14 | * Constructor for ExitException. 15 | *
16 | * 17 | * @param st 18 | * a int. 19 | */ 20 | public ExitException(int st) { 21 | super("No exit"); 22 | status = st; 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /seqware-common/src/main/java/net/sourceforge/seqware/common/util/NullBeanUtils.java: -------------------------------------------------------------------------------- 1 | package net.sourceforge.seqware.common.util; 2 | 3 | import java.lang.reflect.InvocationTargetException; 4 | import org.apache.commons.beanutils.BeanUtilsBean; 5 | 6 | /** 7 | *8 | * NullBeanUtils class. 9 | *
10 | * 11 | * @author boconnor 12 | * @version $Id: $Id 13 | */ 14 | public class NullBeanUtils extends BeanUtilsBean { 15 | 16 | /** 17 | * {@inheritDoc} 18 | * 19 | * @throws java.lang.IllegalAccessException 20 | * @throws java.lang.reflect.InvocationTargetException 21 | */ 22 | @Override 23 | public void copyProperty(Object dest, String name, Object value) throws IllegalAccessException, InvocationTargetException { 24 | if (value == null) return; 25 | super.copyProperty(dest, name, value); 26 | } 27 | 28 | } 29 | -------------------------------------------------------------------------------- /seqware-common/src/main/java/net/sourceforge/seqware/common/util/Rethrow.java: -------------------------------------------------------------------------------- 1 | package net.sourceforge.seqware.common.util; 2 | 3 | public class Rethrow { 4 | 5 | /** 6 | *7 | * Rethrows t if unchecked, otherwise throws t wrapped in a RuntimeException. 8 | * 9 | *
10 | * Use pattern: 11 | * 12 | *
13 | * try {
14 | * foobar();
15 | * } catch (Exception e) {
16 | * rethrow(e); // import static
17 | * }
18 | *
19 | *
20 | * @param t
21 | * @return
22 | */
23 | public static RuntimeException rethrow(Throwable t) {
24 | if (t instanceof RuntimeException) throw (RuntimeException) t;
25 | if (t instanceof Error) throw (Error) t;
26 | throw new RuntimeException(t);
27 | }
28 |
29 | }
30 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/configtools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Handle reading of SeqWare .seqware/settings files.
3 | *
4 | * @since 0.12
5 | */
6 | package net.sourceforge.seqware.common.util.configtools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/exceptiontools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Rather redundant way of printing out exceptions.
3 | *
4 | * TODO: remove this
5 | *
6 | * @since 0.12
7 | */
8 | package net.sourceforge.seqware.common.util.exceptiontools;
9 |
10 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/filetools/lock/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Lock files with an old Java API.
3 | *
4 | * TODO: Update this to NIO2
5 | *
6 | * @since 0.12
7 | */
8 | package net.sourceforge.seqware.common.util.filetools.lock;
9 |
10 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/filetools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Tools for dealing with files.
3 | *
4 | * @since 0.12
5 | */
6 | package net.sourceforge.seqware.common.util.filetools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/iotools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Buffer outputs.
3 | *
4 | * @since 0.12
5 | */
6 | package net.sourceforge.seqware.common.util.iotools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/jsontools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Tools for json files.
3 | *
4 | * @since 0.13
5 | */
6 | package net.sourceforge.seqware.common.util.jsontools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/maptools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Tools for converting ini files to maps.
3 | *
4 | * @since 0.12
5 | */
6 | package net.sourceforge.seqware.common.util.maptools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Various utility classes.
3 | *
4 | * @since 0.13
5 | */
6 | package net.sourceforge.seqware.common.util;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/processtools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Tools for sleeping processes.
3 | *
4 | * TODO: merge this somewhere else
5 | *
6 | * @since 0.12
7 | */
8 | package net.sourceforge.seqware.common.util.processtools;
9 |
10 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/runtools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Tools for running commands.
3 | *
4 | * TODO: Consider converting this to Apache CLI
5 | *
6 | * @since 0.12
7 | */
8 | package net.sourceforge.seqware.common.util.runtools;
9 |
10 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/testtools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * More tools for creating and manipulating tests databases.
3 | *
4 | * @since 0.13
5 | */
6 | package net.sourceforge.seqware.common.util.testtools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/workflowtools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * A strange couple of tools for manipulating workflows.
3 | *
4 | * This is probably redundant and should be merged.
5 | *
6 | * @since 0.12
7 | */
8 | package net.sourceforge.seqware.common.util.workflowtools;
9 |
10 |
--------------------------------------------------------------------------------
/seqware-common/src/main/java/net/sourceforge/seqware/common/util/xmltools/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * XML Tools.
3 | *
4 | * @since 0.12
5 | */
6 | package net.sourceforge.seqware.common.util.xmltools;
7 |
8 |
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/log4j.properties:
--------------------------------------------------------------------------------
1 | log4j.rootLogger=WARN, R
2 |
3 | log4j.appender.R=org.apache.log4j.RollingFileAppender
4 | log4j.appender.R.File=dao-test.log
5 |
6 | log4j.appender.R.MaxFileSize=100KB
7 | # Keep one backup file
8 | log4j.appender.R.MaxBackupIndex=1
9 |
10 | log4j.appender.R.layout=org.apache.log4j.PatternLayout
11 | log4j.appender.R.layout.ConversionPattern=%p %t %c - %m%n
12 |
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/MD5GeneratorTest_leading_zero.txt:
--------------------------------------------------------------------------------
1 | 48
2 |
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/MD5GeneratorTest_md5file.txt:
--------------------------------------------------------------------------------
1 | Test
2 | file
3 | for
4 | checking
5 | md5sum.
6 |
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/configtools/ConfigToolsTest_settings:
--------------------------------------------------------------------------------
1 | setting1=one
2 | SETTING2=TWO
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/filetools/FileToolsTest.txt:
--------------------------------------------------------------------------------
1 | This file should be owned by you.
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/maptools/normal.ini:
--------------------------------------------------------------------------------
1 | # key=input_file:type=file:display=F:file_meta_type=text/plain
2 | input_file=${workflow_bundle_dir}/Workflow_Bundle_helloWorld/1.0-SNAPSHOT/data/input.txt
3 | # this is just a comment, the output directory is a conventions and used in many workflows to specify a relative output path
4 | output_dir=seqware-results
5 | # the output_prefix is a convension and used to specify the root of the absolute output path or an S3 bucket name
6 | # you should pick a path that is available on all custer nodes and can be written by your user
7 | # ends in a "/"
8 | output_prefix=./provisioned/
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/maptools/normal_withBlanks.ini:
--------------------------------------------------------------------------------
1 | # key=input_file:type=file:display=F:file_meta_type=text/plain
2 | input_file=${workflow_bundle_dir}/Workflow_Bundle_helloWorld/1.0-SNAPSHOT/data/input.txt
3 | boogydown=
4 | funkyparameter_with_extraSpace=
5 | # this is just a comment, the output directory is a conventions and used in many workflows to specify a relative output path
6 | output_dir=seqware-results
7 | # the output_prefix is a convension and used to specify the root of the absolute output path or an S3 bucket name
8 | # you should pick a path that is available on all custer nodes and can be written by your user
9 | # ends in a "/"
10 | output_prefix=./provisioned/
11 | funkyparameter=
12 | # key=funky_annotated:type=file:display=F:file_meta_type=text/plain
13 | funky_annotated=
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/net/sourceforge/seqware/common/util/maptools/vars.ini:
--------------------------------------------------------------------------------
1 | test-multi=a${foo}c${bar}e
2 | foo=b
3 | bar=d
4 |
5 | test-bundle-dir=${sqw.bundle-dir}
6 | test-legacy-bundle-dir=${workflow_bundle_dir}
7 |
8 | test-random=${sqw.random}
9 | test-legacy-random=${random}
10 |
11 | test-date=${sqw.date}
12 | test-legacy-date=${date}
13 |
14 | test-datetime=${sqw.datetime}
15 |
16 | test-timestamp=${sqw.timestamp}
17 |
18 | test-uuid=${sqw.uuid}
19 |
20 | test-bundle-seqware-version=${sqw.bundle-seqware-version}
21 |
22 |
--------------------------------------------------------------------------------
/seqware-common/src/test/resources/noTestConfig.json:
--------------------------------------------------------------------------------
1 | {
2 | "defaults": {
3 | "description": "Empty tests",
4 | "metrics_calculate": "calculate.sh",
5 | "metrics_compare": "compare.sh",
6 | "input_config_dir": "/Incoming/error/incoming/",
7 | "output_metrics_dir": "/Are/you/ready/for/the/error/output_expectation/"
8 | },
9 |
10 | "tests": [
11 |
12 | ]
13 | }
14 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/.gitignore:
--------------------------------------------------------------------------------
1 | /crash.log
2 | /output.diff
3 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/Checks:
--------------------------------------------------------------------------------
1 | #deploy_check :css
2 | #deploy_check :html
3 | deploy_check :external_links
4 | deploy_check :internal_links
5 | deploy_check :stale
6 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/Gemfile:
--------------------------------------------------------------------------------
1 | source :rubygems
2 |
3 | gem 'adsf' # for viewing
4 | gem 'builder' # for feeds
5 | gem 'coderay' # for syntax highlighting
6 | gem 'compass' # for advanced CSS
7 | gem 'haml' # for layouts with clean sources
8 | gem 'kramdown' # for advanced markdown
9 | gem 'nanoc' # for compiling the site
10 | gem 'nokogiri' # for parsing HTML
11 | gem 'rainpress' # for compact CSS
12 | gem 'rdiscount' # for fast Markdown
13 | gem 'rubypants' # for pretty typography
14 | gem 'systemu' # for invoking rsync etc
15 | gem "sass", "~> 3.2.7"
16 |
17 | # Enable this if you want to use fast-aleck
18 | # Commented out because fast-aleck has not been released yet
19 | # and because building it is not trivial.
20 | gem 'fast-aleck'
21 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/Rakefile:
--------------------------------------------------------------------------------
1 | require 'nanoc/tasks'
2 |
3 | Dir['tasks/**/*.rake'].sort.each { |rakefile| load rakefile }
4 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/compass_config.rb:
--------------------------------------------------------------------------------
1 | project_path = File.dirname(__FILE__)
2 | http_path = '/'
3 | output_style = :compressed
4 | sass_dir = 'content/assets/style'
5 | css_dir = 'output/assets/style'
6 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/404.yaml:
--------------------------------------------------------------------------------
1 | title: "Page Not Found"
2 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/about.yaml:
--------------------------------------------------------------------------------
1 | title: "About"
2 | markdown: basic
3 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/assets/style/_code.yaml:
--------------------------------------------------------------------------------
1 | is_hidden: true
2 | is_partial: true
3 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/assets/style/_fonts.yaml:
--------------------------------------------------------------------------------
1 | is_hidden: true
2 | is_partial: true
3 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/assets/style/_main.yaml:
--------------------------------------------------------------------------------
1 | is_hidden: true
2 | is_partial: true
3 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/assets/style/screen.sass:
--------------------------------------------------------------------------------
1 | @import fonts.sass
2 | @import main.sass
3 | @import code.sass
4 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/assets/style/screen.yaml:
--------------------------------------------------------------------------------
1 | version: 17
2 | is_hidden: true
3 | is_dynamic: true
4 |
--------------------------------------------------------------------------------
/seqware-distribution/docs/site/content/blog.html:
--------------------------------------------------------------------------------
1 | You can follow SeqWare on Twitter where we will announce new releases and other key events.
2 | 3 |4 | Follow @SeqWare 5 | 6 |
7 | 8 | 9 | <%= render 'article', :article => sorted_articles.first %> 10 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog.yaml: -------------------------------------------------------------------------------- 1 | title: "News" 2 | short_title: "News" 3 | is_dynamic: true 4 | toc_includes_children: true 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/12.html.erb: -------------------------------------------------------------------------------- 1 | --- 2 | kind: "articles_category" 3 | title: "Articles about v0.12.x" 4 | group: "SeqWare v0.12.x" 5 | is_dynamic: true 6 | --- 7 | 8 | <%= render 'articles' %> 9 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/12/2012-08-06.md: -------------------------------------------------------------------------------- 1 | We have released the final version in the 0.12.x series of SeqWare. Check out the [full release notes](/release-notes/) for details. 2 | 3 | If you have any questions, be sure to ask them on [the mailing list](https://groups.google.com/forum/?fromgroups#!forum/seqware). 4 | 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/12/2012-08-06.yaml: -------------------------------------------------------------------------------- 1 | kind: "article" 2 | title: "SeqWare 0.12.5 released" 3 | created_at: "August 6th, 2012" 4 | markdown: basic 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/13.html.erb: -------------------------------------------------------------------------------- 1 | --- 2 | kind: "articles_category" 3 | title: "Articles about v0.13.x" 4 | group: "SeqWare v0.13.x" 5 | is_dynamic: true 6 | --- 7 | 8 | <%= render 'articles' %> 9 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/13/2012-09-02.md: -------------------------------------------------------------------------------- 1 | We are slowly transitioning from SourceForge to GitHub. Part of this transition will involve the migration of our MediaWiki content to this new nanoc-based website which will make it much easier to manage and redistribute our documentation. 2 | 3 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/13/2012-09-02.yaml: -------------------------------------------------------------------------------- 1 | kind: "article" 2 | title: "New SeqWare Website for 0.13.x" 3 | created_at: "September 2th, 2012" 4 | markdown: basic 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/blog/13/2012-09-21.yaml: -------------------------------------------------------------------------------- 1 | kind: "article" 2 | title: "Talk from Genome Informatics" 3 | created_at: "September 21th, 2012" 4 | markdown: basic 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/community.yaml: -------------------------------------------------------------------------------- 1 | title: "Community" 2 | markdown: basic 3 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/13-code.md: -------------------------------------------------------------------------------- 1 | ../../../../../README.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/13-code.yaml: -------------------------------------------------------------------------------- 1 | title: "Source Code" 2 | toc_includes_sections: false 3 | markdown: basic 4 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/2a-installation-from-scratch.md: -------------------------------------------------------------------------------- 1 | ../../../../../seqware-pipeline/README.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/2a-installation-from-scratch.yaml: -------------------------------------------------------------------------------- 1 | title: "Installation From Scratch" 2 | toc_includes_sections: true 3 | markdown: advanced 4 | is_dynamic: true 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/basic_deciders.md: -------------------------------------------------------------------------------- 1 | ../18-deciders.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/config_files.md: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | title: "Workflow Config Files" 4 | markdown: advanced 5 | is_dynamic: true 6 | toc_includes_sections: true 7 | 8 | --- 9 | 10 | ## Overview 11 | 12 | <%= render '/includes/workflow_conf/' %> 13 | 14 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/file-types.md: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | title: "File Type Conventions" 4 | toc_includes_sections: true 5 | markdown: advanced 6 | is_dynamic: true 7 | 8 | --- 9 | 10 | ## MIME Types 11 | 12 | <%= render '/includes/MIME/' %> 13 | 14 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/file_export.md: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | title: File Export 4 | toc_includes_sections: true 5 | markdown: advanced 6 | is_dynamic: false 7 | 8 | --- 9 | 10 | 14 | 15 | ## Overview 16 | 17 | The reporting tools for the file provenance report (seqware files report) and [workflow 18 | runs](/docs/19-workflow-run-reporter/) each generate tab-delimited reports that 19 | also include file output URLs. We currently do not have a bulk export tool in 20 | SeqWare but the ProvisionFiles module can be used to copy remote files from 21 | these reports to a local system. 22 | 23 | For more information on using ProvisionFiles see the module descriptions [page](/docs/17a-modules/#provisionfiles). 24 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/file_import.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SeqWare/seqware/bab036957ee7182a5932a0716fcc16ebe3f09bc7/seqware-distribution/docs/site/content/docs/6-pipeline/file_import.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/metadata_files.md: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | title: "Workflow Metadata File" 4 | markdown: advanced 5 | is_dynamic: true 6 | toc_includes_sections: true 7 | 8 | --- 9 | 10 | ## Overview 11 | 12 | <%= render '/includes/workflow_man/' %> 13 | 14 | 15 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/6-pipeline/workflow_bundles.md: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | title: "Workflow Bundle Conventions" 4 | markdown: advanced 5 | is_dynamic: true 6 | toc_includes_sections: true 7 | 8 | --- 9 | 10 | ## Overview 11 | 12 | <%= render '/includes/workflow_org/' %> 13 | 14 | 15 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/0-overview.md: -------------------------------------------------------------------------------- 1 | ../../../../../../README.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/0-overview.yaml: -------------------------------------------------------------------------------- 1 | title: "Source Code - Overview" 2 | toc_includes_sections: true 3 | markdown: advanced 4 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/1-pipeline.md: -------------------------------------------------------------------------------- 1 | ../../../../../../seqware-pipeline/README.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/1-pipeline.yaml: -------------------------------------------------------------------------------- 1 | title: "SeqWare Pipeline - Install Guide" 2 | toc_includes_sections: true 3 | markdown: advanced 4 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/3-metadb.md: -------------------------------------------------------------------------------- 1 | ../../../../../../seqware-meta-db/README.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/3-metadb.yaml: -------------------------------------------------------------------------------- 1 | title: "SeqWare MetaDB - Install Guide" 2 | toc_includes_sections: true 3 | markdown: advanced 4 | 5 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/4-webservice.md: -------------------------------------------------------------------------------- 1 | ../../../../../../seqware-webservice/README.md -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/4-webservice.yaml: -------------------------------------------------------------------------------- 1 | title: "SeqWare WebService - Install Guide" 2 | toc_includes_sections: true 3 | markdown: advanced 4 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/github_readme/5-portal.yaml: -------------------------------------------------------------------------------- 1 | title: "SeqWare Portal - Install Guide" 2 | toc_includes_sections: true 3 | markdown: advanced 4 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/template.md: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | title: "Title" 4 | toc_includes_sections: true 5 | markdown: advanced 6 | 7 | --- 8 | 9 | 10 | ## Overview 11 | 12 | ## Features 13 | 14 | ## Installation 15 | 16 | ## Configuration 17 | 18 | 19 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/experiment_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /experiments/(experimentSWID) 6 | uri: /experiments/(experimentSWID) 7 | method: GET 8 | summary: Retrieves a list of experiments. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/experiments_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: Metadata DB Experiments 6 | uri: /experiments 7 | method: GET 8 | summary: Retrieves one or more experiments, depending on parameters. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/experiments_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST experiment 6 | uri: /experiments 7 | method: POST 8 | summary: Adds a new experiment to the experiment table. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | 18 | Parameters 19 | -------------- 20 | show 21 | : 22 | id 23 | : 24 | 25 | Example Requests 26 | -------------- 27 | <%= server_name %> 28 | 29 | ~~~~~ 30 | 31 | Code Block 32 | 33 | ~~~~~ 34 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/file_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET file 6 | uri: /files/(fileSWID) 7 | method: GET 8 | summary: Retrieves a file using its SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/file_put.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: PUT file 6 | uri: /files/(fileSWID) 7 | method: PUT 8 | summary: Updates a file with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/files_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET files 6 | uri: /files 7 | method: GET 8 | summary: Retrieves a list of files. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | id 20 | : Returns the file with the given id (primary key) 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/files_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST /files 6 | uri: /experiments 7 | method: POST 8 | summary: Adds metadata about a file to the database. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/ius_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /ius/(iusSWID) 6 | uri: /ius/(iusSWID) 7 | method: GET 8 | summary: Retrieves an experiment based on the SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/ius_put.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: PUT ius 6 | uri: /ius/(iusSWID) 7 | method: PUT 8 | summary: Update an ius with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/iuses_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET iuses 6 | uri: /ius 7 | method: GET 8 | summary: Retrieves a list of IUSes. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | id 20 | : Returns the IUS with the given id (primary key, not SWID) 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/lane_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a lane 6 | uri: /lane/(laneSWID) 7 | method: GET 8 | summary: Retrieves a lane with a particular SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | :sequencerRun - shows the lane with its sequencer run 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/lane_put.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: PUT lane 6 | uri: /lane/(laneSWID) 7 | method: PUT 8 | summary: Updates a lane with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/lanes_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET lanes 6 | uri: /lanes 7 | method: GET 8 | summary: Retrieves a list of lanes. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | id 20 | : Returns the Lane with the given id (primary key, not SWID) 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/processing_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET processing 6 | uri: /processes/(processSWID) 7 | method: GET 8 | summary: Retrieves a processing object by its SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : workflowRun - shows the processing with its workflow run 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/processing_put.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: PUT processing 6 | uri: /processes/(processSWID) 7 | method: PUT 8 | summary: Updates a processing object with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/processingparents_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET the parents of the given processing 6 | uri: /processes/{processSWID}/parents 7 | method: GET 8 | summary: Retrieves the parent processing events of the processing event with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | 20 | Example Requests 21 | -------------- 22 | <%= server_name %> 23 | 24 | ~~~~~ 25 | 26 | Code Block 27 | 28 | ~~~~~ 29 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/processings_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET processings 6 | uri: /processes 7 | method: GET 8 | summary: Retrieves a list of processings. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : files - shows the processing with its attached files 21 | id 22 | : Returns the Processing with the given id (primary key, not SWID) 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/processings_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST processing 6 | uri: /processes 7 | method: POST 8 | summary: Add a new processing object to the database. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/sample_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a sample 6 | uri: /samples/(sampleSWID) 7 | method: GET 8 | summary: Retrieves a sample using its SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | 18 | Parameters 19 | -------------- 20 | show 21 | : lanes - Returns the sample with its lanes 22 | : ius - Returns the sample with its IUSes 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/samples_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET samples 6 | uri: /samples 7 | method: GET 8 | summary: Retrieves a list of samples 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | title 20 | : Returns the Sample with the given title (most samples have names, all samples have titles) 21 | name 22 | : Returns the Sample with the given name (most samples have names, all samples have titles) 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/samples_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST a sample 6 | uri: /samples 7 | method: POST 8 | summary: Add a new sample to the database. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/samples_root_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET samples/root 6 | uri: /samples/root 7 | method: GET 8 | summary: Retrieves a list of root samples (samples without parents in the sample hierarchy) 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | 20 | Example Requests 21 | -------------- 22 | <%= server_name %> 23 | 24 | ~~~~~ 25 | 26 | Code Block 27 | 28 | ~~~~~ 29 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/sequencerrun_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a sequencer run 6 | uri: /sequencerrun/(sequencerRunSWID) 7 | method: GET 8 | summary: Retrieves a sequencer run by SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : lanes - returns a sequencer run with its lanes 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/sequencerruns_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /sequencerruns 6 | uri: /sequencerruns 7 | method: GET 8 | summary: Retrieves a list of sequencer runs. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | name 20 | : Returns the sequencer run with the given name 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/studies_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /studies 6 | uri: /studies 7 | method: GET 8 | summary: Retrieves a list of studies 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | title 20 | : Returns the study with the given title 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/studies_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST /studies 6 | uri: /studies 7 | method: POST 8 | summary: Adds a new study to the database 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/study_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a study 6 | uri: /studies/(studySWID) 7 | method: GET 8 | summary: Retrieves a study using its SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflow_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a workflow 6 | uri: /workflows/(workflowSWID) 7 | method: GET 8 | summary: Retrieves a workflow using its SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : params - Returns the Workflow with its possible parameters 20 | 21 | Example Requests 22 | -------------- 23 | <%= server_name %> 24 | 25 | ~~~~~ 26 | 27 | Code Block 28 | 29 | ~~~~~ 30 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowparams_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET workflowparams 6 | uri: /workflowparams 7 | method: GET 8 | summary: Retrieves a list of workflow parameters. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | id 20 | : Returns the WorkflowParam with the given id (primary key, not SWID, since workflow parameters do not have SWIDs). 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowparams_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST workflow param 6 | uri: /workflowparams 7 | method: POST 8 | summary: Add a new workflow parameter to the database. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowparamvalues_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /workflowparamvalues 6 | uri: /workflowparamvalues 7 | method: GET 8 | summary: Retrieves a list of workflow parameter values. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | id 20 | : Returns the WorkflowParamValue with the given id (primary key, not SWID, since workflow parameter values do not have SWIDs). 21 | 22 | Example Requests 23 | -------------- 24 | <%= server_name %> 25 | 26 | ~~~~~ 27 | 28 | Code Block 29 | 30 | ~~~~~ 31 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowparamvalues_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST /workflowparamvalues 6 | uri: /workflowparamvalues 7 | method: POST 8 | summary: Adds a workflow parameter value to the database 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowrun_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a workflow run 6 | uri: /workflowruns/(workflowRunSWID) 7 | method: GET 8 | summary: Retrieves a workflow run by SWID 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : lanes - return the workflow run with all of its lanes 21 | : ius - return the workflow run with all of its IUSes 22 | : processes - return the workflow run with all of its processing events 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowrun_put.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: PUT a workflow run 6 | uri: /workflowruns/(workflowRunSWID) 7 | method: PUT 8 | summary: Updates a workflow run with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowrunfiles_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET the files produced by the given workflow run 6 | uri: /workflowruns/{workflowRunId}/files 7 | method: GET 8 | summary: Retrieves the files produced by the workflow run with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | 20 | Example Requests 21 | -------------- 22 | <%= server_name %> 23 | 24 | ~~~~~ 25 | 26 | Code Block 27 | 28 | ~~~~~ 29 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowrunprocessings_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET the processing events produced by the given workflow run 6 | uri: /workflowruns/{workflowRunId}/processings 7 | method: GET 8 | summary: Retrieves the processing events produced by the workflow run with the given SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | 20 | Example Requests 21 | -------------- 22 | <%= server_name %> 23 | 24 | ~~~~~ 25 | 26 | Code Block 27 | 28 | ~~~~~ 29 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowruns_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET workflow runs 6 | uri: /workflowruns 7 | method: GET 8 | summary: Retrieves a list of workflow runs. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : Returns the WorkflowRun with the given id (primary key, not SWID). 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowruns_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST /workflowruns 6 | uri: /workflowruns 7 | method: POST 8 | summary: Inserts a new workflow run into the database. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | show 20 | : 21 | id 22 | : 23 | 24 | Example Requests 25 | -------------- 26 | <%= server_name %> 27 | 28 | ~~~~~ 29 | 30 | Code Block 31 | 32 | ~~~~~ 33 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflows_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /workflows 6 | uri: /workflows 7 | method: GET 8 | summary: Retrieves a list of workflows. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | 17 | Parameters 18 | -------------- 19 | id 20 | : Returns the Workflow with the given id (primary key, not SWID) 21 | name 22 | : Returns the Workflow(s) with the given name 23 | version 24 | : Must be used in combination with the "name" parameter. Returns the named workflow with the given version. 25 | 26 | Example Requests 27 | -------------- 28 | <%= server_name %> 29 | 30 | ~~~~~ 31 | 32 | Code Block 33 | 34 | ~~~~~ 35 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflows_post.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: POST a workflow 6 | uri: /workflows 7 | method: POST 8 | summary: Adds a new workflow to the database. 9 | --- 10 | 11 | <%= @item[:summary] %> 12 | 13 | Resource URL 14 | -------------- 15 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 16 | 17 | 18 | Parameters 19 | -------------- 20 | show 21 | : 22 | id 23 | : 24 | 25 | Example Requests 26 | -------------- 27 | <%= server_name %> 28 | 29 | ~~~~~ 30 | 31 | Code Block 32 | 33 | ~~~~~ 34 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/db/workflowworkflowruns_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET all workflow runs for a particular workflow through the web service 6 | uri: /workflows/{workflowId}/runs 7 | method: GET 8 | summary: Retrieves all of the workflow runs for a particular workflow using the workflow's SWID. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/job.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: Metadata - Job Resources 6 | --- 7 | 8 | Overview 9 | -------------- 10 | Jobs are processes that cause considerable processing on the server side and include PUT and POST operations. Some are asynchronous and will immediately return a status ID and indication of a different URI to monitor the progress of the job. 11 | 12 | Resources 13 | -------------- 14 | None so far! 15 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/report/workflow_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a summary of all runs of a workflow 6 | uri: /reports/workflows/{workflowSWID} 7 | method: GET 8 | summary: Retrieves a summary of all runs of a workflow. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/report/workflowrun_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET a workflow run report 6 | uri: /reports/workflowruns/{workflowRunSWID} 7 | method: GET 8 | summary: Retrieves a single workflow run report, including input and output files, using its SeqWare accession. 9 | --- 10 | <%= @item[:summary] %> For more information on this resource, see [Workflow Run Reporter](/docs/19-workflow-run-reporter/) on the SeqWare wiki. 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/report/workflowruns_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET workflow run reports for all runs 6 | uri: /reports/workflowruns 7 | method: GET 8 | summary: Retrieves workflow run report for all runs, including input and output files. 9 | --- 10 | <%= @item[:summary] %> For more information on this resource, see [Workflow Run Reporter](/docs/19-workflow-run-reporter/) on the SeqWare wiki. 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/docs/webservice-api/metadata/report/workflowruntime_get.html: -------------------------------------------------------------------------------- 1 | --- 2 | markdown: advanced 3 | toc_includes_sections: true 4 | is_dynamic: true 5 | title: GET /experiments/(experimentSWID) 6 | uri: /experiments/(experimentSWID) 7 | method: GET 8 | summary: Retrieves a list of experiments. 9 | --- 10 | <%= @item[:summary] %> 11 | 12 | Resource URL 13 | -------------- 14 | <%= @item[:method] %> <%= server_name %><%= @item[:uri] %> 15 | 16 | Parameters 17 | -------------- 18 | show 19 | : 20 | id 21 | : 22 | 23 | Example Requests 24 | -------------- 25 | <%= server_name %> 26 | 27 | ~~~~~ 28 | 29 | Code Block 30 | 31 | ~~~~~ 32 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/index.yaml: -------------------------------------------------------------------------------- 1 | title: "SeqWare » Home" 2 | short_title: "Home" 3 | has_full_title: true 4 | raw_layout: true 5 | markdown: basic 6 | is_dynamic: true 7 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/content/partners.yaml: -------------------------------------------------------------------------------- 1 | title: "Partners" 2 | markdown: basic 3 | -------------------------------------------------------------------------------- /seqware-distribution/docs/site/layouts/article.html.erb: -------------------------------------------------------------------------------- 1 |#!xml
2 | <!-- VARS -->
3 | <#-- workflow and seqware versions -->
4 | <#assign seqware_version = "0.13.6.5"/>
5 | <#assign workflow_version = "1.0"/>
6 | <#assign java_version = "1.6.0"/>
7 | <#assign perl_version = "5.14.1"/>
8 | <#-- make sure it is a string -->
9 | <#assign parentAccessions = "${parent_accessions}"/>
10 | <#-- Set relative paths for files within the run-->
11 | <#assign bin_dir = "bin"/>
12 | <#assign data_dir = "data"/>
13 | <#assign lib_dir = "lib"/>
14 | #!java
2 | @Override
3 | public void setupDirectory() {
4 | // creates a dir1 directory in the current working directory where the workflow runs
5 | this.addDirectory("dir1");
6 | }
7 | #!java
2 | @Override
3 | public Map setupFiles() {
4 | try {
5 | // register an plaintext input file using the information from the INI
6 | // provisioning this file to the working directory will be the first step in the workflow
7 | SqwFile file0 = this.createFile("file_in_0");
8 | file0.setSourcePath(getProperty("input_file"));
9 | file0.setType("text/plain");
10 | file0.setIsInput(true);
11 |
12 | } catch (Exception ex) {
13 | ex.printStackTrace();
14 | System.exit(1);
15 | }
16 | return this.getFiles();
17 | }
18 |
19 | #!java
2 |
3 | // showing how to access the workflow bundle install location
4 | file0.setSourcePath(this.getWorkflowBaseDir()+"/data/input.txt");
5 |
6 | // showing how to access a property from the INI file
7 | file0.setSourcePath(getProperty("input_file"));
8 |
9 | // showing how to access variables out of the ini file
10 | this.getProperty("output_file_1");
11 |