+ d. No term or provision of this License shall be deemed waived and no breach
+ consented to unless such waiver or consent shall be in writing and signed
+ by the party to be charged with such waiver or consent.
+
+ e. This License constitutes the entire agreement between the parties with
+ respect to the Work licensed here. There are no understandings, agreements
+ or representations with respect to the Work not specified here. Licensor
+ shall not be bound by any additional provisions that may appear in any
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+
+Creative Commons Notice
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gem 'zenweb'
gem 'liquid'
gem 'RedCloth'
-gem 'colorize'
\ No newline at end of file
+gem 'colorize'
--- /dev/null
+Arvados Documentation
+
+0. Install dependencies
+
+ $ bundle install
+
+
+1. To build or update documentation:
+ $ rake generate
+
+
+2. To view documentation:
+ $ rake run
+[2014-03-10 09:03:41] INFO WEBrick 1.3.1
+[2014-03-10 09:03:41] INFO ruby 2.1.1 (2014-02-24) [x86_64-linux]
+[2014-03-10 09:03:41] INFO WEBrick::HTTPServer#start: pid=8926 port=8000
+
+ Then go to http://localhost:8000
+
+
+2. You can set 'baseurl' (the URL prefix for all internal links),
+'arvados_api_host' and 'arvados_workbench_host' without changing _config.yml:
+
+ $ rake generate baseurl=/example arvados_api_host=example.com
+
+
+4. To delete generated files:
+ $ rake realclean
require "rubygems"
require "colorize"
+task :generate do
+ vars = ['baseurl', 'arvados_api_host', 'arvados_workbench_host']
+ vars.each do |v|
+ if ENV[v]
+ website.config.h[v] = ENV[v]
+ end
+ end
+end
+
require "zenweb/tasks"
load "zenweb-textile.rb"
load "zenweb-liquid.rb"
# file:///tmp/arvados/doc/.site). To make docs show up inside
# workbench, use /doc here and add a symlink at
# apps/workbench/public/doc pointing to ../../../doc/.site
+# You can also set these on the command line:
+# $ rake generate baseurl=/example arvados_api_host=example.comA
-baseurl: /doc
+baseurl:
+arvados_api_host: localhost
+arvados_workbench_host: localhost
exclude: ["Rakefile", "tmp", "vendor"]
-arvados_api_host: qr1hi.arvadosapi.com
navbar:
userguide:
- user/getting_started/community.html.textile.liquid
- Tutorials:
- user/tutorials/tutorial-keep.html.textile.liquid
- - user/tutorials/tutorial-job1.html.textile.liquid
+ - user/tutorials/intro-crunch.html.textile.liquid
+ - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
- user/tutorials/tutorial-firstscript.html.textile.liquid
- - user/tutorials/tutorial-job-debug.html.textile.liquid
- - user/tutorials/tutorial-parallel.html.textile.liquid
- user/tutorials/tutorial-new-pipeline.html.textile.liquid
- - user/tutorials/tutorial-trait-search.html.textile.liquid
- - user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
- user/tutorials/running-external-program.html.textile.liquid
+ - Intermediate topics:
+ - user/topics/running-pipeline-command-line.html.textile.liquid
+ - user/topics/tutorial-job1.html.textile.liquid
+ - user/topics/tutorial-job-debug.html.textile.liquid
+ - user/topics/tutorial-parallel.html.textile.liquid
+ - user/topics/tutorial-trait-search.html.textile.liquid
+ - user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+ - user/topics/keep.html.textile.liquid
- Examples:
- user/examples/crunch-examples.html.textile.liquid
- Reference:
- user/reference/api-tokens.html.textile.liquid
- user/reference/sdk-cli.html.textile.liquid
+ - Arvados License:
+ - user/copying/copying.html.textile.liquid
+ - user/copying/agpl-3.0.html
+ - user/copying/LICENSE-2.0.html
+ - user/copying/by-sa-3.0.html
sdk:
- Overview:
- sdk/index.html.textile.liquid
- admin/cheat_sheet.html.textile.liquid
installguide:
- Install:
- - install/install-api-server.html.md.liquid
- install/index.html.md.liquid
- - install/install-workbench-app.html.md.liquid
+ - install/install-sso.html.textile.liquid
+ - install/install-api-server.html.textile.liquid
+ - install/install-workbench-app.html.textile.liquid
- install/client.html.textile.liquid
- install/create-standard-objects.html.textile.liquid
- install/install-crunch-dispatch.html.textile.liquid
import arvados
-arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)
-this_task = arvados.current_task()
+# Automatically parallelize this job by running one task per file.
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=True)
-# Get the input collection for this task
-this_task_input = this_task['parameters']['input']
+# Get the input file for the task
+input_file = arvados.get_task_param_mount('input')
-# Create a CollectionReader to access the collection
-input_collection = arvados.CollectionReader(this_task_input)
+# Run the external 'md5sum' program on the input file
+stdoutdata, stderrdata = arvados.util.run_command(['md5sum', input_file])
-# Get the name of the first file in the collection
-input_file = list(input_collection.all_files())[0].name()
-
-# Extract the file to a temporary directory
-# Returns the directory that the file was written to
-input_dir = arvados.util.collection_extract(this_task_input,
- 'tmp',
- files=[input_file],
- decompress=False)
-
-# Run the external 'md5sum' program on the input file, with the current working
-# directory set to the location the input file was extracted to.
-stdoutdata, stderrdata = arvados.util.run_command(
- ['md5sum', input_file],
- cwd=input_dir)
-
-# Save the standard output (stdoutdata) "md5sum.txt" in the output collection
+# Save the standard output (stdoutdata) to "md5sum.txt" in the output collection
out = arvados.CollectionWriter()
out.set_current_file_name("md5sum.txt")
out.write(stdoutdata)
-
-this_task.set_output(out.finish())
+arvados.current_task().set_output(out.finish())
#!/usr/bin/env python
-# Import the hashlib module (part of the Python standard library) to compute md5.
-import hashlib
+import hashlib # Import the hashlib module to compute md5.
+import arvados # Import the Arvados sdk module
-# Import the Arvados sdk module
-import arvados
+# Automatically parallelize this job by running one task per file.
+# This means that if the input consists of many files, each file will
+# be processed in parallel on different nodes enabling the job to
+# be completed quicker.
+arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True,
+ input_as_path=True)
-# Get information about the task from the environment
-this_task = arvados.current_task()
-
-# Get the "input" field from "script_parameters" on the job creation object
-this_job_input = arvados.getjobparam('input')
-
-# Create the object access to the collection referred to in the input
-collection = arvados.CollectionReader(this_job_input)
-
-# Create an object to write a new collection as output
-out = arvados.CollectionWriter()
-
-# Set the name of output file within the collection
-out.set_current_file_name("md5sum.txt")
+# Create the message digest object that will compute the md5 hash
+digestor = hashlib.new('md5')
-# Get an iterator over the files listed in the collection
-all_files = collection.all_files()
-
-# Iterate over each file
-for input_file in all_files:
- # Create the object that will actually compute the md5 hash
- digestor = hashlib.new('md5')
+# Get the input file for the task
+input_file = arvados.get_task_param_mount('input')
+# Open the input file for reading
+with open(input_file) as f:
while True:
- # read a 1 megabyte block from the file
- buf = input_file.read(2**20)
-
- # break when there is no more data left
- if len(buf) == 0:
+ buf = f.read(2**20) # read a 1 megabyte block from the file
+ if len(buf) == 0: # break when there is no more data left
break
+ digestor.update(buf) # update the md5 hash object
- # update the md5 hash object
- digestor.update(buf)
-
- # Get the final hash code
- hexdigest = digestor.hexdigest()
+# Get object representing the current task
+this_task = arvados.current_task()
- # Get the file name from the StreamFileReader object
- file_name = input_file.name()
+ # Write a new collection as output
+out = arvados.CollectionWriter()
- # The "stream name" is the subdirectory inside the collection in which
- # the file is located; '.' is the root of the collection.
- if input_file.stream_name() != '.':
- file_name = os.join(input_file.stream_name(), file_name)
+ # Set output file within the collection
+out.set_current_file_name("md5sum.txt")
- # Write an output line with the md5 value and file name.
- out.write("%s %s\n" % (hexdigest, file_name))
+# Write an output line with the md5 value and input
+out.write("%s %s\n" % (digestor.hexdigest(), this_task['parameters']['input']))
-# Commit the output to keep. This returns a Keep id.
+ # Commit the output to keep. This returns a Keep id.
output_id = out.finish()
# Set the output for this task to the Keep id
-this_task.set_output(output_id)
+this_task.set_output(output_id)
# Done!
--- /dev/null
+{% assign n = 0 %}
+{% assign prev = "" %}
+{% assign nx = 0 %}
+{% for section in site.navbar[page.navsection] %}
+ {% for entry in section %}
+ {% for item in entry[1] %}
+ {% assign p = site.pages[item] %}
+ {% if nx == 1 %}
+ <hr>
+ {% if prev != "" %}
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a></li>
+ {% endif %}
+ <a href="{{ site.baseurl }}{{ p.url }}" class="pull-right">Next: {{ p.title }}</a></li>
+ {% assign nx = 0 %}
+ {% assign n = 1 %}
+ {% endif %}
+ {% if p.url == page.url %}
+ {% assign nx = 1 %}
+ {% else %}
+ {% assign prev = p %}
+ {% endif %}
+ {% endfor %}
+ {% endfor %}
+{% endfor %}
+{% if n == 0 && prev != "" %}
+ <hr>
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a></li>
+ {% assign n = 1 %}
+{% endif %}
\ No newline at end of file
<link href="{{ site.baseurl }}/css/bootstrap.css" rel="stylesheet">
<link href="{{ site.baseurl }}/css/nav-list.css" rel="stylesheet">
<link href="{{ site.baseurl }}/css/badges.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/code.css" rel="stylesheet">
<style>
html {
height:100%;
text-align: center;
margin-bottom: 1em;
}
- .userinput {
- color: #d14;
- }
:target {
padding-top: 61px;
margin-top: -61px;
}
</style>
- <link href="{{ site.baseurl }}/css/bootstrap-responsive.min.css" rel="stylesheet">
+
<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="../assets/js/html5shiv.js"></script>
<div class="row">
{% include 'navbar_left' %}
<div class="col-sm-9">
+ <h1>{{ page.title }}</h1>
{{ content }}
+ {% include 'webring' %}
</div>
</div>
</script>
-<p style="text-align: center">
-The content of this documentation is licensed under a
-<a href="https://creativecommons.org/licenses/by-sa/3.0/us/">Creative
- Commons Attribution-Share Alike 3.0 United States</a> licence.
+<p style="text-align: center"><small>
+The content of this documentation is licensed under the
+<a href="{{ site.baseurl }}/user/copying/by-sa-3.0.html">Creative
+ Commons Attribution-Share Alike 3.0 United States</a> licence.<br>
+Code samples in this documentation are licensed under the
+<a href="{{ site.baseurl }}/user/copying/LICENSE-2.0.html">Apache License, Version 2.0.</a></small>
</p>
</body>
title: Cheat Sheet
...
-h1. Cheat Sheet
+
h3. CLI setup
...
-h1. Authentication
+
Every API request (except the authentication API itself) includes an @access_token@ parameter.
...
-h1. API Reference
+
h2. Concepts
...
-h1. REST Methods
+
(using Group as an example)
...
-h1. api_client_authorizations
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. api_clients
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. authorized_keys
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. collections
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. groups
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. humans
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. job_tasks
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. jobs
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. keep_disks
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. links
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. logs
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. nodes
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. pipeline_instances
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. pipeline_templates
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. repositories
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. specimens
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. traits
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. users
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. virtual_machines
+
Required arguments are displayed in %{background:#ccffcc}green%.
...
-h1. Permission model
+
Each API transaction (read, write, create, etc.) is done on behalf of a person.
...
-h1. Resources
+
This page describes the common attributes of Arvados resources.
...
-h1. ApiClient
+
An **ApiClient** represents a client program that has issued a request to the API server.
...
-h1. ApiClientAuthorization
+
A **ApiClientAuthorization** represents the API authorization token that has been issued to each "ApiClient":ApiClient.html known to this Arvados instance.
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client_authorization@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client_authorizations@
h2. Creation
...
-h1. AuthorizedKey
+
A **AuthorizedKey** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/authorized_key@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/authorized_keys@
h2. Creation
...
-h1. Collection
+
This resource concerns metadata, usage accounting, and integrity checks for data stored on the cloud. Reading and writing the data _per se_ is achieved by the "Keep":/user/tutorials/tutorial-keep.html storage system.
...
-h1. Commit
+
A **Commit** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commits@
h2. Creation
...
-h1. CommitAncestor
+
A **CommitAncestor** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit_ancestor@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit_ancestors@
h2. Creation
...
-h1. Group
+
A **Group** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/group@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/groups@
h2. Creation
...
-h1. Human
+
A **Human** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/human@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/humans@
h2. Creation
...
-h1. Job
+
Applications submit compute jobs when:
* Provenance is important, i.e., it is worth recording how the output was produced; or
...
-h1. JobTask
+
A Job Task is a well defined independently-computable portion of a "Job":Job.html.
...
-h1. KeepDisk
+
A **KeepDisk** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disk@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disks@
h2. Creation
...
-h1. Link
+
**Links** describe relationships between Arvados objects, and from objects to primitives.
...
-h1. Log
+
**Log** objects record events that occur in an Arvados cluster. Both user-written pipelines and the Arvados system itself may generate Log events.
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/log@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/logs@
h2. Creation
...
-h1. Node
+
A **Node** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/node@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/nodes@
h2. Creation
...
-h1. PipelineInstance
+
A **PipelineInstance** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instance@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instances@
h2. Creation
...
-h1. PipelineTemplate
+
A **PipelineTemplate** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_template@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_templates@
h2. Creation
...
-h1. Repository
+
A **Repository** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repository@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repositories@
h2. Creation
...
-h1. Specimen
+
A **Specimen** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimen@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimens@
h2. Creation
...
-h1. Trait
+
A **Trait** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/trait@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/traits@
h2. Creation
...
-h1. User
+
A **User** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/user@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/users@
h2. Creation
...
-h1. VirtualMachine
+
A **VirtualMachine** represents...
See "REST methods for working with Arvados resources":/api/methods.html
-API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/virtual_machine@
+API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/virtual_machines@
h2. Creation
--- /dev/null
+table.code {
+ font-family: Menlo,Monaco,Consolas,"Courier New",monospace;
+ display: block;
+ padding: 9.5px;
+ margin: 0px 0px 10px;
+ font-size: 13px;
+ line-height: 1.42857;
+ color: rgb(51, 51, 51);
+ word-break: break-all;
+ word-wrap: break-word;
+ background-color: rgb(245, 245, 245);
+ border: 1px solid rgb(204, 204, 204);
+ border-radius: 4px 4px 4px 4px;
+}
+
+table.code tr td {
+ white-space: pre;
+}
+
+table.code tr td:nth-child(2) {
+ color: #d14;
+ padding-left: .5em;
+}
+
+.userinput {
+ color: #d14;
+}
text-shadow: 0 -1px 0 rgba(0,0,0,.2);
background-color: rgb(66, 139, 202);
}
+
+.spaced-out li {
+ padding-bottom: 1em;
+}
\ No newline at end of file
"script":"file-select",
"script_parameters":{
"names":[
- "human_g1k_v37.fasta.gz", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
+ "human_g1k_v37.fasta.gz",
+ "human_g1k_v37.fasta.fai.gz",
+ "human_g1k_v37.dict.gz"
],
"input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
},
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153"
},
"bwa-index":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-index",
"script_parameters":{
"input":{
"output_of":"extract-reference"
},
"bwa_tbz":{
- "optional":false
+ "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+ "required":true
}
}
},
"bwa-aln":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"bwa-aln",
"script_parameters":{
"input":{
- "optional":"false"
+ "dataclass":"Collection",
+ "required":"true"
},
"reference_index":{
"output_of":"bwa-index"
},
"samtools_tgz":{
- "optional":false
+ "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+ "required":true
},
"bwa_tbz":{
- "optional":false
+ "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+ "required":true
}
},
"runtime_constraints":{
}
},
"picard-gatk2-prep":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"picard-gatk2-prep",
"script_parameters":{
"input":{
- "output_of":"bwa-aln"
+ "output_of":"bwa-aln"
},
"reference":{
"output_of":"extract-reference"
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
}
},
"runtime_constraints":{
}
},
"GATK2-realign":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-realign",
"script_parameters":{
"input":{
- "output_of":"picard-gatk2-prep"
+ "output_of":"picard-gatk2-prep"
},
"gatk_bundle":{
- "optional":false
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
},
"gatk_tbz":{
- "optional":false
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
},
"regions":{
- "optional":true
+ "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
},
"region_padding":{
- "optional":true
+ "value":10
}
},
"runtime_constraints":{
}
},
"GATK2-bqsr":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-bqsr",
"script_parameters":{
"input":{
- "output_of":"GATK2-realign"
+ "output_of":"GATK2-realign"
},
"gatk_bundle":{
- "optional":false
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
},
"gatk_tbz":{
- "optional":false
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
}
}
},
"GATK2-merge-call":{
- "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
"script":"GATK2-merge-call",
"script_parameters":{
"input":{
- "output_of":"GATK2-bqsr"
+ "output_of":"GATK2-bqsr"
},
"gatk_bundle":{
- "optional":false
+ "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi",
+ "required":true
},
"picard_zip":{
- "optional":false
+ "value":"687f74675c6a0e925dec619cc2bec25f+77",
+ "required":true
},
"gatk_tbz":{
- "optional":false
+ "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+ "required":true
},
"regions":{
- "optional":true
+ "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
},
"region_padding":{
- "optional":true
+ "value":10
},
"GATK2_UnifiedGenotyper_args":{
- "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
+ "default":[
+ "-stand_call_conf",
+ "30.0",
+ "-stand_emit_conf",
+ "30.0",
+ "-dcov",
+ "200"
+ ]
}
}
}
</div>
<div class="col-sm-7" style="border-left: solid; border-width: 1px">
<p>
- <a href="{{ site.baseurl }}/user/">User Guide</a> — How to manage data and do analysis with Arvados.
+ <a href="{{ site.baseurl }}/user/index.html">User Guide</a> — How to manage data and do analysis with Arvados.
</p>
<p>
- <a href="{{ site.baseurl }}/sdk/">SDK Reference</a> — Details about the accessing Arvados from various programming languages.
+ <a href="{{ site.baseurl }}/sdk/index.html">SDK Reference</a> — Details about the accessing Arvados from various programming languages.
</p>
<p>
- <a href="{{ site.baseurl }}/api/">API Reference</a> — Details about the the Arvados REST API.
+ <a href="{{ site.baseurl }}/api/index.html">API Reference</a> — Details about the the Arvados REST API.
</p>
<p>
- <a href="{{ site.baseurl }}/admin/">Admin Guide</a> — How to administer an Arvados system.
+ <a href="{{ site.baseurl }}/admin/index.html">Admin Guide</a> — How to administer an Arvados system.
</p>
<p>
- <a href="{{ site.baseurl }}/install/">Install Guide</a> — How to install Arvados on a cloud platform.
+ <a href="{{ site.baseurl }}/install/index.html">Install Guide</a> — How to install Arvados on a cloud platform.
</p>
</div>
</div>
...
-h1. Install client libraries
+
h3. Python
...
-h1. Create standard objects
+
h3. "All users" group
1. Set up a cluster, or use Amazon
1. Create and mount Keep volumes
+1. [Install the Single Sign On (SSO) server](install-sso.html)
1. [Install the Arvados REST API server](install-api-server.html)
1. [Install the Arvados workbench application](install-workbench-app.html)
1. [Install the Crunch dispatcher](install-crunch-dispatch.html)
+++ /dev/null
----
-layout: default
-navsection: installguide
-title: Install the API server
-navorder: 1
-...
-
-{% include 'alert_stub' %}
-
-# API server setup
-
-## Prerequisites
-
-1. A GNU/linux (virtual) machine
-2. A domain name for your api server
-
-## Download the source tree
-
-Please follow the instructions on the [Download page](https://arvados.org/projects/arvados/wiki/Download) in the wiki.
-
-## Configure the API server
-
-First install the gems:
-
- cd arvados/services/api
- bundle install
-
-Next, configure the database:
-
- cp config/database.yml.sample config/database.yml
-
-Edit database.yml to your liking and make sure the database and db user exist.
-Then set up the database:
-
- RAILS_ENV=production rake db:setup
-
-Then set up omniauth:
-
- cp config/initializers/omniauth.rb.example config/initializers/omniauth.rb
-
-Edit config/initializers/omniauth.rb. Choose an *APP_SECRET* and *APP_ID*. Also set
-*CUSTOM_PROVIDER_URL*.
-
-Make sure your Omniauth provider knows about your *APP_ID* and *APP_SECRET*
-combination.
-
-You also need to update config/initializers/secret_token.rb. Generate a new secret with
-
- rake secret
-
-and put it in config/initializers/secret_token.rb:
-
- Server::Application.config.secret_token = 'your-new-secret-here'
-
-Finally, edit the main configuration:
-
- cp config/environments/production.rb.example config/environments/production.rb
-
-First, you want to make sure that
-
- config.uuid_prefix
-
-is set to a unique 5-digit hex string. You can replace the 'cfi-aws-0' string
-with a string of your choice to make that happen.
-
-The *config.uuid_prefix* string is a unique identifier for your API server. It
-also serves as the first part of the hostname for your API server, for instance
-
- {{ site.arvados_api_host }}
-
-You should use your own domain instead of arvadosapi.com
-
-Second, unless you are running on AWS, you will want to change the definition of
-
- config.compute_node_nameservers
-
-If you know your nameservers and they are fixed, you can hardcode them, and
-make sure to remove the code that tries to look them up from the AWS metadata:
-
- config.compute_node_nameservers = ['1.2.3.4','2.3.4.5','3.4.5.6']
- #require 'net/http'
- #config.compute_node_nameservers = ['local', 'public'].collect do |iface|
- # Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
- #end << '172.16.0.23'
-
-## Apache/Passenger
-
-Set up Apache and Passenger. Point them to the services/api directory in the source tree.
-
-To enable streaming so users can monitor crunch jobs in real time, add
-to your Apache configuration:
-
- PassengerBufferResponse off
-
-## Add an admin user
-
-Point browser to the API endpoint. Log in with a google account.
-
-In the rails console:
-
- Thread.current[:user] = User.find(1)
- Thread.current[:user].is_admin = true
- User.find(1).update_attributes is_admin: true, is_active: true
- User.find(1).is_admin
-
-This should be
-
- => true
-
-## Create a token
-
-In rails console
-
- a = ApiClient.new(owner_uuid:'0'); a.save!
- x = ApiClientAuthorization.new(api_client_id:a.id, user_id:1); x.save; x.api_token
-
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install the API server
+...
+
+h2. Prerequisites:
+
+# A GNU/Linux (virtual) machine
+# A domain name for your api server
+# Ruby >= 2.0.0
+# Bundler: @gem install bundler@
+# Curl libraries: @sudo apt-get install libcurl3 libcurl3-gnutls libcurl4-openssl-dev@
+
+h2. Download the source tree
+
+<notextile>
+<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+</code></pre></notextile>
+
+See also: "Downloading the source code:https://arvados.org/projects/arvados/wiki/Download on the Arvados wiki.
+
+h2. Install gem dependencies
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd arvados/services/api</span>
+~/arvados/services/api$ <span class="userinput">bundle install</span>
+</code></pre></notextile>
+
+h2. Configure the API server
+
+Edit the main configuration:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/application.yml.example config/application.yml</span>
+</code></pre></notextile>
+
+Choose a unique 5-character alphanumeric string to use as your @uuid_prefix@. An example is given that generates a 5-character string based on a hash of your hostname. The @uuid_prefix@ is a unique identifier for your API server. It also serves as the first part of the hostname for your API server.
+
+For a development site, use your own domain instead of arvadosapi.com.
+
+Make sure a clone of the arvados repository exists in @git_repositories_dir@:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">sudo mkdir -p /var/cache/git</span>
+~/arvados/services/api$ <span class="userinput">sudo git clone --bare ../../.git /var/cache/git/arvados.git</span>
+</code></pre></notextile>
+
+Generate a new secret token for signing cookies:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">rake secret
+zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
+</code></pre></notextile>
+
+Put it in @config/application.yml@ in the production or common section:
+
+<notextile>
+<pre><code><span class="userinput"> secret_token: zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz</span>
+</code></pre>
+</notextile>
+
+Consult @application.default.yml@ for a full list of configuration options. Always put your local configuration in @application.yml@ instead of editing @application.default.yml@.
+
+Configure the database:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/database.yml.sample config/database.yml</span>
+</code></pre></notextile>
+
+By default, the development database will use the sqlite3 driver, so no configuration is necessary. If you wish to use mysql or postgres, edit @config/database.yml@ to your liking and make sure the database and db user exist. Then initialize the database:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=development bundle exec rake db:setup</span>
+</code></pre></notextile>
+
+Set up omniauth:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">cp -i config/initializers/omniauth.rb.example config/initializers/omniauth.rb
+</code></pre></notextile>
+
+Edit @config/initializers/omniauth.rb@. Set @APP_SECRET@ to the value of @app_secret@ from "installing the single sign on server":install-sso.html .
+
+You can now run the development server:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">rails server
+</code></pre></notextile>
+
+h3. Apache/Passenger (optional)
+
+You can use "Passenger":https://www.phusionpassenger.com/ for deployment. Point it to the services/api directory in the source tree.
+
+To enable streaming so users can monitor crunch jobs in real time, add to your Passenger configuration in Apache:
+
+<notextile>
+<pre><code><span class="userinput">PassengerBufferResponse off</span>
+</code></pre>
+</notextile>
+
+h2. Add an admin user
+
+Point browser to the API endpoint. Log in with a google account.
+
+In the rails console:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">rails console</span>
+irb(main):001:0> <span class="userinput">Thread.current[:user] = User.find(1)</span>
+irb(main):002:0> <span class="userinput">Thread.current[:user].is_admin = true</span>
+irb(main):003:0> <span class="userinput">User.find(1).update_attributes is_admin: true, is_active: true</span>
+irb(main):004:0> <span class="userinput">User.find(1).is_admin</span>
+=> true
+</code></pre></notextile>
+
+h2. Create an API token
+
+In rails console:
+
+<notextile>
+<pre><code>~/arvados/services/api$ <span class="userinput">rails console</span>
+irb(main):001:0> <span class="userinput">a = ApiClient.new(owner_uuid:'0')</span>
+irb(main):002:0> <span class="userinput">a.save!</span>
+irb(main):003:0> <span class="userinput">x = ApiClientAuthorization.new(api_client_id:a.id, user_id:1)</span>
+irb(main):004:0> <span class="userinput">x.save</span>
+irb(main):005:0> <span class="userinput">x.api_token</span>
+</code></pre></notextile>
...
-h1. Crunch setup
+
The dispatcher normally runs on the same host/VM as the API server.
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install Single Sign On (SSO) server
+...
+
+<notextile>
+<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/sso-devise-omniauth-provider.git</span>
+~$ <span class="userinput">cd sso-devise-omniauth-provider</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">bundle install</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">rake db:create</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">rake db:migrate</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">rake secret</span>
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+~/sso-devise-omniauth-provider$ <span class="userinput">rails console</span>
+irb(main):001:0> <span class="userinput">c = Client.new</span>
+irb(main):002:0> <span class="userinput">c.name = "joshid"</span>
+irb(main):003:0> <span class="userinput">c.app_id = "arvados-server"</span>
+irb(main):004:0> <span class="userinput">c.app_secret = "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"</span>
+irb(main):005:0> <span class="userinput">c.save!</span>
+irb(main):006:0> <span class="userinput">quit</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">rails server --port=3002</span>
+</code></pre>
+</notextile>
+++ /dev/null
----
-layout: default
-navsection: installguide
-title: Install the Arvados workbench application
-navorder: 2
-...
-
-{% include 'alert_stub' %}
-
-# Workbench setup
-
-## Prerequisites
-
-1. A GNU/linux (virtual) machine (can be shared with the API server)
-2. A hostname for your workbench application
-
-## Download the source tree
-
-Please follow the instructions on the [Download page](https://arvados.org/projects/arvados/wiki/Download) in the wiki.
-
-The workbench application is in `apps/workbench`.
-
-## Configure the Workbench application
-
-You need to update config/initializers/secret_token.rb. Generate a new secret with
-
- rake secret
-
-and put it in `config/initializers/secret_token.rb`
-
- Server::Application.config.secret_token = 'your-new-secret-here'
-
-Adjust the following fields in your `environments/production.rb` file.
-
-* `config.site_name` can be the URL of your workbench install.
-* `config.arvados_login_base` and `config.arvados_v1_base` should point to
-your API server. Use the example values as a guide.
-* If you choose not to use https, make sure to also set
-`config.force_ssl = false` in the API server's `production.rb` file.
-
-Copy `config/piwik.yml.example` to `config/piwik.yml` and edit to suit.
-
-## Apache/Passenger
-
-Set up Apache and Passenger. Point them to the apps/workbench directory in the source tree.
-
-## "Trusted client" setting
-
-Log in to Workbench once (this ensures that the Arvados API server has
-a record of the Workbench client).
-
-In the API server project root, start the rails console.
-
- RAILS_ENV=production bundle exec rails c
-
-Locate the ApiClient record for your Workbench installation.
-
- ApiClient.where('url_prefix like ?', '%workbench%')
-
-Set the `is_trusted` flag for the appropriate client record.
-
- ApiClient.find(1234).update_attributes is_trusted: true
-
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Install the Arvados Workbench application
+...
+
+h2. Prerequisites
+
+# A GNU/linux (virtual) machine (can be shared with the API server)
+# A hostname for your Workbench application
+
+h2. Download the source tree
+
+Please follow the instructions on the "Download page":https://arvados.org/projects/arvados/wiki/Download in the wiki.
+
+The Workbench application is in @arvados/apps/workbench@.
+
+h2. Configure the Workbench application
+
+This application needs a secret token. Generate a new secret:
+
+<notextile>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">rake secret</span>
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+</code></pre>
+</notextile>
+
+Copy @config/application.yml.example@ to @config/application.yml@ and edit it appropriately for your environment.
+
+* Set @secret_token@ to the string you generated with @rake secret@.
+* Point @arvados_login_base@ and @arvados_v1_base@ at your "API server":install-api-server.html
+* @site_name@ can be any string to identify this Workbench.
+* Assuming that the SSL certificate you use for development isn't signed by a CA, make sure @arvados_insecure_https@ is @true@.
+
+Copy @config/piwik.yml.example@ to @config/piwik.yml@ and edit to suit.
+
+h3. Apache/Passenger (optional)
+
+Set up Apache and Passenger. Point them to the apps/workbench directory in the source tree.
+
+h2. Trusted client setting
+
+Log in to Workbench once (this ensures that the Arvados API server has a record of the Workbench client).
+
+In the API server project root, start the rails console. Locate the ApiClient record for your Workbench installation, then set the `is_trusted` flag for the appropriate client record:
+
+<notextile><pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=development bundle exec rails console</span>
+irb(main):001:0> <span class="userinput">ApiClient.where('url_prefix like ?', '%workbench%')</span>
+=> {:id => 1234}
+irb(main):002:0> <span class="userinput">ApiClient.find(1234).update_attributes is_trusted: true</span>
+</code></pre>
+</notextile>
+
+
---
layout: default
navsection: sdk
-title: "SDK Reference"
-
+title: "Arvados SDK Reference"
...
-h1. Arvados SDK Reference
-
This section documents how to access the Arvados API and Keep using various programming languages.
* "Python SDK":python/sdk-python.html
...
-h1. Crunch utility libraries
-
Several utility libraries are included with Arvados. They are intended to make it quicker and easier to write your own crunch scripts.
* "Python SDK extras":#pythonsdk
...
-h1. Python SDK
-
The Python SDK provides a generic set of wrappers so you can make API calls easily. It performs some validation before connecting to the API server: for example, it refuses to do an API call if a required parameter is missing.
The library also includes some conveniences for use in Crunch scripts; see "Crunch utility libraries":crunch-utility-libraries.html for details.
<notextile>
<pre>
-$ <code class="userinput">sudo apt-get install python-dev libattr1-dev libfuse-dev pkg-config</code>
+$ <code class="userinput">sudo apt-get install python-pip python-dev libattr1-dev libfuse-dev pkg-config</code>
$ <code class="userinput">sudo pip install arvados-python-client</code>
</pre>
</notextile>
+_If your version of @pip@ is 1.4 or newer, the @pip install@ command might give an error: "Could not find a version that satisfies the requirement arvados-python-client". If this happens, fix it by adding a @--pre@ flag:_
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo pip install --pre arvados-python-client</code>
+</pre>
+</notextile>
+
h4. Option 2: build and install from source
<notextile>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Apache License"
+...
+
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+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+</pre></div></div></div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "GNU Affero General Public License"
+...
+
+<p style="text-align: center;">Version 3, 19 November 2007</p>
+
+<p>Copyright © 2007 Free Software Foundation,
+Inc. <<a href="http://fsf.org/">http://fsf.org/</a>>
+ <br />
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.</p>
+
+<h3><a name="preamble"></a>Preamble</h3>
+
+<p>The GNU Affero General Public License is a free, copyleft license
+for software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.</p>
+
+<p>The licenses for most software and other practical works are
+designed to take away your freedom to share and change the works. By
+contrast, our General Public Licenses are intended to guarantee your
+freedom to share and change all versions of a program--to make sure it
+remains free software for all its users.</p>
+
+<p>When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.</p>
+
+<p>Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.</p>
+
+<p>A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate. Many developers of free software are heartened and
+encouraged by the resulting cooperation. However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.</p>
+
+<p>The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community. It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server. Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.</p>
+
+<p>An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.</p>
+
+<p>The precise terms and conditions for copying, distribution and
+modification follow.</p>
+
+<h3><a name="terms"></a>TERMS AND CONDITIONS</h3>
+
+<h4><a name="section0"></a>0. Definitions.</h4>
+
+<p>"This License" refers to version 3 of the GNU Affero General Public
+License.</p>
+
+<p>"Copyright" also means copyright-like laws that apply to other kinds
+of works, such as semiconductor masks.</p>
+
+<p>"The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.</p>
+
+<p>To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy. The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.</p>
+
+<p>A "covered work" means either the unmodified Program or a work based
+on the Program.</p>
+
+<p>To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.</p>
+
+<p>To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.</p>
+
+<p>An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License. If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.</p>
+
+<h4><a name="section1"></a>1. Source Code.</h4>
+
+<p>The "source code" for a work means the preferred form of the work
+for making modifications to it. "Object code" means any non-source
+form of a work.</p>
+
+<p>A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.</p>
+
+<p>The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form. A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.</p>
+
+<p>The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities. However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.</p>
+
+<p>The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+Source.</p>
+
+<p>The Corresponding Source for a work in source code form is that
+same work.</p>
+
+<h4><a name="section2"></a>2. Basic Permissions.</h4>
+
+<p>All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.</p>
+
+<p>You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force. You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright. Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.</p>
+
+<p>Conveying under any other circumstances is permitted solely under
+the conditions stated below. Sublicensing is not allowed; section 10
+makes it unnecessary.</p>
+
+<h4><a name="section3"></a>3. Protecting Users' Legal Rights From Anti-Circumvention Law.</h4>
+
+<p>No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.</p>
+
+<p>When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.</p>
+
+<h4><a name="section4"></a>4. Conveying Verbatim Copies.</h4>
+
+<p>You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.</p>
+
+<p>You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.</p>
+
+<h4><a name="section5"></a>5. Conveying Modified Source Versions.</h4>
+
+<p>You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:</p>
+
+<ul>
+
+<li>a) The work must carry prominent notices stating that you modified
+ it, and giving a relevant date.</li>
+
+<li>b) The work must carry prominent notices stating that it is
+ released under this License and any conditions added under section
+ 7. This requirement modifies the requirement in section 4 to
+ "keep intact all notices".</li>
+
+<li>c) You must license the entire work, as a whole, under this
+ License to anyone who comes into possession of a copy. This
+ License will therefore apply, along with any applicable section 7
+ additional terms, to the whole of the work, and all its parts,
+ regardless of how they are packaged. This License gives no
+ permission to license the work in any other way, but it does not
+ invalidate such permission if you have separately received it.</li>
+
+<li>d) If the work has interactive user interfaces, each must display
+ Appropriate Legal Notices; however, if the Program has interactive
+ interfaces that do not display Appropriate Legal Notices, your
+ work need not make them do so.</li>
+
+</ul>
+
+<p>A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.</p>
+
+<h4><a name="section6"></a>6. Conveying Non-Source Forms.</h4>
+
+<p>You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:</p>
+
+<ul>
+
+<li>a) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by the
+ Corresponding Source fixed on a durable physical medium
+ customarily used for software interchange.</li>
+
+<li>b) Convey the object code in, or embodied in, a physical product
+ (including a physical distribution medium), accompanied by a
+ written offer, valid for at least three years and valid for as
+ long as you offer spare parts or customer support for that product
+ model, to give anyone who possesses the object code either (1) a
+ copy of the Corresponding Source for all the software in the
+ product that is covered by this License, on a durable physical
+ medium customarily used for software interchange, for a price no
+ more than your reasonable cost of physically performing this
+ conveying of source, or (2) access to copy the
+ Corresponding Source from a network server at no charge.</li>
+
+<li>c) Convey individual copies of the object code with a copy of the
+ written offer to provide the Corresponding Source. This
+ alternative is allowed only occasionally and noncommercially, and
+ only if you received the object code with such an offer, in accord
+ with subsection 6b.</li>
+
+<li>d) Convey the object code by offering access from a designated
+ place (gratis or for a charge), and offer equivalent access to the
+ Corresponding Source in the same way through the same place at no
+ further charge. You need not require recipients to copy the
+ Corresponding Source along with the object code. If the place to
+ copy the object code is a network server, the Corresponding Source
+ may be on a different server (operated by you or a third party)
+ that supports equivalent copying facilities, provided you maintain
+ clear directions next to the object code saying where to find the
+ Corresponding Source. Regardless of what server hosts the
+ Corresponding Source, you remain obligated to ensure that it is
+ available for as long as needed to satisfy these requirements.</li>
+
+<li>e) Convey the object code using peer-to-peer transmission, provided
+ you inform other peers where the object code and Corresponding
+ Source of the work are being offered to the general public at no
+ charge under subsection 6d.</li>
+
+</ul>
+
+<p>A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.</p>
+
+<p>A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling. In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage. For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product. A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.</p>
+
+<p>"Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source. The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.</p>
+
+<p>If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information. But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).</p>
+
+<p>The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed. Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.</p>
+
+<p>Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.</p>
+
+<h4><a name="section7"></a>7. Additional Terms.</h4>
+
+<p>"Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.</p>
+
+<p>When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.</p>
+
+<p>Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:</p>
+
+<ul>
+
+<li>a) Disclaiming warranty or limiting liability differently from the
+ terms of sections 15 and 16 of this License; or</li>
+
+<li>b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or</li>
+
+<li>c) Prohibiting misrepresentation of the origin of that material, or
+ requiring that modified versions of such material be marked in
+ reasonable ways as different from the original version; or</li>
+
+<li>d) Limiting the use for publicity purposes of names of licensors or
+ authors of the material; or</li>
+
+<li>e) Declining to grant rights under trademark law for use of some
+ trade names, trademarks, or service marks; or</li>
+
+<li>f) Requiring indemnification of licensors and authors of that
+ material by anyone who conveys the material (or modified versions of
+ it) with contractual assumptions of liability to the recipient, for
+ any liability that these contractual assumptions directly impose on
+ those licensors and authors.</li>
+
+</ul>
+
+<p>All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further restriction,
+you may remove that term. If a license document contains a further
+restriction but permits relicensing or conveying under this License, you
+may add to a covered work material governed by the terms of that license
+document, provided that the further restriction does not survive such
+relicensing or conveying.</p>
+
+<p>If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.</p>
+
+<p>Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.</p>
+
+<h4><a name="section8"></a>8. Termination.</h4>
+
+<p>You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).</p>
+
+<p>However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.</p>
+
+<p>Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.</p>
+
+<p>Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.</p>
+
+<h4><a name="section9"></a>9. Acceptance Not Required for Having Copies.</h4>
+
+<p>You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.</p>
+
+<h4><a name="section10"></a>10. Automatic Licensing of Downstream Recipients.</h4>
+
+<p>Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.</p>
+
+<p>An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.</p>
+
+<p>You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.</p>
+
+<h4><a name="section11"></a>11. Patents.</h4>
+
+<p>A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".</p>
+
+<p>A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.</p>
+
+<p>Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.</p>
+
+<p>In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.</p>
+
+<p>If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.</p>
+
+<p>If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.</p>
+
+<p>A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.</p>
+
+<p>Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.</p>
+
+<h4><a name="section12"></a>12. No Surrender of Others' Freedom.</h4>
+
+<p>If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.</p>
+
+<h4><a name="section13"></a>13. Remote Network Interaction; Use with the GNU General Public License.</h4>
+
+<p>Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.</p>
+
+<p>Notwithstanding any other provision of this License, you have permission
+to link or combine any covered work with a work licensed under version 3
+of the GNU General Public License into a single combined work, and to
+convey the resulting work. The terms of this License will continue to
+apply to the part which is the covered work, but the work with which it is
+combined will remain governed by version 3 of the GNU General Public
+License.</p>
+
+<h4><a name="section14"></a>14. Revised Versions of this License.</h4>
+
+<p>The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may differ
+in detail to address new problems or concerns.</p>
+
+<p>Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero
+General Public License "or any later version" applies to it, you have
+the option of following the terms and conditions either of that
+numbered version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number
+of the GNU Affero General Public License, you may choose any version
+ever published by the Free Software Foundation.</p>
+
+<p>If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that
+proxy's public statement of acceptance of a version permanently
+authorizes you to choose that version for the Program.</p>
+
+<p>Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.</p>
+
+<h4><a name="section15"></a>15. Disclaimer of Warranty.</h4>
+
+<p>THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
+
+<h4><a name="section16"></a>16. Limitation of Liability.</h4>
+
+<p>IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.</p>
+
+<h4><a name="section17"></a>17. Interpretation of Sections 15 and 16.</h4>
+
+<p>If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.</p>
+
+<p>END OF TERMS AND CONDITIONS</p>
+
+<h3><a name="howto"></a>How to Apply These Terms to Your New Programs</h3>
+
+<p>If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.</p>
+
+<p>To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.</p>
+
+<pre> <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as
+ published by the Free Software Foundation, either version 3 of the
+ License, or (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+</pre>
+
+<p>Also add information on how to contact you by electronic and paper mail.</p>
+
+<p>If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.</p>
+
+<p>You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<<a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>>.</p>
+
+
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Creative Commons"
+...
+
+<div id="deed" class="green">
+ <div id="deed-head">
+
+ <div id="deed-license">
+ <h2>Attribution-ShareAlike 3.0 United States</h2>
+ </div>
+ </div>
+
+ <h3><em>License</em></h3>
+
+ <p>THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS
+ OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR
+ "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER
+ APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS
+ AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS
+ PROHIBITED.</p>
+
+ <p>BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU
+ ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE.
+ TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A
+ CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE
+ IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND
+ CONDITIONS.</p>
+
+ <p><strong>1. Definitions</strong></p>
+
+ <ol type="a">
+ <li><strong>"Collective Work"</strong> means a work, such
+ as a periodical issue, anthology or encyclopedia, in
+ which the Work in its entirety in unmodified form, along
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+ constitutes a Collective Work will not be considered a
+ Derivative Work (as defined below) for the purposes of
+ this License.</li>
+
+ <li><strong>"Creative Commons Compatible
+ License"</strong> means a license that is listed at
+ http://creativecommons.org/compatiblelicenses that has
+ been approved by Creative Commons as being essentially
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+ because that license: (i) contains terms that have the
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+
+ <li><strong>"License Elements"</strong> means the
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+
+ <li><strong>"Licensor"</strong> means the individual,
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+
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+ exercising rights under this License who has not
+ previously violated the terms of this License with
+ respect to the Work, or who has received express
+ permission from the Licensor to exercise rights under
+ this License despite a previous violation.</li>
+ </ol>
+
+ <p><strong>2. Fair Use Rights.</strong> Nothing in this
+ license is intended to reduce, limit, or restrict any
+ rights arising from fair use, first sale or other
+ limitations on the exclusive rights of the copyright owner
+ under copyright law or other applicable laws.</p>
+
+ <p><strong>3. License Grant.</strong> Subject to the terms
+ and conditions of this License, Licensor hereby grants You
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+ the duration of the applicable copyright) license to
+ exercise the rights in the Work as stated below:</p>
+
+ <ol type="a">
+ <li>to reproduce the Work, to incorporate the Work into
+ one or more Collective Works, and to reproduce the Work
+ as incorporated in the Collective Works;</li>
+
+ <li>to create and reproduce Derivative Works provided
+ that any such Derivative Work, including any translation
+ in any medium, takes reasonable steps to clearly label,
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+ the original Work. For example, a translation could be
+ marked "The original work was translated from English to
+ Spanish," or a modification could indicate "The original
+ work has been modified.";</li>
+
+ <li>to distribute copies or phonorecords of, display
+ publicly, perform publicly, and perform publicly by means
+ of a digital audio transmission the Work including as
+ incorporated in Collective Works;</li>
+
+ <li>to distribute copies or phonorecords of, display
+ publicly, perform publicly, and perform publicly by means
+ of a digital audio transmission Derivative Works.</li>
+
+ <li>
+ <p>For the avoidance of doubt, where the Work is a
+ musical composition:</p>
+
+ <ol type="i">
+ <li><strong>Performance Royalties Under Blanket
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+
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+ Agency), royalties for any phonorecord You create
+ from the Work ("cover version") and distribute,
+ subject to the compulsory license created by 17 USC
+ Section 115 of the US Copyright Act (or the
+ equivalent in other jurisdictions).</li>
+ </ol>
+ </li>
+
+ <li><strong>Webcasting Rights and Statutory
+ Royalties</strong>. For the avoidance of doubt, where the
+ Work is a sound recording, Licensor waives the exclusive
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+ performance-rights society (e.g. SoundExchange),
+ royalties for the public digital performance (e.g.
+ webcast) of the Work, subject to the compulsory license
+ created by 17 USC Section 114 of the US Copyright Act (or
+ the equivalent in other jurisdictions).</li>
+ </ol>
+
+ <p>The above rights may be exercised in all media and
+ formats whether now known or hereafter devised. The above
+ rights include the right to make such modifications as are
+ technically necessary to exercise the rights in other media
+ and formats. All rights not expressly granted by Licensor
+ are hereby reserved.</p>
+
+ <p><strong>4. Restrictions.</strong> The license granted in
+ Section 3 above is expressly made subject to and limited by
+ the following restrictions:</p>
+
+ <ol type="a">
+ <li>You may distribute, publicly display, publicly
+ perform, or publicly digitally perform the Work only
+ under the terms of this License, and You must include a
+ copy of, or the Uniform Resource Identifier for, this
+ License with every copy or phonorecord of the Work You
+ distribute, publicly display, publicly perform, or
+ publicly digitally perform. You may not offer or impose
+ any terms on the Work that restrict the terms of this
+ License or the ability of a recipient of the Work to
+ exercise of the rights granted to that recipient under
+ the terms of the License. You may not sublicense the
+ Work. You must keep intact all notices that refer to this
+ License and to the disclaimer of warranties. When You
+ distribute, publicly display, publicly perform, or
+ publicly digitally perform the Work, You may not impose
+ any technological measures on the Work that restrict the
+ ability of a recipient of the Work from You to exercise
+ of the rights granted to that recipient under the terms
+ of the License. This Section 4(a) applies to the Work as
+ incorporated in a Collective Work, but this does not
+ require the Collective Work apart from the Work itself to
+ be made subject to the terms of this License. If You
+ create a Collective Work, upon notice from any Licensor
+ You must, to the extent practicable, remove from the
+ Collective Work any credit as required by Section 4(c),
+ as requested. If You create a Derivative Work, upon
+ notice from any Licensor You must, to the extent
+ practicable, remove from the Derivative Work any credit
+ as required by Section 4(c), as requested.</li>
+
+ <li>You may distribute, publicly display, publicly
+ perform, or publicly digitally perform a Derivative Work
+ only under: (i) the terms of this License; (ii) a later
+ version of this License with the same License Elements as
+ this License; (iii) either the Creative Commons
+ (Unported) license or a Creative Commons jurisdiction
+ license (either this or a later license version) that
+ contains the same License Elements as this License (e.g.
+ Attribution-ShareAlike 3.0 (Unported)); (iv) a Creative
+ Commons Compatible License. If you license the Derivative
+ Work under one of the licenses mentioned in (iv), you
+ must comply with the terms of that license. If you
+ license the Derivative Work under the terms of any of the
+ licenses mentioned in (i), (ii) or (iii) (the "Applicable
+ License"), you must comply with the terms of the
+ Applicable License generally and with the following
+ provisions: (I) You must include a copy of, or the
+ Uniform Resource Identifier for, the Applicable License
+ with every copy or phonorecord of each Derivative Work
+ You distribute, publicly display, publicly perform, or
+ publicly digitally perform; (II) You may not offer or
+ impose any terms on the Derivative Works that restrict
+ the terms of the Applicable License or the ability of a
+ recipient of the Work to exercise the rights granted to
+ that recipient under the terms of the Applicable License;
+ (III) You must keep intact all notices that refer to the
+ Applicable License and to the disclaimer of warranties;
+ and, (IV) when You distribute, publicly display, publicly
+ perform, or publicly digitally perform the Work, You may
+ not impose any technological measures on the Derivative
+ Work that restrict the ability of a recipient of the
+ Derivative Work from You to exercise the rights granted
+ to that recipient under the terms of the Applicable
+ License. This Section 4(b) applies to the Derivative Work
+ as incorporated in a Collective Work, but this does not
+ require the Collective Work apart from the Derivative
+ Work itself to be made subject to the terms of the
+ Applicable License.</li>
+
+ <li>If You distribute, publicly display, publicly
+ perform, or publicly digitally perform the Work (as
+ defined in Section 1 above) or any Derivative Works (as
+ defined in Section 1 above) or Collective Works (as
+ defined in Section 1 above), You must, unless a request
+ has been made pursuant to Section 4(a), keep intact all
+ copyright notices for the Work and provide, reasonable to
+ the medium or means You are utilizing: (i) the name of
+ the Original Author (or pseudonym, if applicable) if
+ supplied, and/or (ii) if the Original Author and/or
+ Licensor designate another party or parties (e.g. a
+ sponsor institute, publishing entity, journal) for
+ attribution ("Attribution Parties") in Licensor's
+ copyright notice, terms of service or by other reasonable
+ means, the name of such party or parties; the title of
+ the Work if supplied; to the extent reasonably
+ practicable, the Uniform Resource Identifier, if any,
+ that Licensor specifies to be associated with the Work,
+ unless such URI does not refer to the copyright notice or
+ licensing information for the Work; and, consistent with
+ Section 3(b) in the case of a Derivative Work, a credit
+ identifying the use of the Work in the Derivative Work
+ (e.g., "French translation of the Work by Original
+ Author," or "Screenplay based on original Work by
+ Original Author"). The credit required by this Section
+ 4(c) may be implemented in any reasonable manner;
+ provided, however, that in the case of a Derivative Work
+ or Collective Work, at a minimum such credit will appear,
+ if a credit for all contributing authors of the
+ Derivative Work or Collective Work appears, then as part
+ of these credits and in a manner at least as prominent as
+ the credits for the other contributing authors. For the
+ avoidance of doubt, You may only use the credit required
+ by this Section for the purpose of attribution in the
+ manner set out above and, by exercising Your rights under
+ this License, You may not implicitly or explicitly assert
+ or imply any connection with, sponsorship or endorsement
+ by the Original Author, Licensor and/or Attribution
+ Parties, as appropriate, of You or Your use of the Work,
+ without the separate, express prior written permission of
+ the Original Author, Licensor and/or Attribution
+ Parties.</li>
+ </ol>
+
+ <p><strong>5. Representations, Warranties and
+ Disclaimer</strong></p>
+
+ <p>UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN
+ WRITING, LICENSOR OFFERS THE WORK AS-IS AND ONLY TO THE
+ EXTENT OF ANY RIGHTS HELD IN THE LICENSED WORK BY THE
+ LICENSOR. THE LICENSOR MAKES NO REPRESENTATIONS OR
+ WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS,
+ IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT
+ LIMITATION, WARRANTIES OF TITLE, MARKETABILITY,
+ MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE,
+ NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS,
+ ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR
+ NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE
+ EXCLUSION OF IMPLIED WARRANTIES, SO SUCH EXCLUSION MAY NOT
+ APPLY TO YOU.</p>
+
+ <p><strong>6. Limitation on Liability.</strong> EXCEPT TO
+ THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL
+ LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY
+ SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY
+ DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK,
+ EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGES.</p>
+
+ <p><strong>7. Termination</strong></p>
+
+ <ol type="a">
+ <li>This License and the rights granted hereunder will
+ terminate automatically upon any breach by You of the
+ terms of this License. Individuals or entities who have
+ received Derivative Works or Collective Works from You
+ under this License, however, will not have their licenses
+ terminated provided such individuals or entities remain
+ in full compliance with those licenses. Sections 1, 2, 5,
+ 6, 7, and 8 will survive any termination of this
+ License.</li>
+
+ <li>Subject to the above terms and conditions, the
+ license granted here is perpetual (for the duration of
+ the applicable copyright in the Work). Notwithstanding
+ the above, Licensor reserves the right to release the
+ Work under different license terms or to stop
+ distributing the Work at any time; provided, however that
+ any such election will not serve to withdraw this License
+ (or any other license that has been, or is required to
+ be, granted under the terms of this License), and this
+ License will continue in full force and effect unless
+ terminated as stated above.</li>
+ </ol>
+
+ <p><strong>8. Miscellaneous</strong></p>
+
+ <ol type="a">
+ <li>Each time You distribute or publicly digitally
+ perform the Work (as defined in Section 1 above) or a
+ Collective Work (as defined in Section 1 above), the
+ Licensor offers to the recipient a license to the Work on
+ the same terms and conditions as the license granted to
+ You under this License.</li>
+
+ <li>Each time You distribute or publicly digitally
+ perform a Derivative Work, Licensor offers to the
+ recipient a license to the original Work on the same
+ terms and conditions as the license granted to You under
+ this License.</li>
+
+ <li>If any provision of this License is invalid or
+ unenforceable under applicable law, it shall not affect
+ the validity or enforceability of the remainder of the
+ terms of this License, and without further action by the
+ parties to this agreement, such provision shall be
+ reformed to the minimum extent necessary to make such
+ provision valid and enforceable.</li>
+
+ <li>No term or provision of this License shall be deemed
+ waived and no breach consented to unless such waiver or
+ consent shall be in writing and signed by the party to be
+ charged with such waiver or consent.</li>
+
+ <li>This License constitutes the entire agreement between
+ the parties with respect to the Work licensed here. There
+ are no understandings, agreements or representations with
+ respect to the Work not specified here. Licensor shall
+ not be bound by any additional provisions that may appear
+ in any communication from You. This License may not be
+ modified without the mutual written agreement of the
+ Licensor and You.</li>
+ </ol>
+ <!-- BREAKOUT FOR CC NOTICE. NOT A PART OF THE LICENSE -->
+
+ <blockquote>
+ <h3>Creative Commons Notice</h3>
+
+ <p>Creative Commons is not a party to this License, and
+ makes no warranty whatsoever in connection with the Work.
+ Creative Commons will not be liable to You or any party
+ on any legal theory for any damages whatsoever, including
+ without limitation any general, special, incidental or
+ consequential damages arising in connection to this
+ license. Notwithstanding the foregoing two (2) sentences,
+ if Creative Commons has expressly identified itself as
+ the Licensor hereunder, it shall have all rights and
+ obligations of Licensor.</p>
+
+ <p>Except for the limited purpose of indicating to the
+ public that the Work is licensed under the CCPL, Creative
+ Commons does not authorize the use by either party of the
+ trademark "Creative Commons" or any related trademark or
+ logo of Creative Commons without the prior written
+ consent of Creative Commons. Any permitted use will be in
+ compliance with Creative Commons' then-current trademark
+ usage guidelines, as may be published on its website or
+ otherwise made available upon request from time to time.
+ For the avoidance of doubt, this trademark restriction
+ does not form part of this License.</p>
+
+ <p>Creative Commons may be contacted at <a href=
+ "http://creativecommons.org/">http://creativecommons.org/</a>.</p>
+ </blockquote>
+ </div>
+ </div>
+
+ </div>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Arvados Free Software Licenses"
+...
+
+Server-side components of Arvados contained in the apps/ and services/ directories, including the API Server, Workbench, and Crunch, are licenced under the "GNU Affero General Public License version 3":agpl-3.0.html.
+
+The Arvados client Software Development Kits contained in the sdk/ directory, example scripts in the crunch_scripts/ directory, and code samples in the Aravados documentation are licensed under the "Apache License, Version 2.0":LICENSE-2.0.html
+
+The Arvados Documentation located in the doc/ directory is licensed under the "Creative Commons Attribution-Share Alike 3.0 United States":by-sa-3.0.html
---
layout: default
navsection: userguide
-navmenu: Examples
title: "Crunch examples"
-
...
-h1. Crunch examples
-
Several crunch scripts are included with Arvados in the "/crunch_scripts directory":https://arvados.org/projects/arvados/repository/revisions/master/show/crunch_scripts. They are intended to provide examples and starting points for writing your own scripts.
h4. bwa-aln
---
layout: default
navsection: userguide
-navmenu: Getting Started
title: "Checking your environment"
-
...
-h1. Checking your environment
-
First you should "log into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login if you have not already done so.
If @arv user current@ is able to access the API server, it will print out information about your account. Check that you are able to access the Arvados API server using the following command:
bc. ARVADOS_API_HOST and ARVADOS_API_TOKEN need to be defined as environment variables
Then follow the instructions for "getting an API token,":{{site.baseurl}}/user/reference/api-tokens.html and try @arv user current@ again.
-
-Once you are able to access the API server, you are ready proceed to the first tutorial: "Storing and retrieving data using Arvados Keep.":{{site.baseurl}}/user/tutorials/tutorial-keep.html
---
layout: default
navsection: userguide
-navmenu: Getting Started
title: Arvados Community and Getting Help
-
...
-h1. Arvados Community and Getting Help
-
h2. On the web
---
layout: default
navsection: userguide
-navmenu: Getting Started
title: Accessing an Arvados VM over ssh
-
...
-h1. Accessing an Arvados Virtual Machine over ssh
-
Arvados requires a public @ssh@ key in order to securely log in to an Arvados VM instance, or to access an Arvados @git@ repository.
This document is divided up into three sections.
h3. From the workbench dashboard
-If you have no @ssh@ keys registered, there should be a notification asking you to provide your @ssh@ public key. On the Workbench dashboard (in this guide, this is "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ ), look for the envelope icon <span class="glyphicon glyphicon-envelope"></span> <span class="badge badge-alert">1</span> in upper right corner (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
+If you have no @ssh@ keys registered, there should be a notification asking you to provide your @ssh@ public key. On the Workbench dashboard (in this guide, this is "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/ ), look for the envelope icon <span class="glyphicon glyphicon-envelope"></span> <span class="badge badge-alert">1</span> in upper right corner (the number indicates there are new notifications). Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
h3. Alternate way to add ssh keys
<notextile>
<pre><code class="userinput">Host *.arvados
ProxyCommand ssh -a -x -p2222 turnout@switchyard.{{ site.arvados_api_host }} $SSH_PROXY_FLAGS %h
+ User <b>you</b>
ForwardAgent yes
ForwardX11 no
</code></pre>
This will recognize any host ending in ".arvados" and automatically apply the proxy, user and forwarding settings from the configuration file, allowing you to log in with a much simpler command:
-notextile. <pre><code>$ <span class="userinput">ssh <b>you@shell</b>.arvados</span></code></pre>
+notextile. <pre><code>$ <span class="userinput">ssh <b>shell</b>.arvados</span></code></pre>
h2(#windowsvm). Logging in using PuTTY (Windows)
---
layout: default
navsection: userguide
-navmenu: Getting Started
title: Accessing Arvados Workbench
-
...
-h1. Accessing Arvados Workbench
Access the Arvados beta test instance available using this link:
-"https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/
+"https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/
If you are accessing Arvados for the first time, you will be asked to log in using a Google account. Arvados uses only your name and email address from Google services for identification, and will never access any personal information. Once you are logged in, the Workbench page may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to activate your account.
Once your account is active, logging in to the Workbench will present you with a system status dashboard. This gives a summary of data, configuration, and activity in the Arvados instance.
-
-Next, we will "configure your account for ssh access to an Arvados virtual machine (VM).":ssh-access.html
layout: default
navsection: userguide
title: Welcome to Arvados!
-
...
-h1. Welcome to Arvados!
-
-This guide is intended to introduce new users to the Arvados system. It covers initial configuration required to use the system and then presents several tutorials on using Arvados to do data processing.
+This guide is intended to introduce new users to the Arvados system. It covers initial configuration required to access the system and then presents several tutorials on using Arvados to do data processing.
This user guide introduces how to use the major components of Arvados. These are:
# Programming in @python@
# Revision control using @git@
-The examples in this guide uses the public Arvados instance located at "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ . You must have an account in order to use this service. If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com .
+We also recommend you read the "Arvados Platform Overview":https://arvados.org/projects/arvados/wiki#Platform-Overview for an introduction and background information about Arvados.
+
+The examples in this guide uses the Arvados instance located at "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/ . If you are using a different Arvados instance replace @{{ site.arvados_workbench_host }}@ with your private instance in all of the examples in this guide.
-If you are using a different Arvados instance replace @{{ site.arvados_api_host }}@ with your private instance in all of the examples in this guide.
+The Arvados public beta instance is located at "https://workbench.qr1hi.arvadosapi.com/":https://workbench.qr1hi.arvadosapi.com/ . You must have an account in order to use this service. If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com .
h2. Typographic conventions
<notextile>
<ul>
-<li>Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type "ls foo" while in your home directory and the expected output will be "foo".
-
+<li>Code blocks which are set aside from the text indicate user input to the system. Commands that should be entered into a Unix shell are indicated by the directory where you should enter the command ('~' indicates your home directory) followed by '$', followed by the highlighted <span class="userinput">command to enter</span> (do not enter the '$'), and possibly followed by example command output in black. For example, the following block indicates that you should type "ls foo.*" while in your home directory and the expected output will be "foo.input" and "foo.output".
<pre><code>~$ <span class="userinput">ls foo</span>
foo
-</code></pre></li>
+</code></pre>
+</li>
<li>Code blocks inline with text emphasize specific <code>programs</code>, <code>files</code>, or <code>options</code> that are being discussed.</li>
<li>Bold text emphasizes <b>specific items</b> to look when discussing Arvados Workbench pages.</li>
</ul>
</notextile>
-Now begin by "accessing the Arvados workbench.":getting_started/workbench.html
---
layout: default
navsection: userguide
-navmenu: Reference
title: "Getting an API token"
-
...
-h1. Reference: Getting an API token
-
The Arvados API token is a secret key that enables the @arv@ command line client to access Arvados with the proper permissions.
-Access the Arvados workbench using this link: "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/
+Access the Arvados workbench using this link: "https://{{ site.arvados_workbench_host }}/":https://{{ site.arvados_workbench_host }}/
(Replace @{{ site.arvados_api_host }}@ with the hostname of your local Arvados instance if necessary.)
---
layout: default
navsection: userguide
-navmenu: Reference
title: "Command line interface"
...
-h1. Reference: Command Line Interface
-
*First, you should be "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
h3. Usage
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "How Keep works"
+...
+
+In Keep, information is stored in *data blocks*. Data blocks are normally between 1 byte and 64 megabytes in size. If a file exceeds the maximum size of a single data block, the file will be split across multiple data blocks until the entire file can be stored. These data blocks may be stored and replicated across multiple disks, servers, or clusters. Each data block has its own identifier for the contents of that specific data block.
+
+In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
+
+In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to Keep in "the first Keep tutorial":{{ site.baseurl }}/users/tutorial/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
+. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
+
+The command @arv keep get@ fetches the contents of the locator @c1bad4b39ca5a924e481008009d94e32+210@. This is a locator for a collection data block, so it fetches the contents of the collection. In this example, this collection consists of a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, <code>204e43b8a1185621ca55a94839582e6f+67108864</code>, <code>b9677abbac956bd3e86b1deb28dfac03+67108864</code>, <code>fc15aff2a762b13f521baf042140acec+67108864</code>, <code>323d2a3ce20370c4ca1d3462a344f8fd+25885655</code>.
+
+Let's use @arv keep get@ to download the first datablock:
+
+notextile. <pre><code>~$ <span class="userinput">cd /scratch/<b>you</b></span>
+/scratch/<b>you</b>$ <span class="userinput">arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1</span></code></pre>
+
+{% include 'notebox_begin' %}
+
+When you run this command, you may get this API warning:
+
+notextile. <pre><code>WARNING:root:API lookup failed for collection 204e43b8a1185621ca55a94839582e6f+67108864 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://qr1hi.arvadosapi.com/arvados/v1/collections/204e43b8a1185621ca55a94839582e6f%2B67108864?alt=json returned "Not Found">)</code></pre>
+
+This happens because @arv keep get@ tries to find a collection with this identifier. When that fails, it emits this warning, then looks for a datablock instead, which succeeds.
+
+{% include 'notebox_end' %}
+
+Let's look at the size and compute the md5 hash of @block1@:
+
+<notextile>
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">ls -l block1</span>
+-rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
+/scratch/<b>you</b>$ <span class="userinput">md5sum block1</span>
+204e43b8a1185621ca55a94839582e6f block1
+</code></pre>
+</notextile>
+
+Notice that the block identifer <code>204e43b8a1185621ca55a94839582e6f+67108864</code> consists of:
+* the md5 hash @204e43b8a1185621ca55a94839582e6f@ which matches the md5 hash of @block1@
+* a size hint @67108864@ which matches the size of @block1@
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Running a pipeline on the command line"
+...
+
+In "Writing a pipeline":{{ site.baseurl }}/user/tutorials/tutorial-firstscript.html, we learned how to create a pipeline template on the command-line. Let's create one that doesn't require any user input to start:
+
+<notextile>
+<pre><code>~$ <span class="userinput">cat >the_pipeline <<EOF
+{
+ "name":"Filter md5 hash values",
+ "components":{
+ "do_hash":{
+ "script":"hash.py",
+ "script_parameters":{
+ "input": "887cd41e9c613463eab2f0d885c6dd96+83"
+ },
+ "script_version":"<b>you</b>:master"
+ },
+ "filter":{
+ "script":"0-filter.py",
+ "script_parameters":{
+ "input":{
+ "output_of":"do_hash"
+ }
+ },
+ "script_version":"<b>you</b>:master"
+ }
+ }
+}
+EOF</span>
+~$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat the_pipeline)"</span></code></pre>
+</notextile>
+
+You can run this pipeline from the command line using @arv pipeline run@, filling in the UUID that you received from @arv pipeline_template create@:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv pipeline run --template qr1hi-p5p6p-xxxxxxxxxxxxxxx</span>
+2013-12-16 14:08:40 +0000 -- pipeline_instance qr1hi-d1hrv-vxzkp38nlde9yyr
+do_hash qr1hi-8i9sb-hoyc2u964ecv1s6 queued 2013-12-16T14:08:40Z
+filter - -
+
+2013-12-16 14:08:51 +0000 -- pipeline_instance qr1hi-d1hrv-vxzkp38nlde9yyr
+do_hash qr1hi-8i9sb-hoyc2u964ecv1s6 8e1b6acdd3f2f1da722538127c5c6202+56
+filter qr1hi-8i9sb-w5k40fztqgg9i2x queued 2013-12-16T14:08:50Z
+
+2013-12-16 14:09:01 +0000 -- pipeline_instance qr1hi-d1hrv-vxzkp38nlde9yyr
+do_hash qr1hi-8i9sb-hoyc2u964ecv1s6 8e1b6acdd3f2f1da722538127c5c6202+56
+filter qr1hi-8i9sb-w5k40fztqgg9i2x 735ac35adf430126cf836547731f3af6+56
+</code></pre>
+</notextile>
+
+This instantiates your pipeline and displays a live feed of its status. The new pipeline instance will also show up on the Workbench %(rarr)→% Compute %(rarr)→% Pipeline instances page.
+
+Arvados adds each pipeline component to the job queue as its dependencies are satisfied (or immediately if it has no dependencies) and finishes when all components are completed or failed and there is no more work left to do.
+
+The Keep locators of the output of each of @"do_hash"@ and @"filter"@ component are available from the output log shown above. The output is also available on the Workbench by navigating to %(rarr)→% Compute %(rarr)→% Pipeline instances %(rarr)→% pipeline uuid under the *id* column %(rarr)→% components.
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep get 8e1b6acdd3f2f1da722538127c5c6202+56/md5sum.txt</span>
+0f1d6bcf55c34bed7f92a805d2d89bbf alice.txt
+504938460ef369cd275e4ef58994cffe bob.txt
+8f3b36aff310e06f3c5b9e95678ff77a carol.txt
+~$ <span class="userinput">arv keep get 735ac35adf430126cf836547731f3af6+56/0-filter.txt</span>
+0f1d6bcf55c34bed7f92a805d2d89bbf alice.txt
+</code></pre>
+</notextile>
+
+Indeed, the filter has picked out just the "alice" file as having a hash that starts with 0.
+
+h3. Running a pipeline with different parameters
+
+Notice that the pipeline template explicitly specifies the Keep locator for the input:
+
+<notextile>
+<pre><code>...
+ "do_hash":{
+ "script_parameters":{
+ "input": "887cd41e9c613463eab2f0d885c6dd96+83"
+ },
+ }
+...
+</code></pre>
+</notextile>
+
+You can specify values for pipeline component script_parameters like this:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv pipeline run --template qr1hi-p5p6p-xxxxxxxxxxxxxxx do_hash::input=c1bad4b39ca5a924e481008009d94e32+210</span>
+2013-12-17 20:31:24 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
+do_hash qr1hi-8i9sb-rffhuay4jryl2n2 queued 2013-12-17T20:31:24Z
+filter - -
+
+2013-12-17 20:31:34 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
+do_hash qr1hi-8i9sb-rffhuay4jryl2n2 {:done=>1, :running=>1, :failed=>0, :todo=>0}
+filter - -
+
+2013-12-17 20:31:55 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
+do_hash qr1hi-8i9sb-rffhuay4jryl2n2 880b55fb4470b148a447ff38cacdd952+54
+filter qr1hi-8i9sb-j347g1sqovdh0op queued 2013-12-17T20:31:55Z
+
+2013-12-17 20:32:05 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
+do_hash qr1hi-8i9sb-rffhuay4jryl2n2 880b55fb4470b148a447ff38cacdd952+54
+filter qr1hi-8i9sb-j347g1sqovdh0op 490cd451c8108824b8a17e3723e1f236+19
+</code></pre>
+</notextile>
+
+Now check the output:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+~$ <span class="userinput">arv keep get 490cd451c8108824b8a17e3723e1f236+19/0-filter.txt</span>
+~$
+</code></pre>
+</notextile>
+
+Since none of the files in the collection have hash code that start with 0, output of the filter component is empty.
---
layout: default
navsection: userguide
-navmenu: Tutorials
title: "Using GATK with Arvados"
-
...
-h1. Using GATK with Arvados
-
This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
h2. Installing GATK
-Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":tutorial-keep.html.
+Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
<notextile>
<pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>
---
layout: default
navsection: userguide
-navmenu: Tutorials
title: "Debugging a Crunch script"
-
...
-h1. Debugging a Crunch script
-
To test changes to a script by running a job, the change must be pushed into @git@, the job queued asynchronously, and the actual execution may be run on any compute server. As a result, debugging a script can be difficult and time consuming. This tutorial demonstrates using @arv-crunch-job@ to run your job in your local VM. This avoids the job queue and allows you to execute the script from your uncomitted git tree.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
-This tutorial uses _you_ to denote your username. Replace _you_ with your user name in all the following examples.
+This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
h2. Create a new script
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script":"hello-world.py",
- "script_version":"/home/you/you",
+ "script_version":"/home/<b>you</b>/<b>you</b>",
"script_parameters":{}
}
EOF</span>
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 node localhost - 1 slots
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 start
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script hello-world.py
-2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script_version /home/you/you
+2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script_version /home/<b>you</b>/<b>you</b>
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 script_parameters {}
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 runtime_constraints {"max_tasks_per_node":0}
2013-12-12_21:36:42 qr1hi-8i9sb-okzukfzkpbrnhst 29827 start level 0
The script's output is captured in the log, which is useful for print statement debugging. However, although this script returned a status code of 0 (success), the job failed. Why? For a job to complete successfully scripts must explicitly add their output to Keep, and then tell Arvados about it. Here is a second try:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >hello-world.py <<EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >hello-world-fixed.py <<EOF
#!/usr/bin/env python
import arvados
~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script":"hello-world-fixed.py",
- "script_version":"/home/you/you",
+ "script_version":"/home/<b>you</b>/<b>you</b>",
"script_parameters":{}
}
EOF</span>
2013-12-12_21:56:59 qr1hi-8i9sb-79260ykfew5trzl 31578 node localhost - 1 slots
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 start
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script hello-world.py
-2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script_version /home/you/you
+2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script_version /home/<b>you</b>/<b>you</b>
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 script_parameters {}
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 runtime_constraints {"max_tasks_per_node":0}
2013-12-12_21:57:00 qr1hi-8i9sb-79260ykfew5trzl 31578 start level 0
notextile. <pre><code>~$ <span class="userinput">export KEEP_LOCAL_STORE=/tmp</span></code></pre>
-Next, "parallel tasks.":tutorial-parallel.html
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Running a Crunch job"
-
+title: "Running a Crunch job on the command line"
...
-h1. Running a crunch job
-
-This tutorial introduces the concepts and use of the Crunch job system using the @arv@ command line tool and Arvados Workbench.
+This tutorial introduces how to run individual Crunch jobs using the @arv@ command line tool.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
-In "retrieving data using Keep,":tutorial-keep.html we downloaded a file from Keep and did some computation with it (specifically, computing the md5 hash of the complete file). While a straightforward way to accomplish a computational task, there are several obvious drawbacks to this approach:
-* Large files require significant time to download.
-* Very large files may exceed the scratch space of the local disk.
-* We are only able to use the local CPU to process the file.
+You will create a job to run the "hash" crunch script. The "hash" script computes the md5 hash of each file in a collection.
-The Arvados "Crunch" framework is designed to support processing very large data batches (gigabytes to terabytes) efficiently, and provides the following benefits:
-* Increase concurrency by running tasks asynchronously, using many CPUs and network interfaces at once (especially beneficial for CPU-bound and I/O-bound tasks respectively).
-* Track inputs, outputs, and settings so you can verify that the inputs, settings, and sequence of programs you used to arrive at an output is really what you think it was.
-* Ensure that your programs and workflows are repeatable with different versions of your code, OS updates, etc.
-* Interrupt and resume long-running jobs consisting of many short tasks.
-* Maintain timing statistics automatically, so they're there when you want them.
+h2. Jobs
-For your first job, you will run the "hash" crunch script using the Arvados system. The "hash" script computes the md5 hash of each file in a collection.
+Crunch pipelines consist of one or more jobs. A "job" is a single run of a specific version of a crunch script with a specific input. You an also run jobs individually.
-Crunch jobs are described using JSON objects. For example:
+A request to run a crunch job are is described using a JSON object. For example:
<notextile>
<pre><code>~$ <span class="userinput">cat >the_job <<EOF
* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
* @>the_job@ redirects standard output to a file called @the_job@
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under _Compute %(rarr)→% Code repositories_.
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories .
* @"script_parameters"@ are provided to the script. In this case, the input is the locator for the collection that we inspected in the previous section.
Use @arv job create@ to actually submit the job. It should print out a JSON object which describes the newly created job:
h2. Monitor job progress
-Go to the Workbench dashboard. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
+Go to the "Workbench dashboard":http://{{site.arvados_workbench_host}}. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
On the command line, you can access log messages while the job runs using @arv job log_tail_follow@:
h2. Inspect the job output
-On the workbench dashboard, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+On the "Workbench dashboard":http://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
On the command line, you can use @arv job get@ to access a JSON object describing the output:
"cancelled_by_user_uuid":null,
"started_at":"2013-12-16T20:44:36Z",
"finished_at":"2013-12-16T20:44:53Z",
- "output":"880b55fb4470b148a447ff38cacdd952+54",
+ "output":"dd755dbc8d49a67f4fe7dc843e4f10a6+54",
"success":true,
"running":false,
"is_locked_by_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
</code></pre>
</notextile>
-* @"output"@ is the unique identifier for this specific job's output. This is a Keep collection. Because the output of Arvados jobs should be deterministic, the known expected output is <code>880b55fb4470b148a447ff38cacdd952+54</code>.
+* @"output"@ is the unique identifier for this specific job's output. This is a Keep collection. Because the output of Arvados jobs should be deterministic, the known expected output is <code>dd755dbc8d49a67f4fe7dc843e4f10a6+54</code>.
Now you can list the files in the collection:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep ls 880b55fb4470b148a447ff38cacdd952+54</span>
+<pre><code>~$ <span class="userinput">arv keep ls dd755dbc8d49a67f4fe7dc843e4f10a6+54</span>
md5sum.txt
</code></pre>
</notextile>
This collection consists of the @md5sum.txt@ file. Use @arv keep get@ to show the contents of the @md5sum.txt@ file:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+<pre><code>~$ <span class="userinput">arv keep get dd755dbc8d49a67f4fe7dc843e4f10a6+54/md5sum.txt</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f ./var-GS000016015-ASM.tsv.bz2
</code></pre>
</notextile>
2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 1 done, 1 running, 0 todo
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 child 7716 on compute13.1 exit 0 signal 0 success=true
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 success in 13 seconds
-2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 output 880b55fb4470b148a447ff38cacdd952+54
+2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 1 output dd755dbc8d49a67f4fe7dc843e4f10a6+54
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 wait for last 0 children to finish
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 2 done, 0 running, 0 todo
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 release job allocation
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 Freeze not implemented
2013-12-16_20:44:52 qr1hi-8i9sb-1pm1t02dezhupss 7575 collate
-2013-12-16_20:44:53 qr1hi-8i9sb-1pm1t02dezhupss 7575 output 880b55fb4470b148a447ff38cacdd952+54
+2013-12-16_20:44:53 qr1hi-8i9sb-1pm1t02dezhupss 7575 output dd755dbc8d49a67f4fe7dc843e4f10a6+54+K@qr1hi
2013-12-16_20:44:53 qr1hi-8i9sb-1pm1t02dezhupss 7575 finish
</code></pre>
</notextile>
-
-This concludes the first tutorial. In the next tutorial, we will "write a script to compute the hash.":tutorial-firstscript.html
---
layout: default
navsection: userguide
-navmenu: Tutorials
title: "Parallel Crunch tasks"
-
...
-h1. Parallel Crunch tasks
-
-In the tutorial "writing a crunch script,":tutorial-firstscript.html our script used a "for" loop to compute the md5 hashes for each file in sequence. This approach, while simple, is not able to take advantage of the compute cluster with multiple nodes and cores to speed up computation by running tasks in parallel. This tutorial will demonstrate how to create parallel Crunch tasks.
+In the previous tutorials, we used @arvados.job_setup.one_task_per_input_file()@ to automatically parallelize our jobs by creating a separate task per file. For some types of jobs, you may need to split the work up differently, for example creating tasks to process different segments of a single large file. In this this tutorial will demonstrate how to create Crunch tasks directly.
Start by entering the @crunch_scripts@ directory of your git repository:
Add the following code to compute the md5 hash of each file in a
-<pre><code class="userinput">{% include 'parallel_hash_script_py' %}</code></pre>
+<notextile> {% code 'parallel_hash_script_py' as python %} </notextile>
Make the file executable:
</code></pre>
</notextile>
-You should now be able to run your new script using Crunch, with "script" referring to our new "parallel-hash.py" script. We will use a different input from our previous examples. We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":tutorial-keep.html).
+You should now be able to run your new script using Crunch, with "script" referring to our new "parallel-hash.py" script. We will use a different input from our previous examples. We will use @887cd41e9c613463eab2f0d885c6dd96+83@ which consists of three files, "alice.txt", "bob.txt" and "carol.txt" (the example collection used previously in "fetching data from Arvados using Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html#dir).
<notextile>
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script": "parallel-hash.py",
- "script_version": "you:master",
+ "script_version": "<b>you</b>:master",
"script_parameters":
{
"input": "887cd41e9c613463eab2f0d885c6dd96+83"
Because the job ran in parallel, each instance of parallel-hash creates a separate @md5sum.txt@ as output. Arvados automatically collates theses files into a single collection, which is the output of the job:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv keep get e2ccd204bca37c77c0ba59fc470cd0f7+162</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv keep ls e2ccd204bca37c77c0ba59fc470cd0f7+162</span>
md5sum.txt
md5sum.txt
md5sum.txt
</code></pre>
</notextile>
-h2. The one job per file pattern
-
-This example demonstrates how to schedule a new task per file. Because this is a common pattern, the Crunch Python API contains a convenience function to "queue a task for each input file":{{site.baseurl}}/sdk/python/crunch-utility-libraries.html#one_task_per_input which reduces the amount of boilerplate code required to handle parallel jobs.
-
-Next, "Constructing a Crunch pipeline":tutorial-new-pipeline.html
---
layout: default
navsection: userguide
-navmenu: Tutorials
title: "Querying the Metadata Database"
-
...
-h1. Querying the Metadata Database
-
This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: Introduction to Crunch
+...
+
+In "getting data from Keep,":tutorial-keep.html#arv-get we downloaded a file from Keep and did some computation with it (specifically, computing the md5 hash of the complete file). While a straightforward way to accomplish a computational task, there are several obvious drawbacks to this approach:
+* Large files require significant time to download.
+* Very large files may exceed the scratch space of the local disk.
+* We are only able to use the local CPU to process the file.
+
+The Arvados "Crunch" framework is designed to support processing very large data batches (gigabytes to terabytes) efficiently, and provides the following benefits:
+* Increase concurrency by running tasks asynchronously, using many CPUs and network interfaces at once (especially beneficial for CPU-bound and I/O-bound tasks respectively).
+* Track inputs, outputs, and settings so you can verify that the inputs, settings, and sequence of programs you used to arrive at an output is really what you think it was.
+* Ensure that your programs and workflows are repeatable with different versions of your code, OS updates, etc.
+* Interrupt and resume long-running jobs consisting of many short tasks.
+* Maintain timing statistics automatically, so they're there when you want them.
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Running external programs"
-
+title: "Using Crunch to run external programs"
...
-h1. Running external programs
-
This tutorial demonstrates how to use Crunch to run an external program by writting a wrapper using the Python SDK.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
Add the following code to use the @md5sum@ program to compute the hash of each file in a collection:
-<pre><code class="userinput">{% include 'run_md5sum_py' %}</code></pre>
+<notextile> {% code 'run_md5sum_py' as python %} </notextile>
Make the file executable:
You should now be able to run your new script using Crunch, with "script" referring to our new "run-md5sum.py" script.
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
-{
- "script": "run-md5sum.py",
- "script_version": "you:master",
- "script_parameters":
- {
- "input": "c1bad4b39ca5a924e481008009d94e32+210"
- }
-}
-EOF</span>
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job create --job "$(cat the_job)"</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_pipeline <<EOF
{
- ...
- "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
- ...
-}
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
-{
- ...
- "output":"4d164b1658c261b9afc6b479130016a3+54",
- ...
+ "name":"Run external md5sum program",
+ "components":{
+ "do_hash":{
+ "script":"run-md5sum.py",
+ "script_parameters":{
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ "script_version":"<b>you</b>:master"
+ }
+ }
}
+EOF
+</span>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat ~/the_pipeline)"</span>
</code></pre>
</notextile>
+
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
layout: default
navsection: userguide
navmenu: Tutorials
-title: "Writing a Crunch script"
-
+title: "Writing a pipeline"
...
-h1. Writing a Crunch script
-
In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, navigate to _Compute %(rarr)→% Code repositories._ You should see two repositories, one named "arvados" (under the *name* column) and a second with your user name. Next to *name* is the column *push_url*. Copy the *push_url* cell associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
+On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
Next, on the Arvados virtual machine, clone your git repository:
Add the following code to compute the md5 hash of each file in a collection:
-<pre><code class="userinput">{% include 'tutorial_hash_script_py' %}</code></pre>
+<notextile> {% code 'tutorial_hash_script_py' as python %} </notextile>
Make the file executable:
notextile. <pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x hash.py</span></code></pre>
{% include 'notebox_begin' %}
-The below steps describe how to execute the script after committing changes to git. To test the script locally, please see the "debugging a crunch script":tutorial-job-debug.html page.
+The steps below describe how to execute the script after committing changes to git. To run a script locally for testing, please see "debugging a crunch script":{{site.baseurl}}/user/topics/tutorial-job-debug.html .
{% include 'notebox_end' %}
* [new branch] master -> master</code></pre>
</notextile>
-You should now be able to run your script using Crunch, similar to how we did it in the "first tutorial.":tutorial-job1.html The field @"script_version"@ should be @you:master@ to tell Crunch to run the script at the head of the "master" git branch, which you just uploaded.
+h2. Create a pipeline template
+
+Next, create a file that contains the pipeline definition:
<notextile>
-<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
-{
- "script": "hash.py",
- "script_version": "you:master",
- "script_parameters":
- {
- "input": "c1bad4b39ca5a924e481008009d94e32+210"
- }
-}
-EOF</span>
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job create --job "$(cat ~/the_job)"</span>
-{
- ...
- "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
- ...
-}
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cd ~</span>
+~$ <span class="userinput">cat >the_pipeline <<EOF
{
- ...
- "output":"880b55fb4470b148a447ff38cacdd952+54",
- ...
+ "name":"My first pipeline",
+ "components":{
+ "do_hash":{
+ "script":"hash.py",
+ "script_parameters":{
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ "script_version":"<b>you</b>:master"
+ }
+ }
}
-~/<b>you</b>/crunch_scripts$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+EOF
+</span></code></pre>
+</notextile>
+
+* @cat@ is a standard Unix utility that simply copies standard input to standard output
+* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
+* @>the_pipeline@ redirects standard output to a file called @the_pipeline@
+* @"name"@ is a human-readable name for the pipeline
+* @"components"@ is a set of scripts that make up the pipeline
+* The component is listed with a human-readable name (@"do_hash"@ in this example)
+* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}//repositories .
+* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection@.
+
+Now, use @arv pipeline_template create@ tell Arvados about your pipeline template:
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat the_pipeline)"</span>
</code></pre>
</notextile>
-Next, "debugging a crunch script.":tutorial-job-debug.html
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Storing and Retrieving data using Arvados Keep"
-
+title: "Storing and Retrieving data using Keep"
...
-h1. Storing and Retrieving data using Arvados Keep
-
This tutorial introduces you to the Arvados file storage system.
The output value @c1bad4b39ca5a924e481008009d94e32+210@ from @arv keep put@ is the Keep locator. This enables you to access the file you just uploaded, and is explained in the next section.
-h2. Putting a directory
+h2(#dir). Putting a directory
You can also use @arv keep put@ to add an entire directory:
</code></pre>
</notextile>
+The locator @887cd41e9c613463eab2f0d885c6dd96+83@ represents a collection with multiple files.
+
h1. Getting Data from Keep
-In Keep, information is stored in *data blocks*. Data blocks are normally between 1 byte and 64 megabytes in size. If a file exceeds the maximum size of a single data block, the file will be split across multiple data blocks until the entire file can be stored. These data blocks may be stored and replicated across multiple disks, servers, or clusters. Each data block has its own identifier for the contents of that specific data block.
+h2. Using Workbench
-In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
+You may access collections through the "Collections section of Arvados Workbench":https://{{ site.arvados_workbench_host }}/collections located at "https://{{ site.arvados_workbench_host }}/collections":https://{{ site.arvados_workbench_host }}/collections . You can also access individual collections and individual files within a collection. Some examples:
-In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to keep in the previous section. First let us examine the contents of this collection using @arv keep get@:
+* "https://{{ site.arvados_workbench_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://{{ site.arvados_workbench_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
+* "https://{{ site.arvados_workbench_host }}/collections/887cd41e9c613463eab2f0d885c6dd96+83/alice.txt":https://{{ site.arvados_workbench_host }}/collections/887cd41e9c613463eab2f0d885c6dd96+83/alice.txt
+
+h2(#arv-get). Using arv-get
+
+You can view the contents of a collection using @arv keep ls@:
<notextile>
-<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
-. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep ls c1bad4b39ca5a924e481008009d94e32+210</span>
+var-GS000016015-ASM.tsv.bz2
</code></pre>
-</notextile>
-The command @arv keep get@ fetches the contents of the locator @c1bad4b39ca5a924e481008009d94e32+210@. This is a locator for a collection data block, so it fetches the contents of the collection. In this example, this collection consists of a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, <code>204e43b8a1185621ca55a94839582e6f+67108864</code>, <code>b9677abbac956bd3e86b1deb28dfac03+67108864</code>, <code>fc15aff2a762b13f521baf042140acec+67108864</code>, <code>323d2a3ce20370c4ca1d3462a344f8fd+25885655</code>.
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep ls 887cd41e9c613463eab2f0d885c6dd96+83</span>
+alice.txt
+bob.txt
+carol.txt
+</code></pre>
+</notextile>
-Let's use @arv keep get@ to download the first datablock:
+Use @-s@ to print file sizes rounded up to the nearest kilobyte:
-notextile. <pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1</span></code></pre>
+<notextile>
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210</span>
+221887 var-GS000016015-ASM.tsv.bz2
+</code></pre>
+</notextile>
-Let's look at the size and compute the md5 hash of @block1@:
+Use @arv keep get@ to download the contents of a collection and place it in the directory specified in the second argument (in this example, @.@ for the current directory):
<notextile>
-<pre><code>/scratch/<b>you</b>$ <span class="userinput">ls -l block1</span>
--rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
-/scratch/<b>you</b>$ <span class="userinput">md5sum block1</span>
-204e43b8a1185621ca55a94839582e6f block1
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210/ .</span>
</code></pre>
</notextile>
-Notice that the block identifer <code>204e43b8a1185621ca55a94839582e6f+67108864</code> of:
-* the md5 hash @204e43b8a1185621ca55a94839582e6f@ which matches the md5 hash of @block1@
-* a size hint @67108864@ which matches the size of @block1@
-
-Next, let's use @arv keep get@ to download and reassemble @var-GS000016015-ASM.tsv.bz2@ using the following command:
+You can also download indvidual files:
<notextile>
-<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2 .</span>
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep get 887cd41e9c613463eab2f0d885c6dd96+83/alice.txt .</span>
</code></pre>
+</notextile>
-This downloads the file @var-GS000016015-ASM.tsv.bz2@ described by collection @c1bad4b39ca5a924e481008009d94e32+210@ from Keep and places it into the local directory. Now that we have the file, we can compute the md5 hash of the complete file:
+With a local copy of the file, we can do some computation, for example computing the md5 hash of the complete file:
<notextile>
<pre><code>/scratch/<b>you</b>$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
</code></pre>
</notextile>
-h2. Accessing Collections
+h2. Using arv-mount
-There are a couple of other ways to access a collection. You may view the contents of a collection using @arv keep ls@:
+Use @arv-mount@ to take advantage of the "File System in User Space / FUSE":http://fuse.sourceforge.net/ feature of the Linux kernel to mount a Keep collection as if it were a regular directory tree.
<notextile>
-<pre><code>/scratch/<b>you</b>$ <span class="userinput">arv keep ls c1bad4b39ca5a924e481008009d94e32+210</span>
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">mkdir mnt</span>
+/scratch/<b>you</b>$ <span class="userinput">arv-mount --collection c1bad4b39ca5a924e481008009d94e32+210 mnt &</span>
+/scratch/<b>you</b>$ <span class="userinput">cd mnt</span>
+/scratch/<b>you</b>/mnt$ <span class="userinput">ls</span>
var-GS000016015-ASM.tsv.bz2
-/scratch/<b>you</b>$ <span class="userinput">arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210</span>
-221887 var-GS000016015-ASM.tsv.bz2
+/scratch/<b>you</b>/mnt$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+/scratch/<b>you</b>/mnt$ <span class="userinput">cd ..</span>
+/scratch/<b>you</b>$ <span class="userinput">fusermount -u mnt</span>
</code></pre>
</notextile>
-* @-s@ prints file sizes in kilobytes
+You can also mount the entire Keep namespace in "magic directory" mode:
-You may also access through the Arvados Workbench using a URI similar to this, where the last part of the path is the Keep locator:
+<notextile>
+<pre><code>/scratch/<b>you</b>$ <span class="userinput">mkdir mnt</span>
+/scratch/<b>you</b>$ <span class="userinput">arv-mount mnt &</span>
+/scratch/<b>you</b>$ <span class="userinput">cd mnt/c1bad4b39ca5a924e481008009d94e32+210</span>
+/scratch/<b>you</b>/mnt/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">ls</span>
+var-GS000016015-ASM.tsv.bz2
+/scratch/<b>you</b>/mnt/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
+44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+/scratch/<b>you</b>/mnt/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">cd ../..</span>
+/scratch/<b>you</b>$ <span class="userinput">fusermount -u mnt</span>
+</code></pre>
+</notextile>
-"https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
+Using @arv-mount@ has several significant benefits:
-You are now ready to proceed to the next tutorial, "running a crunch job.":tutorial-job1.html
+* You can browse, open and read Keep entries as if they are regular files.
+* It is easy for existing tools to access files in Keep.
+* Data is downloaded on demand, it is not necessary to download an entire file or collection to start processing
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Constructing a Crunch pipeline"
-
+title: "Writing a multi-step pipeline"
...
-h1. Constructing a Crunch pipeline
-
A pipeline in Arvados is a collection of crunch scripts, in which the output from one script may be used as the input to another script.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples.
+
h2. Create a new script
-Our second script will filter the output of @parallel_hash.py@ and only include hashes that start with 0. Create a new script in @crunch_scripts/@ called @0-filter.py@:
+Our second script will filter the output of @hash.py@ and only include hashes that start with 0. Create a new script in <notextile><code>~/<b>you</b>/crunch_scripts/</code></notextile> called @0-filter.py@:
-<pre><code class="userinput">{% include '0_filter_py' %}</code></pre>
+<notextile> {% code '0_filter_py' as python %} </notextile>
Now add it to git:
<notextile>
-<pre><code>$ <span class="userinput">git add 0-filter.py</span>
-$ <span class="userinput">git commit -m"zero filter"</span>
-$ <span class="userinput">git push origin master</span>
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">chmod +x 0-filter.py</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">git add 0-filter.py</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">git commit -m"zero filter"</span>
+~/<b>you</b>/crunch_scripts$ <span class="userinput">git push origin master</span>
</code></pre>
</notextile>
Next, create a file that contains the pipeline definition:
<notextile>
-<pre><code>$ <span class="userinput">cat >the_pipeline <<EOF
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_pipeline <<EOF
{
- "name":"my_first_pipeline",
+ "name":"Filter md5 hash values",
"components":{
"do_hash":{
- "script":"parallel-hash.py",
+ "script":"hash.py",
"script_parameters":{
- "input": "887cd41e9c613463eab2f0d885c6dd96+83"
+ "input":{
+ "required": true,
+ "dataclass": "Collection"
+ }
},
- "script_version":"you:master"
+ "script_version":"<b>you</b>:master"
},
"filter":{
"script":"0-filter.py",
"output_of":"do_hash"
}
},
- "script_version":"you:master"
+ "script_version":"<b>you</b>:master"
}
}
}
EOF
-</code></pre>
+</span></code></pre>
</notextile>
-* @"name"@ is a human-readable name for the pipeline
-* @"components"@ is a set of scripts that make up the pipeline
-* Each component is listed with a human-readable name (@"do_hash"@ and @"filter"@ in this example)
-* Each item in @"components"@ is a single Arvados job, and uses the same format that we saw previously with @arv job create@
-* @"output_of"@ indicates that the @"input"@ of @"filter"@ is the @"output"@ of the @"do_hash"@ component. This is a _dependency_. Arvados uses the dependencies between jobs to automatically determine the correct order to run the jobs.
+* @"output_of"@ indicates that the @input@ of the @do_hash@ component is connected to the @output@ of @filter@. This is a _dependency_. Arvados uses the dependencies between jobs to automatically determine the correct order to run the jobs.
Now, use @arv pipeline_template create@ tell Arvados about your pipeline template:
<notextile>
-<pre><code>$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat the_pipeline)"</span>
-qr1hi-p5p6p-xxxxxxxxxxxxxxx
+<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">arv pipeline_template create --pipeline-template "$(cat ~/the_pipeline)"</span>
</code></pre>
</notextile>
-Your new pipeline template will appear on the Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates page.
-
-h3. Running a pipeline
-
-Run the pipeline using @arv pipeline run@, using the UUID that you received from @arv pipeline create@:
-
-<notextile>
-<pre><code>$ <span class="userinput">arv pipeline run --template qr1hi-p5p6p-xxxxxxxxxxxxxxx</span>
-2013-12-16 14:08:40 +0000 -- pipeline_instance qr1hi-d1hrv-vxzkp38nlde9yyr
-do_hash qr1hi-8i9sb-hoyc2u964ecv1s6 queued 2013-12-16T14:08:40Z
-filter - -
-2013-12-16 14:08:51 +0000 -- pipeline_instance qr1hi-d1hrv-vxzkp38nlde9yyr
-do_hash qr1hi-8i9sb-hoyc2u964ecv1s6 e2ccd204bca37c77c0ba59fc470cd0f7+162
-filter qr1hi-8i9sb-w5k40fztqgg9i2x queued 2013-12-16T14:08:50Z
-2013-12-16 14:09:01 +0000 -- pipeline_instance qr1hi-d1hrv-vxzkp38nlde9yyr
-do_hash qr1hi-8i9sb-hoyc2u964ecv1s6 e2ccd204bca37c77c0ba59fc470cd0f7+162
-filter qr1hi-8i9sb-w5k40fztqgg9i2x 735ac35adf430126cf836547731f3af6+56
-</code></pre>
-</notextile>
-
-This instantiates your pipeline and displays a live feed of its status. The new pipeline instance will also show up on the Workbench %(rarr)→% Compute %(rarr)→% Pipeline instances page.
-
-Arvados adds each pipeline component to the job queue as its dependencies are satisfied (or immediately if it has no dependencies) and finishes when all components are completed or failed and there is no more work left to do.
-
-The Keep locators of the output of each of @"do_hash"@ and @"filter"@ component are available from the output log shown above. The output is also available on the Workbench by navigating to %(rarr)→% Compute %(rarr)→% Pipeline instances %(rarr)→% pipeline uuid under the *id* column %(rarr)→% components.
-
-<notextile>
-<pre><code>$ <span class="userinput">arv keep get e2ccd204bca37c77c0ba59fc470cd0f7+162/md5sum.txt</span>
-0f1d6bcf55c34bed7f92a805d2d89bbf alice.txt
-504938460ef369cd275e4ef58994cffe bob.txt
-8f3b36aff310e06f3c5b9e95678ff77a carol.txt
-$ <span class="userinput">arv keep get 735ac35adf430126cf836547731f3af6+56</span>
-0f1d6bcf55c34bed7f92a805d2d89bbf alice.txt
-</code></pre>
-</notextile>
-
-Indeed, the filter has picked out just the "alice" file as having a hash that starts with 0.
-
-h3. Running a pipeline with different parameters
-
-Notice that the pipeline definition explicitly specifies the Keep locator for the input:
-
-<notextile>
-<pre><code>...
- "do_hash":{
- "script_parameters":{
- "input": "887cd41e9c613463eab2f0d885c6dd96+83"
- },
- }
-...
-</code></pre>
-</notextile>
-
-What if we want to run the pipeline on a different input block? One option is to define a new pipeline template, but would potentially result in clutter with many pipeline templates defined for one-off jobs. Instead, you can override values in the input of the component like this:
-
-<notextile>
-<pre><code>$ <span class="userinput">arv pipeline run --template qr1hi-d1hrv-vxzkp38nlde9yyr do_hash::input=33a9f3842b01ea3fdf27cc582f5ea2af+242</span>
-2013-12-17 20:31:24 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
-do_hash qr1hi-8i9sb-rffhuay4jryl2n2 queued 2013-12-17T20:31:24Z
-filter - -
-2013-12-17 20:31:34 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
-do_hash qr1hi-8i9sb-rffhuay4jryl2n2 {:done=>1, :running=>1, :failed=>0, :todo=>0}
-filter - -
-2013-12-17 20:31:44 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
-do_hash qr1hi-8i9sb-rffhuay4jryl2n2 {:done=>1, :running=>1, :failed=>0, :todo=>0}
-filter - -
-2013-12-17 20:31:55 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
-do_hash qr1hi-8i9sb-rffhuay4jryl2n2 880b55fb4470b148a447ff38cacdd952+54
-filter qr1hi-8i9sb-j347g1sqovdh0op queued 2013-12-17T20:31:55Z
-2013-12-17 20:32:05 +0000 -- pipeline_instance qr1hi-d1hrv-tlkq20687akys8e
-do_hash qr1hi-8i9sb-rffhuay4jryl2n2 880b55fb4470b148a447ff38cacdd952+54
-filter qr1hi-8i9sb-j347g1sqovdh0op fb728f0ffe152058fa64b9aeed344cb5+54
-</code></pre>
-</notextile>
-
-Now check the output:
-
-<notextile>
-<pre><code>$ <span class="userinput">arv keep ls -s fb728f0ffe152058fa64b9aeed344cb5+54</span>
-0 0-filter.txt
-</code></pre>
-</notextile>
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page.
-Here the filter script output is empty, so none of the files in the collection have hash code that start with 0.
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Running a pipeline using Workbench"
+...
+
+notextile. <div class="spaced-out">
+
+# Go to "Collections":http://{{ site.arvados_workbench_host }}/collections .
+# On the collections page, go to the search box <span class="glyphicon glyphicon-search"></span> and search for "tutorial".
+# This should yield a collection with the contents "var-GS000016015-ASM.tsv.bz2"
+# Click on the check box to the left of "var-GS000016015-ASM.tsv.bz2". This puts the collection in your persistent selection list. Click on the paperclip <span class="glyphicon glyphicon-paperclip"></span> in the upper right to get a dropdown menu listing your current selections.
+# Go to "Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_templates .
+# Look for a pipeline named "Tutorial pipeline".
+# Click on the play button <span class="glyphicon glyphicon-play"></span> to the left of "Tutorial pipeline". This will take you to a new page to configure the pipeline.
+# Under *parameter* look for "input". Set the value of "input" by clicking on on "none" to get a editing popup. At the top of the selection list in the editing popup will be the collection that you selected in step 4.
+# You can now click on "Run pipeline" in the upper right to start the pipeline.
+# This will reload the page with the pipeline queued to run.
+# The page refreshes automatically every 15 seconds. You should see the pipeline running, and then finish successfully.
+# Once it is finished, click on the link under the *output* column. This will take you to the collection page for the output of this pipeline.
+# Click on "md5sum.txt" to see the actual file that is the output of this pipeline.
+# On the collection page, click on the "Provenance graph" tab to see a graphical representation of the data elements and pipelines that were involved in generating this file.
+
+notextile. </div>
+
require 'zenweb'
+require 'liquid'
module ZenwebLiquid
VERSION = '0.0.1'
##
# Render a page's liquid and return the intermediate result
def liquid template, content, page, binding = TOPLEVEL_BINDING
- require 'liquid'
Liquid::Template.file_system = Liquid::LocalFileSystem.new(File.join(File.dirname(Rake.application().rakefile), "_includes"))
unless defined? @liquid_template
@liquid_template = Liquid::Template.parse(template)
@liquid_template.render(vars)
end
end
+
+ class LiquidCode < Liquid::Include
+ Syntax = /(#{Liquid::QuotedFragment}+)(\s+(?:as)\s+(#{Liquid::QuotedFragment}+))?/o
+
+ def initialize(tag_name, markup, tokens)
+ Liquid::Tag.instance_method(:initialize).bind(self).call(tag_name, markup, tokens)
+
+ if markup =~ Syntax
+ @template_name = $1
+ @language = $3
+ @attributes = {}
+ else
+ raise SyntaxError.new("Error in tag 'code' - Valid syntax: include '[code_file]' as '[language]'")
+ end
+ end
+
+ def render(context)
+ require 'coderay'
+
+ partial = load_cached_partial(context)
+ html = ''
+
+ context.stack do
+ html = CodeRay.scan(partial.root.nodelist.join, @language).div
+ end
+
+ html
+ end
+
+ Liquid::Template.register_tag('code', LiquidCode)
+ end
end
none /cgroup cgroup defaults 0 0
$ sudo mount /cgroup
</pre>
-
- 3. Enable IPv4 forwarding:
-
- <pre>
- $ grep ipv4.ip_forward /etc/sysctl.conf
- net.ipv4.ip_forward=1
- $ sudo sysctl net.ipv4.ip_forward=1
- </pre>
- 4. [Download and run a docker binary from docker.io.](http://docs.docker.io/en/latest/installation/binaries/)
+ 3. [Download and run a docker binary from docker.io.](http://docs.docker.io/en/latest/installation/binaries/)
-* Ruby (any version)
+* Ruby (version 1.9.3 or greater)
* sudo privileges to run `debootstrap`
Building
--------
-1. Copy `config.yml.example` to `config.yml` and edit it with settings
- for your installation.
-2. Run `make` to build the following Docker images:
+Type `./build.sh` to configure and build the following Docker images:
* arvados/api - the Arvados API server
* arvados/doc - Arvados documentation
* arvados/workbench - the Arvados console
* arvados/sso - the Arvados single-signon authentication server
- You may also build Docker images for individual Arvados services:
-
- $ make api-image
- $ make doc-image
- $ make warehouse-image
- $ make workbench-image
- $ make sso-image
+`build.sh` will generate reasonable defaults for all configuration
+settings. If you want more control over the way Arvados is
+configured, first copy `config.yml.example` to `config.yml` and edit
+it with appropriate configuration settings, and then run `./build.sh`.
Running
-------
# == Synopsis
#
-# wh-run-pipeline-instance --template pipeline-template-uuid [options] [--] [parameters]
-# wh-run-pipeline-instance --instance pipeline-instance-uuid [options]
+# arv-run-pipeline-instance --template pipeline-template-uuid [options] [--] [parameters]
+# arv-run-pipeline-instance --instance pipeline-instance-uuid [options]
#
# Satisfy a pipeline template by finding or submitting a mapreduce job
# for each pipeline component.
# to finish. Just find out whether jobs are finished,
# queued, or running for each component
#
-# [--create-instance-only] Do not try to satisfy any components. Just
+# [--submit] Do not try to satisfy any components. Just
# create an instance, print its UUID to
# stdout, and exit.
#
begin
require 'rubygems'
- require 'google/api_client'
require 'json'
require 'pp'
require 'trollop'
-rescue LoadError
+ require 'google/api_client'
+rescue LoadError => l
+ puts $:
abort <<-EOS
-#{$0}: fatal: some runtime dependencies are missing.
+#{$0}: fatal: #{l.message}
+Some runtime dependencies may be missing.
Try: gem install pp google-api-client json trollop
EOS
end
"UUID of pipeline instance.",
:short => :none,
:type => :string)
- opt(:create_instance_only,
+ opt(:submit,
"Do not try to satisfy any components. Just create a pipeline instance and output its UUID.",
:short => :none,
:type => :boolean)
+ opt(:run_here,
+ "Manage the pipeline in process.",
+ :short => :none,
+ :type => :boolean)
stop_on [:'--']
end
$options = Trollop::with_standard_exception_handling p do
$debuglevel = $options[:debug_level] || ($options[:debug] && 1) || 0
if $options[:instance]
- if $options[:template] or $options[:create_instance_only]
- abort "#{$0}: syntax error: --instance cannot be combined with --template or --create-instance-only."
+ if $options[:template] or $options[:submit]
+ abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
end
elsif not $options[:template]
abort "#{$0}: syntax error: you must supply a --template or --instance."
end
+if $options[:run_here] == $options[:submit]
+ abort "#{$0}: syntax error: you must supply either --run-here or --submit."
+end
+
+# Suppress SSL certificate checks if ARVADOS_API_HOST_INSECURE
+
+module Kernel
+ def suppress_warnings
+ original_verbosity = $VERBOSE
+ $VERBOSE = nil
+ result = yield
+ $VERBOSE = original_verbosity
+ return result
+ end
+end
+
+if ENV['ARVADOS_API_HOST_INSECURE']
+ suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
+end
+
# Set up the API client.
$client ||= Google::APIClient.
if p.is_a? Hash and p[:output_of] == cname.to_s
debuglog "parameter #{c2name}::#{pname} == #{c[:job][:output]}"
c2[:script_parameters][pname] = c[:job][:output]
+ moretodo = true
end
end
end
elsif c[:job][:running] ||
(!c[:job][:started_at] && !c[:job][:cancelled_at])
- moretodo ||= !@options[:no_wait]
+ moretodo = true
elsif c[:job][:cancelled_at]
debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
end
@instance[:components] = @components
@instance[:active] = moretodo
report_status
+
+ if @options[:no_wait]
+ moretodo = false
+ end
+
if moretodo
begin
sleep 10
end
end
end
- @instance[:success] = @components.reject { |cname,c| c[:job] and c[:job][:success] }.empty?
+
+ ended = 0
+ succeeded = 0
+ failed = 0
+ @components.each do |cname, c|
+ if c[:job]
+ if c[:job][:finished_at]
+ ended += 1
+ if c[:job][:success] == true
+ succeeded += 1
+ end
+ end
+ end
+ end
+
+ if ended == @components.length
+ @instance[:active] = false
+ @instance[:success] = (succeeded == @components.length)
+ end
+
@instance.save
end
end
runner.apply_parameters(p.leftovers)
runner.setup_instance
- if $options[:create_instance_only]
+ if $options[:submit]
runner.instance.save
puts runner.instance[:uuid]
else
$command .=
"&& perl -";
}
- $ENV{"PYTHONPATH"} =~ s{^}{:} if $ENV{"PYTHONPATH"};
- $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/sdk/python}; # xxx hack
- $ENV{"PYTHONPATH"} =~ s{^}{$ENV{CRUNCH_SRC}/arvados/sdk/python:}; # xxx hack
- $ENV{"PYTHONPATH"} =~ s{$}{:/usr/local/arvados/src/sdk/python}; # xxx hack
$command .=
"&& exec arv-mount $ENV{TASK_KEEPMOUNT} --exec $ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
my @execargs = ('bash', '-c', $command);
from stream import *
import config
import errors
+import util
def normalize_stream(s, stream):
stream_tokens = [s]
class CollectionReader(object):
def __init__(self, manifest_locator_or_text):
- if re.search(r'^[a-f0-9]{32}\+\d+(\+\S)*$', manifest_locator_or_text):
+ if re.search(r'^[a-f0-9]{32}(\+\d+)?(\+\S+)*$', manifest_locator_or_text):
self._manifest_locator = manifest_locator_or_text
self._manifest_text = None
- else:
+ elif re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)*( \d+:\d+:\S+)+\n', manifest_locator_or_text):
self._manifest_text = manifest_locator_or_text
self._manifest_locator = None
+ else:
+ raise errors.ArgumentError(
+ "Argument to CollectionReader must be a manifest or a collection UUID")
self._streams = None
def __enter__(self):
# errors.py - Arvados-specific exceptions.
+class ArgumentError(Exception):
+ pass
class SyntaxError(Exception):
pass
class AssertionError(Exception):
# wait until the driver is finished initializing
operations.initlock.wait()
+ rc = 255
try:
rc = subprocess.call(args.exec_args, shell=False)
- except:
- rc = 255
+ except OSError as e:
+ sys.stderr.write('arv-mount: %s -- exec %s\n' % (str(e), args.exec_args))
+ rc = e.errno
+ except Exception as e:
+ sys.stderr.write('arv-mount: %s\n' % str(e))
finally:
subprocess.call(["fusermount", "-u", "-z", args.mountpoint])
parser = argparse.ArgumentParser(
description='Read manifest on standard input and put normalized manifest on standard output.')
+parser.add_argument('--extract', type=str, help="The file to extract from the input manifest")
+
args = parser.parse_args()
import arvados
cr = arvados.CollectionReader(r)
-print cr.manifest_text()
+if args.extract:
+ i = args.extract.rfind('/')
+ if i == -1:
+ stream = '.'
+ fn = args.extract
+ else:
+ stream = args.extract[:i]
+ fn = args.extract[(i+1):]
+ for s in cr.all_streams():
+ if s.name() == stream:
+ if fn in s.files():
+ sys.stdout.write(s.files()[fn].as_manifest())
+else:
+ sys.stdout.write(cr.manifest_text())
'bin/arv-put',
'bin/arv-mount',
'bin/arv-ls',
+ 'bin/arv-normalize',
],
install_requires=[
'python-gflags',
os.environ['KEEP_LOCAL_STORE'] = '/tmp'
LocalCollectionWriterTest().runTest()
def runTest(self):
- cr = arvados.CollectionReader('d6c3b8e571f1b81ebb150a45ed06c884+114')
+ cr = arvados.CollectionReader('d6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle')
got = []
for s in cr.all_streams():
for f in s.all_files():
/config/api.clinicalfuture.com.*
/config/database.yml
/config/initializers/omniauth.rb
+/config/application.yml
# asset cache
/public/assets/
# Bundle edge Rails instead:
# gem 'rails', :git => 'git://github.com/rails/rails.git'
-#gem 'sqlite3'
+group :test, :development do
+ gem 'sqlite3'
+end
+
+# This might not be needed in :test and :development, but we load it
+# anyway to make sure it always gets in Gemfile.lock and to help
+# reveal install problems sooner rather than later.
gem 'pg'
# Start using multi_json once we are on Rails 3.2;
gem 'redis'
gem 'test_after_commit', :group => :test
+
+gem 'google-api-client', '~> 0.6.3'
+gem 'trollop'
+
+gem 'arvados-cli', '>= 0.1.20140311162926'
activemodel (>= 3.0.0)
activesupport (>= 3.0.0)
rack (>= 1.1.0)
+ addressable (2.3.5)
andand (1.3.3)
arel (3.0.2)
+ arvados-cli (0.1.20140311162926)
+ activesupport (~> 3.2, >= 3.2.13)
+ andand (~> 1.3, >= 1.3.3)
+ curb (~> 0.8)
+ google-api-client (~> 0.6.3)
+ json (~> 1.7, >= 1.7.7)
+ oj (~> 2.0, >= 2.0.3)
+ trollop (~> 2.0)
+ autoparse (0.3.3)
+ addressable (>= 2.3.1)
+ extlib (>= 0.9.15)
+ multi_json (>= 1.0.0)
builder (3.0.4)
capistrano (2.15.5)
highline
coffee-script-source
execjs
coffee-script-source (1.6.3)
+ curb (0.8.5)
daemon_controller (1.1.7)
erubis (2.7.0)
execjs (2.0.2)
+ extlib (0.9.16)
faraday (0.8.8)
multipart-post (~> 1.2.0)
+ google-api-client (0.6.4)
+ addressable (>= 2.3.2)
+ autoparse (>= 0.3.3)
+ extlib (>= 0.9.15)
+ faraday (~> 0.8.4)
+ jwt (>= 0.1.5)
+ launchy (>= 2.1.1)
+ multi_json (>= 1.0.0)
+ signet (~> 0.4.5)
+ uuidtools (>= 2.1.0)
hashie (1.2.0)
highline (1.6.20)
hike (1.2.3)
json (1.8.1)
jwt (0.1.8)
multi_json (>= 1.5)
+ launchy (2.4.2)
+ addressable (~> 2.3)
libv8 (3.16.14.3)
mail (2.5.4)
mime-types (~> 1.16)
railties (~> 3.2.0)
sass (>= 3.1.10)
tilt (~> 1.3)
+ signet (0.4.5)
+ addressable (>= 2.2.3)
+ faraday (~> 0.8.1)
+ jwt (>= 0.1.5)
+ multi_json (>= 1.0.0)
sprockets (2.2.2)
hike (~> 1.2)
multi_json (~> 1.0)
rack (~> 1.0)
tilt (~> 1.1, != 1.3.0)
+ sqlite3 (1.3.8)
test_after_commit (0.2.2)
therubyracer (0.12.0)
libv8 (~> 3.16.14.0)
treetop (1.4.15)
polyglot
polyglot (>= 0.3.1)
+ trollop (2.0)
tzinfo (0.3.38)
uglifier (2.3.0)
execjs (>= 0.3.0)
json (>= 1.8.0)
+ uuidtools (2.1.4)
PLATFORMS
ruby
DEPENDENCIES
acts_as_api
andand
+ arvados-cli (>= 0.1.20140311162926)
coffee-rails (~> 3.2.0)
+ google-api-client (~> 0.6.3)
jquery-rails
multi_json
oj
redis
rvm-capistrano
sass-rails (>= 3.2.0)
+ sqlite3
test_after_commit
therubyracer
+ trollop
uglifier (>= 1.0.3)
if @object.save
show
else
- render_error "Save failed"
+ raise "Save failed"
end
end
if @object.update_attributes attrs_to_update
show
else
- render_error "Update failed"
+ raise "Update failed"
end
end
def render_error(e)
logger.error e.inspect
- logger.error e.backtrace.collect { |x| x + "\n" }.join('') if e.backtrace
+ if e.respond_to? :backtrace and e.backtrace
+ logger.error e.backtrace.collect { |x| x + "\n" }.join('')
+ end
if @object and @object.errors and @object.errors.full_messages and not @object.errors.full_messages.empty?
errors = @object.errors.full_messages
else
when '=', '<', '<=', '>', '>=', 'like'
if operand.is_a? String
cond_out << "#{table_name}.#{attr} #{operator} ?"
- if operator.match(/[<=>]/) and
- model_class.attribute_column(attr).type == :datetime
+ if (# any operator that operates on value rather than
+ # representation:
+ operator.match(/[<=>]/) and
+ model_class.attribute_column(attr).type == :datetime)
operand = Time.parse operand
end
param_out << operand
if supplied_token
api_client_auth = ApiClientAuthorization.
includes(:api_client, :user).
- where('api_token=? and (expires_at is null or expires_at > now())', supplied_token).
+ where('api_token=? and (expires_at is null or expires_at > CURRENT_TIMESTAMP)', supplied_token).
first
if api_client_auth.andand.user
session[:user_id] = api_client_auth.user.id
end
def render *opts
- response = opts.first[:json]
- if response.is_a?(Hash) &&
- params[:_profile] &&
- Thread.current[:request_starttime]
- response[:_profile] = {
- request_time: Time.now - Thread.current[:request_starttime]
- }
+ if opts.first
+ response = opts.first[:json]
+ if response.is_a?(Hash) &&
+ params[:_profile] &&
+ Thread.current[:request_starttime]
+ response[:_profile] = {
+ request_time: Time.now - Thread.current[:request_starttime]
+ }
+ end
end
super *opts
end
resource_attrs[:user_id] =
User.where(uuid: resource_attrs.delete(:owner_uuid)).first.andand.id
end
+ resource_attrs[:api_client_id] = Thread.current[:api_client].id
super
end
api_client_auth = ApiClientAuthorization.
new(user: user,
api_client: @api_client,
- created_by_ip_address: remote_ip)
+ created_by_ip_address: remote_ip,
+ scopes: ["all"])
api_client_auth.save!
if callback_url.index('?')
def self.searchable_columns
self.columns.collect do |col|
- if [:string, :text, :datetime].index(col.type) && col.name != 'owner_uuid'
+ if [:string, :text, :datetime, :integer].index(col.type) && col.name != 'owner_uuid'
col.name
end
end.compact
def update_modified_by_fields
self.created_at ||= Time.now
- self.owner_uuid ||= current_default_owner
+ self.owner_uuid ||= current_default_owner if self.respond_to? :owner_uuid=
self.modified_at = Time.now
self.modified_by_user_uuid = current_user ? current_user.uuid : nil
self.modified_by_client_uuid = current_api_client ? current_api_client.uuid : nil
--- /dev/null
+class Blob
+
+ # In order to get a Blob from Keep, you have to prove either
+ # [a] you have recently written it to Keep yourself, or
+ # [b] apiserver has recently decided that you should be able to read it
+ #
+ # To ensure that the requestor of a blob is authorized to read it,
+ # Keep requires clients to timestamp the blob locator with an expiry
+ # time, and to sign the timestamped locator with their API token.
+ #
+ # A signed blob locator has the form:
+ # locator_hash +A blob_signature @ timestamp
+ # where the timestamp is a Unix time expressed as a hexadecimal value,
+ # and the blob_signature is the signed locator_hash + API token + timestamp.
+ #
+ class InvalidSignatureError < StandardError
+ end
+
+ # Blob.sign_locator: return a signed and timestamped blob locator.
+ #
+ # The 'opts' argument should include:
+ # [required] :key - the Arvados server-side blobstore key
+ # [required] :api_token - user's API token
+ # [optional] :ttl - number of seconds before this request expires
+ #
+ def self.sign_locator blob_locator, opts
+ # We only use the hash portion for signatures.
+ blob_hash = blob_locator.split('+').first
+
+ # Generate an expiry timestamp (seconds since epoch, base 16)
+ timestamp = (Time.now.to_i + (opts[:ttl] || 600)).to_s(16)
+ # => "53163cb4"
+
+ # Generate a signature.
+ signature =
+ generate_signature opts[:key], blob_hash, opts[:api_token], timestamp
+
+ blob_locator + '+A' + signature + '@' + timestamp
+ end
+
+ # Blob.verify_signature
+ # Safely verify the signature on a blob locator.
+ # Return value: true if the locator has a valid signature, false otherwise
+ # Arguments: signed_blob_locator, opts
+ #
+ def self.verify_signature *args
+ begin
+ self.verify_signature! *args
+ true
+ rescue Blob::InvalidSignatureError
+ false
+ end
+ end
+
+ # Blob.verify_signature!
+ # Verify the signature on a blob locator.
+ # Return value: true if the locator has a valid signature
+ # Arguments: signed_blob_locator, opts
+ # Exceptions:
+ # Blob::InvalidSignatureError if the blob locator does not include a
+ # valid signature
+ #
+ def self.verify_signature! signed_blob_locator, opts
+ blob_hash = signed_blob_locator.split('+').first
+ given_signature, timestamp = signed_blob_locator.
+ split('+A').last.
+ split('+').first.
+ split('@')
+
+ if !timestamp
+ raise Blob::InvalidSignatureError.new 'No signature provided.'
+ end
+ if !timestamp.match /^[\da-f]+$/
+ raise Blob::InvalidSignatureError.new 'Timestamp is not a base16 number.'
+ end
+ if timestamp.to_i(16) < Time.now.to_i
+ raise Blob::InvalidSignatureError.new 'Signature expiry time has passed.'
+ end
+
+ my_signature =
+ generate_signature opts[:key], blob_hash, opts[:api_token], timestamp
+
+ if my_signature != given_signature
+ raise Blob::InvalidSignatureError.new 'Signature is invalid.'
+ end
+
+ true
+ end
+
+ def self.generate_signature key, blob_hash, api_token, timestamp
+ OpenSSL::HMAC.hexdigest('sha1', key,
+ [blob_hash,
+ api_token,
+ timestamp].join('@'))
+ end
+end
MAX_SLOTS = 64
- @@confdir = if Rails.configuration.respond_to? :dnsmasq_conf_dir
- Rails.configuration.dnsmasq_conf_dir
- elsif File.exists? '/etc/dnsmasq.d/.'
- '/etc/dnsmasq.d'
- else
- nil
- end
+ @@confdir = Rails.configuration.dnsmasq_conf_dir
@@domain = Rails.configuration.compute_node_domain rescue `hostname --domain`.strip
@@nameservers = Rails.configuration.compute_node_nameservers
def start!(ping_url_method)
ensure_permission_to_update
ping_url = ping_url_method.call({ uuid: self.uuid, ping_secret: self.info[:ping_secret] })
- if (Rails.configuration.compute_node_ec2run_args rescue false) and
- (Rails.configuration.compute_node_ami rescue false)
+ if (Rails.configuration.compute_node_ec2run_args and
+ Rails.configuration.compute_node_ami)
ec2_args = ["--user-data '#{ping_url}'",
"-t c1.xlarge -n 1",
Rails.configuration.compute_node_ec2run_args,
t.collect { |r| r[2] }.inject(0.0) { |sum,a| sum += a } / t.size
end
+ def self.queue
+ self.where('active = true')
+ end
+
protected
def bootstrap_components
if pipeline_template and (!components or components.empty?)
end
def check_auto_admin
- if User.where("uuid not like '%-000000000000000'").where(:is_admin => true).count == 0 and not Rails.configuration.auto_admin_user.nil?
+ if User.where("uuid not like '%-000000000000000'").where(:is_admin => true).count == 0 and Rails.configuration.auto_admin_user
if current_user.email == Rails.configuration.auto_admin_user
self.is_admin = true
self.is_active = true
--- /dev/null
+# Do not use this file for site configuration. Create application.yml
+# instead (see application.yml.example).
+
+development:
+ force_ssl: false
+ cache_classes: false
+ whiny_nils: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_mailer.raise_delivery_errors: false
+ action_mailer.perform_deliveries: false
+ active_support.deprecation: :log
+ action_dispatch.best_standards_support: :builtin
+ active_record.mass_assignment_sanitizer: :strict
+ active_record.auto_explain_threshold_in_seconds: 0.5
+ assets.compress: false
+ assets.debug: true
+
+production:
+ force_ssl: true
+ cache_classes: true
+ consider_all_requests_local: false
+ action_controller.perform_caching: true
+ serve_static_assets: false
+ assets.compress: true
+ assets.compile: false
+ assets.digest: true
+
+test:
+ force_ssl: false
+ cache_classes: true
+ serve_static_assets: true
+ static_cache_control: public, max-age=3600
+ whiny_nils: true
+ consider_all_requests_local: true
+ action_controller.perform_caching: false
+ action_dispatch.show_exceptions: false
+ action_controller.allow_forgery_protection: false
+ action_mailer.delivery_method: :test
+ active_support.deprecation: :stderr
+ active_record.mass_assignment_sanitizer: :strict
+ uuid_prefix: zzzzz
+
+common:
+ secret_token: ~
+ uuid_prefix: <%= Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4] %>
+
+ git_repositories_dir: /var/cache/git
+
+ # :none or :slurm_immediate
+ crunch_job_wrapper: :none
+
+ # username, or false = do not set uid when running jobs.
+ crunch_job_user: crunch
+
+ # The web service must be able to create/write this file, and
+ # crunch-job must be able to stat() it.
+ crunch_refresh_trigger: /tmp/crunch_refresh_trigger
+
+ # Path to /etc/dnsmasq.d, or false = do not update dnsmasq data.
+ dnsmasq_conf_dir: false
+
+ # Set to AMI id (ami-123456) to auto-start nodes. See app/models/node.rb
+ compute_node_ami: false
+ compute_node_ec2run_args: -g arvados-compute
+ compute_node_spot_bid: 0.11
+
+ compute_node_domain: <%= `hostname`.split('.')[1..-1].join('.').strip %>
+ compute_node_nameservers:
+ - 192.168.1.1
+ compute_node_ec2_tag_enable: false
+
+ accept_api_token: {}
+
+ new_users_are_active: false
+ admin_notifier_email_from: arvados@example.com
+ email_subject_prefix: "[ARVADOS] "
+
+ # Visitors to the API server will be redirected to the workbench
+ workbench_address: https://workbench.local:3001/
+
+ # The e-mail address of the user you would like to become marked as an admin
+ # user on their first login.
+ # In the default configuration, authentication happens through the Arvados SSO
+ # server, which uses openid against Google's servers, so in that case this
+ # should be an address associated with a Google account.
+ auto_admin_user: false
+
+ ## Set Time.zone default to the specified zone and make Active
+ ## Record auto-convert to this zone. Run "rake -D time" for a list
+ ## of tasks for finding time zone names. Default is UTC.
+ #time_zone: Central Time (US & Canada)
+
+ ## Default encoding used in templates for Ruby 1.9.
+ encoding: utf-8
+
+ # Enable the asset pipeline
+ assets.enabled: true
+
+ # Version of your assets, change this if you want to expire all your assets
+ assets.version: "1.0"
# Activate observers that should always be running.
# config.active_record.observers = :cacher, :garbage_collector, :forum_observer
- # Set Time.zone default to the specified zone and make Active Record auto-convert to this zone.
- # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
- # config.time_zone = 'Central Time (US & Canada)'
-
# The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
# config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
# config.i18n.default_locale = :de
- # Configure the default encoding used in templates for Ruby 1.9.
- config.encoding = "utf-8"
-
# Configure sensitive parameters which will be filtered from the log file.
config.filter_parameters += [:password]
-
- # Enable the asset pipeline
- config.assets.enabled = true
-
- # Version of your assets, change this if you want to expire all your assets
- config.assets.version = '1.0'
-
- config.force_ssl = true
-
- def config.uuid_prefix(x=nil)
- if x and @uuid_prefix
- raise "uuid_prefix was already set to #{@uuid_prefix}"
- end
- @uuid_prefix ||= Digest::MD5.hexdigest(x || `hostname`.strip).to_i(16).to_s(36)[-5..-1]
- end
- def config.uuid_prefix=(x)
- @uuid_prefix = x
- end
end
-
end
--- /dev/null
+# Copy this file to application.yml and edit to suit.
+#
+# Consult application.default.yml for the full list of configuration
+# settings.
+#
+# The order of precedence is:
+# 1. config/environments/{RAILS_ENV}.rb (deprecated)
+# 2. Section in application.yml corresponding to RAILS_ENV (e.g., development)
+# 3. Section in application.yml called "common"
+# 4. Section in application.default.yml corresponding to RAILS_ENV
+# 5. Section in application.default.yml called "common"
+
+development:
+
+production:
+ # At minimum, you need a nice long randomly generated secret_token here.
+ secret_token: ~
+
+ uuid_prefix: bogus
+
+ # This is suitable for AWS; see common section below for a static example.
+ #
+ #compute_node_nameservers: <%#
+ require 'net/http'
+ ['local', 'public'].collect do |iface|
+ Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
+ end << '172.16.0.23'
+ %>
+
+test:
+ uuid_prefix: zzzzz
+ secret_token: <%= rand(2**512).to_s(36) %>
+
+common:
+
+ # Git repositories must be readable by api server, or you won't be
+ # able to submit crunch jobs. To pass the test suites, put a clone
+ # of the arvados tree in {git_repositories_dir}/arvados.git or
+ # {git_repositories_dir}/arvados/.git
+ #
+ #git_repositories_dir: /var/cache/git
development:
- adapter: mysql
- encoding: utf8
- database: arvados_development
- username: arvados
- password: ********
- host: localhost
+ adapter: sqlite3
+ database: db/arvados_development.sqlite3
test:
- adapter: mysql
+ adapter: postgresql
encoding: utf8
database: arvados_test
username: arvados
host: localhost
production:
- adapter: mysql
+ adapter: postgresql
encoding: utf8
database: arvados_production
username: arvados
# Visitors to the API server will be redirected to the workbench
config.workbench_address = "http://localhost:3000/"
+
+ # The e-mail address of the user you would like to become marked as an admin
+ # user on their first login.
+ # In the default configuration, authentication happens through the Arvados SSO
+ # server, which uses openid against Google's servers, so in that case this
+ # should be an address associated with a Google account.
+ config.auto_admin_user = ''
end
APP_SECRET = rand(2**512).to_s(36) # CHANGE ME!
# Update your custom Omniauth provider URL here
-CUSTOM_PROVIDER_URL = 'http://auth.clinicalfuture.com'
+CUSTOM_PROVIDER_URL = 'http://localhost:3002'
Rails.application.config.middleware.use OmniAuth::Builder do
provider :josh_id, APP_ID, APP_SECRET, CUSTOM_PROVIDER_URL
--- /dev/null
+$application_config = {}
+
+%w(application.default application).each do |cfgfile|
+ path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
+ if File.exists? path
+ yaml = ERB.new(IO.read path).result(binding)
+ confs = YAML.load(yaml)
+ $application_config.merge!(confs['common'] || {})
+ $application_config.merge!(confs[::Rails.env.to_s] || {})
+ end
+end
+
+Server::Application.configure do
+ nils = []
+ $application_config.each do |k, v|
+ # "foo.bar: baz" --> { config.foo.bar = baz }
+ cfg = config
+ ks = k.split '.'
+ k = ks.pop
+ ks.each do |kk|
+ cfg = cfg.send(kk)
+ end
+ if cfg.respond_to?(k.to_sym) and !cfg.send(k).nil?
+ # Config must have been set already in environments/*.rb.
+ #
+ # After config files have been migrated, this mechanism should
+ # be deprecated, then removed.
+ elsif v.nil?
+ # Config variables are not allowed to be nil. Make a "naughty"
+ # list, and present it below.
+ nils << k
+ else
+ cfg.send "#{k}=", v
+ end
+ end
+ if !nils.empty?
+ raise <<EOS
+Refusing to start in #{::Rails.env.to_s} mode with missing configuration.
+
+The following configuration settings must be specified in
+config/application.yml:
+* #{nils.join "\n* "}
+
+EOS
+ end
+end
--- /dev/null
+namespace :config do
+ desc 'Ensure site configuration has all required settings'
+ task check: :environment do
+ $application_config.sort.each do |k, v|
+ $stderr.puts "%-32s %s" % [k, eval("Rails.configuration.#{k}")]
+ end
+ end
+end
def refresh_todo
@todo = Job.queue
+ @todo_pipelines = PipelineInstance.queue
end
def sinfo
api_client_id: 0)
job_auth.save
- cmd_args << (ENV['CRUNCH_JOB_BIN'] || `which crunch-job`.strip)
+ crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
+ if crunch_job_bin == ''
+ raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
+ end
+
+ cmd_args << crunch_job_bin
cmd_args << '--job-api-token'
cmd_args << job_auth.api_token
cmd_args << '--job'
cmd_args << job.uuid
- if cmd_args[0] == ''
- raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
- end
-
commit = Commit.where(sha1: job.script_version).first
if commit
cmd_args << '--git-dir'
@running.delete job_done.uuid
end
+ def update_pipelines
+ @todo_pipelines.each do |p|
+ pipe_auth = ApiClientAuthorization.
+ new(user: User.where('uuid=?', p.modified_by_user_uuid).first,
+ api_client_id: 0)
+ pipe_auth.save
+
+ puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-here --no-wait --instance #{p.uuid}`
+ end
+ end
+
def run
act_as_system_user
@running ||= {}
unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
start_jobs
end
+ unless @todo_pipelines.empty? or did_recently(:update_pipelines, 5.0)
+ update_pipelines
+ end
end
reap_children
select(@running.values.collect { |j| [j[:stdout], j[:stderr]] }.flatten,
end
end
+
+
protected
def did_recently(thing, min_interval)
'zzzzz-8i9sb-pshmckwoma9plh7']
end
+ test "search jobs by started_at with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '<', Time.now.to_s]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs by started_at with > query" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>', Time.now.to_s]]
+ }
+ assert_response :success
+ assert_equal 0, assigns(:objects).count
+ end
+
+ test "search jobs by started_at with >= query on metric date" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>=', '2014-01-01']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs by started_at with >= query on metric date and time" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>=', '2014-01-01 01:23:45']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'pshmckw'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
test "search jobs by nonexistent column with < query" do
authorize_with :active
get :index, {
end
end
+ test "search keep_disks by service_port with >= query" do
+ authorize_with :active
+ get :index, {
+ filters: [['service_port', '>=', 25107]]
+ }
+ assert_response :success
+ assert_equal true, assigns(:objects).any?
+ end
+
+ test "search keep_disks by service_port with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['service_port', '<', 25107]]
+ }
+ assert_response :success
+ assert_equal false, assigns(:objects).any?
+ end
+
+ test "search keep_disks with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'o2t1q5w'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-penuu-5w2o2t1q5wy7fhn')
+ end
+
end
assert_response :success
end
+ test "create token for different user" do
+ post "/arvados/v1/api_client_authorizations", {
+ :format => :json,
+ :api_client_authorization => {
+ :owner_uuid => users(:spectator).uuid
+ }
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin_trustedclient).api_token}"}
+ assert_response :success
+
+ get "/arvados/v1/users/current", {
+ :format => :json
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{jresponse['api_token']}"}
+ @jresponse = nil
+ assert_equal users(:spectator).uuid, jresponse['uuid']
+ end
+
+ test "refuse to create token for different user if not trusted client" do
+ post "/arvados/v1/api_client_authorizations", {
+ :format => :json,
+ :api_client_authorization => {
+ :owner_uuid => users(:spectator).uuid
+ }
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:admin).api_token}"}
+ assert_response 403
+ end
+
+ test "refuse to create token for different user if not admin" do
+ post "/arvados/v1/api_client_authorizations", {
+ :format => :json,
+ :api_client_authorization => {
+ :owner_uuid => users(:spectator).uuid
+ }
+ }, {'HTTP_AUTHORIZATION' => "OAuth2 #{api_client_authorizations(:active_trustedclient).api_token}"}
+ assert_response 403
+ end
+
end
--- /dev/null
+require 'test_helper'
+
+class BlobTest < ActiveSupport::TestCase
+ @@api_token = rand(2**512).to_s(36)[0..49]
+ @@key = rand(2**2048).to_s(36)
+ @@blob_data = 'foo'
+ @@blob_locator = Digest::MD5.hexdigest(@@blob_data) +
+ '+' + @@blob_data.size.to_s
+
+ test 'correct' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key
+ assert_equal true, Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+
+ test 'expired' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key, ttl: -1
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'expired, but no raise' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key, ttl: -1
+ assert_equal false, Blob.verify_signature(signed,
+ api_token: @@api_token,
+ key: @@key)
+ end
+
+ test 'bogus, wrong block hash' do
+ signed = Blob.sign_locator @@blob_locator, api_token: @@api_token, key: @@key
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed.sub('acbd','abcd'), api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, expired' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa@531641bf'
+ assert_raises Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, wrong key' do
+ signed = Blob.sign_locator(@@blob_locator,
+ api_token: @@api_token,
+ key: (@@key+'x'))
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, wrong api token' do
+ signed = Blob.sign_locator(@@blob_locator,
+ api_token: @@api_token.reverse,
+ key: @@key)
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, signature format 1' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa@'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, signature format 2' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+A@531641bf'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, signature format 3' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Axyzzy@531641bf'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'bogus, timestamp format' do
+ signed = 'acbd18db4cc2f85cedef654fccc4a4d8+3+Aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa@xyzzy'
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(signed, api_token: @@api_token, key: @@key)
+ end
+ end
+
+ test 'no signature at all' do
+ assert_raise Blob::InvalidSignatureError do
+ Blob.verify_signature!(@@blob_locator, api_token: @@api_token, key: @@key)
+ end
+ end
+end
projects / arvados.git / commitdiff