arvados.git
10 years agoUse arvados.api('v1') accessor instead of arvados.service. refs #1773
Tom Clegg [Mon, 23 Dec 2013 16:21:00 +0000 (08:21 -0800)]
Use arvados.api('v1') accessor instead of arvados.service. refs #1773

10 years agoRemove extra `shift' screwing up argument processing.
Tim Pierce [Fri, 20 Dec 2013 21:51:33 +0000 (16:51 -0500)]
Remove extra `shift' screwing up argument processing.

10 years agoUpdate favicon to Dax
Tom Clegg [Thu, 19 Dec 2013 21:41:41 +0000 (13:41 -0800)]
Update favicon to Dax

10 years agoAdd Python SDK doc page. closes #1754
Tom Clegg [Thu, 19 Dec 2013 20:46:24 +0000 (12:46 -0800)]
Add Python SDK doc page. closes #1754

10 years agoAccept an API version argument to arvados.api(). refs #1772
Tom Clegg [Thu, 19 Dec 2013 20:52:06 +0000 (12:52 -0800)]
Accept an API version argument to arvados.api(). refs #1772

10 years agoUpdated documentation for clarity.
Tim Pierce [Thu, 19 Dec 2013 18:51:24 +0000 (13:51 -0500)]
Updated documentation for clarity.

10 years agoFix up usage error message
Tom Clegg [Tue, 17 Dec 2013 17:39:46 +0000 (09:39 -0800)]
Fix up usage error message

10 years agoMerge branch '1495-crunch-documentation'
Peter Amstutz [Wed, 18 Dec 2013 17:01:59 +0000 (12:01 -0500)]
Merge branch '1495-crunch-documentation'

10 years ago* mailto:arvados@clinicalfuture.com is now arvados@curoverse.com
Peter Amstutz [Wed, 18 Dec 2013 17:00:38 +0000 (12:00 -0500)]
* mailto:arvados@clinicalfuture.com is now arvados@curoverse.com
* git clone in install guide now clones from github

10 years ago* Fixed template so subsections only show up in userguide
Peter Amstutz [Tue, 17 Dec 2013 22:09:18 +0000 (17:09 -0500)]
* Fixed template so subsections only show up in userguide
* Removed obsolete tutorial files
* Copy edits

10 years ago* Finished trait search tutorial
Peter Amstutz [Tue, 17 Dec 2013 19:56:42 +0000 (14:56 -0500)]
* Finished trait search tutorial
* Finished GATK tutorial
* Noted that arv ls -s print size in kilobytes

10 years ago* Almost done with trait search tutorial
Peter Amstutz [Tue, 17 Dec 2013 17:13:13 +0000 (12:13 -0500)]
* Almost done with trait search tutorial
* Working on GATK tutorial
* Added section on putting directories into Keep

10 years agoAdd new user activation + setup script. closes #1738
Tom Clegg [Tue, 17 Dec 2013 16:15:40 +0000 (08:15 -0800)]
Add new user activation + setup script. closes #1738

10 years agoReturn API response objects as Models (with save() etc) instead of Hashes
Tom Clegg [Tue, 17 Dec 2013 16:13:58 +0000 (08:13 -0800)]
Return API response objects as Models (with save() etc) instead of Hashes

closes #1756

10 years agoPropagate API errors as exceptions
Tom Clegg [Tue, 17 Dec 2013 14:51:38 +0000 (06:51 -0800)]
Propagate API errors as exceptions

10 years agoWorking on traits document
Peter Amstutz [Mon, 16 Dec 2013 23:14:09 +0000 (18:14 -0500)]
Working on traits document

10 years agoChange arv-put default behavior: write a manifest, even for a single file.
Tom Clegg [Mon, 16 Dec 2013 21:27:14 +0000 (13:27 -0800)]
Change arv-put default behavior: write a manifest, even for a single file.

refs #1646

10 years agoReturn empty-block locator in data_locators() for zero-byte stream
Tom Clegg [Mon, 16 Dec 2013 21:26:35 +0000 (13:26 -0800)]
Return empty-block locator in data_locators() for zero-byte stream

10 years agoRemove extra trailing newline in --raw mode output
Tom Clegg [Mon, 16 Dec 2013 21:04:47 +0000 (13:04 -0800)]
Remove extra trailing newline in --raw mode output

10 years agoFix some typos and long lines
Tom Clegg [Mon, 16 Dec 2013 17:23:55 +0000 (09:23 -0800)]
Fix some typos and long lines

10 years ago* Fixed links
Peter Amstutz [Mon, 16 Dec 2013 17:16:22 +0000 (12:16 -0500)]
* Fixed links
* Added bootstrap and jquery snapshots

10 years agoReorganized user manual into sections
Peter Amstutz [Mon, 16 Dec 2013 16:24:52 +0000 (11:24 -0500)]
Reorganized user manual into sections

10 years agoReorganization, added parallel jobs and new pipeline tutorial.
Peter Amstutz [Mon, 16 Dec 2013 15:33:01 +0000 (10:33 -0500)]
Reorganization, added parallel jobs and new pipeline tutorial.

10 years agoAdd example ruby client: list idle/busy worker nodes and age of last ping
Tom Clegg [Fri, 13 Dec 2013 21:35:52 +0000 (13:35 -0800)]
Add example ruby client: list idle/busy worker nodes and age of last ping

closes #1729

10 years agoObey ARVADOS_API_HOST_INSECURE if host came from ARVADOS_API_HOST env var
Tom Clegg [Fri, 13 Dec 2013 21:34:18 +0000 (13:34 -0800)]
Obey ARVADOS_API_HOST_INSECURE if host came from ARVADOS_API_HOST env var

10 years agoSet jobs.log_tail_follow default buffer size in discovery document.
Tom Clegg [Fri, 13 Dec 2013 18:09:50 +0000 (10:09 -0800)]
Set jobs.log_tail_follow default buffer size in discovery document.

refs #1743

10 years agoFix parsing of buffer_size parameter in jobs.log_tail_follow
Tom Clegg [Fri, 13 Dec 2013 16:50:00 +0000 (08:50 -0800)]
Fix parsing of buffer_size parameter in jobs.log_tail_follow

refs #1743

10 years agoStream API responses for jobs.log_tail_follow and users.log_stream
Tom Clegg [Thu, 12 Dec 2013 23:21:26 +0000 (15:21 -0800)]
Stream API responses for jobs.log_tail_follow and users.log_stream

10 years ago * Mostly done on "Debug a Crunch Script"
Peter Amstutz [Thu, 12 Dec 2013 22:04:39 +0000 (17:04 -0500)]
 * Mostly done on "Debug a Crunch Script"

10 years agoHandle unexpected server responses better, clean up usage/help code
Tom Clegg [Thu, 12 Dec 2013 21:40:24 +0000 (13:40 -0800)]
Handle unexpected server responses better, clean up usage/help code

10 years agoMerge remote-tracking branch 'origin' into 1495-crunch-documentation
Peter Amstutz [Thu, 12 Dec 2013 20:21:54 +0000 (15:21 -0500)]
Merge remote-tracking branch 'origin' into 1495-crunch-documentation

10 years ago* split out sections into their own documents
Peter Amstutz [Thu, 12 Dec 2013 20:17:28 +0000 (15:17 -0500)]
* split out sections into their own documents
* defined typeface conventions and applied them some existing
  documents
* finished writing/documenting/testing tutorial hash crunch script
* split out first crunch script into a standalone runnable python file

10 years agoRemove TMP/src.commit too, when removing TMP/src.
Tom Clegg [Thu, 12 Dec 2013 19:46:26 +0000 (11:46 -0800)]
Remove TMP/src.commit too, when removing TMP/src.

10 years agoFix left nav link order
Tom Clegg [Thu, 12 Dec 2013 17:41:00 +0000 (09:41 -0800)]
Fix left nav link order

10 years agoStore crunch-job log in a collection instead of just raw data blocks.
Tom Clegg [Thu, 12 Dec 2013 17:28:48 +0000 (09:28 -0800)]
Store crunch-job log in a collection instead of just raw data blocks.

10 years agoFix gatk_tbz locator.
Tom Clegg [Thu, 12 Dec 2013 15:28:47 +0000 (07:28 -0800)]
Fix gatk_tbz locator.

10 years agoRevert "Rename annotation DepthOfCoverage to Coverage"
Tom Clegg [Thu, 12 Dec 2013 15:27:52 +0000 (07:27 -0800)]
Revert "Rename annotation DepthOfCoverage to Coverage"

This reverts commit 6d21143f763a0a3a5098acb5698cb549f37a6db5.

10 years agoRename annotation DepthOfCoverage to Coverage
Tom Clegg [Thu, 12 Dec 2013 04:10:53 +0000 (20:10 -0800)]
Rename annotation DepthOfCoverage to Coverage

GATK 2.6-4-g3e5ff60 says:

Annotation DepthOfCoverage is no longer available in the GATK; it has
been deprecated since version 2.4 (renamed to Coverage)

10 years agoAdd input parameter tables and source code link for each crunch example.
Tom Clegg [Thu, 12 Dec 2013 03:59:25 +0000 (19:59 -0800)]
Add input parameter tables and source code link for each crunch example.

closes #1656

10 years agoFix reference to picard source distribution -> binary distribution.
Tom Clegg [Thu, 12 Dec 2013 04:00:37 +0000 (20:00 -0800)]
Fix reference to picard source distribution -> binary distribution.

refs #1656

10 years agoRemove unused module import.
Tom Clegg [Thu, 12 Dec 2013 04:01:44 +0000 (20:01 -0800)]
Remove unused module import.

10 years agoUse git@git.[...] not git://git.[...] as default repository fetch_url.
Tom Clegg [Wed, 11 Dec 2013 15:44:20 +0000 (07:44 -0800)]
Use git@git.[...] not git://git.[...] as default repository fetch_url.

closes #1691

10 years agoFormatting tweaks, mosting changing <pre> to textiles block code (bc.) mark.
Peter Amstutz [Wed, 11 Dec 2013 14:15:06 +0000 (09:15 -0500)]
Formatting tweaks, mosting changing <pre> to textiles block code (bc.) mark.

10 years agoMerge branch '1637-improve-arv-tutorial'
Peter Amstutz [Wed, 11 Dec 2013 13:35:36 +0000 (08:35 -0500)]
Merge branch '1637-improve-arv-tutorial'

10 years agoFixed formatting.
Tim Pierce [Wed, 11 Dec 2013 05:14:38 +0000 (00:14 -0500)]
Fixed formatting.

10 years agoAdded Keep tutorial (refs #1647)
Tim Pierce [Wed, 11 Dec 2013 04:02:10 +0000 (23:02 -0500)]
Added Keep tutorial (refs #1647)

10 years agoAdd "crunch examples" and "crunch utility libraries" pages
Tom Clegg [Wed, 11 Dec 2013 02:04:24 +0000 (18:04 -0800)]
Add "crunch examples" and "crunch utility libraries" pages
in doc/user/.

refs #1513
refs #1656

10 years agoClear $CRUNCH_TMP/src when starting a job.
Tom Clegg [Wed, 11 Dec 2013 01:38:42 +0000 (17:38 -0800)]
Clear $CRUNCH_TMP/src when starting a job.

closes #1687

10 years agoAdd GATK2 exome fastq->vcf pipeline example
Tom Clegg [Wed, 11 Dec 2013 01:37:34 +0000 (17:37 -0800)]
Add GATK2 exome fastq->vcf pipeline example

closes #1574

10 years agoWhen running "arv-get -n", it is OK if destination files already exist.
Tom Clegg [Wed, 11 Dec 2013 00:06:22 +0000 (16:06 -0800)]
When running "arv-get -n", it is OK if destination files already exist.

refs #1646

10 years agoAdd docstrings to arvados_samtools module.
Tom Clegg [Tue, 10 Dec 2013 22:39:44 +0000 (14:39 -0800)]
Add docstrings to arvados_samtools module.

closes #1639

10 years agoRemoved numbering and put navorder for tutorial 2 at 102 to hide it.
Peter Amstutz [Tue, 10 Dec 2013 22:00:17 +0000 (17:00 -0500)]
Removed numbering and put navorder for tutorial 2 at 102 to hide it.

10 years agoMissing file
Peter Amstutz [Tue, 10 Dec 2013 21:50:17 +0000 (16:50 -0500)]
Missing file

10 years agoCleaned up comments to be hidden from rendered page (still visible in
Peter Amstutz [Tue, 10 Dec 2013 21:50:08 +0000 (16:50 -0500)]
Cleaned up comments to be hidden from rendered page (still visible in
page source).  Tutorial 2 is glaringly unfinished but otherwise we can
go ahead and merge into master to end the sprint.

10 years agoCleaned up old files and reorganized navigation order.
Peter Amstutz [Tue, 10 Dec 2013 21:18:15 +0000 (16:18 -0500)]
Cleaned up old files and reorganized navigation order.

10 years agoFinished first tutorial.
Peter Amstutz [Tue, 10 Dec 2013 20:44:46 +0000 (15:44 -0500)]
Finished first tutorial.

10 years agoMerge branch '1646-arv-put'
Tom Clegg [Tue, 10 Dec 2013 20:13:26 +0000 (12:13 -0800)]
Merge branch '1646-arv-put'

10 years agoPoint "arv keep get/put" to arv-get/put and unsupport "arv get/put"
Tom Clegg [Tue, 10 Dec 2013 20:08:04 +0000 (12:08 -0800)]
Point "arv keep get/put" to arv-get/put and unsupport "arv get/put"
style.

refs #1646

10 years agoAdd "Install client libraries" page to doc/install/.
Tom Clegg [Tue, 10 Dec 2013 20:04:44 +0000 (12:04 -0800)]
Add "Install client libraries" page to doc/install/.

refs #1646

10 years agoSupport invoking arv-get and arv-put via "arv get" and "arv put".
Tom Clegg [Tue, 10 Dec 2013 19:38:41 +0000 (11:38 -0800)]
Support invoking arv-get and arv-put via "arv get" and "arv put".

refs #1646

10 years agoAdd python client library package: arv-get, arv-put, arvados module
Tom Clegg [Tue, 10 Dec 2013 19:22:44 +0000 (11:22 -0800)]
Add python client library package: arv-get, arv-put, arvados module

refs #1646

10 years agoFix port flags for "run.sh start".
Tim Pierce [Tue, 10 Dec 2013 18:31:18 +0000 (13:31 -0500)]
Fix port flags for "run.sh start".

10 years agoRename doc page to match title.
Tom Clegg [Tue, 10 Dec 2013 17:08:11 +0000 (09:08 -0800)]
Rename doc page to match title.

10 years agoAdd "Create standard objects" page in install docs.
Tom Clegg [Tue, 10 Dec 2013 17:07:11 +0000 (09:07 -0800)]
Add "Create standard objects" page in install docs.

10 years agoSupport the use of groups to grant repository permissions.
Tom Clegg [Tue, 10 Dec 2013 17:03:28 +0000 (09:03 -0800)]
Support the use of groups to grant repository permissions.

Now, if user A can_read group B, and group B can_read repository C,
then /arvados/v1/repositories/get_all_permissions will indicate that
user A has gitolite_permissions "R" on repository C.

10 years agoClean up arvados_bwa module and add docstrings.
Tom Clegg [Tue, 10 Dec 2013 05:58:43 +0000 (21:58 -0800)]
Clean up arvados_bwa module and add docstrings.

closes #1638

10 years agoMerge branch 'master' into 1646-arv-put
Tom Clegg [Tue, 10 Dec 2013 04:56:19 +0000 (20:56 -0800)]
Merge branch 'master' into 1646-arv-put

Conflicts:
sdk/python/arvados.py

10 years agoMerge branch '1587-fix-test-suites-in-devsandbox'
Tim Pierce [Mon, 9 Dec 2013 23:36:23 +0000 (18:36 -0500)]
Merge branch '1587-fix-test-suites-in-devsandbox'

10 years agoAdd arv-get -f (force overwrite) and --skip-existing flags.
Tom Clegg [Mon, 9 Dec 2013 23:26:42 +0000 (15:26 -0800)]
Add arv-get -f (force overwrite) and --skip-existing flags.

If neither is specified, and local destination files exist, refuse to
write anything.

refs #1646

10 years agoSupport "arv-get {locator}/filename path/to/localdir" invocation:
Tom Clegg [Mon, 9 Dec 2013 20:54:28 +0000 (12:54 -0800)]
Support "arv-get {locator}/filename path/to/localdir" invocation:
write file data to path/to/localdir/file

refs #1646

10 years agoFail gracefully when fetching a raw block that does not exist
Tom Clegg [Mon, 9 Dec 2013 20:45:00 +0000 (12:45 -0800)]
Fail gracefully when fetching a raw block that does not exist

10 years agoFail more gracefully on some common error conditions
Tom Clegg [Mon, 9 Dec 2013 20:34:51 +0000 (12:34 -0800)]
Fail more gracefully on some common error conditions

10 years agoUse our own exception classes, instead of just Exception
Tom Clegg [Mon, 9 Dec 2013 20:33:45 +0000 (12:33 -0800)]
Use our own exception classes, instead of just Exception

10 years agoFix crash when destination directory supplied without trailing slash,
Tom Clegg [Mon, 9 Dec 2013 19:45:56 +0000 (11:45 -0800)]
Fix crash when destination directory supplied without trailing slash,
and crash when asked to copy a directory to a file.

refs #1646

10 years agoUse body={...} instead of object_type=json.dumps({...})
Tom Clegg [Mon, 9 Dec 2013 19:15:39 +0000 (11:15 -0800)]
Use body={...} instead of object_type=json.dumps({...})

10 years agoAdd example scripts and libraries for bwa, samtools, picard, gatk2
Tom Clegg [Mon, 9 Dec 2013 18:25:48 +0000 (10:25 -0800)]
Add example scripts and libraries for bwa, samtools, picard, gatk2

closes #1598

10 years agoMerge remote-tracking branch 'origin/master' into 1637-improve-arv-tutorial
Peter Amstutz [Mon, 9 Dec 2013 14:58:46 +0000 (09:58 -0500)]
Merge remote-tracking branch 'origin/master' into 1637-improve-arv-tutorial

10 years agoA little bit of documentation work from home
Peter Amstutz [Sun, 8 Dec 2013 02:30:57 +0000 (21:30 -0500)]
A little bit of documentation work from home

10 years agoAdding 'run.sh test api' to run API server Rails tests.
Tim Pierce [Fri, 6 Dec 2013 22:49:40 +0000 (17:49 -0500)]
Adding 'run.sh test api' to run API server Rails tests.

10 years agoDocumentation work in progress, making evening check-in.
Peter Amstutz [Fri, 6 Dec 2013 22:03:15 +0000 (17:03 -0500)]
Documentation work in progress, making evening check-in.

10 years agoIgnore config/environments/test.rb and production.rb
Tom Clegg [Fri, 6 Dec 2013 20:45:26 +0000 (12:45 -0800)]
Ignore config/environments/test.rb and production.rb

10 years agoIgnore tmp directory created by cli tests
Tom Clegg [Fri, 6 Dec 2013 20:36:05 +0000 (12:36 -0800)]
Ignore tmp directory created by cli tests

10 years agoAdded 'test' command to run.sh.
Tim Pierce [Fri, 6 Dec 2013 19:46:48 +0000 (14:46 -0500)]
Added 'test' command to run.sh.

10 years agorun.sh: bug fixes
Tim Pierce [Thu, 5 Dec 2013 22:40:02 +0000 (17:40 -0500)]
run.sh: bug fixes

10 years agoRewriting documentation work in progress.
Peter Amstutz [Thu, 5 Dec 2013 22:01:39 +0000 (17:01 -0500)]
Rewriting documentation work in progress.

10 years agorun.sh: add "stop" command, also remove old containers before trying to start them
Tim Pierce [Thu, 5 Dec 2013 21:40:02 +0000 (16:40 -0500)]
run.sh: add "stop" command, also remove old containers before trying to start them

10 years agoRemove spurious "if".
Tom Clegg [Thu, 5 Dec 2013 21:27:51 +0000 (13:27 -0800)]
Remove spurious "if".

10 years agoUse some helpful HTTP status codes, not just generic 422.
Tom Clegg [Thu, 5 Dec 2013 21:08:28 +0000 (13:08 -0800)]
Use some helpful HTTP status codes, not just generic 422.

* 403 for PermissionDeniedError
* 401 for UnauthorizedError

10 years agoCheck permission before deleting objects
Tom Clegg [Thu, 5 Dec 2013 21:12:50 +0000 (13:12 -0800)]
Check permission before deleting objects

10 years agoReorganized code to support 'start' command.
Tim Pierce [Thu, 5 Dec 2013 19:26:39 +0000 (14:26 -0500)]
Reorganized code to support 'start' command.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados into 1637-improve-arv-tutorial
Peter Amstutz [Thu, 5 Dec 2013 14:41:28 +0000 (09:41 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados into 1637-improve-arv-tutorial

10 years agorun.sh prints instructions/settings for running a test suite.
Tim Pierce [Wed, 4 Dec 2013 22:43:48 +0000 (17:43 -0500)]
run.sh prints instructions/settings for running a test suite.

10 years agoNotes on new user documentation
peter [Wed, 4 Dec 2013 21:32:39 +0000 (16:32 -0500)]
Notes on new user documentation

10 years agoAdd support for ARVADOS_API_PORT.
Tim Pierce [Wed, 4 Dec 2013 20:50:58 +0000 (15:50 -0500)]
Add support for ARVADOS_API_PORT.

10 years agoSuperuser script must be run as ./script/create_superuser_token.rb.
Tim Pierce [Wed, 4 Dec 2013 20:10:09 +0000 (15:10 -0500)]
Superuser script must be run as ./script/create_superuser_token.rb.

10 years agoAPI_SUPERUSER_TOKEN must be named API_SUPERUSER_SECRET to be autogenerated.
Tim Pierce [Wed, 4 Dec 2013 19:35:00 +0000 (14:35 -0500)]
API_SUPERUSER_TOKEN must be named API_SUPERUSER_SECRET to be autogenerated.

10 years agorun.sh bug fixes.
Tim Pierce [Wed, 4 Dec 2013 18:38:20 +0000 (13:38 -0500)]
run.sh bug fixes.

10 years agoMount separate volumes for each keep container launched.
Tim Pierce [Wed, 4 Dec 2013 16:51:12 +0000 (11:51 -0500)]
Mount separate volumes for each keep container launched.

10 years agoAllow overriding of default ports for API, doc, SSO, and workbench
Ward Vandewege [Wed, 4 Dec 2013 02:34:05 +0000 (21:34 -0500)]
Allow overriding of default ports for API, doc, SSO, and workbench
servers when started with run.sh

10 years agoFix failing test by parsing timestamp correctly.
Tom Clegg [Tue, 3 Dec 2013 23:19:22 +0000 (15:19 -0800)]
Fix failing test by parsing timestamp correctly.