From: Peter Amstutz Date: Thu, 26 Apr 2018 18:13:27 +0000 (-0400) Subject: 13282: doc updates X-Git-Tag: 1.2.0~184^2 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/da8714584a1649fb128e0f13718c2507c518a210 13282: doc updates * Improve presentation of R SDK * Move obsolete crunch1 documentation to "Obsolete" section. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- diff --git a/doc/Rakefile b/doc/Rakefile index 855b829855..079f7da27f 100644 --- a/doc/Rakefile +++ b/doc/Rakefile @@ -54,7 +54,7 @@ navmenu: R title: "R SDK Overview" ... -#{rd.read.gsub("```", "\n~~~\n").gsub(/^[ ]+/, "")} +#{rd.read.gsub(/^```$/, "~~~").gsub(/^```(\w)$/, "~~~\\1")} EOF ) end diff --git a/doc/_config.yml b/doc/_config.yml index 50a9f7a2cf..4766e3f589 100644 --- a/doc/_config.yml +++ b/doc/_config.yml @@ -40,8 +40,6 @@ navbar: - Running workflows at the command line: - user/cwl/cwl-runner.html.textile.liquid - user/cwl/cwl-run-options.html.textile.liquid - # - user/topics/running-pipeline-command-line.html.textile.liquid - # - user/topics/arv-run.html.textile.liquid - Working with git repositories: - user/tutorials/add-new-repository.html.textile.liquid - user/tutorials/git-arvados-guide.html.textile.liquid @@ -51,23 +49,25 @@ navbar: - user/cwl/cwl-style.html.textile.liquid - user/cwl/cwl-extensions.html.textile.liquid - user/topics/arv-docker.html.textile.liquid - # - user/tutorials/running-external-program.html.textile.liquid - # - user/topics/crunch-tools-overview.html.textile.liquid - # - user/tutorials/tutorial-firstscript.html.textile.liquid - # - user/tutorials/tutorial-submit-job.html.textile.liquid - # - user/topics/tutorial-parallel.html.textile.liquid - Reference: - user/reference/cookbook.html.textile.liquid - # - user/topics/run-command.html.textile.liquid - # - user/reference/job-pipeline-ref.html.textile.liquid - # - user/examples/crunch-examples.html.textile.liquid - #- Query the metadata database: - # - user/topics/tutorial-trait-search.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 + - Obsolete documentation: + - user/topics/running-pipeline-command-line.html.textile.liquid + - user/topics/arv-run.html.textile.liquid + - user/tutorials/running-external-program.html.textile.liquid + - user/topics/crunch-tools-overview.html.textile.liquid + - user/tutorials/tutorial-firstscript.html.textile.liquid + - user/tutorials/tutorial-submit-job.html.textile.liquid + - user/topics/tutorial-parallel.html.textile.liquid + - user/topics/run-command.html.textile.liquid + - user/reference/job-pipeline-ref.html.textile.liquid + - user/examples/crunch-examples.html.textile.liquid + - user/topics/tutorial-trait-search.html.textile.liquid sdk: - Overview: - sdk/index.html.textile.liquid @@ -75,10 +75,10 @@ navbar: - sdk/python/sdk-python.html.textile.liquid - sdk/python/example.html.textile.liquid - sdk/python/python.html.textile.liquid - # - sdk/python/crunch-utility-libraries.html.textile.liquid - sdk/python/arvados-fuse.html.textile.liquid - sdk/python/events.html.textile.liquid - sdk/python/cookbook.html.textile.liquid + - sdk/python/crunch-utility-libraries.html.textile.liquid - CLI: - sdk/cli/install.html.textile.liquid - sdk/cli/index.html.textile.liquid diff --git a/doc/architecture/Arvados arch.odg b/doc/architecture/Arvados_arch.odg similarity index 100% rename from doc/architecture/Arvados arch.odg rename to doc/architecture/Arvados_arch.odg diff --git a/doc/sdk/python/crunch-utility-libraries.html.textile.liquid b/doc/sdk/python/crunch-utility-libraries.html.textile.liquid index 64019bba33..3e2631512b 100644 --- a/doc/sdk/python/crunch-utility-libraries.html.textile.liquid +++ b/doc/sdk/python/crunch-utility-libraries.html.textile.liquid @@ -11,6 +11,8 @@ Copyright (C) The Arvados Authors. All rights reserved. SPDX-License-Identifier: CC-BY-SA-3.0 {% endcomment %} +{% include 'pipeline_deprecation_notice' %} + 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 @@ -224,5 +226,3 @@ On qr1hi.arvadosapi.com, the binary distribution @picard-tools-1.82.zip@ is avai ... } - - diff --git a/doc/user/topics/tutorial-trait-search.html.textile.liquid b/doc/user/topics/tutorial-trait-search.html.textile.liquid index 7015d413f9..d396802f72 100644 --- a/doc/user/topics/tutorial-trait-search.html.textile.liquid +++ b/doc/user/topics/tutorial-trait-search.html.textile.liquid @@ -9,23 +9,27 @@ Copyright (C) The Arvados Authors. All rights reserved. SPDX-License-Identifier: CC-BY-SA-3.0 {% endcomment %} +{% include 'notebox_begin_warning' %} +The humans, specimens and traits tables are deprecated and will be removed in a future release. The recommended way to store and search on user-defined metadata is using the "properties" field of Arvados resources. +{% include 'notebox_end' %} + 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. {% include 'tutorial_expectations' %} In the tutorial examples, three angle brackets (>>>) will be used to denote code to enter at the interactive Python prompt. -Start by running Python. +Start by running Python. 
~$ python
-Python 2.7.3 (default, Jan  2 2013, 13:56:14) 
+Python 2.7.3 (default, Jan  2 2013, 13:56:14)
 [GCC 4.7.2] on linux2
 Type "help", "copyright", "credits" or "license" for more information.
 >>>
- + If everything is set up correctly, you will be able to import the arvados SDK. notextile. 
>>> import arvados
@@ -248,7 +252,7 @@ After the jobs have completed, check output file sizes. job_uuid = job[collection_uuid]['uuid'] job_output = arvados.api('v1').jobs().get(uuid=job_uuid).execute()['output'] output_files = arvados.api('v1').collections().get(uuid=job_output).execute()['files'] - # Test the output size. If greater than zero, that means 'grep' found the variant + # Test the output size. If greater than zero, that means 'grep' found the variant if output_files[0][2] > 0: print("%s has variant rs1126809" % (pgpid[collection_uuid])) else: diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd index 8a64e93d0a..cfa0ce5ae6 100644 --- a/sdk/R/README.Rmd +++ b/sdk/R/README.Rmd @@ -5,312 +5,318 @@ The API is not final and feedback is solicited from users on ways in which it co ### Installation -```install.packages("ArvadosR", repos=c("http://r.arvados.org", getOption("repos")["CRAN"]), dependencies=TRUE)``` +```{r include=FALSE} +knitr::opts_chunk$set(eval=FALSE) +``` + +```{r} +install.packages("ArvadosR", repos=c("http://r.arvados.org", getOption("repos")["CRAN"]), dependencies=TRUE) +``` Note: on Linux, you may have to install supporting packages. On Centos 7, this is: -```yum install libxml2-devel openssl-devel curl-devel``` +```{bash} +yum install libxml2-devel openssl-devel curl-devel +``` On Debian, this is: -```apt-get install build-essential libxml2-dev libssl-dev libcurl4-gnutls-dev``` +```{bash} +apt-get install build-essential libxml2-dev libssl-dev libcurl4-gnutls-dev +``` ### Usage #### Initializing API -```{r include=FALSE} -knitr::opts_chunk$set(eval = FALSE) -``` - * Load Library and Initialize API: - ```{r} - library('ArvadosR') - # use environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST - arv <- Arvados$new() +```{r} +library('ArvadosR') +# use environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST +arv <- Arvados$new() - # provide them explicitly - arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") - ``` +# provide them explicitly +arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") +``` - Optionally, add numRetries parameter to specify number of times to retry failed service requests. - Default is 0. +Optionally, add numRetries parameter to specify number of times to retry failed service requests. +Default is 0. - ```{r} - arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3) - ``` +```{r} +arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3) +``` - This parameter can be set at any time using setNumRetries +This parameter can be set at any time using setNumRetries - ```{r} - arv$setNumRetries(5) - ``` +```{r} +arv$setNumRetries(5) +``` #### Working with collections * Get a collection: - ```{r} - collection <- arv$collections.get("uuid") - ``` +```{r} +collection <- arv$collections.get("uuid") +``` * List collections: - ```{r} - # offset of 0 and default limit of 100 - collectionList <- arv$collections.list(list(list("name", "like", "Test%"))) +```{r} +# offset of 0 and default limit of 100 +collectionList <- arv$collections.list(list(list("name", "like", "Test%"))) - collectionList <- arv$collections.list(list(list("name", "like", "Test%")), limit = 10, offset = 2) - ``` +collectionList <- arv$collections.list(list(list("name", "like", "Test%")), limit = 10, offset = 2) +``` - ```{r} - # count of total number of items (may be more than returned due to paging) - collectionList$items_available +```{r} +# count of total number of items (may be more than returned due to paging) +collectionList$items_available - # items which match the filter criteria - collectionList$items - ``` +# items which match the filter criteria +collectionList$items +``` * List all collections even if the number of items is greater than maximum API limit: - ```{r} - collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%"))) - ``` +```{r} +collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%"))) +``` * Delete a collection: - ```{r} - deletedCollection <- arv$collections.delete("uuid") - ``` +```{r} +deletedCollection <- arv$collections.delete("uuid") +``` * Update a collection's metadata: - ```{r} - updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), "uuid") - ``` +```{r} +updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), "uuid") +``` * Create collection: - ```{r} - newCollection <- arv$collections.create(list(name = "Example", description = "This is a test collection")) - ``` +```{r} +newCollection <- arv$collections.create(list(name = "Example", description = "This is a test collection")) +``` #### Manipulating collection content * Create collection object: - ```{r} - collection <- Collection$new(arv, "uuid") - ``` +```{r} +collection <- Collection$new(arv, "uuid") +``` * Get list of files: - ```{r} - files <- collection$getFileListing() - ``` +```{r} +files <- collection$getFileListing() +``` * Get ArvadosFile or Subcollection from internal tree-like structure: - ```{r} - arvadosFile <- collection$get("location/to/my/file.cpp") - ``` +```{r} +arvadosFile <- collection$get("location/to/my/file.cpp") +``` or - ```{r} - arvadosSubcollection <- collection$get("location/to/my/directory/") - ``` +```{r} +arvadosSubcollection <- collection$get("location/to/my/directory/") +``` * Read a table: - ```{r} - arvadosFile <- collection$get("myinput.txt") - arvConnection <- arvadosFile$connection("r") - mytable <- read.table(arvConnection) - ``` +```{r} +arvadosFile <- collection$get("myinput.txt") +arvConnection <- arvadosFile$connection("r") +mytable <- read.table(arvConnection) +``` * Write a table: - ```{r} - arvadosFile <- collection$create("myoutput.txt") - arvConnection <- arvadosFile$connection("w") - write.table(mytable, arvConnection) - arvadosFile$flush() - ``` +```{r} +arvadosFile <- collection$create("myoutput.txt") +arvConnection <- arvadosFile$connection("w") +write.table(mytable, arvConnection) +arvadosFile$flush() +``` * Write to existing file (override current content of the file): - ```{r} - arvadosFile <- collection$get("location/to/my/file.cpp") - arvadosFile$write("This is new file content") - ``` +```{r} +arvadosFile <- collection$get("location/to/my/file.cpp") +arvadosFile$write("This is new file content") +``` * Read whole file or just a portion of it: - ```{r} - fileContent <- arvadosFile$read() - fileContent <- arvadosFile$read("text") - fileContent <- arvadosFile$read("raw", offset = 1024, length = 512) - ``` +```{r} +fileContent <- arvadosFile$read() +fileContent <- arvadosFile$read("text") +fileContent <- arvadosFile$read("raw", offset = 1024, length = 512) +``` * Get ArvadosFile or Subcollection size: - ```{r} - size <- arvadosFile$getSizeInBytes() - ``` +```{r} +size <- arvadosFile$getSizeInBytes() +``` or - ```{r} - size <- arvadosSubcollection$getSizeInBytes() - ``` +```{r} +size <- arvadosSubcollection$getSizeInBytes() +``` * Create new file in a collection: - ```{r} - collection$create(fileNames, optionalRelativePath) - ``` +```{r} +collection$create(fileNames, optionalRelativePath) +``` Example: - ```{r} - mainFile <- collection$create("main.cpp", "cpp/src/") - fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/") - ``` +```{r} +mainFile <- collection$create("main.cpp", "cpp/src/") +fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/") +``` * Add existing ArvadosFile or Subcollection to a collection: - ```{r} - folder <- Subcollection$new("src") - file <- ArvadosFile$new("main.cpp") - folder$add(file) - ``` +```{r} +folder <- Subcollection$new("src") +file <- ArvadosFile$new("main.cpp") +folder$add(file) +``` - ```{r} - collection$add(folder, "cpp") - ``` +```{r} +collection$add(folder, "cpp") +``` - This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists. - If subcollection contains more files or folders they will be added recursively. +This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists. +If subcollection contains more files or folders they will be added recursively. * Delete file from a collection: - ```{r} - collection$remove("location/to/my/file.cpp") - ``` +```{r} +collection$remove("location/to/my/file.cpp") +``` - You can remove both Subcollection and ArvadosFile. - If subcollection contains more files or folders they will be removed recursively. +You can remove both Subcollection and ArvadosFile. +If subcollection contains more files or folders they will be removed recursively. - You can also remove multiple files at once: +You can also remove multiple files at once: - ```{r} - collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp")) - ``` +```{r} +collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp")) +``` * Delete file or folder from a Subcollection: - ```{r} - subcollection <- collection$get("mySubcollection/") - subcollection$remove("fileInsideSubcollection.exe") - subcollection$remove("folderInsideSubcollection/") - ``` +```{r} +subcollection <- collection$get("mySubcollection/") +subcollection$remove("fileInsideSubcollection.exe") +subcollection$remove("folderInsideSubcollection/") +``` * Move file or folder inside collection: - Directley from collection +Directley from collection - ```{r} - collection$move("folder/file.cpp", "file.cpp") - ``` +```{r} +collection$move("folder/file.cpp", "file.cpp") +``` - Or from file +Or from file - ```{r} - file <- collection$get("location/to/my/file.cpp") - file$move("newDestination/file.cpp") - ``` +```{r} +file <- collection$get("location/to/my/file.cpp") +file$move("newDestination/file.cpp") +``` - Or from subcollection +Or from subcollection - ```{r} - subcollection <- collection$get("location/to/folder") - subcollection$move("newDestination/folder") - ``` +```{r} +subcollection <- collection$get("location/to/folder") +subcollection$move("newDestination/folder") +``` - Make sure to include new file name in destination. - In second example file$move("newDestination/") will not work. +Make sure to include new file name in destination. +In second example file$move("newDestination/") will not work. #### Working with Aravdos projects * Get a project: - ```{r} - project <- arv$projects.get("uuid") - ``` +```{r} +project <- arv$projects.get("uuid") +``` * List projects: - ```{r} - # list subprojects of a project - projects <- arv$projects.list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) +```{r} +list subprojects of a project +projects <- arv$projects.list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc"))) - # list projects which have names beginning with Example - examples <- arv$projects.list(list(list("name","like","Example%"))) - ``` +list projects which have names beginning with Example +examples <- arv$projects.list(list(list("name","like","Example%"))) +``` * List all projects even if the number of items is greater than maximum API limit: - ```{r} - projects <- listAll(arv$projects.list, list(list("name","like","Example%"))) - ``` +```{r} +projects <- listAll(arv$projects.list, list(list("name","like","Example%"))) +``` * Delete a project: - ```{r} - deletedProject <- arv$projects.delete("uuid") - ``` +```{r} +deletedProject <- arv$projects.delete("uuid") +``` * Update project: - ```{r} - updatedProject <- arv$projects.update(list(name = "new_name", description = "new description"), "uuid") - ``` +```{r} +updatedProject <- arv$projects.update(list(name = "new_name", description = "new description"), "uuid") +``` * Create project: - ```{r} - newProject <- arv$projects.update(list(name = "project_name", description = "project description")) - ``` +```{r} +newProject <- arv$projects.update(list(name = "project_name", description = "project description")) +``` #### Help * View help page of Arvados classes by puting ? before class name: - ```{r} - ?Arvados - ?Collection - ?Subcollection - ?ArvadosFile - ``` +```{r} +?Arvados +?Collection +?Subcollection +?ArvadosFile +``` * View help page of any method defined in Arvados class by puting ? before method name: - ```{r} - ?collections.update - ?jobs.get - ``` +```{r} +?collections.update +?jobs.get +``` ### Building the ArvadosR package - ``` - cd arvados/sdk && R CMD build R - ``` +```{bash} +cd arvados/sdk && R CMD build R +``` This will create a tarball of the ArvadosR package in the current directory.