Merge branch 'Reports_newpage' of https://github.com/Airistotal/galaxy into Reports_newpage

Author: Airistotal

.ci/pep8_sources.txt

@@ -2,6 +2,7 @@ cron/parse_builds.py
 lib/galaxy/auth
 lib/galaxy/config.py
 lib/galaxy/datatypes/{data,proteomics}.py
+lib/galaxy/datatypes/converters/{bedgraph_to_array_tree_converter,wiggle_to_array_tree_converter}.py
 lib/galaxy/exceptions/error_codes.py
 lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py
 lib/galaxy/main.py
@@ -16,6 +17,7 @@ lib/galaxy/queue_worker.py
 lib/galaxy/tags
 lib/galaxy/tools
 lib/galaxy/util/{__init__,json,permutations,plugin_config,properties,simplegraph,sockets,sleeper,streamball,submodules,xml_macros}.py
+lib/galaxy/visualization/data_providers/{__init__,genome,registry}.py
 lib/galaxy/web/{proxy,security}
 lib/galaxy/web/base/{__init__,interactive_environments}.py
 lib/galaxy/web/formatting.py

client/galaxy/scripts/libs/jquery.sparklines.js

@@ -1705,3 +1705,32 @@ div.toolTitleNoSection
 #for_bears {
     display: none;
 }
+
+// ============================================================================ Reports Webapp
+
+.dir_arrow {
+    visibility: hidden
+}
+
+#spark_time_select {
+    display: inline-block;
+}
+
+#spark_select {
+    height: 23px;
+    width: 30px;
+    padding: 0;
+    border-radius: 2px;
+}
+
+.quarter_width {
+    width: 25%;
+}
+
+.third_width {
+    width: 30%;
+}
+
+.half_width {
+    width: 50%
+} 

client/galaxy/style/less/base.less

@@ -23,9 +23,11 @@
 
         <!--  Sample S3 Object Store
         <object_store type="s3">
-            <auth access_key="...." secret_key="....." />
-            <bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" />
-            <cache path="database/files/" size="1000" />
+             <auth access_key="...." secret_key="....." />
+             <bucket name="unique_bucket_name_all_lowercase" use_reduced_redundancy="False" />
+             <cache path="database/object_store_cache" size="1000" />
+             <extra_dir type="job_work" path="database/job_working_directory_s3"/>
+             <extra_dir type="temp" path="database/tmp_s3"/>
         </object_store>
         -->
 
@@ -34,7 +36,9 @@
              <auth access_key="...." secret_key="....." />
              <bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/>
              <connection host="" port="" is_secure="" conn_path="" multipart="True"/>
-             <cache path="database/files/" size="1000" />
+             <cache path="database/object_store_cache" size="1000" />
+             <extra_dir type="job_work" path="database/job_working_directory_swift"/>
+             <extra_dir type="temp" path="database/tmp_swift"/>
          </object_store>
          -->
 

config/object_store_conf.xml.sample

@@ -0,0 +1,282 @@
+Galaxy API Documentation
+************************
+
+Background
+==========
+In addition to being accessible through a web interface, Galaxy can also be
+accessed programmatically, through shell scripts and other programs. The web
+interface is appropriate for things like exploratory analysis, visualization,
+construction of workflows, and rerunning workflows on new datasets.
+
+The web interface is less suitable for things like
+    - Connecting a Galaxy instance directly to your sequencer and running
+      workflows whenever data is ready.
+    - Running a workflow against multiple datasets (which can be done with the
+      web interface, but is tedious).
+    - When the analysis involves complex control, such as looping and
+      branching.
+
+The Galaxy API addresses these and other situations by exposing Galaxy
+internals through an additional interface, known as an Application Programming
+Interface, or API.
+
+Quickstart
+==========
+
+Log in as your user, navigate to the API Keys page in the User menu, and
+generate a new API key.  Make a note of the API key, and then pull up a
+terminal.  Now we'll use the display.py script in your galaxy/scripts/api
+directory for a short example::
+
+        % ./display.py my_key http://localhost:4096/api/histories
+        Collection Members
+        ------------------
+        #1: /api/histories/8c49be448cfe29bc
+          name: Unnamed history
+          id: 8c49be448cfe29bc
+        #2: /api/histories/33b43b4e7093c91f
+          name: output test
+          id: 33b43b4e7093c91f
+
+The result is a Collection of the histories of the user specified by the API
+key (you).  To look at the details of a particular history, say #1 above, do
+the following::
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc
+        Member Information
+        ------------------
+        state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
+        state: ok
+        contents_url: /api/histories/8c49be448cfe29bc/contents
+        id: 8c49be448cfe29bc
+        name: Unnamed history
+
+This gives detailed information about the specific member in question, in this
+case the History.  To view history contents, do the following::
+
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents
+        Collection Members
+        ------------------
+        #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+          name: Pasted Entry
+          type: file
+          id: 6f91353f3eb0fa4a
+
+What we have here is another Collection of items containing all of the datasets
+in this particular history.  Finally, to view details of a particular dataset
+in this collection, execute the following::
+
+        % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
+        Member Information
+        ------------------
+        misc_blurb: 1 line
+        name: Pasted Entry
+        data_type: txt
+        deleted: False
+        file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
+        state: ok
+        download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
+        visible: True
+        genome_build: ?
+        model_class: HistoryDatasetAssociation
+        file_size: 17
+        metadata_data_lines: 1
+        id: 6f91353f3eb0fa4a
+        misc_info: uploaded txt file
+        metadata_dbkey: ?
+
+And now you've successfully used the API to request and select a history,
+browse the contents of that history, and then look at detailed information
+about a particular dataset.
+
+For a more comprehensive Data Library example, set the following option in your
+galaxy.ini as well, and restart galaxy again::
+
+        admin_users = you@example.org
+        library_import_dir = /path/to/some/directory
+
+In the directory you specified for 'library_import_dir', create some
+subdirectories, and put (or symlink) files to import into Galaxy into those
+subdirectories.
+
+In Galaxy, create an account that matches the address you put in 'admin_users',
+then browse to that user's preferences and generate a new API Key.  Copy the
+key to your clipboard and then use these scripts::
+
+        % ./display.py my_key http://localhost:4096/api/libraries
+        Collection Members
+        ------------------
+
+        0 elements in collection
+
+        % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library'
+        Response
+        --------
+        /api/libraries/f3f73e481f432006
+          name: api_test
+          id: f3f73e481f432006
+
+        % ./display.py my_key http://localhost:4096/api/libraries
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006
+          name: api_test
+          id: f3f73e481f432006
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006
+        Member Information
+        ------------------
+        synopsis: None
+        contents_url: /api/libraries/f3f73e481f432006/contents
+        description: API Test Library
+        name: api_test
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+          name: /
+          type: folder
+          id: 28202595c0d2591f61ddda595d2c3670
+
+        % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
+        Response
+        --------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+          name: api_test_folder1
+          id: 28202595c0d2591fa4f9089d2303fd89
+
+        % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
+        Response
+        --------
+        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+          name: 2.bed
+          id: e9ef7fdb2db87d7b
+        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+          name: 3.bed
+          id: 3b7f6a31f80a5018
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 
+        Collection Members
+        ------------------
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
+          name: /
+          type: folder
+          id: 28202595c0d2591f61ddda595d2c3670
+        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
+          name: /api_test_folder1
+          type: folder
+          id: 28202595c0d2591fa4f9089d2303fd89
+        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+          name: /api_test_folder1/2.bed
+          type: file
+          id: e9ef7fdb2db87d7b
+        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
+          name: /api_test_folder1/3.bed
+          type: file
+          id: 3b7f6a31f80a5018
+
+        % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
+        Member Information
+        ------------------
+        misc_blurb: 68 regions
+        metadata_endCol: 3
+        data_type: bed
+        metadata_columns: 6
+        metadata_nameCol: 4
+        uploaded_by: nate@...
+        metadata_strandCol: 6
+        name: 2.bed
+        genome_build: hg19
+        metadata_comment_lines: None
+        metadata_startCol: 2
+        metadata_chromCol: 1
+        file_size: 4272
+        metadata_data_lines: 68
+        message:
+        metadata_dbkey: hg19
+        misc_info: uploaded bed file
+        date_uploaded: 2010-06-22T17:01:51.266119
+        metadata_column_types: str, int, int, str, int, str
+
+Other parameters are valid when uploading, they are the same parameters as are
+used in the web form, like 'link_data_only' and etc.
+
+The request and response format should be considered alpha and are subject to change.
+
+API Design Guidelines
+=====================
+
+The following section outlines guidelines related to extending and/or modifing
+the Galaxy API. The Galaxy API has grown in an ad-hoc fashion over time by
+many contributors and so clients SHOULD NOT expect the API will conform to
+these guidelines - but developers contributing to the Galaxy API SHOULD follow
+these guidelines.
+
+    - API functionality should include docstring documentation for consumption
+      by readthedocs.org.
+    - Developers should familiarize themselves with the HTTP status code definitions
+      http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html. The API responses
+      should properly set the status code according to the result - in particular
+      2XX responses should be used for successful requests, 4XX for various
+      kinds of client errors, and 5XX for the errors on the server side.
+    - If there is an error processing some part of request (one item in a list
+      for instance), the status code should be set to reflect the error and the
+      partial result may or may not be returned depending on the controller -
+      this behavior should be documented.
+    - API methods should throw a finite number of exceptions 
+      (defined in :doc:`galaxy.exceptions`) and these should subclass 
+      `MessageException` and not paste/wsgi HTTP exceptions. When possible, 
+      the framework itself should be responsible catching these exceptions, 
+      setting the status code, and building an error response.
+    - Error responses should not consist of plain text strings - they should be
+      dictionaries describing the error and containing the following::
+
+          {
+            "status_code": 400,
+            "err_code": 400007,
+            "err_msg": "Request contained invalid parameter, action could not be completed.",
+            "type": "error",
+            "extra_error_info": "Extra information."
+          }
+
+      Various error conditions (once a format has been chosen and framework to
+      enforce it in place) should be spelled out in this document.
+    - Backward compatibility is important and should be maintained when possible.
+      If changing behavior in a non-backward compatibile way please ensure one
+      of the following holds - there is a strong reason to believe no consumers
+      depend on a behavior, the behavior is effectively broken, or the API
+      method being modified has not been part of a tagged dist release.
+
+The following bullet points represent good practices more than guidelines, please
+consider them when modifying the API.
+
+    - Functionality should not be copied and pasted between controllers -
+      consider refactoring functionality into associated classes or short of
+      that into Mixins (http://en.wikipedia.org/wiki/Composition_over_inheritance)
+      or into Managers (:doc:`galaxy.managers`).
+    - API additions are more permanent changes to Galaxy than many other potential
+      changes and so a second opinion on API changes should be sought. (Consider a
+      pull request!)
+    - New API functionality should include functional tests. These functional
+      tests should be implemented in Python and placed in
+      `test/functional/api`. (Once such a framework is in place - it is not
+      right now).
+    - Changes to reflect modifications to the API should be pushed upstream to
+      the BioBlend project if possible.
+
+Longer term goals/notes.
+
+    - It would be advantageous to have a clearer separation of anonymous and
+      admin handling functionality.
+    - If at some point in the future, functionality needs to be added that
+      breaks backward compatibility in a significant way to a component used by
+      the community - a "dev" variant of the API will be established and
+      the community should be alerted and given a timeframe for when the old
+      behavior will be replaced with the new behavior.
+    - Consistent standards for range-based requests, batch requests, filtered
+      requests, etc... should be established and documented here.
+
+
+.. include:: lib/galaxy.webapps.galaxy.api.rst

doc/source/api_doc.rst

@@ -17,8 +17,6 @@
 ####### REQUIRED GALAXY INCLUDES
 
 sys.path.append(os.path.join(os.getcwd(), '../../lib'))
-import galaxy
-from galaxy import eggs
 
 #######
 
@@ -103,7 +101,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -274,6 +272,6 @@ def __getattr__(cls, name):
             return Mock()
 
 # adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect.
-MOCK_MODULES = ['tables', 'decorator', 'numpy']
+MOCK_MODULES = ['tables', 'decorator']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

doc/source/conf.py

@@ -42,7 +42,7 @@ Contents
 .. toctree::
    :maxdepth: 5
 
-   API Documentation <lib/galaxy.webapps.galaxy.api>
+   API Documentation <api_doc>
 
    Application Documentation <lib/modules>