1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/592af505e4e6/ changeset: 592af505e4e6 user: greg date: 2013-03-05 18:36:58 summary: 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. affected #: 4 files
diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -672,20 +672,32 @@ 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 @@ 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 @@ 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 @@ 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 @@ 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,
diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -2134,13 +2134,12 @@ 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
diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako --- /dev/null +++ b/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>${test_results_dict.get( 'traceback', '' )}</td> + </tr> + %endif + %endfor + </table> + <div style="clear: both"></div> + </div> + </div> + </div> +%endif
diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -26,6 +26,13 @@ can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated can_upload = can_push can_view_change_log = not is_new + if repository_metadata: + if repository_metadata.includes_tools and repository_metadata.tool_test_errors is not None: + can_display_tool_functional_test_results = True + else: + can_display_tool_functional_test_results = False + else: + can_display_tool_functional_test_results = False
if can_push: browse_label = 'Browse or delete repository tip files' @@ -105,6 +112,9 @@ %if can_undeprecate: <a class="action-button" href="${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>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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