- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 1684: Modified sort options in grouping tool to work...
by Nate Coraor 23 Dec '08

23 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c1d3004f0613 changeset: 1684:c1d3004f0613 user: guru date: Mon Dec 22 12:15:02 2008 -0500 description: Modified sort options in grouping tool to work correctly on older and newer versions of unix sort. Also included functional tests. 4 file(s) affected in this change: test-data/groupby_out1.dat test-data/groupby_out2.dat tools/stats/grouping.py tools/stats/grouping.xml diffs (126 lines): diff -r 96f2c4630e62 -r c1d3004f0613 test-data/groupby_out1.dat --- a/test-data/groupby_out1.dat Fri Dec 19 14:25:43 2008 -0500 +++ b/test-data/groupby_out1.dat Mon Dec 22 12:15:02 2008 -0500 @@ -1,21 +1,20 @@ -chr10 55251623.000000 -chr11 87588756.250000 -chr1 148052568.250000 -chr12 38440094.000000 -chr13 112381694.000000 -chr14 98710240.000000 -chr15 41666442.500000 -chr16 206638.000000 -chr18 50562378.250000 -chr19 59226196.750000 -chr20 33504194.750000 -chr2 118341365.500000 -chr21 33160676.750000 -chr2 220209905.500000 -chr22 30471242.250000 -chr5 131612441.500000 -chr6 108564320.750000 -chr7 115958079.000000 -chr8 118881131.000000 -chr9 128842832.750000 -chrX 145194871.500000 +chr1 1.48053e+08 +chr10 5.52516e+07 +chr11 8.75888e+07 +chr12 3.84401e+07 +chr13 1.12382e+08 +chr14 9.87102e+07 +chr15 4.16664e+07 +chr16 206638 +chr18 5.05624e+07 +chr19 5.92262e+07 +chr2 1.69276e+08 +chr20 3.35042e+07 +chr21 3.31607e+07 +chr22 3.04712e+07 +chr5 1.31612e+08 +chr6 1.08564e+08 +chr7 1.15958e+08 +chr8 1.18881e+08 +chr9 1.28843e+08 +chrX 1.45195e+08 diff -r 96f2c4630e62 -r c1d3004f0613 test-data/groupby_out2.dat --- a/test-data/groupby_out2.dat Fri Dec 19 14:25:43 2008 -0500 +++ b/test-data/groupby_out2.dat Mon Dec 22 12:15:02 2008 -0500 @@ -1,2 +1,2 @@ -chr10 1700.00 ['NM_11', 'NM_10', 'test'] -chr22 1533.33 ['NM_17', 'NM_19', 'NM_18'] \ No newline at end of file +chr10 1700 +chr22 1533.33 \ No newline at end of file diff -r 96f2c4630e62 -r c1d3004f0613 tools/stats/grouping.py --- a/tools/stats/grouping.py Fri Dec 19 14:25:43 2008 -0500 +++ b/tools/stats/grouping.py Mon Dec 22 12:15:02 2008 -0500 @@ -69,8 +69,9 @@ start a key at POS1, end it at POS2 (origin 1) In other words, column positions start at 1 rather than 0, so we need to add 1 to group_col. + if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1. """ - command_line = "sort -f -k " + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile + command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile except Exception, exc: stop_err( 'Initialization error -> %s' %str(exc) ) diff -r 96f2c4630e62 -r c1d3004f0613 tools/stats/grouping.xml --- a/tools/stats/grouping.xml Fri Dec 19 14:25:43 2008 -0500 +++ b/tools/stats/grouping.xml Mon Dec 22 12:15:02 2008 -0500 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.3.0"> +<tool id="Grouping1" name="Group" version="1.4.0"> <description>data by a column and perform aggregate operation on other columns.</description> <command interpreter="python"> grouping.py @@ -38,28 +38,26 @@ <requirements> <requirement type="python-module">rpy</requirement> </requirements> - <tests> -  -  + <test> + <param name="input1" value="1.bed"/> + <param name="groupcol" value="1"/> + <param name="optype" value="mean"/> + <param name="opcol" value="2"/> + <param name="opround" value="no"/> + <output name="out_file1" file="groupby_out1.dat"/> + </test> + +  + <test> + <param name="input1" value="1.tabular"/> + <param name="groupcol" value="1"/> + <param name="optype" value="mean"/> + <param name="opcol" value="2"/> + <param name="opround" value="no"/> + <output name="out_file1" file="groupby_out2.dat"/> </test> - --> -  -  </tests> <help>

1 0

[hg] galaxy 1683: fix for short read score distribution tool. re...
by Greg Von Kuster 20 Dec '08

20 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/96f2c4630e62 changeset: 1683:96f2c4630e62 user: wychung date: Fri Dec 19 14:25:43 2008 -0500 description: fix for short read score distribution tool. restore test data. 3 file(s) affected in this change: test-data/454Score.png test-data/solexaScore.png tools/metag_tools/short_reads_figure_score.py diffs (35 lines): diff -r b7aabc2553fc -r 96f2c4630e62 test-data/454Score.png Binary file test-data/454Score.png has changed diff -r b7aabc2553fc -r 96f2c4630e62 test-data/solexaScore.png Binary file test-data/solexaScore.png has changed diff -r b7aabc2553fc -r 96f2c4630e62 tools/metag_tools/short_reads_figure_score.py --- a/tools/metag_tools/short_reads_figure_score.py Fri Dec 19 12:25:52 2008 -0500 +++ b/tools/metag_tools/short_reads_figure_score.py Fri Dec 19 14:25:43 2008 -0500 @@ -62,9 +62,9 @@ return score_points def __main__(): - + invalid_lines = 0 - + infile_score_name = sys.argv[1].strip() outfile_R_name = sys.argv[2].strip() @@ -153,7 +153,6 @@ number_of_points = 20 else: number_of_points = read_length - read_length_threshold = 100 # minimal read length for 454 file score_points = [] score_matrix = [] @@ -180,7 +179,6 @@ big = 0 tmp_array.append( big ) score_points.append( tmp_array ) - elif seq_method == '454': # skip the last fasta sequence score = ''

1 0

[hg] galaxy 1682: fixed for short read build distribution tool. ...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b7aabc2553fc changeset: 1682:b7aabc2553fc user: wychung date: Fri Dec 19 12:25:52 2008 -0500 description: fixed for short read build distribution tool. remove unused arrays. also update test data output. 3 file(s) affected in this change: test-data/454Score.png test-data/solexaScore.png tools/metag_tools/short_reads_figure_score.py diffs (87 lines): diff -r d38b593a27b4 -r b7aabc2553fc test-data/454Score.png Binary file test-data/454Score.png has changed diff -r d38b593a27b4 -r b7aabc2553fc test-data/solexaScore.png Binary file test-data/solexaScore.png has changed diff -r d38b593a27b4 -r b7aabc2553fc tools/metag_tools/short_reads_figure_score.py --- a/tools/metag_tools/short_reads_figure_score.py Fri Dec 19 11:05:54 2008 -0500 +++ b/tools/metag_tools/short_reads_figure_score.py Fri Dec 19 12:25:52 2008 -0500 @@ -62,6 +62,9 @@ return score_points def __main__(): + + invalid_lines = 0 + infile_score_name = sys.argv[1].strip() outfile_R_name = sys.argv[2].strip() @@ -150,7 +153,7 @@ number_of_points = 20 else: number_of_points = read_length - quality_score = {} # quantile dictionary + read_length_threshold = 100 # minimal read length for 454 file score_points = [] score_matrix = [] @@ -177,12 +180,7 @@ big = 0 tmp_array.append( big ) score_points.append( tmp_array ) - # quartile - for j, k in enumerate( tmp_array ): - if quality_score.has_key( ( j, k ) ): - quality_score[ ( j, k ) ] += 1 - else: - quality_score[ ( j, k ) ] = 1 + elif seq_method == '454': # skip the last fasta sequence score = '' @@ -203,12 +201,6 @@ score_points_tmp = merge_to_20_datapoints( score ) score_points.append( score_points_tmp ) tmp_array = score_points_tmp - # quartile - for j, k in enumerate( tmp_array ): - if quality_score.has_key( ( j, k ) ): - quality_score[ ( j, k ) ] += 1 - else: - quality_score[ ( j ,k ) ] = 1 score = '' else: score = "%s %s" % ( score, line ) @@ -222,19 +214,16 @@ score_points_tmp = merge_to_20_datapoints( score ) score_points.append( score_points_tmp ) tmp_array = score_points_tmp - for j, k in enumerate( tmp_array ): - if quality_score.has_key( ( j, k ) ): - quality_score[ ( j, k ) ] += 1 - else: - quality_score[ ( j, k ) ] = 1 # reverse the matrix, for R - tmp_array = [] for i in range( number_of_points - 1 ): + tmp_array = [] for j in range( len( score_points ) ): - tmp_array.append( int( score_points[j][i] ) ) + try: + tmp_array.append( int( score_points[j][i] ) ) + except: + invalid_lines += 1 score_matrix.append( tmp_array ) - tmp_array = [] # generate pdf figures #outfile_R_pdf = outfile_R_name @@ -268,6 +257,8 @@ if invalid_scores > 0: print 'Skipped %d invalid scores. ' % invalid_scores + if invalid_lines > 0: + print 'Skipped %d invalid lines. ' % invalid_lines if empty_score_matrix_columns > 0: print '%d missing scores in score_matrix. ' % empty_score_matrix_columns

1 0

[hg] galaxy 1681: Yet another fix for the deleted histories report.
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d38b593a27b4 changeset: 1681:d38b593a27b4 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 19 11:05:54 2008 -0500 description: Yet another fix for the deleted histories report. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/system.py diffs (12 lines): diff -r e7c679451988 -r d38b593a27b4 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 10:55:42 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 11:05:54 2008 -0500 @@ -93,7 +93,7 @@ if not hda.dataset.purged: dataset_count += 1 try: - disk_space += dataset.file_size + disk_space += hda.dataset.file_size except: pass history_count += 1

1 0

[hg] galaxy 1680: Fix for deleted histories report in the system...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/e7c679451988 changeset: 1680:e7c679451988 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 19 10:55:42 2008 -0500 description: Fix for deleted histories report in the system controller. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/system.py diffs (14 lines): diff -r 48f3b242c75e -r e7c679451988 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 09:53:32 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/system.py Fri Dec 19 10:55:42 2008 -0500 @@ -89,8 +89,8 @@ histories = h.query().filter( where ).options( eagerload( 'datasets' ) ) for history in histories: - for dataset in history.datasets: - if not dataset.purged: + for hda in history.datasets: + if not hda.dataset.purged: dataset_count += 1 try: disk_space += dataset.file_size

1 0

[hg] galaxy 1679: Add security to reports app, fixes reports.
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/48f3b242c75e changeset: 1679:48f3b242c75e user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Dec 19 09:53:32 2008 -0500 description: Add security to reports app, fixes reports. 1 file(s) affected in this change: lib/galaxy/webapps/reports/app.py diffs (18 lines): diff -r c0efda325046 -r 48f3b242c75e lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py Thu Dec 18 16:35:26 2008 -0500 +++ b/lib/galaxy/webapps/reports/app.py Fri Dec 19 09:53:32 2008 -0500 @@ -1,5 +1,6 @@ import sys, config import galaxy.model +from galaxy.web import security class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -19,5 +20,7 @@ db_url, self.config.database_engine_options, create_tables = True ) + # Security helper + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) def shutdown( self ): pass

1 0

[hg] galaxy 1678: Enhance the tool panel, now supports following...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c0efda325046 changeset: 1678:c0efda325046 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Dec 18 16:35:26 2008 -0500 description: Enhance the tool panel, now supports following tags: <toolbox> <tool file="data_source/upload.xml"/> # tools outside sections <label text="Basic Tools" id="basic_tools" /> # labels outside sections <workflow id="529fd61ab1c6cc36" /> # workflows outside sections <section name="Get Data" id="getext"> # sections <tool file="data_source/biomart.xml" /> # tools inside sections <label text="In Section" id="in_section" /> # labels inside sections <workflow id="adb5f5c93f827949" /> # workflows inside sections </section> </toolbox> 16 file(s) affected in this change: lib/galaxy/app.py lib/galaxy/config.py lib/galaxy/tools/__init__.py lib/galaxy/web/controllers/workflow.py lib/galaxy/web/framework/__init__.py lib/galaxy/webapps/reports/config.py reports_wsgi.ini.sample static/june_2007_style/blue/tool_menu.css static/june_2007_style/make_style.py static/june_2007_style/tool_menu.css.tmpl templates/admin_main.mako templates/root/tool_menu.mako templates/workflow/editor.mako test/functional/test_toolbox.py tool_conf.xml.sample universe_wsgi.ini.sample diffs (891 lines): diff -r d86bacb600db -r c0efda325046 lib/galaxy/app.py --- a/lib/galaxy/app.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/app.py Thu Dec 18 16:35:26 2008 -0500 @@ -1,6 +1,7 @@ import sys, os, atexit from galaxy import config, jobs, util, tools, web +from galaxy.web import security import galaxy.model import galaxy.model.mapping import galaxy.datatypes.registry @@ -26,6 +27,8 @@ db_url, self.config.database_engine_options, create_tables = True ) + # Security helper + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Initialize the tools self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self ) #Load datatype converters diff -r d86bacb600db -r c0efda325046 lib/galaxy/config.py --- a/lib/galaxy/config.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/config.py Thu Dec 18 16:35:26 2008 -0500 @@ -35,9 +35,6 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) - # CRITICAL: the value of id_secret MUST be the same in universe_wsgi.ini and reports_wsgi.ini - # or the framework's __ensure_valid_session method will throw exceptions when switching between - # Galaxy and the reports in the same browser. self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) diff -r d86bacb600db -r c0efda325046 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Dec 18 16:35:26 2008 -0500 @@ -42,8 +42,8 @@ individual tool config files. """ self.tools_by_id = {} - self.tools_and_sections_by_id = {} - self.sections = [] + self.workflows_by_id = {} + self.tool_panel = odict() self.tool_root_dir = tool_root_dir self.app = app try: @@ -54,24 +54,68 @@ def init_tools( self, config_filename ): """ Read the configuration file and load each tool. + The following tags are currently supported: + <toolbox> + <tool file="data_source/upload.xml"/> # tools outside sections + <label text="Basic Tools" id="basic_tools" /> # labels outside sections + <workflow id="529fd61ab1c6cc36" /> # workflows outside sections + <section name="Get Data" id="getext"> # sections + <tool file="data_source/biomart.xml" /> # tools inside sections + <label text="In Section" id="in_section" /> # labels inside sections + <workflow id="adb5f5c93f827949" /> # workflows inside sections + </section> + </toolbox> """ + def load_tool( elem, panel_dict ): + try: + path = elem.get( "file" ) + tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) + self.tools_by_id[ tool.id ] = tool + key = 'tool_' + tool.id + panel_dict[ key ] = tool + log.debug( "Loaded tool: %s %s" % ( tool.id, tool.version ) ) + except: + log.exception( "error reading tool from path: %s" % path ) + def load_workflow( elem, panel_dict ): + try: + # TODO: should id be encoded? + workflow_id = elem.get( 'id' ) + workflow = self.load_workflow( workflow_id ) + self.workflows_by_id[ workflow_id ] = workflow + key = 'workflow_' + workflow_id + panel_dict[ key ] = workflow + log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) + except: + log.exception( "error loading workflow: %s" % workflow_id ) + def load_label( elem, panel_dict ): + label = ToolSectionLabel( elem ) + key = 'label_' + label.id + panel_dict[ key ] = label + def load_section( elem, panel_dict ): + section = ToolSection( elem ) + log.debug( "Loading section: %s" % section.name ) + for section_elem in elem: + if section_elem.tag == 'tool': + load_tool( section_elem, section.elems ) + elif section_elem.tag == 'workflow': + load_workflow( section_elem, section.elems ) + elif section_elem.tag == 'label': + load_label( section_elem, section.elems ) + key = 'section_' + section.id + panel_dict[ key ] = section + log.info("parsing the tool configuration") tree = util.parse_xml( config_filename ) root = tree.getroot() - for elem in root.findall("section"): - section = ToolSection(elem) - log.debug( "Loading tools in section: %s" % section.name ) - for tool in elem.findall("tool"): - try: - path = tool.get("file") - tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) - log.debug( "Loaded tool: %s %s" %( tool.id, tool.version ) ) - self.tools_by_id[tool.id] = tool - self.tools_and_sections_by_id[tool.id] = tool, section - section.tools.append(tool) - except Exception, exc: - log.exception( "error reading tool from path: %s" % path ) - self.sections.append(section) + for elem in root: + if elem.tag == 'tool': + load_tool( elem, self.tool_panel ) + elif elem.tag == 'workflow': + load_workflow( elem, self.tool_panel ) + elif elem.tag == 'section' : + load_section( elem, self.tool_panel ) + elif elem.tag == 'label': + load_label( elem, self.tool_panel ) def load_tool( self, config_file ): """ @@ -94,28 +138,36 @@ def reload( self, tool_id ): """ - Attempt to reload the tool identified by 'tool_id', if successfull + Attempt to reload the tool identified by 'tool_id', if successful replace the old tool. """ - if tool_id not in self.tools_and_sections_by_id: + if tool_id not in self.tools_by_id: raise ToolNotFoundException( "No tool with id %s" % tool_id ) - old_tool, section = self.tools_and_sections_by_id[ tool_id ] + old_tool = self.tools_by_id[ tool_id ] new_tool = self.load_tool( old_tool.config_file ) + # Replace old_tool with new_tool in self.tool_panel + tool_key = 'tool_' + tool_id + for key, val in self.tool_panel.items(): + if key == tool_key: + self.tool_panel[ key ] = new_tool + break + elif key.startswith( 'section' ): + section = val + for section_key, section_val in section.elems.items(): + if section_key == tool_key: + self.tool_panel[ key ].elems[ section_key ] = new_tool + break + self.tools_by_id[ tool_id ] = new_tool log.debug( "Reloaded tool %s %s" %( old_tool.id, old_tool.version ) ) - # Is there a potential sync problem here? This should be roughly - # atomic. Too many indexes for tools... - section.tools[ section.tools.index( old_tool ) ] = new_tool - self.tools_by_id[ tool_id ] = new_tool - self.tools_and_sections_by_id[ tool_id ] = new_tool, section - - def itertools( self ): + + def load_workflow( self, workflow_id ): """ - Iterate over all the tools in the toolbox (ordered by section but - without grouping). + Return an instance of 'Workflow' identified by `id`, + which is encoded in the tool panel. """ - for section in self.sections: - for tool in section.tools: - yield tool + id = self.app.security.decode_id( workflow_id ) + stored = self.app.model.StoredWorkflow.get( id ) + return stored.latest_workflow class ToolSection( object ): """ @@ -126,7 +178,17 @@ self.name = elem.get( "name" ) self.id = elem.get( "id" ) self.version = elem.get( "version" ) - self.tools = [] + self.elems = odict() + +class ToolSectionLabel( object ): + """ + A label for a set of tools that can be displayed above groups of tools + and sections in the user interface + """ + def __init__( self, elem ): + self.text = elem.get( "text" ) + self.id = elem.get( "id" ) + self.version = elem.get( "version" ) class DefaultToolState( object ): """ diff -r d86bacb600db -r c0efda325046 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Thu Dec 18 16:35:26 2008 -0500 @@ -439,13 +439,14 @@ ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) @web.expose - def run( self, trans, id, **kwargs ): + def run( self, trans, id, check_user=True, **kwargs ): stored = get_stored_workflow( trans, id, check_ownership=False ) - user = trans.get_user() - if stored.user != user: - if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).count() == 0: - error( "Workflow is not owned by or shared with current user" ) + if check_user: + user = trans.get_user() + if stored.user != user: + if trans.sa_session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).count() == 0: + error( "Workflow is not owned by or shared with current user" ) # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps diff -r d86bacb600db -r c0efda325046 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Dec 18 16:35:26 2008 -0500 @@ -86,8 +86,7 @@ module_directory = galaxy_app.config.template_cache, collection_size = 500 ) # Security helper - from galaxy.web import security - self.security = security.SecurityHelper( id_secret = galaxy_app.config.id_secret ) + self.security = galaxy_app.security def handle_controller_exception( self, e, trans, **kwargs ): if isinstance( e, MessageException ): return trans.show_message( e.message, e.type ) diff -r d86bacb600db -r c0efda325046 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py Thu Dec 18 09:32:43 2008 -0500 +++ b/lib/galaxy/webapps/reports/config.py Thu Dec 18 16:35:26 2008 -0500 @@ -25,9 +25,6 @@ # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) - # CRITICAL: the value of id_secret MUST be the same in universe_wsgi.ini and reports_wsgi.ini - # or the framework's __ensure_valid_session method will throw exceptions when switching between - # Galaxy and the reports in the same browser. self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) diff -r d86bacb600db -r c0efda325046 reports_wsgi.ini.sample --- a/reports_wsgi.ini.sample Thu Dec 18 09:32:43 2008 -0500 +++ b/reports_wsgi.ini.sample Thu Dec 18 16:35:26 2008 -0500 @@ -37,7 +37,6 @@ session_secret = changethisinproduction # Galaxy session security -# The value of id_secret MUST be the same as the value of id_secret in universe_wsgi.ini id_secret = changethisinproductiontoo # Configuration for debugging middleware diff -r d86bacb600db -r c0efda325046 static/june_2007_style/blue/tool_menu.css --- a/static/june_2007_style/blue/tool_menu.css Thu Dec 18 09:32:43 2008 -0500 +++ b/static/june_2007_style/blue/tool_menu.css Thu Dec 18 16:35:26 2008 -0500 @@ -35,6 +35,13 @@ font-weight: bold; } +div.toolPanelLabel +{ + padding-top: 5px; + padding-bottom: 5px; + font-weight: bold; +} + div.toolTitle { padding-top: 5px; @@ -44,3 +51,10 @@ display: list-item; list-style: square outside; } + + +div.toolTitleNoSection +{ + padding-bottom: 0px; + font-weight: bold; +} diff -r d86bacb600db -r c0efda325046 static/june_2007_style/make_style.py --- a/static/june_2007_style/make_style.py Thu Dec 18 09:32:43 2008 -0500 +++ b/static/june_2007_style/make_style.py Thu Dec 18 16:35:26 2008 -0500 @@ -1,12 +1,17 @@ #!/usr/bin/env python -import sys +import sys, string, os.path +from galaxy import eggs +import pkg_resources +pkg_resources.require( "Cheetah" ) + from Cheetah.Template import Template -import string from subprocess import Popen, PIPE -import os.path assert sys.version_info[:2] >= ( 2, 4 ) + +# To create a new style ( this is an example ): +# python make_style.py blue_colors.ini blue def run( cmd ): return Popen( cmd, stdout=PIPE).communicate()[0] diff -r d86bacb600db -r c0efda325046 static/june_2007_style/tool_menu.css.tmpl --- a/static/june_2007_style/tool_menu.css.tmpl Thu Dec 18 09:32:43 2008 -0500 +++ b/static/june_2007_style/tool_menu.css.tmpl Thu Dec 18 16:35:26 2008 -0500 @@ -35,6 +35,13 @@ font-weight: bold; } +div.toolPanelLabel +{ + padding-top: 5px; + padding-bottom: 5px; + font-weight: bold; +} + div.toolTitle { padding-top: 5px; @@ -44,3 +51,10 @@ display: list-item; list-style: square outside; } + + +div.toolTitleNoSection +{ + padding-bottom: 0px; + font-weight: bold; +} diff -r d86bacb600db -r c0efda325046 templates/admin_main.mako --- a/templates/admin_main.mako Thu Dec 18 09:32:43 2008 -0500 +++ b/templates/admin_main.mako Thu Dec 18 16:35:26 2008 -0500 @@ -2,32 +2,38 @@ <%def name="title()">Galaxy Administration</%def> <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> - <tr> - <td> - <h3 align="center">Galaxy Administration</h3> - %if msg: - <p class="ok_bgr">${msg}</p> - %endif - </td> - </tr> - <tr> - <td> - <form method="post" action="admin"> - <p>Admin password: <input type="password" name="passwd" size="8"></p> - <p> - Reload tool: - <select name="tool_id"> - %for i, section in enumerate( toolbox.sections ): - <optgroup label="${section.name}"> - %for t in section.tools: - <option value="${t.id}">${t.name}</option> - %endfor - %endfor - </select> - <button name="action" value="tool_reload">Reload</button> - </p> - </form> - </td> - </tr> + <tr> + <td> + <h3 align="center">Galaxy Administration</h3> + %if msg: + <p class="ok_bgr">${msg}</p> + %endif + </td> + </tr> + <tr> + <td> + <form method="post" action="admin"> + <p>Admin password: <input type="password" name="passwd" size="8"></p> + <p> + Reload tool: + <select name="tool_id"> + %for key, val in toolbox.tool_panel.items(): + %if key.startswith( 'tool' ): + <option value="${val.id}">${val.name}</option> + %elif key.startswith( 'section' ): + <optgroup label="${val.name}"> + <% section = val %> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + <option value="${section_val.id}">${section_val.name}</option> + %endif + %endfor + %endif + %endfor + </select> + <button name="action" value="tool_reload">Reload</button> + </p> + </form> + </td> + </tr> </table> - diff -r d86bacb600db -r c0efda325046 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako Thu Dec 18 09:32:43 2008 -0500 +++ b/templates/root/tool_menu.mako Thu Dec 18 16:35:26 2008 -0500 @@ -1,113 +1,148 @@ +## Render a tool +<%def name="render_tool( tool, section )"> + %if not tool.hidden: + %if section: + <div class="toolTitle"> + %else: + <div class="toolTitleNoSection"> + %endif + <% + if tool.input_required: + link = h.url_for( controller='tool_runner', tool_id=tool.id ) + else: + link = h.url_for( tool.action, ** tool.get_static_param_values( t ) ) + %> + ## FIXME: This doesn't look right + ## %if "[[" in tool.description and "]]" in tool.description: + ## ${tool.description.replace( '[[', '<a href="link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" ) + %if tool.name: + <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.name}</a> ${tool.description} + %else: + <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.description}</a> + %endif + </div> + %endif +</%def> + +## Render a workflow +<%def name="render_workflow( key, workflow, section )"> + %if section: + <div class="toolTitle"> + %else: + <div class="toolTitleNoSection"> + %endif + <% encoded_id = key.lstrip( 'workflow_' ) %> + <a id="link-${workflow.id}" href="${ h.url_for( controller='workflow', action='run', id=encoded_id, check_user=False )}" target="galaxy_main"}">${workflow.name}</a> + </div> +</%def> + +## Render a label +<%def name="render_label( label )"> + <div class="toolSectionPad"></div> + <div class="toolPanelLabel" id="title_${label.id}"> + <span>${label.text}</span> + </div> + <div class="toolSectionPad"></div> +</%def> + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> + <head> + <title>Galaxy Tools</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> + <link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" /> -<head> -<title>Galaxy Tools</title> -<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> -<link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" /> + <script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> -<script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script> + <script type="text/javascript"> + var q = jQuery.noConflict(); + q(document).ready(function() { + q( "div.toolSectionBody" ).hide(); + q( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" ) + var last_expanded = null; + q( "div.toolSectionTitle" ).each( function() { + var body = q(this).next( "div.toolSectionBody" ); + q(this).click( function() { + if ( body.is( ":hidden" ) ) { + if ( last_expanded ) last_expanded.slideUp( "fast" ); + last_expanded = body; + body.slideDown( "fast" ); + } + else { + body.slideUp( "fast" ); + last_expanded = null; + } + return false; + }); + }); + q( "a[@minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( q(this).attr( "minsizehint" ) ); + } + }); + }); + </script> + </head> -<script type="text/javascript"> - var q = jQuery.noConflict(); - q(document).ready(function() { - q( "div.toolSectionBody" ).hide(); - q( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" ) - var last_expanded = null; - q( "div.toolSectionTitle" ).each( function() { - var body = q(this).next( "div.toolSectionBody" ); - q(this).click( function() { - if ( body.is( ":hidden" ) ) { - if ( last_expanded ) last_expanded.slideUp( "fast" ); - last_expanded = body; - body.slideDown( "fast" ); - } - else { - body.slideUp( "fast" ); - last_expanded = null; - } - return false; - }); - }); - q( "a[@minsizehint]" ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( q(this).attr( "minsizehint" ) ); - } - }); - }); -</script> + <body class="toolMenuPage"> + <div class="toolMenu"> + <div class="toolSectionList"> + %for key, val in toolbox.tool_panel.items(): + %if key.startswith( 'tool' ): + ${render_tool( val, False )} + <div class="toolSectionPad"></div> + %elif key.startswith( 'workflow' ): + ${render_workflow( key, val, False )} + %elif key.startswith( 'section' ): + <% section = val %> + <div class="toolSectionTitle" id="title_${section.id}"> + <span>${section.name}</span> + </div> + <div id="${section.id}" class="toolSectionBody"> + <div class="toolSectionBg"> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + ${render_tool( section_val, True )} + %elif section_key.startswith( 'workflow' ): + ${render_workflow( section_key, section_val, True )} + %elif section_key.startswith( 'label' ): + ${render_label( section_val )} + %endif + %endfor + </div> + </div> + <div class="toolSectionPad"></div> + %elif key.startswith( 'label' ): + ${render_label( val )} + %endif + %endfor -</head> + ## Link to workflow management. The location of this may change, but eventually + ## at least some workflows will appear here (the user should be able to + ## configure which of their stored workflows appear in the tools menu). -<body class="toolMenuPage"> - -<div class="toolMenu"> - -<div class="toolSectionList"> -%for i, section in enumerate( toolbox.sections ): - %if i > 0: - <div class="toolSectionPad"></div> - %endif - <div class="toolSectionTitle" id="title_${section.id}"> - <span>${section.name}</span> - </div> - <div id="${section.id}" class="toolSectionBody"> - <div class="toolSectionBg"> - %for tool in section.tools: - %if not tool.hidden: - <div class="toolTitle"> - <% - if tool.input_required: - link = h.url_for( controller='tool_runner', tool_id=tool.id ) - else: - link = h.url_for( tool.action, ** tool.get_static_param_values( t ) ) - %> - ## FIXME: This doesn't look right - ## %if "[[" in tool.description and "]]" in tool.description: - ## ${tool.description.replace( '[[', '<a href="link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" ) - %if tool.name: - <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.name}</a> ${tool.description} - %else: - <a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.description}</a> - %endif + <div class="toolSectionPad"></div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle" id="title_XXinternalXXworkflow"> + <span>Workflow <i>(beta)</i></span> + </div> + <div id="XXinternalXXworkflow" class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows + </div> + %if t.user: + %for m in t.user.stored_workflow_menu_entries: + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + </div> + %endfor + %endif + </div> + </div> </div> - %endif - %endfor - </div> - </div> -%endfor - -## Link to workflow management. The location of this may change, but eventually -## at least some workflows will appear here (the user should be able to -## configure which of their stored workflows appear in the tools menu). - -<div class="toolSectionPad"></div> -<div class="toolSectionPad"></div> -<div class="toolSectionTitle" id="title_XXinternalXXworkflow"> - <span>Workflow <i>(beta)</i></span> -</div> -<div id="XXinternalXXworkflow" class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows </div> - %if t.user: - %for m in t.user.stored_workflow_menu_entries: - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> - </div> - %endfor - %endif - </div> -</div> - -</div> - -</div> - -<div style="height: 20px"></div> - -</body> - -</html> \ No newline at end of file + <div style="height: 20px"></div> + </body> +</html> diff -r d86bacb600db -r c0efda325046 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Dec 18 09:32:43 2008 -0500 +++ b/templates/workflow/editor.mako Thu Dec 18 16:35:26 2008 -0500 @@ -344,6 +344,11 @@ padding-bottom: 0px; font-weight: bold; } + div.toolPanelLabel { + padding-top: 5px; + padding-bottom: 5px; + font-weight: bold; + } div.toolMenuGroupHeader { font-weight: bold; padding-top: 0.5em; @@ -353,7 +358,6 @@ border-bottom: dotted #333 1px; margin-bottom: 0.5em; } - div.toolTitle { padding-top: 5px; padding-bottom: 5px; @@ -361,6 +365,10 @@ margin-right: 10px; display: list-item; list-style: square outside; + } + div.toolTitleNoSection { + padding-bottom: 0px; + font-weight: bold; } div.toolTitleDisabled { padding-top: 5px; @@ -371,6 +379,11 @@ list-style: square outside; font-style: italic; color: gray; + } + div.toolTitleNoSectionDisabled { + padding-bottom: 0px; + font-style: italic; + color: gray; } div.toolFormRow { position: relative; @@ -467,6 +480,50 @@ </style> </%def> +## Render a tool in the tool panel +<%def name="render_tool( tool, section )"> + %if not tool.hidden: + %if tool.is_workflow_compatible: + %if section: + <div class="toolTitle"> + %else: + <div class="toolTitleNoSection"> + %endif + %if "[[" in tool.description and "]]" in tool.description: + ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )} + %elif tool.name: + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} + %else: + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> + %endif + </div> + %else: + %if section: + <div class="toolTitleDisabled"> + %else: + <div class="toolTitleNoSectionDisabled"> + %endif + %if "[[" in tool.description and "]]" in tool.description: + ${tool.description.replace( '[[', '' % tool.id ).replace( "]]", "" )} + %elif tool.name: + ${tool.name} ${tool.description} + %else: + ${tool.description} + %endif + </div> + %endif + %endif +</%def> + +## Render a label in the tool panel +<%def name="render_label( label )"> + <div class="toolSectionPad"></div> + <div class="toolPanelLabel" id="title_${label.id}"> + <span>${label.text}</span> + </div> + <div class="toolSectionPad"></div> +</%def> + <div id="overlay"> ## Need a table here for centering in IE6 <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0"><tr><td> @@ -501,43 +558,30 @@ <div class="unified-panel-body" style="overflow: auto;"> <div class="toolMenu"> <div class="toolSectionList"> - %for i, section in enumerate( app.toolbox.sections ): - %if i > 0: - <div class="toolSectionPad"></div> - %endif - <div class="toolSectionTitle" id="title_${section.id}"> - <span>${section.name}</span> - </div> - <div id="${section.id}" class="toolSectionBody"> - <div class="toolSectionBg"> - %for tool in section.tools: - %if not tool.hidden: - %if tool.is_workflow_compatible: - <div class="toolTitle "> - %if "[[" in tool.description and "]]" in tool.description: - ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )} - %elif tool.name: - <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} - %else: - <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> + %for key, val in app.toolbox.tool_panel.items(): + %if key.startswith( 'tool' ): + ${render_tool( val, False )} + %elif key.startswith( 'section' ): + <% section = val %> + <div class="toolSectionTitle" id="title_${section.id}"> + <span>${section.name}</span> + </div> + <div id="${section.id}" class="toolSectionBody"> + <div class="toolSectionBg"> + %for section_key, section_val in section.elems.items(): + %if section_key.startswith( 'tool' ): + ${render_tool( section_val, True )} + %elif section_key.startswith( 'label' ): + ${render_label( section_val )} %endif - </div> - %else: - <div class="toolTitleDisabled"> - %if "[[" in tool.description and "]]" in tool.description: - ${tool.description.replace( '[[', '' % tool.id ).replace( "]]", "" )} - %elif tool.name: - ${tool.name} ${tool.description} - %else: - ${tool.description} - %endif - </div> - %endif - %endif - %endfor - </div> - </div> - %endfor + %endfor + </div> + </div> + <div class="toolSectionPad"></div> + %elif key.startswith( 'label' ): + ${render_label( val )} + %endif + %endfor </div> <div> </div> <div class="toolMenuGroupHeader">Workflow control</div> diff -r d86bacb600db -r c0efda325046 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Thu Dec 18 09:32:43 2008 -0500 +++ b/test/functional/test_toolbox.py Thu Dec 18 16:35:26 2008 -0500 @@ -1,5 +1,4 @@ -import sys -import new +import sys, new from galaxy.tools.parameters import grouping from galaxy.tools.parameters import basic from base.twilltestcase import TwillTestCase @@ -9,6 +8,7 @@ class ToolTestCase( TwillTestCase ): """Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`""" def do_it( self ): + print "###self.testdef: ", self.testdef # If the test generation had an error, raise if self.testdef.error: if self.testdef.exception: @@ -126,10 +126,10 @@ return # Push all the toolbox tests to module level G = globals() - for i, section in enumerate( toolbox.sections ): - for j, tool in enumerate( section.tools ): - if tool.tests: - for k, testdef in enumerate( tool.tests ): - name = "%s > %s > %s" % ( section.name, tool.name, testdef.name ) - testcase = get_testcase( testdef, name ) - G[ 'testcase_%d_%d_%d' % ( i, j, k ) ] = testcase + for i, tool_id in enumerate( toolbox.tools_by_id ): + tool = toolbox.tools_by_id[ tool_id ] + if tool.tests: + for j, testdef in enumerate( tool.tests ): + name = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) + testcase = get_testcase( testdef, name ) + G[ 'testcase_%d_%d' % ( i, j ) ] = testcase diff -r d86bacb600db -r c0efda325046 tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Dec 18 09:32:43 2008 -0500 +++ b/tool_conf.xml.sample Thu Dec 18 16:35:26 2008 -0500 @@ -2,7 +2,6 @@ <toolbox> <section name="Get Data" id="getext"> <tool file="data_source/upload.xml"/> - <tool file="data_source/access_libraries.xml" /> <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> diff -r d86bacb600db -r c0efda325046 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Thu Dec 18 09:32:43 2008 -0500 +++ b/universe_wsgi.ini.sample Thu Dec 18 16:35:26 2008 -0500 @@ -73,7 +73,6 @@ session_secret = changethisinproduction # Galaxy session security -# The value of id_secret MUST be the same as the value of id_secret in reports_wsgi.ini id_secret = changethisinproductiontoo # Use user provided in an upstream server's $REMOTE_USER variable

1 0

[hg] galaxy 1677: Pass in a session cookie name when building th...
by Greg Von Kuster 19 Dec '08

19 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d86bacb600db changeset: 1677:d86bacb600db user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Dec 18 09:32:43 2008 -0500 description: Pass in a session cookie name when building the app - this enables the Galaxy session to use a different cookie from the Galaxy reports session. Also add exception handling to decoding the session key so server errors won't result from attempting to retrieve an invalid session key from the db. 3 file(s) affected in this change: lib/galaxy/web/buildapp.py lib/galaxy/web/framework/__init__.py lib/galaxy/webapps/reports/buildapp.py diffs (160 lines): diff -r b83da0b74595 -r d86bacb600db lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Wed Dec 17 12:13:38 2008 -0500 +++ b/lib/galaxy/web/buildapp.py Thu Dec 18 09:32:43 2008 -0500 @@ -55,7 +55,7 @@ app = UniverseApplication( global_conf = global_conf, **kwargs ) atexit.register( app.shutdown ) # Create the universe WSGI application - webapp = galaxy.web.framework.WebApplication( app ) + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) add_controllers( webapp, app ) # These two routes handle our simple needs at the moment webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) diff -r b83da0b74595 -r d86bacb600db lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Wed Dec 17 12:13:38 2008 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Dec 18 09:32:43 2008 -0500 @@ -77,9 +77,9 @@ return FormBuilder( *args, **kwargs ) class WebApplication( base.WebApplication ): - def __init__( self, galaxy_app ): + def __init__( self, galaxy_app, session_cookie='galaxysession' ): base.WebApplication.__init__( self ) - self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self ) ) + self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) # Mako support self.mako_template_lookup = mako.lookup.TemplateLookup( directories = [ galaxy_app.config.template_path ] , @@ -101,7 +101,7 @@ Encapsulates web transaction specific state for the Universe application (specifically the user's "cookie" session and history) """ - def __init__( self, environ, app, webapp ): + def __init__( self, environ, app, webapp, session_cookie ): self.app = app self.webapp = webapp self.security = webapp.security @@ -118,7 +118,7 @@ # and such). self.workflow_building_mode = False # Always have a valid galaxy session - self.__ensure_valid_session() + self.__ensure_valid_session( session_cookie ) @property def sa_session( self ): """ @@ -148,7 +148,7 @@ event.session_id = self.galaxy_session.id event.flush() def get_cookie( self, name='galaxysession' ): - """Convienience method for getting the galaxysession cookie""" + """Convenience method for getting a session cookie""" try: # If we've changed the cookie during the request return the new value if name in self.response.cookies: @@ -158,7 +158,7 @@ except: return None def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): - """Convienience method for setting the galaxysession cookie""" + """Convenience method for setting a session cookie""" # The galaxysession cookie value must be a high entropy 128 bit random number encrypted # using a server secret key. Any other value is invalid and could pose security issues. self.response.cookies[name] = value @@ -172,7 +172,7 @@ # if not self.__galaxy_session: # self.__ensure_valid_session() # return self.__galaxy_session - def __ensure_valid_session( self ): + def __ensure_valid_session( self, session_cookie ): """ Ensure that a valid Galaxy session exists and is available as trans.session (part of initialization) @@ -182,7 +182,7 @@ """ sa_session = self.sa_session # Try to load an existing session - secure_id = self.get_cookie( name='galaxysession' ) + secure_id = self.get_cookie( name=session_cookie ) galaxy_session = None prev_galaxy_session = None user_for_new_session = None @@ -193,11 +193,17 @@ if secure_id: # Decode the cookie value to get the session_key session_key = self.security.decode_session_key( secure_id ) - # Retrieve the galaxy_session id via the unique session_key - galaxy_session = self.app.model.GalaxySession.filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, - self.app.model.GalaxySession.table.c.is_valid==True ) ).first() - # If remote user is in use it can invalidate the session, so we need to - # to check some things now. + try: + # Make sure we have a valid UTF-8 string + session_key = session_key.encode( 'utf8' ) + except UnicodeDecodeError: + # We'll end up creating a new galaxy_session + session_key = None + if session_key: + # Retrieve the galaxy_session id via the unique session_key + galaxy_session = self.app.model.GalaxySession.filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, + self.app.model.GalaxySession.table.c.is_valid==True ) ).first() + # If remote user is in use it can invalidate the session, so we need to to check some things now. if self.app.config.use_remote_user: assert "HTTP_REMOTE_USER" in self.environ, \ "use_remote_user is set but no HTTP_REMOTE_USER variable" @@ -232,7 +238,7 @@ galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) galaxy_session_requires_flush = True self.galaxy_session = galaxy_session - self.__update_session_cookie() + self.__update_session_cookie( name=session_cookie ) else: self.galaxy_session = galaxy_session # Do we need to flush the session? @@ -279,11 +285,11 @@ user.external = True #self.log_event( "Automatically created account '%s'", user.email ) return user - def __update_session_cookie( self ): + def __update_session_cookie( self, name='galaxysession' ): """ - Update the 'galaxysession' cookie to match the current session. + Update the session cookie to match the current session. """ - self.set_cookie( self.security.encode_session_key( self.galaxy_session.session_key ), name='galaxysession' ) + self.set_cookie( self.security.encode_session_key( self.galaxy_session.session_key ), name=name ) def handle_user_login( self, user ): """ @@ -304,7 +310,8 @@ self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] ) else: self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) - self.__update_session_cookie() + # This method is not called from the Galaxy reports, so the cookie will always be galaxysession + self.__update_session_cookie( name='galaxysession' ) def handle_user_logout( self ): """ Logout the current user: @@ -315,7 +322,8 @@ prev_galaxy_session.is_valid = False self.galaxy_session = self.__create_new_session( prev_galaxy_session, None ) self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) - self.__update_session_cookie() + # This method is not called from the Galaxy reports, so the cookie will always be galaxysession + self.__update_session_cookie( name='galaxysession' ) def get_galaxy_session( self ): """ diff -r b83da0b74595 -r d86bacb600db lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py Wed Dec 17 12:13:38 2008 -0500 +++ b/lib/galaxy/webapps/reports/buildapp.py Thu Dec 18 09:32:43 2008 -0500 @@ -52,7 +52,7 @@ app = UniverseApplication( global_conf = global_conf, **kwargs ) atexit.register( app.shutdown ) # Create the universe WSGI application - webapp = galaxy.web.framework.WebApplication( app ) + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxyreportssession' ) add_controllers( webapp, app ) # These two routes handle our simple needs at the moment webapp.add_route( '/:controller/:action', controller="root", action='index' )

1 0

[hg] galaxy 1676: speed enhancement for incorrect_gops_jobs script.
by Nate Coraor 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b83da0b74595 changeset: 1676:b83da0b74595 user: guru date: Wed Dec 17 12:13:38 2008 -0500 description: speed enhancement for incorrect_gops_jobs script. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (30 lines): diff -r 3a9c9da987a2 -r b83da0b74595 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:25:35 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Dec 17 12:13:38 2008 -0500 @@ -42,13 +42,19 @@ try: for job in app.model.Job.filter( sa.and_( app.model.Job.table.c.create_time.between( '2008-05-23', '2008-11-29' ), app.model.Job.table.c.state == 'ok', - sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', - app.model.Job.table.c.tool_id == 'gops_subtract_1', - app.model.Job.table.c.tool_id == 'gops_merge_1', - app.model.Job.table.c.tool_id == 'gops_coverage_1', - app.model.Job.table.c.tool_id == 'gops_complement_1', - ), - sa.not_( app.model.Job.table.c.command_line.like( '%-2 1,2,3%' ) ) + sa.or_( + sa.and_( sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1', + ), + sa.not_( app.model.Job.table.c.command_line.like( '%-2 1,2,3%' ) ) + ), + sa.and_( sa.or_( app.model.Job.table.c.tool_id == 'gops_complement_1', + app.model.Job.table.c.tool_id == 'gops_merge_1', + ), + sa.not_( app.model.Job.table.c.command_line.like( '%-1 1,2,3%' ) ) + ) + ) ) ).all(): print "# processing job id %s" % str( job.id )

1 0

[hg] galaxy 1674: Enhancing incorrect_Gops_job script to output ...
by Nate Coraor 17 Dec '08

17 Dec '08

details: http://www.bx.psu.edu/hg/galaxy/rev/006bfb42e335 changeset: 1674:006bfb42e335 user: guru date: Wed Dec 17 11:01:57 2008 -0500 description: Enhancing incorrect_Gops_job script to output only those jobs whose output has changed since the BitSetSafeReaderWrapper was fixed. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (45 lines): diff -r f61f2128c692 -r 006bfb42e335 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Tue Dec 16 17:30:19 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Dec 17 11:01:57 2008 -0500 @@ -5,7 +5,7 @@ """ from galaxy import eggs -import sys, os, ConfigParser +import sys, os, ConfigParser, tempfile import galaxy.app import galaxy.model.mapping import pkg_resources @@ -62,6 +62,23 @@ history = app.model.History.get( hda.history_id ) print "# ------> processing history id %s" % str( history.id ) if history.user_id: + cmd_line = str( job.command_line ) + new_output = tempfile.NamedTemporaryFile('w') + if (sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1' + ) + ): + new_cmd_line = " ".join(map(str,cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[5:])) + job_output = cmd_line.split()[4] + else: + new_cmd_line = " ".join(map(str,cmd_line.split()[:3])) + " " + new_output.name + " " + " ".join(map(str,cmd_line.split()[4:])) + job_output = cmd_line.split()[3] + os.system(new_cmd_line) + diff_status = os.system('diff %s %s >> /dev/null' %(new_output.name, job_output)) + if diff_status == 0: + continue + print "# --------> Outputs differ" user = app.model.User.get( history.user_id ) jobs[ job.id ] = {} jobs[ job.id ][ 'hda_id' ] = hda.id @@ -77,7 +94,7 @@ print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email" for jid in jobs: - print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % \ + print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \ ( str( jid ), str( jobs[ jid ][ 'hda_id' ] ), jobs[ jid ][ 'hda_name' ],

1 0