Add baseline support for reviewing functional test results for installing repositories and executing functional tests on the contained tool inside a Galaxy instance for tools included in repositories in the tool shed.

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -672,20 +672,32 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
                                                           status='error' ) )
 
     @web.expose
-    def display_tool_functional_test_errors( self, trans, repository_id, repository_metadata_id, **kwd ):
+    def display_tool_functional_test_results( self, trans, repository_id, repository_metadata_id, **kwd ):
+        """
+        The test framework in ~/test/install_and_test_tool_shed_repositories can be executed on a regularly defined schedule (e.g., via cron) to install appropriate
+        repositories from a tool shed into a Galaxy instance and run defined functional tests for the tools included in the repository.  This process affects the values
+        if these columns in the repository_metadata table: tools_functionally_correct, do_not_test, time_last_tested and tool_test_errors.  The tool_test_errors is
+        slightly mis-named (it should have been named tool_test_results) it will contain a dictionary that includes information about the test environment even if all
+        tests passed and the tools_functionally_correct column is set to True.
+        The value of the tool_test_errors column will be a dictionary with the key / value pairs: 
+        "test_environment", {"architecture": "i386", "python_version": "2.5.4", "system": "Darwin 10.8.0"}
+        "test_errors" [ { "test_id":<some test id>, "stdout":<stdout of running the test>, "stderr":<stderr of running the test>, "traceback":<traceback of running the test>]
+        """
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = suc.get_repository_by_id( trans.app, repository_id )
+        repository = suc.get_repository_by_id( trans, repository_id )
         if repository:
             repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
             changeset_revision = repository_metadata.changeset_revision
             if repository_metadata:
                 metadata = repository_metadata.metadata
                 if metadata:
-                    return trans.fill_template( '/webapps/tool_shed/repository/display_tool_functional_test_errors.mako',
+                    revision_label = suc.get_revision_label( trans, repository, repository_metadata.changeset_revision )
+                    return trans.fill_template( '/webapps/tool_shed/repository/display_tool_functional_test_results.mako',
                                                 repository=repository,
                                                 repository_metadata=repository_metadata,
+                                                revision_label=revision_label,
                                                 message=message,
                                                 status=status )
                 else:
@@ -1636,7 +1648,6 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
                                                                                             downloadable=False )
         revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ) )
         repository_metadata = None
-        repository_metadata_id = None
         metadata = None
         is_malicious = False
         repository_dependencies = None
@@ -1644,7 +1655,6 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
             repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
             if repository_metadata:
                 revision_label = suc.get_revision_label( trans, repository, changeset_revision )
-                repository_metadata_id = trans.security.encode_id( repository_metadata.id )
                 metadata = repository_metadata.metadata
                 is_malicious = repository_metadata.malicious
             else:
@@ -1654,7 +1664,6 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
                     repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision )
                     if repository_metadata:
                         revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision )
-                        repository_metadata_id = trans.security.encode_id( repository_metadata.id )
                         metadata = repository_metadata.metadata
                         is_malicious = repository_metadata.malicious
             if repository_metadata:
@@ -1702,7 +1711,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
                                     repo=repo,
                                     repository=repository,
                                     containers_dict=containers_dict,
-                                    repository_metadata_id=repository_metadata_id,
+                                    repository_metadata=repository_metadata,
                                     changeset_revision=changeset_revision,
                                     reviewed_by_user=reviewed_by_user,
                                     review_id=review_id,

lib/tool_shed/util/shed_util_common.py

@@ -2134,13 +2134,12 @@ def get_repo_info_tuple_contents( repo_info_tuple ):
     elif len( repo_info_tuple ) == 7:
         description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
     return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies
-def get_repository_by_id( app, id ):
+def get_repository_by_id( trans, id ):
     """Get a repository from the database via id."""
-    sa_session = app.model.context.current
-    if app.name == 'galaxy':
-        return sa_session.query( app.model.ToolShedRepository ).get( id )
+    if trans.webapp.name == 'galaxy':
+        return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
     else:
-        return sa_session.query( app.model.Repository ).get( id )
+        return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) )
 def get_repository_by_name( app, name ):
     """Get a repository from the database via name."""
     sa_session = app.model.context.current

templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako

@@ -0,0 +1,185 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
+<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
+
+<%
+    from galaxy.web.framework.helpers import time_ago
+
+    changeset_revision = repository_metadata.changeset_revision
+    has_metadata = repository.metadata_revisions
+    has_readme = metadata and 'readme' in metadata
+    is_admin = trans.user_is_admin()
+    is_new = repository.is_new( trans.app )
+    is_deprecated = repository.deprecated
+
+    can_browse_contents = trans.webapp.name == 'tool_shed' and not is_new
+    can_contact_owner = trans.user and trans.user != repository.user
+    can_download = not is_new and ( not is_malicious or can_push )
+    can_manage = is_admin or repository.user == trans.user
+    can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
+    can_rate = repository.user != trans.user
+    can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
+    can_upload = can_push
+    can_view_change_log = trans.webapp.name == 'tool_shed' and not is_new
+    if repository_metadata.tool_test_errors:
+        # The tool_test_errors is mis-named (it should have been named tool_test_results) it will contain a dictionary that includes information
+        # about the test environment even if all tests passed and the repository_metadata.tools_functionally_correct column is set to True.
+        tool_test_errors = repository_metadata.tool_test_errors
+        test_environment_dict = tool_test_errors.get( 'test_environment', None )
+        test_errors = tool_test_errors.get( 'test_errors', [] )
+    else:
+        tool_test_errors = None
+        test_environment_dict = {}
+        test_errors = []
+
+    if can_push:
+        browse_label = 'Browse or delete repository tip files'
+    else:
+        browse_label = 'Browse repository tip files'
+%>
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/tool_shed/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+<br/><br/>
+<ul class="manage-table-actions">
+    %if is_new:
+        <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
+    %else:
+        <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+        <div popupmenu="repository-${repository.id}-popup">
+            %if can_review_repository:
+                %if reviewed_by_user:
+                    <a class="action-button" href="${h.url_for( controller='repository_review', action='edit_review', id=review_id )}">Manage my review of this revision</a>
+                %else:
+                    <a class="action-button" href="${h.url_for( controller='repository_review', action='create_review', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Add a review to this revision</a>
+                %endif
+            %endif
+            %if can_manage:
+                <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a>
+            %else:
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a>
+            %endif
+            %if can_upload:
+                <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
+            %endif
+            %if can_view_change_log:
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+            %endif
+            %if can_browse_contents:
+                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+            %endif
+            %if can_contact_owner:
+                <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a>
+            %endif
+            %if can_download:
+                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a>
+            %endif
+        </div>
+    %endif
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Repository revision</div>
+    <div class="toolFormBody">
+        <div class="form-row">
+            <label>Revision:</label>
+            %if can_view_change_log:
+                <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a>
+            %else:
+                ${revision_label}
+            %endif
+        </div>
+    </div>
+</div>
+<p/>
+%if can_download:
+    <div class="toolForm">
+        <div class="toolFormTitle">Repository '${repository.name}'</div>
+        <div class="toolFormBody">
+            <div class="form-row">
+                <label>Clone this repository:</label>
+                ${render_clone_str( repository )}
+            </div>
+        </div>
+    </div>
+%else:
+    <b>Repository name:</b><br/>
+    ${repository.name}
+%endif
+%if tool_test_errors:
+    <p/>
+    <div class="toolForm">
+        <div class="toolFormTitle">Tool functional test results</div>
+        <div class="toolFormBody">
+            <div class="form-row">
+                <label>Time tested:</label>
+                ${time_ago( repository_metadata.time_last_tested ) | h}
+            </div>
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%"><td><b>Test environment</td></tr>
+                </table>
+            </div>
+            <div class="form-row">
+                <label>Architecture:</label>
+                ${test_environment_dict.get( 'architecture', 'unknown' ) | h}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Python version:</label>
+                ${test_environment_dict.get( 'python_version', 'unknown' ) | h}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Operating system:</label>
+                ${test_environment_dict.get( 'system', 'unknown' ) | h}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <table width="100%">
+                    <tr bgcolor="#D8D8D8" width="100%"><td><b>Test results</td></tr>
+                </table>
+            </div>
+            <div class="form-row">
+                <table class="grid">
+                    %for test_results_dict in test_errors:
+                        <tr>
+                            <td bgcolor="#FFFFCC"><b>Test id</b></td>
+                            <td bgcolor="#FFFFCC">${test_results_dict.get( 'test_id', 'unknown' )}</td>
+                        </tr>
+                        %if repository_metadata.tools_functionally_correct:
+                            <tr>
+                                <td><b>Stdout</b></td>
+                                <td>${test_results_dict.get( 'stdout', '' )}</td>
+                            </tr>
+                        %else:
+                            <tr>
+                                <td><b>Stderr</b></td>
+                                <td>${test_results_dict.get( 'stderr', '' )}</td>
+                            </tr>
+                            <tr>
+                                <td><b>Traceback</b></td>
+                                <td>${test_results_dict.get( 'traceback', '' )}</td>
+                            </tr>
+                        %endif
+                    %endfor
+                </table>
+                <div style="clear: both"></div>
+            </div>
+        </div>
+    </div>
+%endif

templates/webapps/tool_shed/repository/manage_repository.mako

@@ -26,6 +26,13 @@
     can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated
     can_upload = can_push
     can_view_change_log = not is_new
+    if repository_metadata:
+        if repository_metadata.includes_tools and repository_metadata.tool_test_errors is not None:
+            can_display_tool_functional_test_results = True
+        else:
+            can_display_tool_functional_test_results = False
+    else:
+        can_display_tool_functional_test_results = False
 
     if can_push:
         browse_label = 'Browse or delete repository tip files'
@@ -105,6 +112,9 @@
             %if can_undeprecate:
                 <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a>
             %endif
+            %if can_display_tool_functional_test_results:
+                <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a>
+            %endif
             %if can_download:
                 <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
                 <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>