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[hg] galaxy 3694: Add missing job_id substitutions to jobs/runne...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1a3bc21d3a8e changeset: 3694:1a3bc21d3a8e user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 26 09:58:21 2010 -0400 description: Add missing job_id substitutions to jobs/runners/pbs.py. diffstat: lib/galaxy/jobs/runners/pbs.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r df8fc06fdac9 -r 1a3bc21d3a8e lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Sun Apr 25 16:18:15 2010 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Mon Apr 26 09:58:21 2010 -0400 @@ -378,7 +378,7 @@ try: # recheck to make sure it wasn't a communication problem self.check_single_job( pbs_server_name, job_id ) - log.warning( "(%s/%s) job was not in state check list, but was found with individual state check" ) + log.warning( "(%s/%s) job was not in state check list, but was found with individual state check" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) except: errno, text = pbs.error()

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[hg] galaxy 3693: Fix multiple issues for history display. Fixes...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df8fc06fdac9 changeset: 3693:df8fc06fdac9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun Apr 25 16:18:15 2010 -0400 description: Fix multiple issues for history display. Fixes include: (a) empty annotations hidden; (b) text 'import XXX' added next to import icon; (c) fix dataset display links; (d) fix dataset view links; and (e) fix peek placement. diffstat: lib/galaxy/datatypes/interval.py | 2 +- lib/galaxy/web/controllers/history.py | 2 -- templates/dataset/display.mako | 5 ++++- templates/display_base.mako | 2 +- templates/history/display.mako | 15 ++++++++++++--- templates/history/view.mako | 12 +----------- templates/page/history_annotation_table.mako | 2 +- templates/root/history.mako | 2 +- templates/root/history_common.mako | 28 ++++++++++++++++++++++------ templates/workflow/display.mako | 7 ++++++- 10 files changed, 49 insertions(+), 28 deletions(-) diffs (237 lines): diff -r 7151ae06bf7a -r df8fc06fdac9 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Sat Apr 24 15:03:22 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Sun Apr 25 16:18:15 2010 -0400 @@ -235,7 +235,7 @@ # if our URL scheme is https. Making this work # requires additional hackery in your upstream proxy. # If UCSC ever supports https, remove this hack. - internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) + internal_url = "%s" % url_for( controller='/dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) if base_url.startswith( 'https://' ): base_url = base_url.replace( 'https', 'http', 1 ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) diff -r 7151ae06bf7a -r df8fc06fdac9 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Sat Apr 24 15:03:22 2010 -0400 +++ b/lib/galaxy/web/controllers/history.py Sun Apr 25 16:18:15 2010 -0400 @@ -590,11 +590,9 @@ error( "Either you are not allowed to view this history or the owner of this history has not made it accessible." ) # View history. datasets = self.get_history_datasets( trans, history_to_view ) - user_owns_history = ( trans.get_user() == history_to_view.user ) return trans.stream_template_mako( "history/view.mako", history = history_to_view, datasets = datasets, - user_owns_history = user_owns_history, show_deleted = False ) @web.expose diff -r 7151ae06bf7a -r df8fc06fdac9 templates/dataset/display.mako --- a/templates/dataset/display.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/dataset/display.mako Sun Apr 25 16:18:15 2010 -0400 @@ -24,7 +24,10 @@ <%def name="render_item_links( data )"> ## Provide links to save data and import dataset. <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}" class="icon-button disk tooltip" title="Save dataset"></a> - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}" class="icon-button import tooltip" title="Import dataset"></a> + <a + href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}" + class="icon-button import tooltip" + title="Import dataset"></a> </%def> <%def name="render_item( data, data_to_render )"> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/display_base.mako --- a/templates/display_base.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/display_base.mako Sun Apr 25 16:18:15 2010 -0400 @@ -114,7 +114,7 @@ <%def name="render_item_header( item )"> <h3>Galaxy ${get_class_display_name( item.__class__ )} '${get_item_name( item )| h}'</h3> - %if hasattr( item, "annotation"): + %if hasattr( item, "annotation") and item.annotation is not None: <div class="annotation">Annotation: ${item.annotation}</div> %endif <hr/> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/history/display.mako --- a/templates/history/display.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/history/display.mako Sun Apr 25 16:18:15 2010 -0400 @@ -38,7 +38,12 @@ </%def> <%def name="render_item_links( history )"> - <a href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" class="icon-button import tooltip" title="Import history"></a> + <a + href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" + class="icon-button import" + ## Needed to overwide initial width so that link is floated left appropriately. + style="width: 100%" + title="Import history">Import history</a> </%def> <%def name="render_item( history, datasets )"> @@ -60,10 +65,14 @@ %if data.visible: <td> <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} </div> </td> - <td class="annotation">${data.annotation}</td> + <td class="annotation"> + %if hasattr( data, "annotation") and data.annotation is not None: + ${data.annotation} + %endif + </td> %endif </tr> %endfor diff -r 7151ae06bf7a -r df8fc06fdac9 templates/history/view.mako --- a/templates/history/view.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/history/view.mako Sun Apr 25 16:18:15 2010 -0400 @@ -64,11 +64,6 @@ </%def> <%def name="center_panel()"> - ## For now, turn off inline editing so that view is external only. - <% - user_owns_history = False - %> - ## Get URL to other histories owned by user that owns this history. <% ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. @@ -84,9 +79,7 @@ <div style="overflow: auto; height: 100%;"> ## Render view of history. <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not user_owns_history: <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | - %endif <a href="${get_history_link( history )}">${_('refresh')}</a> %if show_deleted: | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> @@ -95,9 +88,6 @@ </div> <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - %if user_owns_history: - <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> - %endif <div id="history-name">${history.get_display_name()}</div> </div> @@ -118,7 +108,7 @@ %for data in datasets: %if data.visible: <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} </div> %endif %endfor diff -r 7151ae06bf7a -r df8fc06fdac9 templates/page/history_annotation_table.mako --- a/templates/page/history_annotation_table.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/page/history_annotation_table.mako Sun Apr 25 16:18:15 2010 -0400 @@ -50,7 +50,7 @@ ##<td valign="top" class="annotation">Describe this step: why was it done? what data does it produce?</td> <td> <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = False )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )} </div> </td> </tr> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/root/history.mako --- a/templates/root/history.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/root/history.mako Sun Apr 25 16:18:15 2010 -0400 @@ -387,7 +387,7 @@ %for data in reversed( datasets ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = True )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = True )} </div> %endif %endfor diff -r 7151ae06bf7a -r df8fc06fdac9 templates/root/history_common.mako --- a/templates/root/history_common.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/root/history_common.mako Sun Apr 25 16:18:15 2010 -0400 @@ -1,6 +1,6 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> +<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True )"> <a name="${trans.security.encode_id( data.id )}"></a> <% if data.state in ['no state','',None]: @@ -29,16 +29,28 @@ ## links should be enough. However the number of datasets being uploaded ## at a time is usually small so the impact of these images is also small. <img src="${h.url_for('/static/images/eye_icon_grey.png')}" width='16' height='16' alt='display data' title='display data' class='button display' border='0'> - %if user_owns_dataset: + %if for_editing: <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='button edit' border='0'> %endif %else: - <a class="icon-button display tooltip" title="Display data in browser" href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), preview=True, filename='' )}" target="galaxy_main"></a> - %if user_owns_dataset: + <% + dataset_id = trans.security.encode_id( data.id ) + if for_editing: + display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) + else: + display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', + username=data.history.user.username, slug=dataset_id ) + %> + <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}" + %if for_editing: + target="galaxy_main" + %endif + ></a> + %if for_editing: <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> %endif %endif - %if user_owns_dataset: + %if for_editing: <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> %endif </div> @@ -89,7 +101,7 @@ <% dataset_id=trans.security.encode_id( data.id ) %> %if data.has_data: <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Save" class="icon-button disk tooltip"></a> - %if user_owns_dataset: + %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): <a class="icon-button vis-chart tooltip trackster" title="Visualize in Trackster" id="visualize_${hid}"></a> @@ -110,6 +122,10 @@ </div> %endif + %else: + ## When displaying datasets for viewing, this is often needed to prevent peek from overlapping + ## icons. + <div style="clear: both"></div> %endif %if data.peek != "no peek": <div><pre id="peek${data.id}" class="peek">${_(data.display_peek())}</pre></div> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/workflow/display.mako --- a/templates/workflow/display.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/workflow/display.mako Sun Apr 25 16:18:15 2010 -0400 @@ -71,7 +71,12 @@ <%def name="render_item_links( workflow )"> - <a href="${h.url_for( controller='/workflow', action='imp', id=trans.security.encode_id(workflow.id) )}" class="icon-button import tooltip" title="Import workflow"></a> + <a + href="${h.url_for( controller='/workflow', action='imp', id=trans.security.encode_id(workflow.id) )}" + class="icon-button import" + ## Needed to overwide initial width so that link is floated left appropriately. + style="width: 100%" + title="Import workflow">Import workflow</a> </%def> <%def name="render_item( workflow, steps )">

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[hg] galaxy 3692: Better labels for rna-seq tools' output datasets.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7151ae06bf7a changeset: 3692:7151ae06bf7a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sat Apr 24 15:03:22 2010 -0400 description: Better labels for rna-seq tools' output datasets. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 4 +++- tools/ngs_rna/cuffcompare_wrapper.xml | 6 +++--- tools/ngs_rna/cuffdiff_wrapper.py | 4 +++- tools/ngs_rna/cuffdiff_wrapper.xml | 22 +++++++++++----------- tools/ngs_rna/cufflinks_wrapper.py | 4 +++- tools/ngs_rna/cufflinks_wrapper.xml | 6 +++--- tools/ngs_rna/tophat_wrapper.xml | 6 +++--- 7 files changed, 29 insertions(+), 23 deletions(-) diffs (130 lines): diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -33,11 +33,13 @@ if options.ignore_nonoverlap: cmd += " -R " + # Output/debugging. + print cmd + # Add input files. if type(args) is list: args = " ".join(args) cmd += " " + args - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -32,9 +32,9 @@ </inputs> <outputs> - <data format="gtf" name="transcripts_combined" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: combined transcripts"/> - <data format="tracking" name="transcripts_tracking" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: transcript tracking"/> - <data format="gtf" name="transcripts_accuracy" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: transcript accuracy"/> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> + <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"/> + <data format="gtf" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -69,9 +69,11 @@ if options.max_mle_iterations: cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + # Output/debugging. + print cmd + # Add inputs. cmd += " " + options.inputA + " " + options.input1 + " " + options.input2 - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -44,17 +44,17 @@ </inputs> <outputs> - <data format="tabular" name="isoforms_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: isoform expression"/> - <data format="tabular" name="genes_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: gene expression"/> - <data format="tabular" name="tss_groups_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: TSS groups expression"/> - <data format="tabular" name="cds_exp_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="splicing_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: splicing diff"/> - <data format="tabular" name="cds_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS diff"/> - <data format="tabular" name="promoters_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: promoters diff"/> - <data format="tabular" name="tss_groups_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: TSS groups FPKM tracking" /> - <data format="tabular" name="cds_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS FPKM tracking"/> - <data format="tabular" name="genes_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: gene FPKM tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: isoform FPKM tracking"/> + <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: isoform expression"/> + <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> + <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> + <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> + <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> + <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -62,9 +62,11 @@ if options.max_mle_iterations: cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + # Output/debugging. + print cmd + # Add input files. cmd += " " + options.input - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -50,9 +50,9 @@ </inputs> <outputs> - <data format="expr" name="genes_expression" label="Cufflinks on data ${input.hid}: gene expression"/> - <data format="expr" name="transcripts_expression" label="Cufflinks on data ${input.hid}: transcript expression"/> - <data format="gtf" name="assembled_isoforms" label="Cufflinks on data ${input.hid}: assembled transcripts"/> + <data format="expr" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> + <data format="expr" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/> + <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -55,9 +55,9 @@ </inputs> <outputs> - <data format="sam" name="accepted_hits"/> - <data format="wig" name="coverage" /> - <data format="bed" name="junctions" /> + <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="wig" name="coverage" label="${tool.name} on ${on_string}: coverage"/> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> </outputs> <tests>

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[hg] galaxy 3691: Some fixes for the async datasource tool contr...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0dd1676e5b6f changeset: 3691:0dd1676e5b6f user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Apr 23 17:04:39 2010 -0400 description: Some fixes for the async datasource tool controller. diffstat: lib/galaxy/web/controllers/async.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (19 lines): diff -r 7ae394334e5c -r 0dd1676e5b6f lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Fri Apr 23 16:32:40 2010 -0400 +++ b/lib/galaxy/web/controllers/async.py Fri Apr 23 17:04:39 2010 -0400 @@ -108,8 +108,8 @@ data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO + trans.sa_session.add( data ) #Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW - trans.sa_session.add( data ) open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) trans.sa_session.add( trans.history ) @@ -135,4 +135,4 @@ trans.sa_session.flush() - return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config ) + return trans.fill_template( 'tool_executed.mako', history=history, toolbox=toolbox, tool=tool, util=util, out_data={} )

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[hg] galaxy 3690: Added missing templates
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7ae394334e5c changeset: 3690:7ae394334e5c user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Apr 23 16:32:40 2010 -0400 description: Added missing templates diffstat: templates/webapps/community/admin/category/category_create.mako | 35 ++ templates/webapps/community/admin/category/category_rename.mako | 44 +++ templates/webapps/community/admin/category/grid.mako | 1 + templates/webapps/community/admin/category/role.mako | 118 ++++++++++ 4 files changed, 198 insertions(+), 0 deletions(-) diffs (214 lines): diff -r a66d849924d2 -r 7ae394334e5c templates/webapps/community/admin/category/category_create.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/admin/category/category_create.mako Fri Apr 23 16:32:40 2010 -0400 @@ -0,0 +1,35 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create Role</div> + <div class="toolFormBody"> + <form name="create_category_form" id="create_category_form" action="${h.url_for( action='create_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <input name="name" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <label>Description:</label> + <input name="description" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <input type="submit" name="create_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r a66d849924d2 -r 7ae394334e5c templates/webapps/community/admin/category/category_rename.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/admin/category/category_rename.mako Fri Apr 23 16:32:40 2010 -0400 @@ -0,0 +1,44 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change category name and description</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='rename_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${category.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input name="description" type="textfield" value="${category.description}" size=40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="rename_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r a66d849924d2 -r 7ae394334e5c templates/webapps/community/admin/category/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/admin/category/grid.mako Fri Apr 23 16:32:40 2010 -0400 @@ -0,0 +1,1 @@ +<%inherit file="/grid_base.mako"/> diff -r a66d849924d2 -r 7ae394334e5c templates/webapps/community/admin/category/role.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/admin/category/role.mako Fri Apr 23 16:32:40 2010 -0400 @@ -0,0 +1,118 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +<%def name="render_select( name, options )"> + <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> + %for option in options: + <option value="${option[0]}">${option[1]}</option> + %endfor + </select> +</%def> + +<script type="text/javascript"> +$().ready(function() { + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('#groups_add_button').click(function() { + return !$('#out_groups option:selected').remove().appendTo('#in_groups'); + }); + $('#groups_remove_button').click(function() { + return !$('#in_groups option:selected').remove().appendTo('#out_groups'); + }); + $('form#associate_role_user_group').submit(function() { + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_groups option').each(function(i) { + $(this).attr("selected", "selected"); + }); + }); +}); +</script> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Role '${role.name}'</div> + <div class="toolFormBody"> + <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='manage_users_and_groups_for_role', id=trans.security.encode_id( role.id ) )}" method="post" > + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Users associated with '${role.name}'</label> + ${render_select( "in_users", in_users )}<br/> + <input type="submit" id="users_remove_button" value=">>"/> + </div> + <div> + <label>Users not associated with '${role.name}'</label> + ${render_select( "out_users", out_users )}<br/> + <input type="submit" id="users_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Groups associated with '${role.name}'</label> + ${render_select( "in_groups", in_groups )}<br/> + <input type="submit" id="groups_remove_button" value=">>"/> + </div> + <div> + <label>Groups not associated with '${role.name}'</label> + ${render_select( "out_groups", out_groups )}<br/> + <input type="submit" id="groups_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <input type="submit" name="role_members_edit_button" value="Save"/> + </div> + </form> + </div> +</div> +<br clear="left"/> +<br/> +%if len( library_dataset_actions ) > 0: + <h3>Data library datasets associated with role '${role.name}'</h3> + <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> + <tr> + <td> + <ul> + %for ctr, library, in enumerate( library_dataset_actions.keys() ): + <li> + <img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> + ${library.name} + <ul> + %for folder_path, permissions in library_dataset_actions[ library ].items(): + <li> + <img src="/static/images/silk/folder_page.png" class="rowIcon"/> + ${folder_path} + <ul> + % for permission in permissions: + <ul> + <li>${permission}</li> + </ul> + %endfor + </ul> + </li> + %endfor + </ul> + </li> + %endfor + </ul> + </td> + </tr> + </table> +%endif

1 0

[hg] galaxy 3689: Move setting categories to the Tool class in t...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a66d849924d2 changeset: 3689:a66d849924d2 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Apr 23 16:24:49 2010 -0400 description: Move setting categories to the Tool class in the model diffstat: lib/galaxy/webapps/community/controllers/tool_browser.py | 17 +--------------- lib/galaxy/webapps/community/model/__init__.py | 9 ++++++++ 2 files changed, 10 insertions(+), 16 deletions(-) diffs (50 lines): diff -r 87cee993fa2d -r a66d849924d2 lib/galaxy/webapps/community/controllers/tool_browser.py --- a/lib/galaxy/webapps/community/controllers/tool_browser.py Fri Apr 23 16:11:55 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool_browser.py Fri Apr 23 16:24:49 2010 -0400 @@ -117,7 +117,7 @@ elif params.save_button: tool.user_description = util.restore_text( params.description ) categories = [] - set_tool_category_associations( trans, tool, util.listify( params.category ) ) + tool.set_categories( trans, util.listify( params.category ) ) trans.sa_session.add( tool ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='tool_browser', @@ -131,18 +131,3 @@ categories=categories, message=message, status=status ) - -## ---- Utility methods ------------------------------------------------------- - -# It may make sense to create something like the security controller to do -# this, but seems unnecessary for this single operation - -def set_tool_category_associations( trans, tool, categories, delete_existing_assocs=True ): - if delete_existing_assocs: - for a in tool.categories: - trans.sa_session.delete( a ) - trans.sa_session.flush() - for category in categories: - if not isinstance( category, trans.model.Category ): - category = trans.sa_session.query( trans.model.Category ).get( int( category ) ) - tool.categories.append( trans.model.ToolCategoryAssociation( tool, category ) ) diff -r 87cee993fa2d -r a66d849924d2 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 23 16:11:55 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 23 16:24:49 2010 -0400 @@ -123,6 +123,15 @@ self.description = datatype_bunch.description self.version = datatype_bunch.version self.user_id = datatype_bunch.user.id + def set_categories( self, trans, categories, delete_existing_assocs=True ): + if delete_existing_assocs: + for a in self.categories: + trans.sa_session.delete( a ) + trans.sa_session.flush() + for category in categories: + if not isinstance( category, Category ): + category = trans.sa_session.query( Category ).get( int( category ) ) + self.categories.append( ToolCategoryAssociation( self, category ) ) class Tag ( object ): def __init__( self, id=None, type=None, parent_id=None, name=None ):

1 0

[hg] galaxy 3688: Add categories to the community app
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/87cee993fa2d changeset: 3688:87cee993fa2d user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Apr 23 16:11:55 2010 -0400 description: Add categories to the community app diffstat: lib/galaxy/webapps/community/controllers/admin.py | 275 ++++++++++ lib/galaxy/webapps/community/controllers/tool_browser.py | 26 +- lib/galaxy/webapps/community/controllers/upload.py | 7 +- lib/galaxy/webapps/community/model/__init__.py | 7 +- lib/galaxy/webapps/community/model/mapping.py | 3 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 3 +- templates/webapps/community/admin/index.mako | 9 + templates/webapps/community/base_panels.mako | 2 +- templates/webapps/community/tool/edit_tool.mako | 4 +- 9 files changed, 323 insertions(+), 13 deletions(-) diffs (452 lines): diff -r 318dc4410301 -r 87cee993fa2d lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 23 15:31:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 23 16:11:55 2010 -0400 @@ -277,8 +277,283 @@ def build_initial_query( self, session ): return session.query( self.model_class ) +class CategoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.description + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, category ): + if category.deleted: + return "deleted" + return "" + + # Grid definition + webapp = "community" + title = "Categories" + model_class = model.Category + template='/webapps/community/admin/category/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Edit category", id=item.id, webapp="community" ) ), + model_class=model.Category, + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", attach_popup=False ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new category", + dict( controller='admin', action='categories', operation='create', webapp="community" ) ) + ] + operations = [ grids.GridOperation( "Rename", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( webapp="community", action="rename_category" ) ), + grids.GridOperation( "Delete", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + url_args=dict( webapp="community", action="mark_category_deleted" ) ), + grids.GridOperation( "Undelete", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( webapp="community", action="undelete_category" ) ), + grids.GridOperation( "Purge", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( webapp="community", action="purge_category" ) ) ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) + class AdminCommunity( BaseController, Admin ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() + category_list_grid = CategoryListGrid() + + @web.expose + @web.require_admin + def categories( self, trans, **kwargs ): + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + if operation == "create": + return self.create_category( trans, **kwargs ) + if operation == "delete": + return self.mark_category_deleted( trans, **kwargs ) + if operation == "undelete": + return self.undelete_category( trans, **kwargs ) + if operation == "purge": + return self.purge_category( trans, **kwargs ) + if operation == "rename": + return self.rename_category( trans, **kwargs ) + # Render the list view + return self.category_list_grid( trans, **kwargs ) + + @web.expose + @web.require_admin + def create_category( self, trans, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'community' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if params.get( 'create_category_button', False ): + name = util.restore_text( params.name ) + description = util.restore_text( params.description ) + if not name or not description: + message = "Enter a valid name and a description" + elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==name ).first(): + message = "A category with that name already exists" + else: + # Create the category + category = trans.app.model.Category( name=name, description=description ) + trans.sa_session.add( category ) + message = "Category '%s' has been created" % category.name + trans.sa_session.flush() + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', + action='create_category', + webapp=webapp, + message=util.sanitize_text( message ), + status='error' ) ) + return trans.fill_template( '/webapps/community/admin/category/category_create.mako', + webapp=webapp, + message=message, + status=status ) + @web.expose + @web.require_admin + def rename_category( self, trans, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + message = "No category ids received for renaming" + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=message, + status='error' ) ) + category = get_category( trans, id ) + if params.get( 'rename_category_button', False ): + old_name = category.name + new_name = util.restore_text( params.name ) + new_description = util.restore_text( params.description ) + if not new_name: + message = 'Enter a valid name' + status = 'error' + elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + message = 'A category with that name already exists' + status = 'error' + else: + category.name = new_name + category.description = new_description + trans.sa_session.add( category ) + trans.sa_session.flush() + message = "Category '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) + return trans.fill_template( '/webapps/community/admin/category/category_rename.mako', + category=category, + webapp=webapp, + message=message, + status=status ) + @web.expose + @web.require_admin + def mark_category_deleted( self, trans, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + id = kwd.get( 'id', None ) + if not id: + message = "No category ids received for deleting" + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=message, + status='error' ) ) + ids = util.listify( id ) + message = "Deleted %d categories: " % len( ids ) + for category_id in ids: + category = get_category( trans, category_id ) + category.deleted = True + trans.sa_session.add( category ) + trans.sa_session.flush() + message += " %s " % category.name + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) + @web.expose + @web.require_admin + def undelete_category( self, trans, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + id = kwd.get( 'id', None ) + if not id: + message = "No category ids received for undeleting" + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=message, + status='error' ) ) + ids = util.listify( id ) + count = 0 + undeleted_categories = "" + for category_id in ids: + category = get_category( trans, category_id ) + if not category.deleted: + message = "Category '%s' has not been deleted, so it cannot be undeleted." % category.name + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='error' ) ) + category.deleted = False + trans.sa_session.add( category ) + trans.sa_session.flush() + count += 1 + undeleted_categories += " %s" % category.name + message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) + @web.expose + @web.require_admin + def purge_category( self, trans, **kwd ): + # This method should only be called for a Category that has previously been deleted. + # Purging a deleted Category deletes all of the following from the database: + # - ToolCategoryAssociations where category_id == Category.id + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + id = kwd.get( 'id', None ) + if not id: + message = "No category ids received for purging" + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='error' ) ) + ids = util.listify( id ) + message = "Purged %d categories: " % len( ids ) + for category_id in ids: + category = get_category( trans, category_id ) + if not category.deleted: + message = "Category '%s' has not been deleted, so it cannot be purged." % category.name + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='error' ) ) + # Delete ToolCategoryAssociations + for tca in category.tools: + trans.sa_session.delete( tca ) + trans.sa_session.flush() + message += " %s " % category.name + trans.response.send_redirect( web.url_for( controller='admin', + action='categories', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) + +## ---- Utility methods ------------------------------------------------------- + +def get_category( trans, id ): + """Get a User from the database by id.""" + # Load user from database + id = trans.security.decode_id( id ) + category = trans.sa_session.query( trans.model.Category ).get( id ) + if not category: + return trans.show_error_message( "Category not found for id (%s)" % str( id ) ) + return category diff -r 318dc4410301 -r 87cee993fa2d lib/galaxy/webapps/community/controllers/tool_browser.py --- a/lib/galaxy/webapps/community/controllers/tool_browser.py Fri Apr 23 15:31:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool_browser.py Fri Apr 23 16:11:55 2010 -0400 @@ -115,8 +115,15 @@ message = 'Uploading new version not implemented' status = 'error' elif params.save_button: - tool.user_description = params.description - tool.category = params.category + tool.user_description = util.restore_text( params.description ) + categories = [] + set_tool_category_associations( trans, tool, util.listify( params.category ) ) + trans.sa_session.add( tool ) + trans.sa_session.flush() + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='browse_tools', + message='Saved categories and description for %s' % tool.name, + status='done' ) ) categories = trans.sa_session.query( trans.model.Category ).order_by( trans.model.Category.table.c.name ).all() return trans.fill_template( '/webapps/community/tool/edit_tool.mako', encoded_id = encoded_id, @@ -124,3 +131,18 @@ categories=categories, message=message, status=status ) + +## ---- Utility methods ------------------------------------------------------- + +# It may make sense to create something like the security controller to do +# this, but seems unnecessary for this single operation + +def set_tool_category_associations( trans, tool, categories, delete_existing_assocs=True ): + if delete_existing_assocs: + for a in tool.categories: + trans.sa_session.delete( a ) + trans.sa_session.flush() + for category in categories: + if not isinstance( category, trans.model.Category ): + category = trans.sa_session.query( trans.model.Category ).get( int( category ) ) + tool.categories.append( trans.model.ToolCategoryAssociation( tool, category ) ) diff -r 318dc4410301 -r 87cee993fa2d lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 23 15:31:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 23 16:11:55 2010 -0400 @@ -49,12 +49,15 @@ os.link( uploaded_file.name, obj.file_name ) except OSError: shutil.copy( uploaded_file.name, obj.file_name ) - message = 'Uploaded %s' % meta.message + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='edit_tool', + message='Uploaded %s' % meta.message, + status='done' ) ) except datatypes.DatatypeVerificationError, e: message = str( e ) status = 'error' except sqlalchemy.exc.IntegrityError: - message = 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please ... ??? ... Otherwise, please choose a new ID.' + message = 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' status = 'error' uploaded_file.close() selected_upload_type = params.get( 'type', 'tool' ) diff -r 318dc4410301 -r 87cee993fa2d lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 23 15:31:52 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 23 16:11:55 2010 -0400 @@ -134,10 +134,10 @@ return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name ) class Category( object ): - def __init__( self, id=None, name=None, description=None ): - self.id = id + def __init__( self, name=None, description=None, deleted=False ): self.name = name self.description = description + self.deleted = deleted class ItemTagAssociation ( object ): def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ): @@ -156,8 +156,7 @@ pass class ToolCategoryAssociation( object ): - def __init__( self, id=None, tool=None, category=None ): - self.id = id + def __init__( self, tool=None, category=None ): self.tool = tool self.category = category diff -r 318dc4410301 -r 87cee993fa2d lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 23 15:31:52 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 23 16:11:55 2010 -0400 @@ -119,7 +119,8 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), index=True, unique=True ), - Column( "description" , TEXT ) ) + Column( "description" , TEXT ), + Column( "deleted", Boolean, index=True, default=False ) ) ToolCategoryAssociation.table = Table( "tool_category_association", metadata, Column( "id", Integer, primary_key=True ), diff -r 318dc4410301 -r 87cee993fa2d lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 23 15:31:52 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 23 16:11:55 2010 -0400 @@ -96,7 +96,8 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), index=True, unique=True ), - Column( "description" , TEXT ) ) + Column( "description" , TEXT ), + Column( "deleted", Boolean, index=True, default=False ) ) ToolCategoryAssociation_table = Table( "tool_category_association", metadata, Column( "id", Integer, primary_key=True ), diff -r 318dc4410301 -r 87cee993fa2d templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Fri Apr 23 15:31:52 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Fri Apr 23 16:11:55 2010 -0400 @@ -88,6 +88,15 @@ <div class="toolTitle"><a href="${h.url_for( controller='tool_browser', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> </div> </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Community</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='categories', webapp='community' )}" target="galaxy_main">Manage categories</a></div> + </div> + </div> </div> </div> </div> diff -r 318dc4410301 -r 87cee993fa2d templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako Fri Apr 23 15:31:52 2010 -0400 +++ b/templates/webapps/community/base_panels.mako Fri Apr 23 16:11:55 2010 -0400 @@ -92,7 +92,7 @@ <div class="title" style="position: absolute; top: 0; left: 0;"> <a href="${app.config.get( 'logo_url', '/' )}"> <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> - Galaxy + Galaxy Community %if app.config.brand: <span class='brand'>/ ${app.config.brand}</span> %endif diff -r 318dc4410301 -r 87cee993fa2d templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 23 15:31:52 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 23 16:11:55 2010 -0400 @@ -25,7 +25,7 @@ <div class="form-row"> <label>Categories:</label> <div class="form-row-input"> - <select name="category" multiple size=5> + <select name="category" multiple size=5 style="min-width: 250px;"> %for category in categories: %if category.id in [ tool_category.id for tool_category in tool.categories ]: <option value="${category.id}" selected>${category.name}</option> @@ -39,7 +39,7 @@ </div> <div class="form-row"> <label>Description:</label> - <div class="form-row-input"><textarea name="description" rows="5" cols="35"></textarea></div> + <div class="form-row-input"><textarea name="description" rows="5" cols="35">${tool.user_description}</textarea></div> <div style="clear: both"></div> </div> <div class="form-row">

1 0

[hg] galaxy 3687: lims:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/318dc4410301 changeset: 3687:318dc4410301 user: rc date: Fri Apr 23 15:31:52 2010 -0400 description: lims: - ui cleanup - fixed a functional test bug diffstat: templates/admin/requests/get_data.mako | 5 ++--- test/functional/test_forms_and_requests.py | 15 ++++++++++----- 2 files changed, 12 insertions(+), 8 deletions(-) diffs (44 lines): diff -r f6e86e26cfe2 -r 318dc4410301 templates/admin/requests/get_data.mako --- a/templates/admin/requests/get_data.mako Fri Apr 23 15:16:24 2010 -0400 +++ b/templates/admin/requests/get_data.mako Fri Apr 23 15:31:52 2010 -0400 @@ -113,9 +113,8 @@ </div> <div class="form-row"> <div class="toolParamHelp" style="clear: both;"> - After clicking <b>Transfer</b> do <i>not</i> close this page or - navigate away from this page. Once the transfer is complete - the dataset(s) will show up on this page. + After selecting dataset(s), be sure to click on the <b>Start transfer</b> button. + Once the transfer is complete the dataset(s) will show up on this page. </div> <input type="submit" name="select_files_button" value="Select"/> </div> diff -r f6e86e26cfe2 -r 318dc4410301 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Fri Apr 23 15:16:24 2010 -0400 +++ b/test/functional/test_forms_and_requests.py Fri Apr 23 15:31:52 2010 -0400 @@ -372,15 +372,20 @@ % ( request_two.name, request_two.states.REJECTED ) def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" - # TODO: RC: add whatever is missing from this method that should be marked - # deleted or purged so that later test runs will correctly test features if the - # database has not be purged. - # # Logged in as admin_user + # remove the request_type permissions + rt_actions = sa_session.query( galaxy.model.RequestTypePermissions ) \ + .filter(and_(galaxy.model.RequestTypePermissions.table.c.request_type_id==request_type.id) ) \ + .order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) ) \ + .all() + for a in rt_actions: + sa_session.delete( a ) + sa_session.flush() + ################## # Eliminate all non-private roles ################## - for role in [ role_one ]: + for role in [ role_one, role_two ]: self.mark_role_deleted( self.security.encode_id( role.id ), role.name ) self.purge_role( self.security.encode_id( role.id ), role.name ) # Manually delete the role from the database

1 0

[hg] galaxy 3686: Miscellaneous community space fixes.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f6e86e26cfe2 changeset: 3686:f6e86e26cfe2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 23 15:16:24 2010 -0400 description: Miscellaneous community space fixes. diffstat: lib/galaxy/web/base/controller.py | 6 +- lib/galaxy/web/framework/__init__.py | 6 +- lib/galaxy/web/security/__init__.py | 6 +- lib/galaxy/webapps/community/controllers/admin.py | 1 - lib/galaxy/webapps/community/controllers/upload.py | 10 +- lib/galaxy/webapps/community/model/__init__.py | 7 +- setup.sh | 2 +- templates/admin/center.mako | 187 --------------------- templates/webapps/community/admin/center.mako | 41 ++++ templates/webapps/community/admin/index.mako | 20 +- templates/webapps/galaxy/admin/center.mako | 187 +++++++++++++++++++++ templates/webapps/galaxy/admin/index.mako | 2 +- 12 files changed, 265 insertions(+), 210 deletions(-) diffs (620 lines): diff -r 34eec4d48cc4 -r f6e86e26cfe2 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Fri Apr 23 13:16:40 2010 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Apr 23 15:16:24 2010 -0400 @@ -330,7 +330,11 @@ @web.expose @web.require_admin def center( self, trans, **kwd ): - return trans.fill_template( '/admin/center.mako' ) + webapp = kwd.get( 'webapp', 'galaxy' ) + if webapp == 'galaxy': + return trans.fill_template( '/webapps/galaxy/admin/center.mako' ) + else: + return trans.fill_template( '/webapps/community/admin/center.mako' ) @web.expose @web.require_admin def reload_tool( self, trans, **kwd ): diff -r 34eec4d48cc4 -r f6e86e26cfe2 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Apr 23 13:16:40 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Apr 23 15:16:24 2010 -0400 @@ -268,7 +268,7 @@ galaxy_session_requires_flush = False if secure_id: # Decode the cookie value to get the session_key - session_key = self.security.decode_session_key( secure_id ) + session_key = self.security.decode_guid( secure_id ) try: # Make sure we have a valid UTF-8 string session_key = session_key.encode( 'utf8' ) @@ -365,7 +365,7 @@ Caller is responsible for flushing the returned session. """ - session_key = self.security.get_new_session_key() + session_key = self.security.get_new_guid() galaxy_session = self.app.model.GalaxySession( session_key=session_key, is_valid=True, @@ -411,7 +411,7 @@ """ Update the session cookie to match the current session. """ - self.set_cookie( self.security.encode_session_key( self.galaxy_session.session_key ), name=name, path=self.app.config.cookie_path ) + self.set_cookie( self.security.encode_guid( self.galaxy_session.session_key ), name=name, path=self.app.config.cookie_path ) def handle_user_login( self, user, webapp ): """ Login a new user (possibly newly created) diff -r 34eec4d48cc4 -r f6e86e26cfe2 lib/galaxy/web/security/__init__.py --- a/lib/galaxy/web/security/__init__.py Fri Apr 23 13:16:40 2010 -0400 +++ b/lib/galaxy/web/security/__init__.py Fri Apr 23 15:16:24 2010 -0400 @@ -43,16 +43,16 @@ return self.id_cipher.encrypt( s ).encode( 'hex' ) def decode_id( self, obj_id ): return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) - def encode_session_key( self, session_key ): + def encode_guid( self, session_key ): # Session keys are strings # Pad to a multiple of 8 with leading "!" s = ( "!" * ( 8 - len( session_key ) % 8 ) ) + session_key # Encrypt return self.id_cipher.encrypt( s ).encode( 'hex' ) - def decode_session_key( self, session_key ): + def decode_guid( self, session_key ): # Session keys are strings return self.id_cipher.decrypt( session_key.decode( 'hex' ) ).lstrip( "!" ) - def get_new_session_key( self ): + def get_new_guid( self ): # Generate a unique, high entropy 128 bit random number return get_random_bytes( 16 ) \ No newline at end of file diff -r 34eec4d48cc4 -r f6e86e26cfe2 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 23 13:16:40 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 23 15:16:24 2010 -0400 @@ -43,7 +43,6 @@ return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' - log.debug("####In UserListGrid, in community" ) # Grid definition webapp = "community" title = "Users" diff -r 34eec4d48cc4 -r f6e86e26cfe2 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 23 13:16:40 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 23 15:16:24 2010 -0400 @@ -41,6 +41,7 @@ try: meta = datatype.verify( uploaded_file ) meta.user = trans.user + meta.guid = trans.app.security.get_new_guid() obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) trans.sa_session.flush() @@ -57,7 +58,8 @@ status = 'error' uploaded_file.close() selected_upload_type = params.get( 'type', 'tool' ) - return trans.fill_template( '/webapps/community/upload/upload.mako', message=message, - status=status, - selected_upload_type=selected_upload_type, - upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list() ) + return trans.fill_template( '/webapps/community/upload/upload.mako', + message=message, + status=status, + selected_upload_type=selected_upload_type, + upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list() ) diff -r 34eec4d48cc4 -r f6e86e26cfe2 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 23 13:16:40 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 23 15:16:24 2010 -0400 @@ -93,7 +93,6 @@ self.name = name or "Unnamed tool" self.description = description self.user_description = user_description - self.category = category self.version = version or "1.0.0" self.user_id = user_id self.external_filename = external_filename @@ -117,11 +116,13 @@ self.external_filename = filename file_name = property( get_file_name, set_file_name ) def create_from_datatype( self, datatype_bunch ): + # TODO: ensure guid is unique and generate a new one if not. + self.guid = datatype_bunch.guid self.tool_id = datatype_bunch.id self.name = datatype_bunch.name + self.description = datatype_bunch.description self.version = datatype_bunch.version - self.description = datatype_bunch.description - self.user_id = datatype_bunch.user + self.user_id = datatype_bunch.user.id class Tag ( object ): def __init__( self, id=None, type=None, parent_id=None, name=None ): diff -r 34eec4d48cc4 -r f6e86e26cfe2 setup.sh --- a/setup.sh Fri Apr 23 13:16:40 2010 -0400 +++ b/setup.sh Fri Apr 23 15:16:24 2010 -0400 @@ -31,7 +31,7 @@ DIRS=" database database/files -database/tools +database/community_files database/tmp database/compiled_templates database/job_working_directory diff -r 34eec4d48cc4 -r f6e86e26cfe2 templates/admin/center.mako --- a/templates/admin/center.mako Fri Apr 23 13:16:40 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,187 +0,0 @@ -<%inherit file="/base.mako"/> - -<%def name="title()">Galaxy Administration</%def> - -<h2>Administration</h2> - -<p>The menu on the left provides the following features</p> -<ul> - <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details - <p/> - <ul> - <li> - <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated - with each user. - </li> - <p/> - <li> - <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with - each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and - roles that are associated with the group. - </li> - <p/> - <li> - <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that - are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated - with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied - to each dataset. - </li> - </ul> - </li> - <p/> - <li><strong>Data</strong> - <p/> - <ul> - <li> - <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, - only administrators can create data libraries. - <p/> - When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even - those that are not logged in. The Galaxy administrator can restrict access to a data library by associating roles with the data library's - "access library" permission. This permission will conservatively override the [dataset] "access" permission for the data library's contained - datasets. - <p/> - For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the - data library will still only be displayed to those users that have Role1. However, if the data library's "access library" permission is - associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, - then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission - is associated with only Role1. - <p/> - In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can - be granted to users (a library item is one of: a data library, a library folder, a library dataset). - <p/> - <ul> - <li><strong>add library item</strong> - Role members can add library items to this data library or folder</li> - <li><strong>modify library item</strong> - Role members can modify this library item</li> - <li><strong>manage library permissions</strong> - Role members can manage permissions applied to this library item</li> - </ul> - <p/> - The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception - of the "access library" permission, which is only available on the data library itself). Because of this, it is important to set desired permissions - on a new data library when it is created. When this is done, new folders and datasets added to the data library will automatically inherit those - permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. - <p/> - The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. - Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This - approach allows for multiple users to use a single (possibly very large) dataset file. - </li> - </ul> - </li> - <p/> - <li><strong>Server</strong> - <p/> - <ul> - <li> - <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running - </li> - <p/> - <li> - <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions - </li> - <p/> - <li> - <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or - running). Administrators are able to cleanly stop long-running jobs. - </li> - </ul> - </li> - <p/> - <li><strong>Forms</strong> - <p/>To be completed - </li> - <p/> - <li><strong>Sequencing Requests</strong> - <p/>To be completed - </li> - <p/> - <li><strong>Cloud</strong> - <p/>To be completed - </li> -</ul> -<p/> -<p><strong>Data Security and Data Libraries</strong></p> -<p/> -<strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found -here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security -process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" -and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and -the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference -in the way Galaxy has behaved in the past. -<ul> - <li> - <strong>Users</strong> - registered Galaxy users that have created a Galaxy account. Users can belong to groups and can - be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any - of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they - will be considered "public", and no one will be allowed to change permissions on them). - </li> - <p/> - <li> - <strong>Groups</strong> - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 - or more roles, simplifying the process of applying permissions to the data between a select group of users. - </li> - <p/> - <li> - <strong>Roles</strong> - associate users and groups with specific permissions on datasets. For example, users in groups A and B - can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently - one of the following: - <ul> - <li> - <strong>private</strong> - every user is associated automatically with their own private role. Administrators cannot - manage private roles. - </li> - <li> - <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role - and this will be it's type. - </li> - <li> - <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with - another user. This can generally be considered a temporary role. - </li> - <li><strong>admin</strong> - a role created by a Galaxy administrator.</li> - </ul> - </li> - <p/> - <li> - <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described. - <ul> - <li> - <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. - <p> - If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone - that can access the data library in which it is contained. See the <strong>Manage data libraries</strong> section above for - details. Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in - during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected. - </p> - <p> - Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. - For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users - and groups who are associated with 'Role A' may access the dataset. - </p> - <p> - If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived - from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are associated with - a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. When - the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and - roles associated with the "access" permission (otherwise the dataset would be restricted from everyone). - </p> - <p> - In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with - their private role (the role identical to their Galaxy user name / email address). Associating additional roles that - include the "access" permission is not possible, since it would render the dataset inaccessible to everyone. - <p> - To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset - with that role, not their "private role". Galaxy makes this easy by telling the user they are about to share a private dataset - and giving them the option of doing so. If they respond positively, the sharing role is automatically created for them. - </p> - <p> - Private data (data associated with roles that include the "access" permission) must be made public in order to be used - with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" - tool. Being made publically accessible means removing the association of all roles that include the "access" permission - from the dataset. - <p> - </li> - <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li> - </ul> - </li> -</ul> -<br/> diff -r 34eec4d48cc4 -r f6e86e26cfe2 templates/webapps/community/admin/center.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/admin/center.mako Fri Apr 23 15:16:24 2010 -0400 @@ -0,0 +1,41 @@ +<%inherit file="/base.mako"/> + +<%def name="title()">Galaxy Administration</%def> + +<h2>Administration</h2> + +<p>The menu on the left provides the following features</p> +<ul> + <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details + <p/> + <ul> + <li> + <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated + with each user. + </li> + <p/> + <li> + <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with + each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and + roles that are associated with the group. + </li> + <p/> + <li> + <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that + are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated + with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied + to each dataset. + </li> + </ul> + </li> + <p/> + <li><strong>Tools</strong> + <p/> + <ul> + <li> + <strong>Manage tools</strong> - coming soon... + </li> + </ul> + </li> +</ul> +<br/> diff -r 34eec4d48cc4 -r f6e86e26cfe2 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Fri Apr 23 13:16:40 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Fri Apr 23 15:16:24 2010 -0400 @@ -74,11 +74,19 @@ <span>Security</span> </div> <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp='community' )}" target="galaxy_main">Manage users</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp='community' )}" target="galaxy_main">Manage groups</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp='community' )}" target="galaxy_main">Manage roles</a></div> - </div> + <div class="toolSectionBg"> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp='community' )}" target="galaxy_main">Manage users</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp='community' )}" target="galaxy_main">Manage groups</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp='community' )}" target="galaxy_main">Manage roles</a></div> + </div> + </div> + <div class="toolSectionTitle"> + <span>Tools</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a href="${h.url_for( controller='tool_browser', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> + </div> </div> </div> </div> @@ -87,7 +95,7 @@ <%def name="center_panel()"> <% - center_url = h.url_for( action='center' ) + center_url = h.url_for( action='center', webapp='community' ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r 34eec4d48cc4 -r f6e86e26cfe2 templates/webapps/galaxy/admin/center.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/galaxy/admin/center.mako Fri Apr 23 15:16:24 2010 -0400 @@ -0,0 +1,187 @@ +<%inherit file="/base.mako"/> + +<%def name="title()">Galaxy Administration</%def> + +<h2>Administration</h2> + +<p>The menu on the left provides the following features</p> +<ul> + <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details + <p/> + <ul> + <li> + <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated + with each user. + </li> + <p/> + <li> + <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with + each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and + roles that are associated with the group. + </li> + <p/> + <li> + <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that + are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated + with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied + to each dataset. + </li> + </ul> + </li> + <p/> + <li><strong>Data</strong> + <p/> + <ul> + <li> + <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, + only administrators can create data libraries. + <p/> + When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even + those that are not logged in. The Galaxy administrator can restrict access to a data library by associating roles with the data library's + "access library" permission. This permission will conservatively override the [dataset] "access" permission for the data library's contained + datasets. + <p/> + For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the + data library will still only be displayed to those users that have Role1. However, if the data library's "access library" permission is + associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, + then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission + is associated with only Role1. + <p/> + In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can + be granted to users (a library item is one of: a data library, a library folder, a library dataset). + <p/> + <ul> + <li><strong>add library item</strong> - Role members can add library items to this data library or folder</li> + <li><strong>modify library item</strong> - Role members can modify this library item</li> + <li><strong>manage library permissions</strong> - Role members can manage permissions applied to this library item</li> + </ul> + <p/> + The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception + of the "access library" permission, which is only available on the data library itself). Because of this, it is important to set desired permissions + on a new data library when it is created. When this is done, new folders and datasets added to the data library will automatically inherit those + permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. + <p/> + The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. + Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This + approach allows for multiple users to use a single (possibly very large) dataset file. + </li> + </ul> + </li> + <p/> + <li><strong>Server</strong> + <p/> + <ul> + <li> + <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running + </li> + <p/> + <li> + <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions + </li> + <p/> + <li> + <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or + running). Administrators are able to cleanly stop long-running jobs. + </li> + </ul> + </li> + <p/> + <li><strong>Forms</strong> + <p/>To be completed + </li> + <p/> + <li><strong>Sequencing Requests</strong> + <p/>To be completed + </li> + <p/> + <li><strong>Cloud</strong> + <p/>To be completed + </li> +</ul> +<p/> +<p><strong>Data Security and Data Libraries</strong></p> +<p/> +<strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found +here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security +process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" +and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and +the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference +in the way Galaxy has behaved in the past. +<ul> + <li> + <strong>Users</strong> - registered Galaxy users that have created a Galaxy account. Users can belong to groups and can + be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any + of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they + will be considered "public", and no one will be allowed to change permissions on them). + </li> + <p/> + <li> + <strong>Groups</strong> - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 + or more roles, simplifying the process of applying permissions to the data between a select group of users. + </li> + <p/> + <li> + <strong>Roles</strong> - associate users and groups with specific permissions on datasets. For example, users in groups A and B + can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently + one of the following: + <ul> + <li> + <strong>private</strong> - every user is associated automatically with their own private role. Administrators cannot + manage private roles. + </li> + <li> + <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role + and this will be it's type. + </li> + <li> + <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with + another user. This can generally be considered a temporary role. + </li> + <li><strong>admin</strong> - a role created by a Galaxy administrator.</li> + </ul> + </li> + <p/> + <li> + <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described. + <ul> + <li> + <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. + <p> + If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone + that can access the data library in which it is contained. See the <strong>Manage data libraries</strong> section above for + details. Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in + during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected. + </p> + <p> + Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. + For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users + and groups who are associated with 'Role A' may access the dataset. + </p> + <p> + If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived + from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are associated with + a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. When + the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and + roles associated with the "access" permission (otherwise the dataset would be restricted from everyone). + </p> + <p> + In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with + their private role (the role identical to their Galaxy user name / email address). Associating additional roles that + include the "access" permission is not possible, since it would render the dataset inaccessible to everyone. + <p> + To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset + with that role, not their "private role". Galaxy makes this easy by telling the user they are about to share a private dataset + and giving them the option of doing so. If they respond positively, the sharing role is automatically created for them. + </p> + <p> + Private data (data associated with roles that include the "access" permission) must be made public in order to be used + with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" + tool. Being made publically accessible means removing the association of all roles that include the "access" permission + from the dataset. + <p> + </li> + <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li> + </ul> + </li> +</ul> +<br/> diff -r 34eec4d48cc4 -r f6e86e26cfe2 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako Fri Apr 23 13:16:40 2010 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Fri Apr 23 15:16:24 2010 -0400 @@ -133,7 +133,7 @@ <%def name="center_panel()"> <% - center_url = h.url_for( action='center' ) + center_url = h.url_for( action='center', webapp='galaxy' ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def>

1 0

[hg] galaxy 3685: lims: add tests for request_type permissions
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/34eec4d48cc4 changeset: 3685:34eec4d48cc4 user: rc date: Fri Apr 23 13:16:40 2010 -0400 description: lims: add tests for request_type permissions diffstat: test/base/twilltestcase.py | 15 ++ test/functional/test_forms_and_requests.py | 214 ++++++++++++++++++---------- 2 files changed, 151 insertions(+), 78 deletions(-) diffs (337 lines): diff -r a77ec2944999 -r 34eec4d48cc4 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Apr 23 11:30:16 2010 -0400 +++ b/test/base/twilltestcase.py Fri Apr 23 13:16:40 2010 -0400 @@ -1526,6 +1526,21 @@ tc.fv("1", "state_desc_%i" % index, state[1]) tc.submit( "save_request_type" ) self.check_page_for_string( "Request type <b>%s</b> has been created" % name ) + def request_type_permissions( self, request_type_id, request_type_name, role_ids_str, permissions_in, permissions_out ): + # role_ids_str must be a comma-separated string of role ids + url = "requests_admin/manage_request_types?operation=permissions&id=%s&update_roles_button=Save" % ( request_type_id ) + for po in permissions_out: + key = '%s_out' % po + url ="%s&%s=%s" % ( url, key, role_ids_str ) + for pi in permissions_in: + key = '%s_in' % pi + url ="%s&%s=%s" % ( url, key, role_ids_str ) + self.home() + self.visit_url( "%s/%s" % ( self.url, url ) ) + print url + check_str = "Permissions updated for request type '%s'" % request_type_name + self.check_page_for_string( check_str ) + self.home() def create_request( self, request_type_id, name, desc, fields ): self.home() self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % ( self.url, diff -r a77ec2944999 -r 34eec4d48cc4 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Fri Apr 23 11:30:16 2010 -0400 +++ b/test/functional/test_forms_and_requests.py Fri Apr 23 13:16:40 2010 -0400 @@ -2,6 +2,7 @@ from galaxy.model.orm import * from galaxy.model.mapping import context as sa_session from base.twilltestcase import * +from base.test_db_util import * not_logged_in_as_admin_security_msg = 'You must be logged in as an administrator to access this feature.' logged_in_as_admin_security_msg = 'You must be an administrator to access this feature.' @@ -37,7 +38,80 @@ class TestFormsAndRequests( TwillTestCase ): - def test_000_create_form( self ): + def test_000_initiate_users( self ): + """Ensuring all required user accounts exist""" + self.logout() + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) + global regular_user1 + regular_user1 = get_user( 'test1(a)bx.psu.edu' ) + assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' + global regular_user1_private_role + regular_user1_private_role = get_private_role( regular_user1 ) + self.logout() + self.login( email='test2(a)bx.psu.edu', username='regular-user2' ) + global regular_user2 + regular_user2 = get_user( 'test2(a)bx.psu.edu' ) + assert regular_user2 is not None, 'Problem retrieving user with email "test2(a)bx.psu.edu" from the database' + global regular_user2_private_role + regular_user2_private_role = get_private_role( regular_user2 ) + self.logout() + self.login( email='test3(a)bx.psu.edu', username='regular-user3' ) + global regular_user3 + regular_user3 = get_user( 'test3(a)bx.psu.edu' ) + assert regular_user3 is not None, 'Problem retrieving user with email "test3(a)bx.psu.edu" from the database' + global regular_user3_private_role + regular_user3_private_role = get_private_role( regular_user3 ) + self.logout() + self.login( email='test(a)bx.psu.edu', username='admin-user' ) + global admin_user + admin_user = get_user( 'test(a)bx.psu.edu' ) + assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' + global admin_user_private_role + admin_user_private_role = get_private_role( admin_user ) + def test_005_create_required_groups_and_roles( self ): + """Testing creating all required groups and roles for this script""" + # Logged in as admin_user + # Create role_one + name = 'Role One' + description = "This is Role One's description" + user_ids = [ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] + self.create_role( name=name, + description=description, + in_user_ids=user_ids, + in_group_ids=[], + create_group_for_role='no', + private_role=admin_user.email ) + # Get the role object for later tests + global role_one + role_one = get_role_by_name( name ) + # Create group_one + name = 'Group One' + self.create_group( name=name, in_user_ids=[ str( regular_user1.id ) ], in_role_ids=[ str( role_one.id ) ] ) + # Get the group object for later tests + global group_one + group_one = get_group_by_name( name ) + assert group_one is not None, 'Problem retrieving group named "Group One" from the database' + # NOTE: To get this to work with twill, all select lists on the ~/admin/role page must contain at least + # 1 option value or twill throws an exception, which is: ParseError: OPTION outside of SELECT + # Due to this bug in twill, we create the role, we bypass the page and visit the URL in the + # associate_users_and_groups_with_role() method. + # + #create role_two + name = 'Role Two' + description = 'This is Role Two' + user_ids = [ str( admin_user.id ) ] + group_ids = [ str( group_one.id ) ] + private_role = admin_user.email + self.create_role( name=name, + description=description, + in_user_ids=user_ids, + in_group_ids=group_ids, + private_role=private_role ) + # Get the role object for later tests + global role_two + role_two = get_role_by_name( name ) + assert role_two is not None, 'Problem retrieving role named "Role Two" from the database' + def test_010_create_form( self ): """Testing creating a new form and editing it""" self.logout() self.login( email='test(a)bx.psu.edu' ) @@ -58,7 +132,7 @@ self.check_page_for_string( new_name ) self.check_page_for_string( new_desc ) form_one_name = new_name - def test_005_add_form_fields( self ): + def test_015_add_form_fields( self ): """Testing adding fields to a form definition""" fields = [dict(name='Test field name one', desc='Test field description one', @@ -78,7 +152,7 @@ field_index=len(form_one.fields), fields=fields) form_one_latest = get_latest_form(form_one_name) assert len(form_one_latest.fields) == len(form_one.fields)+len(fields) - def test_015_create_sample_form( self ): + def test_020_create_sample_form( self ): """Testing creating another form (for samples)""" global form_two_name desc = "This is Form Two's description" @@ -90,7 +164,7 @@ self.check_page_for_string( form_two_name ) self.check_page_for_string( desc ) self.check_page_for_string( formtype ) - def test_020_create_request_type( self ): + def test_025_create_request_type( self ): """Testing creating a new requestype""" request_form = get_latest_form(form_one_name) sample_form = get_latest_form(form_two_name) @@ -102,93 +176,77 @@ .order_by( desc( galaxy.model.RequestType.table.c.create_time ) ) \ .first() assert request_type is not None, 'Problem retrieving request type named "%s" from the database' % request_type_name - def test_025_create_address_and_library( self ): + # Set permissions + permissions_in = [ k for k, v in galaxy.model.RequestType.permitted_actions.items() ] + permissions_out = [] + # Role one members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for + # REQUEST_TYPE_ACCESS on this request_type + self.request_type_permissions(self.security.encode_id( request_type.id ), + request_type.name, + str( role_one.id ), + permissions_in, + permissions_out ) + # Make sure the request_type is not accessible by regular_user2 since regular_user2 does not have Role1. + self.logout() + self.login( email=regular_user2.email ) + self.visit_url( '%s/requests/new?create=True&select_request_type=%i' % (self.url, request_type.id) ) + try: + self.check_page_for_string( 'There are no request types created for a new request.' ) + raise AssertionError, 'The request_type %s is accessible by %s when it should be restricted' % ( request_type.name, regular_user2.email ) + except: + pass + self.logout() + self.login( email=admin_user.email ) + + def test_030_create_address_and_library( self ): """Testing address & library creation""" - # first create a regular user - self.logout() - self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) - self.logout() - self.login( email='test(a)bx.psu.edu' ) # first create a library for the request so that it can be submitted later - lib_name = 'TestLib001' - self.create_library( lib_name, '' ) - self.visit_page( 'library_admin/browse_libraries' ) - self.check_page_for_string( lib_name ) + name = "TestLib001" + description = "TestLib001 description" + synopsis = "TestLib001 synopsis" + self.create_library( name=name, description=description, synopsis=synopsis ) # Get the library object for later tests global library_one - library_one = sa_session.query( galaxy.model.Library ) \ - .filter( and_( galaxy.model.Library.table.c.name==lib_name, - galaxy.model.Library.table.c.deleted==False ) ) \ - .first() - assert library_one is not None, 'Problem retrieving library named "%s" from the database' % lib_name - global admin_user - admin_user = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ) \ - .first() - assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' - # Get the admin user's private role for later use - global admin_user_private_role - admin_user_private_role = None - for role in admin_user.all_roles(): - if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email: - admin_user_private_role = role - break - if not admin_user_private_role: - raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) - global regular_user1 - regular_user1 = sa_session.query( galaxy.model.User ) \ - .filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ) \ - .first() - assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' - # Get the regular user's private role for later use - global regular_user1_private_role - regular_user1_private_role = None - for role in regular_user1.all_roles(): - if role.name == regular_user1.email and role.description == 'Private Role for %s' % regular_user1.email: - regular_user1_private_role = role - break - if not regular_user1_private_role: - raise AssertionError( "Private role not found for user '%s'" % regular_user1.email ) - # Set permissions on the library, sort for later testing + library_one = get_library( name, description, synopsis ) + assert library_one is not None, 'Problem retrieving library named "%s" from the database' % name + # Make sure library_one is public + assert 'access library' not in [ a.action for a in library_one.actions ], 'Library %s is not public when first created' % library_one.name + # Set permissions on the library, sort for later testing. permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] permissions_out = [] - name = 'Role for testing forms' - description = "This is Role Ones description" - user_ids=[ str( admin_user.id ), str( regular_user1.id ) ] - self.create_role( name=name, - description=description, - in_user_ids=user_ids, - in_group_ids=[], - create_group_for_role='yes', - private_role=admin_user.email ) - # Get the role object for later tests - global role_one - role_one = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() - assert role_one is not None, 'Problem retrieving role named "Role for testing forms" from the database' - # Role one members are: admin_user, regular_user1. Each of these users will be permitted to - # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items. + # Role one members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on this library and it's contents. self.library_permissions( self.security.encode_id( library_one.id ), library_one.name, str( role_one.id ), permissions_in, permissions_out ) - # create a folder in the library + # Make sure the library is accessible by admin_user + self.visit_url( '%s/library/browse_libraries' % self.url ) + self.check_page_for_string( library_one.name ) + # Make sure the library is not accessible by regular_user2 since regular_user2 does not have Role1. + self.logout() + self.login( email=regular_user2.email ) + self.visit_url( '%s/library/browse_libraries' % self.url ) + try: + self.check_page_for_string( library_one.name ) + raise AssertionError, 'Library %s is accessible by %s when it should be restricted' % ( library_one.name, regular_user2.email ) + except: + pass + self.logout() + self.login( email=admin_user.email ) + # create folder root_folder = library_one.root_folder - name = "Folder One" + name = "Root Folder's Folder One" + description = "This is the root folder's Folder One" self.add_folder( 'library_admin', self.security.encode_id( library_one.id ), self.security.encode_id( root_folder.id ), name=name, - description='' ) + description=description ) global folder_one - folder_one = sa_session.query( galaxy.model.LibraryFolder ) \ - .filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id, - galaxy.model.LibraryFolder.table.c.name==name ) ) \ - .first() + folder_one = get_folder( root_folder.id, name, description ) assert folder_one is not None, 'Problem retrieving library folder named "%s" from the database' % name - self.home() - self.visit_url( '%s/library_common/browse_library?cntrller=library_admin&id=%s' % ( self.url, self.security.encode_id( library_one.id ) ) ) - self.check_page_for_string( name ) # create address self.logout() self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) @@ -202,7 +260,7 @@ .filter( and_( galaxy.model.UserAddress.table.c.desc==address1[ 'short_desc' ], galaxy.model.UserAddress.table.c.deleted==False ) ) \ .first() - def test_030_create_request( self ): + def test_035_create_request( self ): """Testing creating, editing and submitting a request as a regular user""" # login as a regular user self.logout() @@ -240,7 +298,7 @@ # check if the request's state is now set to 'submitted' assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ % ( request_one.name, request_one.states.SUBMITTED ) - def test_035_request_lifecycle( self ): + def test_040_request_lifecycle( self ): """Testing request lifecycle as it goes through all the states""" # goto admin manage requests page self.logout() @@ -264,7 +322,7 @@ self.check_request_grid(state='Complete', request_name=request_one.name) assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ % ( request_one.name, request_one.states.COMPLETE ) - def test_040_admin_create_request_on_behalf_of_regular_user( self ): + def test_045_admin_create_request_on_behalf_of_regular_user( self ): """Testing creating and submitting a request as an admin on behalf of a regular user""" self.logout() self.login( email='test(a)bx.psu.edu' ) @@ -301,7 +359,7 @@ # check if both the requests is showing in the 'All' filter self.check_request_admin_grid(state='All', request_name=request_one.name) self.check_request_admin_grid(state='All', request_name=request_two.name) - def test_045_reject_request( self ): + def test_050_reject_request( self ): '''Testing rejecting a request''' self.logout() self.login( email='test(a)bx.psu.edu' ) @@ -312,7 +370,7 @@ # check if the request's state is now set to 'submitted' assert request_two.state is not request_two.states.REJECTED, "The state of the request '%s' should be set to '%s'" \ % ( request_two.name, request_two.states.REJECTED ) - def test_050_reset_data_for_later_test_runs( self ): + def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # TODO: RC: add whatever is missing from this method that should be marked # deleted or purged so that later test runs will correctly test features if the

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