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[hg] galaxy 1540: Fix all root controller methods so that histor...
by Greg Von Kuster 02 Oct '08

02 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/0041f2ba49ed changeset: 1540:0041f2ba49ed user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Oct 02 12:45:03 2008 -0400 description: Fix all root controller methods so that history_dataset_association.id is not confused with history_dataset_association.dataset_id. 1 file(s) affected in this change: lib/galaxy/web/controllers/root.py diffs (415 lines): diff -r dd58d5aeb274 -r 0041f2ba49ed lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Oct 01 12:43:59 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 02 12:45:03 2008 -0400 @@ -21,9 +21,7 @@ @web.expose def index(self, trans, id=None, tool_id=None, mode=None, m_c=None, m_a=None, **kwd): - return trans.fill_template( "root/index.mako", - tool_id=tool_id, - m_c=m_c, m_a=m_a ) + return trans.fill_template( "root/index.mako", tool_id=tool_id, m_c=m_c, m_a=m_a ) ## ---- Tool related ----------------------------------------------------- @@ -68,10 +66,10 @@ @web.expose def dataset_state ( self, trans, id=None, stamp=None ): if id is not None: - try: - data = self.app.model.HistoryDatasetAssociation.get( id ) + try: + data = self.app.model.Dataset.get( id ) except: - return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) + return trans.show_error_message( "Unable to check dataset id %s." %str( id ) ) trans.response.headers['X-Dataset-State'] = data.state trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' @@ -82,13 +80,13 @@ @web.expose def dataset_code( self, trans, id=None, hid=None, stamp=None ): if id is not None: - try: - data = self.app.model.HistoryDatasetAssociation.get( id ) + try: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() except: - return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) + return trans.show_error_message( "Unable to check dataset id %s." % str( id ) ) trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - return trans.fill_template("root/history_item.mako", data=data, hid=hid) + return trans.fill_template( "root/history_item.mako", data=hda.dataset, hid=hid ) else: return trans.show_error_message( "Must specify a dataset id.") @@ -103,11 +101,11 @@ ids = map( int, ids.split( "," ) ) states = states.split( "," ) for id, state in zip( ids, states ): - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data.state != state: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda.dataset.state != state: rval[id] = { - "state": data.state, - "html": trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ) + "state": hda.dataset.state, + "html": trans.fill_template( "root/history_item.mako", data=hda, hid=hda.hid ) } return rval @@ -133,7 +131,6 @@ raise Exception( "History_dataset_association with hid '%s' does not exist." % str( hid ) ) else: try: - id = int( id ) history_dataset_assoc = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() except: return "Dataset id '%s' is invalid." %str( id ) @@ -163,36 +160,36 @@ Returns child data directly into the browser, based upon parent_id and designation. """ try: - data = self.app.model.HistoryDatasetAssociation.get( parent_id ) - if data: - child = data.get_child_by_designation(designation) + hda = self.app.model.HistoryDatasetAssociation.get( parent_id ) + if hda: + child = hda.get_child_by_designation( designation ) if child: return self.display(trans, id=child.id, tofile=tofile, toext=toext) except Exception: pass - return "A child named %s could not be found for data %s" % ( designation, parent_id ) + return "A child named '%s' could not be found for history_dataset_association id '%s'" % ( designation, str( parent_id ) ) @web.expose def display_as( self, trans, id=None, display_app=None, **kwd ): """Returns a file in a format that can successfully be displayed in display_app""" - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: - trans.response.set_content_type(data.get_mime()) + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda: + trans.response.set_content_type( hda.get_mime() ) trans.log_event( "Formatted dataset id %s for display at %s" % ( str(id), display_app ) ) - return data.as_display_type(display_app, **kwd) + return hda.as_display_type( display_app, **kwd ) else: - return "No data with id=%d" % id + return "Dataset 'id' %s does not exist." % str( id ) @web.expose def peek(self, trans, id=None): """Returns a 'peek' at the data""" - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda: yield "<html><body><pre>" - yield data.peek + yield hda.peek yield "</pre></body></html>" else: - yield "No data with id=%d" % id + yield "Dataset 'id' %s does not exist." % str( id ) @web.expose def edit(self, trans, id=None, hid=None, **kwd): @@ -200,76 +197,75 @@ if hid is not None: history = trans.get_history() # TODO: hid handling - data = history.datasets[ int( hid ) - 1 ] + hda = history.datasets[ int( hid ) - 1 ] elif id is None: - return trans.show_error_message( "Problem loading dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) + return trans.show_error_message( "Problem loading dataset id '%s' with history id '%s'." % ( str( id ), str( hid ) ) ) else: - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data is None: - return trans.show_error_message( "Problem retrieving dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda is None: + return trans.show_error_message( "Problem retrieving dataset 'id' %s with history id '%s'." % ( str( id ), str( hid ) ) ) p = util.Params(kwd, safe=False) if p.change: # The user clicked the Save button on the 'Change data type' form - trans.app.datatypes_registry.change_datatype( data, p.datatype ) + trans.app.datatypes_registry.change_datatype( hda, p.datatype ) trans.app.model.flush() elif p.save: # The user clicked the Save button on the 'Edit Attributes' form - data.name = p.name - data.info = p.info + hda.name = p.name + hda.info = p.info # The following for loop will save all metadata_spec items - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in hda.datatype.metadata_spec.items(): if spec.get("readonly"): continue optional = p.get("is_"+name, None) if optional and optional == 'true': # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr(data.metadata,name,None) + setattr( hda.metadata, name, None ) else: - setattr(data.metadata,name,spec.unwrap(p.get(name, None), p)) + setattr( hda.metadata, name, spec.unwrap( p.get( name, None ), p ) ) - data.datatype.after_edit( data ) + hda.datatype.after_edit( hda ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in hda.datatype.metadata_spec.items(): # We need to be careful about the attributes we are resetting if name != 'name' and name != 'info' and name != 'dbkey': if spec.get( 'default' ): - setattr( data.metadata,name,spec.unwrap( spec.get( 'default' ), spec )) - data.datatype.set_meta( data ) - data.datatype.after_edit( data ) + setattr( hda.metadata, name, spec.unwrap( spec.get( 'default' ), spec ) ) + hda.datatype.set_meta( hda ) + hda.datatype.after_edit( hda ) trans.app.model.flush() return trans.show_ok_message( "Attributes updated", refresh_frames=['history'] ) elif p.convert_data: """The user clicked the Convert button on the 'Convert to new format' form""" target_type = kwd.get("target_type", None) if target_type: - msg = data.datatype.convert_dataset(trans, data, target_type) + msg = hda.datatype.convert_dataset(trans, hda, target_type) return trans.show_ok_message( msg, refresh_frames=['history'] ) - data.datatype.before_edit( data ) + hda.datatype.before_edit( hda ) - if "dbkey" in data.datatype.metadata_spec and not data.metadata.dbkey: + if "dbkey" in hda.datatype.metadata_spec and not hda.metadata.dbkey: # Copy dbkey into metadata, for backwards compatability # This looks like it does nothing, but getting the dbkey # returns the metadata dbkey unless it is None, in which # case it resorts to the old dbkey. Setting the dbkey # sets it properly in the metadata - data.metadata.dbkey = data.dbkey + hda.metadata.dbkey = hda.dbkey metadata = list() # a list of MetadataParemeters - for name, spec in data.datatype.metadata_spec.items(): + for name, spec in hda.datatype.metadata_spec.items(): if spec.visible: - metadata.append( spec.wrap( data.metadata.get(name), data ) ) + metadata.append( spec.wrap( hda.metadata.get( name ), hda ) ) # let's not overwrite the imported datatypes module with the variable datatypes? ldatatypes = [x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys()] ldatatypes.sort() - trans.log_event( "Opened edit view on dataset %s" % str(id) ) - return trans.fill_template( "/dataset/edit_attributes.mako", data=data, metadata=metadata, - datatypes=ldatatypes, err=None ) + trans.log_event( "Opened edit view on dataset id '%s'" % str( id ) ) + return trans.fill_template( "/dataset/edit_attributes.mako", data=hda, metadata=metadata, datatypes=ldatatypes, err=None ) @web.expose def delete( self, trans, id = None, **kwd): @@ -284,21 +280,22 @@ int( id ) except: continue - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: - # Walk up parent datasets to find the containing history - topmost_parent = data + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + log.debug("***hda.dataset_id: %s" % str( hda.dataset_id)) + if hda: + # Walk up parent hdas to find the containing history + topmost_parent = hda while topmost_parent.parent: topmost_parent = topmost_parent.parent assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark deleted and cleanup - data.mark_deleted() - data.clear_associated_files() + hda.mark_deleted() + hda.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id %s marked as deleted" % str(id) ) - if data.parent_id is None: + trans.log_event( "Dataset id '%s' marked as deleted" % str( id ) ) + if hda.parent_id is None: try: - self.app.job_stop_queue.put( data.creating_job_associations[0].job ) + self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return self.history( trans ) @@ -311,21 +308,21 @@ except: return "Dataset id '%s' is invalid" %str( id ) history = trans.get_history() - data = self.app.model.HistoryDatasetAssociation.get( id ) - if data: + hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + if hda: # Walk up parent datasets to find the containing history - topmost_parent = data + topmost_parent = hda while topmost_parent.parent: topmost_parent = topmost_parent.parent assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark deleted and cleanup - data.mark_deleted() - data.clear_associated_files() + hda.mark_deleted() + hda.clear_associated_files() self.app.model.flush() - trans.log_event( "Dataset id %s marked as deleted async" % str(id) ) - if data.parent_id is None: + trans.log_event( "Dataset id '%s' marked as deleted async" % str( id ) ) + if hda.parent_id is None: try: - self.app.job_stop_queue.put( data.creating_job_associations[0].job ) + self.app.job_stop_queue.put( hda.creating_job_associations[0].job ) except IndexError: pass # upload tool will cause this since it doesn't have a job return "OK" @@ -335,8 +332,7 @@ @web.expose def history_options( self, trans ): """Displays a list of history related actions""" - return trans.fill_template( "/history/options.mako", - user = trans.get_user(), history = trans.get_history() ) + return trans.fill_template( "/history/options.mako", user=trans.get_user(), history=trans.get_history() ) @web.expose def history_delete( self, trans, id=None, **kwd): @@ -368,16 +364,16 @@ trans.log_event( "History id %s marked as deleted" % str(hid) ) else: return trans.show_message( "You must select at least one history to delete." ) - return trans.show_message( "History deleted: %s" % ",".join(history_names), - refresh_frames=['history']) + return trans.show_message( "History deleted: %s" % ",".join(history_names), refresh_frames=['history'] ) @web.expose def clear_history( self, trans ): """Clears the history for a user""" history = trans.get_history() - for dataset in history.datasets: - dataset.deleted = True - dataset.clear_associated_files() + for hda in history.datasets: + hda.deleted = True + hda.dataset.deleted = True + hda.clear_associated_files() self.app.model.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @@ -425,9 +421,7 @@ if not isinstance( id, list ): id = [ id ] trans.log_event( "History id %s available" % str( id ) ) - return trans.fill_template( "/history/list.mako", ids=id, - user=trans.get_user(), - current_history=trans.get_history() ) + return trans.fill_template( "/history/list.mako", ids=id, user=trans.get_user(), current_history=trans.get_history() ) @web.expose def history_import( self, trans, id=None, confirm=False, **kwd ): @@ -553,23 +547,23 @@ """Adds a POSTed file to a History""" try: history = trans.app.model.History.get( history_id ) - data = trans.app.model.HistoryDatasetAssociation( name = name, info = info, extension = ext, dbkey = dbkey, create_dataset = True ) - data.flush() - data_file = open( data.file_name, "wb" ) + hda = trans.app.model.HistoryDatasetAssociation( name=name, info=info, extension=ext, dbkey=dbkey, create_dataset=True ) + hda.flush() + data_file = open( hda.file_name, "wb" ) file_data.file.seek( 0 ) data_file.write( file_data.file.read() ) data_file.close() - data.state = data.states.OK - data.init_meta() - data.set_meta() - data.flush() - history.add_dataset( data ) + hda.dataset.state = hda.dataset.states.OK + hda.init_meta() + hda.set_meta() + hda.flush() + history.add_dataset( hda ) history.flush() - data.set_peek() - data.set_size() - data.flush() - trans.log_event("Added dataset %d to history %d" %(data.id, trans.history.id)) - return trans.show_ok_message("Dataset "+str(data.hid)+" added to history "+str(history_id)+".") + hda.set_peek() + hda.set_size() + hda.flush() + trans.log_event( "Added dataset id '%s' to history id '%s'." % ( str( hda.dataset_id ), str( history_id ) ) ) + return trans.show_ok_message( "Dataset id " + str( hda.dataset_id ) + " added to history id " + str( history_id ) + "." ) except: return trans.show_error_message("Adding File to History has Failed") @@ -577,13 +571,11 @@ def dataset_make_primary( self, trans, id=None): """Copies a dataset and makes primary""" try: - old_data = self.app.model.HistoryDatasetAssociation.get( id ) - new_data = old_data.copy() - ## new_data.parent = None - ## history = trans.app.model.History.get( old_data.history_id ) + old_hda = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() + new_hda = old_hda.copy() history = trans.get_history() - history.add_dataset(new_data) - new_data.flush() + history.add_dataset( new_hda ) + new_hda.flush() return trans.show_message( "<p>Secondary dataset has been made primary.</p>", refresh_frames=['history'] ) except: return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) @@ -603,7 +595,7 @@ @web.expose def dataset_errors( self, trans, id=None, **kwd ): """View/fix errors associated with dataset""" - data = trans.app.model.HistoryDatasetAssociation.get( id ) + hda = trans.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() p = kwd if p.get("fix_errors", None): # launch tool to create new, (hopefully) error free dataset @@ -611,18 +603,19 @@ tool_params["tool_id"] = 'fix_errors' tool_params["runtool_btn"] = 'T' tool_params["input"] = id - tool_params["ext"] = data.ext + tool_params["ext"] = hda.ext # send methods selected - repair_methods = data.datatype.repair_methods( data ) + repair_methods = hda.datatype.repair_methods( hda ) methods = [] for method, description in repair_methods: - if method in p: methods.append(method) + if method in p: + methods.append( method ) tool_params["methods"] = ",".join(methods) url = "/tool_runner/index?" + urllib.urlencode(tool_params) trans.response.send_redirect(url) else: - history = trans.app.model.History.get( data.history_id ) - return trans.fill_template('dataset/validation.tmpl', data=data, history=history) + history = trans.app.model.History.get( hda.history_id ) + return trans.fill_template('dataset/validation.tmpl', data=hda, history=history) # ---- Debug methods ----------------------------------------------------

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[hg] galaxy 1539: Fix for root/display() - history_dataset_assoc...
by Greg Von Kuster 01 Oct '08

01 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/dd58d5aeb274 changeset: 1539:dd58d5aeb274 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Oct 01 12:43:59 2008 -0400 description: Fix for root/display() - history_dataset_association.dataset_id no longer confused with history_dataset_association.id. 1 file(s) affected in this change: lib/galaxy/web/controllers/root.py diffs (56 lines): diff -r f9431ad593b4 -r dd58d5aeb274 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Oct 01 10:17:58 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Wed Oct 01 12:43:59 2008 -0400 @@ -125,36 +125,37 @@ except: return "hid '%s' is invalid" %str( hid ) history = trans.get_history() - for dataset in history.datasets: - if dataset.hid == hid: - data = dataset + for hda in history.datasets: + if hda.hid == hid: + history_dataset_assoc = hda break else: - raise Exception( "No dataset with hid '%d'" % hid ) + raise Exception( "History_dataset_association with hid '%s' does not exist." % str( hid ) ) else: try: - data = self.app.model.HistoryDatasetAssociation.get( id ) + id = int( id ) + history_dataset_assoc = self.app.model.HistoryDatasetAssociation.filter_by( dataset_id=id ).first() except: - return "Dataset id '%s' is invalid" %str( id ) - if data: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) + return "Dataset id '%s' is invalid." %str( id ) + if history_dataset_assoc: + mime = trans.app.datatypes_registry.get_mimetype_by_extension( history_dataset_assoc.extension.lower() ) trans.response.set_content_type(mime) if tofile: - fStat = os.stat(data.file_name) + fStat = os.stat(history_dataset_assoc.file_name) trans.response.headers['Content-Length'] = int(fStat.st_size) if toext[0:1] != ".": toext = "." + toext valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name + fname = history_dataset_assoc.name fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, toext) - trans.log_event( "Display dataset id: %s" % str(id) ) + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (history_dataset_assoc.hid, fname, toext) + trans.log_event( "Display dataset id: '%s'." % str(id) ) try: - return open( data.file_name ) + return open( history_dataset_assoc.file_name ) except: - return "This dataset contains no content" + return "Dataset id '%s' contains no content." % str( id ) else: - return "No dataset with id '%s'" % str( id ) + return "Dataset id '%s' does not exist." % str( id ) @web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"):

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[hg] galaxy 1538: Fix for histogram tool when input dataset is e...
by Greg Von Kuster 01 Oct '08

01 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f9431ad593b4 changeset: 1538:f9431ad593b4 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Oct 01 10:17:58 2008 -0400 description: Fix for histogram tool when input dataset is empty. 1 file(s) affected in this change: tools/stats/gsummary.py diffs (11 lines): diff -r 1dbd88fb9e57 -r f9431ad593b4 tools/stats/gsummary.py --- a/tools/stats/gsummary.py Tue Sep 30 16:40:42 2008 -0400 +++ b/tools/stats/gsummary.py Wed Oct 01 10:17:58 2008 -0400 @@ -57,6 +57,7 @@ tmp_file.write( "%s\n" % hdr_str ) skipped_lines = 0 first_invalid_line = 0 + i = 0 for i, line in enumerate( file( datafile ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ):

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[hg] galaxy 1537: add error msg for shrimp_wrapper when memory e...
by Greg Von Kuster 01 Oct '08

01 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1dbd88fb9e57 changeset: 1537:1dbd88fb9e57 user: wychung date: Tue Sep 30 16:40:42 2008 -0400 description: add error msg for shrimp_wrapper when memory error and zero hits. convert last column of megablast output to float. 3 file(s) affected in this change: tools/metag_tools/megablast_wrapper.py tools/metag_tools/shrimp_wrapper.py tools/metag_tools/shrimp_wrapper.xml diffs (111 lines): diff -r 8ab38aa72998 -r 1dbd88fb9e57 tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Tue Sep 30 16:17:12 2008 -0400 +++ b/tools/metag_tools/megablast_wrapper.py Tue Sep 30 16:40:42 2008 -0400 @@ -55,7 +55,9 @@ chunk = db[(db_build)] megablast_command = "megablast -d %s -i %s -o %s -m 8 -a 8 -W %s -p %s -e %s -F %s > /dev/null 2>&1 " \ % ( chunk, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, mega_filter ) - + + print megablast_command + try: os.system( megablast_command ) except Exception, e: @@ -67,8 +69,12 @@ line = line.rstrip( '\r\n' ) fields = line.split() try: + # get gi and length of that gi seq gi, gi_len = fields[1].split('_') - new_line = "%s\t%s\t%s\t%s" % ( fields[0], gi, gi_len, '\t'.join( fields[2:] ) ) + # convert the last column (causing problem in filter tool) to float + fields[-1] = float(fields[-1]) + + new_line = "%s\t%s\t%s\t%s\t%0.1f" % ( fields[0], gi, gi_len, '\t'.join( fields[2:-1] ), fields[-1] ) except: new_line = line invalid_lines += 1 diff -r 8ab38aa72998 -r 1dbd88fb9e57 tools/metag_tools/shrimp_wrapper.py --- a/tools/metag_tools/shrimp_wrapper.py Tue Sep 30 16:17:12 2008 -0400 +++ b/tools/metag_tools/shrimp_wrapper.py Tue Sep 30 16:40:42 2008 -0400 @@ -1,15 +1,21 @@ #! /usr/bin/python """ +TODO +1. decrease memory usage +2. multi-fasta fastq file, ex. 454 +3. split reads into small chuncks? + SHRiMP wrapper Inputs: - reference seq and reads +1. reference seq +2. reads Outputs: - table of 8 columns: +1. table of 8 columns: chrom ref_loc read_id read_loc ref_nuc read_nuc quality coverage - SHRiMP output +2. SHRiMP output Parameters: -s Spaced Seed (default: 111111011111) @@ -37,13 +43,9 @@ >7:2:1147:982/1 chr3 + 95338194 95338225 4 35 36 2700 9T7C14 >7:2:587:93/1 chr3 + 14913541 14913577 1 35 36 2960 19--16 -Testing: -%python shrimp_wrapper.py single ~/Desktop/shrimp_wrapper/phix_anc.fa tmp tmp1 ~/Desktop/shrimp_wrapper/phix.10.solexa.fastq -%python shrimp_wrapper.py paired ~/Desktop/shrimp_wrapper/eca_ref_chrMT.fa tmp tmp1 ~/Desktop/shrimp_wrapper/eca.5.solexa_1.fastq ~/Desktop/shrimp_wrapper/eca.5.solexa_2.fastq - """ -import os, sys, tempfile, os.path +import os, sys, tempfile, os.path, re assert sys.version_info[:2] >= (2.4) @@ -575,6 +577,29 @@ if os.path.exists(query_qual_end1): os.remove(query_qual_end1) if os.path.exists(query_qual_end2): os.remove(query_qual_end2) stop_err(str(e)) + + # check SHRiMP output: count number of lines + num_hits = 0 + if shrimp_outfile: + for i, line in enumerate(file(shrimp_outfile)): + line = line.rstrip('\r\n') + if not line or line.startswith('#'): continue + try: + fields = line.split() + num_hits += 1 + except Exception, e: + stop_err(str(e)) + + if num_hits == 0: # no hits generated + err_msg = '' + if shrimp_log: + for i, line in enumerate(file(shrimp_log)): + if line.startswith('error'): # deal with memory error: + err_msg += line # error: realloc failed: Cannot allocate memory + if re.search('Reads Matched', line): # deal with zero hits + if int(line[8:].split()[2]) == 0: + err_msg = 'Zero hits found.\n' + stop_err('SHRiMP Failed due to:\n' + err_msg) # convert to table if type_of_reads == 'single': diff -r 8ab38aa72998 -r 1dbd88fb9e57 tools/metag_tools/shrimp_wrapper.xml --- a/tools/metag_tools/shrimp_wrapper.xml Tue Sep 30 16:17:12 2008 -0400 +++ b/tools/metag_tools/shrimp_wrapper.xml Tue Sep 30 16:40:42 2008 -0400 @@ -1,5 +1,5 @@ <tool id="shrimp_wrapper" name="SHRiMP" version="1.0.0"> - <description>SHort Read Mapping Package</description> + <description>: SHort Read Mapping Package</description> <command interpreter="python"> #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $input_query #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size

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[hg] galaxy 1536: Add a change_format tag to output datasets in ...
by Greg Von Kuster 01 Oct '08

01 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8ab38aa72998 changeset: 1536:8ab38aa72998 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Sep 30 16:17:12 2008 -0400 description: Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values. Several tools have been updated to take advantage of this, eliminating their need for code_files. 12 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py tools/annotation_profiler/annotation_profiler.xml tools/annotation_profiler/annotation_profiler_code.py tools/extract/extract_genomic_dna.xml tools/extract/extract_genomic_dna_code.py tools/filters/pasteWrapper.xml tools/filters/pasteWrapper_code.py tools/maf/maf_stats.xml tools/maf/maf_stats_code.py tools/sr_mapping/lastz_code.py tools/sr_mapping/lastz_wrapper.xml diffs (222 lines): diff -r 931d6ca549d3 -r 8ab38aa72998 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Sep 30 15:30:57 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Sep 30 16:17:12 2008 -0400 @@ -299,6 +299,7 @@ for data_elem in out_elem.findall("data"): output = ToolOutput( data_elem.get("name") ) output.format = data_elem.get("format", "data") + output.change_format = data_elem.findall("change_format") output.metadata_source = data_elem.get("metadata_source", "") output.parent = data_elem.get("parent", None) output.label = util.xml_text( data_elem, "label" ) diff -r 931d6ca549d3 -r 8ab38aa72998 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Sep 30 15:30:57 2008 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Tue Sep 30 16:17:12 2008 -0400 @@ -115,6 +115,21 @@ ext = output.format if ext == "input": ext = input_ext + #process change_format tags + if output.change_format: + for change_elem in output.change_format: + for when_elem in change_elem.findall( 'when' ): + check = incoming.get( when_elem.get( 'input' ), None ) + if check is not None: + if check == when_elem.get( 'value', None ): + ext = when_elem.get( 'format', ext ) + else: + check = when_elem.get( 'input_dataset', None ) + if check is not None: + check = inp_data.get( check, None ) + if check is not None: + if str( getattr( check, when_elem.get( 'attribute' ) ) ) == when_elem.get( 'value', None ): + ext = when_elem.get( 'format', ext ) data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True ) # Commit the dataset immediately so it gets database assigned unique id data.flush() diff -r 931d6ca549d3 -r 8ab38aa72998 tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Tue Sep 30 15:30:57 2008 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Tue Sep 30 16:17:12 2008 -0400 @@ -16,9 +16,12 @@ <param name="table_names" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Tables to Use" help="Selecting no tables will result in using all tables." from_file="annotation_profiler_options.xml"/> </inputs> <outputs> - <data format="input" name="out_file1"/> + <data format="input" name="out_file1"> + <change_format> + <when input="summary" value="-S" format="tabular" /> + </change_format> + </data> </outputs> - <code file="annotation_profiler_code.py" /> <tests> <test> <param name="input1" value="4.bed" dbkey="hg18"/> diff -r 931d6ca549d3 -r 8ab38aa72998 tools/annotation_profiler/annotation_profiler_code.py --- a/tools/annotation_profiler/annotation_profiler_code.py Tue Sep 30 15:30:57 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#Change format from Interval to tabular if needed -def exec_before_job(app, inp_data, out_data, param_dict, tool): - if param_dict['summary']: - out_data['out_file1'].change_datatype('tabular') \ No newline at end of file diff -r 931d6ca549d3 -r 8ab38aa72998 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Tue Sep 30 15:30:57 2008 -0400 +++ b/tools/extract/extract_genomic_dna.xml Tue Sep 30 16:17:12 2008 -0400 @@ -12,9 +12,12 @@ </param> </inputs> <outputs> - <data format="fasta" name="out_file1" /> + <data format="fasta" name="out_file1"> + <change_format> + <when input="out_format" value="interval" format="interval" /> + </change_format> + </data> </outputs> - <code file="extract_genomic_dna_code.py" /> <tests> <test> <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> diff -r 931d6ca549d3 -r 8ab38aa72998 tools/extract/extract_genomic_dna_code.py --- a/tools/extract/extract_genomic_dna_code.py Tue Sep 30 15:30:57 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -# by dan -#Change format from FASTA to Interval if needed; use metadata from input file -def exec_before_job(app, inp_data, out_data, param_dict, tool): - if param_dict['out_format'] == "interval": - out_data['out_file1'].change_datatype('interval') - out_data['out_file1'].init_meta( copy_from=inp_data['input'] ) diff -r 931d6ca549d3 -r 8ab38aa72998 tools/filters/pasteWrapper.xml --- a/tools/filters/pasteWrapper.xml Tue Sep 30 15:30:57 2008 -0400 +++ b/tools/filters/pasteWrapper.xml Tue Sep 30 16:17:12 2008 -0400 @@ -15,7 +15,11 @@ </param> </inputs> <outputs> - <data format="input" name="out_file1" metadata_source="input1" /> + <data format="input" name="out_file1" metadata_source="input1"> + <change_format> + <when input_dataset="input1" attribute="ext" value="bed" format="interval"/> + </change_format> + </data> </outputs> <tests> <test> @@ -60,5 +64,4 @@ a 3 40 </help> -<code file="pasteWrapper_code.py"/> </tool> diff -r 931d6ca549d3 -r 8ab38aa72998 tools/filters/pasteWrapper_code.py --- a/tools/filters/pasteWrapper_code.py Tue Sep 30 15:30:57 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -#post processing, if bed file, change to interval file -from galaxy import datatypes -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - for name, data in out_data.items(): - if data.ext == "bed": - data = app.datatypes_registry.change_datatype(data, "interval") - data.flush() \ No newline at end of file diff -r 931d6ca549d3 -r 8ab38aa72998 tools/maf/maf_stats.xml --- a/tools/maf/maf_stats.xml Tue Sep 30 15:30:57 2008 -0400 +++ b/tools/maf/maf_stats.xml Tue Sep 30 16:17:12 2008 -0400 @@ -44,7 +44,11 @@ </param> </inputs> <outputs> - <data format="interval" name="out_file1" metadata_source="input1"/> + <data format="interval" name="out_file1" metadata_source="input1"> + <change_format> + <when input="summary" value="true" format="tabular" /> + </change_format> + </data> </outputs> <requirements> <requirement type="python-module">numpy</requirement> @@ -95,5 +99,4 @@ where **coverage** is the number of nucleotides divided by the total length of the provided intervals. </help> - <code file="maf_stats_code.py"/> </tool> diff -r 931d6ca549d3 -r 8ab38aa72998 tools/maf/maf_stats_code.py --- a/tools/maf/maf_stats_code.py Tue Sep 30 15:30:57 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -import os - -def load_maf_data( GALAXY_DATA_INDEX_DIR, sep='\t' ): - # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to - # set data.name in exec_before_job(). - maf_sets = {} - filename = "%s/maf_index.loc" % GALAXY_DATA_INDEX_DIR - for i, line in enumerate( file( filename ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( sep ) - #read each line, if not enough fields, go to next line - try: - maf_desc = fields[0] - maf_uid = fields[1] - builds = fields[2] - build_list =[] - split_builds = builds.split( "," ) - for build in split_builds: - this_build = build.split( "=" )[0] - build_list.append( this_build ) - paths = fields[3] - maf_sets[ maf_uid ] = {} - maf_sets[ maf_uid ][ 'description' ] = maf_desc - maf_sets[ maf_uid ][ 'builds' ] = build_list - except: - continue - return maf_sets -def exec_before_job(app, inp_data, out_data, param_dict, tool): - maf_sets = load_maf_data( app.config.tool_data_path, sep='\t' ) - if param_dict[ 'maf_source_type' ][ 'maf_source' ] == "cached": - for name, data in out_data.items(): - try: - data.name = data.name + " [" + maf_sets[ str( param_dict[ 'maf_source_type' ][ 'mafType' ] ) ][ 'description' ] + "]" - except KeyError: - data.name = data.name + " [unknown MAF source specified]" - if param_dict[ 'summary' ].lower() == "true": - for name, data in out_data.items(): - data.change_datatype( 'tabular' ) diff -r 931d6ca549d3 -r 8ab38aa72998 tools/sr_mapping/lastz_code.py --- a/tools/sr_mapping/lastz_code.py Tue Sep 30 15:30:57 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -# by dan -#Change format from tabular to maf if needed; use metadata from input file -def exec_before_job(app, inp_data, out_data, param_dict, tool): - if param_dict['out_format'] == "maf": - out_data['output1'].change_datatype('maf') -# out_data['output1'].init_meta( copy_from=inp_data['input1'] ) diff -r 931d6ca549d3 -r 8ab38aa72998 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Tue Sep 30 15:30:57 2008 -0400 +++ b/tools/sr_mapping/lastz_wrapper.xml Tue Sep 30 16:17:12 2008 -0400 @@ -77,13 +77,16 @@ <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this fraction (%) of each read"/> </inputs> <outputs> - <data format="tabular" name="output1" /> + <data format="tabular" name="output1"> + <change_format> + <when input="out_format" value="maf" format="maf" /> + </change_format> + </data> <data format="tabular" name="output2" /> </outputs> <requirements> <requirement type="binary">lastz</requirement> </requirements> - <code file="lastz_code.py" /> <tests> <test> <param name="input1" value="phiX.fa" ftype="fasta" />

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[hg] galaxy 1534: Fix for disk usage report in the webapps syste...
by Greg Von Kuster 30 Sep '08

30 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1706aadf16b2 changeset: 1534:1706aadf16b2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Sep 29 10:37:54 2008 -0400 description: Fix for disk usage report in the webapps system controller. 1 file(s) affected in this change: lib/galaxy/webapps/reports/controllers/system.py diffs (20 lines): diff -r 3830fefb07da -r 1706aadf16b2 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Fri Sep 26 14:22:37 2008 -0400 +++ b/lib/galaxy/webapps/reports/controllers/system.py Mon Sep 29 10:37:54 2008 -0400 @@ -157,13 +157,15 @@ disk_usage = self.get_disk_usage( file_path ) min_file_size = 2**32 # 4 Gb file_size_str = nice_size( min_file_size ) + hda = trans.model.HistoryDatasetAssociation d = trans.model.Dataset datasets = [] where = ( d.table.c.file_size > min_file_size ) dataset_rows = d.query().filter( where ).order_by( desc( d.table.c.file_size ) ) for dataset in dataset_rows: - datasets.append( ( dataset.id, str( dataset.update_time )[0:10], dataset.history_id, dataset.deleted, dataset.file_size ) ) + history_dataset_assoc = hda.filter_by( dataset_id=dataset.id ).order_by( desc( hda.table.c.history_id ) ).all()[0] + datasets.append( ( dataset.id, str( dataset.update_time )[0:10], history_dataset_assoc.history_id, dataset.deleted, dataset.file_size ) ) return file_path, disk_usage, datasets, file_size_str def nice_size( size ):

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[hg] galaxy 1535: Modified the way biomart tool runs: output gen...
by Greg Von Kuster 30 Sep '08

30 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/931d6ca549d3 changeset: 1535:931d6ca549d3 user: guru date: Tue Sep 30 15:30:57 2008 -0400 description: Modified the way biomart tool runs: output generation will be completed before exec_afer_process hook is called. 4 file(s) affected in this change: tools/data_source/biomart.py tools/data_source/biomart.xml tools/data_source/biomart_filter.py tools/data_source/biomart_test.xml diffs (148 lines): diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/biomart.py Tue Sep 30 15:30:57 2008 -0400 @@ -0,0 +1,55 @@ +#!/usr/bin/env python +#Retreives data from BIOMART and stores in a file. Biomart parameters are provided in the input/output file. +#guruprasad Ananda + +import urllib, sys, os, gzip, tempfile, shutil +from galaxy import eggs + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + filename = sys.argv[1] + params = {} + for line in open(filename, 'r'): + try: + line = line.strip() + fields = line.split('\t') + params[fields[0]] = fields[1] + except: + continue + + URL = params.get( 'URL', None ) + if not URL: + open( filename, 'w' ).write( "" ) + stop_err( 'Datasource has not sent back a URL parameter.' ) + URL = URL + '&_export=1&GALAXY_URL=0' + CHUNK_SIZE = 2**20 # 1Mb + MAX_SIZE = CHUNK_SIZE * 100 + try: + page = urllib.urlopen(URL) + except Exception, exc: + stop_err('Problems connecting to %s (%s)' % (URL, exc) ) + + fp = open(filename, 'w') + size = 0 + max_size_exceeded = False + while 1: + chunk = page.read(CHUNK_SIZE) + if not chunk: + break + size += len(chunk) + if size > MAX_SIZE: + max_size_exceeded = True + break + fp.write(chunk) + fp.close() + + if max_size_exceeded: + print 'Maximum data size of 100 MB exceeded, incomplete data retrieval.' + +if __name__ == "__main__": + __main__() diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart.xml --- a/tools/data_source/biomart.xml Mon Sep 29 10:37:54 2008 -0400 +++ b/tools/data_source/biomart.xml Tue Sep 30 15:30:57 2008 -0400 @@ -1,14 +1,14 @@ <?xml version="1.0"?> <tool name="BioMart" id="biomart"> - <description>Central server</description> - - <command/> - + <command interpreter="python"> + biomart.py + $output + </command> <inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> - </inputs> + </inputs> <uihints minwidth="800"/> diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart_filter.py --- a/tools/data_source/biomart_filter.py Mon Sep 29 10:37:54 2008 -0400 +++ b/tools/data_source/biomart_filter.py Tue Sep 30 15:30:57 2008 -0400 @@ -14,41 +14,16 @@ data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) data = app.datatypes_registry.change_datatype(data, data_type) data.name = data_name + #store BIOMART parameters temporarily in output file + out = open(data.file_name,'w') + for key, value in param_dict.items(): + print >> out, "%s\t%s" % (key,value) + out.close() out_data[name] = data + def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): - """Verifies the data after the run""" - URL = param_dict.get( 'URL', None ) - if not URL: - raise Exception('Datasource has not sent back a URL parameter') - URL = URL + '&_export=1&GALAXY_URL=0' - CHUNK_SIZE = 2**20 # 1Mb - MAX_SIZE = CHUNK_SIZE * 100 - try: - page = urllib.urlopen(URL) - except Exception, exc: - raise Exception('Problems connecting to %s (%s)' % (URL, exc) ) name, data = out_data.items()[0] - fp = open(data.file_name, 'wb') - size = 0 - max_size_exceeded = False - - while 1: - chunk = page.read(CHUNK_SIZE) - if not chunk: - break - size += len(chunk) - if size > MAX_SIZE: - max_size_exceeded = True - break - fp.write(chunk) - fp.close() - - if max_size_exceeded: - data.info = 'Maximum data size of 100 MB exceeded, incomplete data retrieval.' - else: - data.info = data.name - if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval): #Set meta data, format file to be valid interval type data.set_meta(first_line_is_header=True) diff -r 1706aadf16b2 -r 931d6ca549d3 tools/data_source/biomart_test.xml --- a/tools/data_source/biomart_test.xml Mon Sep 29 10:37:54 2008 -0400 +++ b/tools/data_source/biomart_test.xml Tue Sep 30 15:30:57 2008 -0400 @@ -3,7 +3,10 @@ <description>Test server</description> - <command/> + <command interpreter="python"> + biomart.py + $output + </command> <inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top"> <display>go to BioMart Central $GALAXY_URL</display>

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[hg] galaxy 1533: Update to implicit converter discovery. Will n...
by Greg Von Kuster 30 Sep '08

30 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/3830fefb07da changeset: 1533:3830fefb07da user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 26 14:22:37 2008 -0400 description: Update to implicit converter discovery. Will now allow the use of converters that create datatypes that are a subclass of what is needed by the tool. i.e. If tool input requires 'interval', and a datatype has a BED converter available but no interval converter, the BED converter can now be used. 5 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/registry.py lib/galaxy/model/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/parameters/basic.py diffs (138 lines): diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/datatypes/data.py Fri Sep 26 14:22:37 2008 -0400 @@ -185,6 +185,10 @@ """Returns available converters by type for this dataset""" return datatypes_registry.get_converters_by_datatype(original_dataset.ext) + def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd ) + def convert_dataset(self, trans, original_dataset, target_type, return_output = False, visible = True ): """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.""" converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type ) diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri Sep 26 14:22:37 2008 -0400 @@ -233,3 +233,16 @@ if target_ext in converters.keys(): return converters[target_ext] return None + def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): + """Returns ( target_ext, exisiting converted dataset )""" + for convert_ext in self.get_converters_by_datatype( dataset.ext ): + if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): + datasets = dataset.get_converted_files_by_type( convert_ext ) + if datasets: + ret_data = datasets[0] + elif not converter_safe: + continue + else: + ret_data = None + return ( convert_ext, ret_data ) + return ( None, None ) \ No newline at end of file diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/model/__init__.py Fri Sep 26 14:22:37 2008 -0400 @@ -254,6 +254,10 @@ def get_converter_types(self): return self.datatype.get_converter_types( self, datatypes_registry) + + def find_conversion_destination( self, accepted_formats, **kwd ): + """Returns ( target_ext, exisiting converted dataset )""" + return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd ) def copy( self, copy_children = False, parent_id = None ): des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self ) diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Fri Sep 26 14:22:37 2008 -0400 @@ -29,22 +29,21 @@ def visitor( prefix, input, value, parent = None ): def process_dataset( data ): if data and not isinstance( data.datatype, input.formats ): - for target_ext in input.extensions: - if target_ext in data.get_converter_types(): - data.refresh() #need to refresh incase this conversion just took place, i.e. input above in tool performed the same conversion - datasets = data.get_converted_files_by_type( target_ext ) - if datasets: data = datasets[0] - elif input.converter_safe( param_values, trans ): - #run converter here - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) - new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] - new_data.hid = data.hid - new_data.name = data.name - new_data.flush() - assoc.dataset = new_data - assoc.flush() - data = new_data - break + data.refresh() #need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion + target_ext, converted_dataset = data.find_conversion_destination( input.formats, converter_safe = input.converter_safe( param_values, trans ) ) + if target_ext: + if converted_dataset: + data = converted_dataset + else: + #run converter here + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) + new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] + new_data.hid = data.hid + new_data.name = data.name + new_data.flush() + assoc.dataset = new_data + assoc.flush() + data = new_data return data if isinstance( input, DataToolParameter ): if isinstance( value, list ): diff -r 3b6771227a43 -r 3830fefb07da lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Fri Sep 26 09:10:04 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Fri Sep 26 14:22:37 2008 -0400 @@ -1059,16 +1059,12 @@ selected = ( value and ( data in value ) ) field.add_option( "%s: %s" % ( hid, data.name[:30] ), data.id, selected ) else: - for target_ext in self.extensions: - if target_ext in data.get_converter_types(): - datasets = data.get_converted_files_by_type( target_ext ) - if datasets: - data = datasets[0] - elif not self.converter_safe( other_values, trans ): - continue - selected = ( value and ( data in value ) ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected ) - break #we only report the first valid converter, assume self.extensions is a priority list + target_ext, converted_dataset = data.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + if target_ext: + if converted_dataset: + data = converted_dataset + selected = ( value and ( data in value ) ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, data.name[:30] ), data.id, selected ) # Also collect children via association object dataset_collector( data.children, hid ) dataset_collector( history.datasets, None ) @@ -1111,9 +1107,9 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - for target_ext in self.extensions: - if target_ext in data.get_converter_types(): - return True + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = True ) #need to assume converter_safe = True, since we don't know about other parameter values here + if target_ext is not None: + return True return False for i, data in enumerate( datasets ): if data.visible and not data.deleted and data.state not in [data.states.ERROR] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): @@ -1184,7 +1180,7 @@ return [] def converter_safe( self, other_values, trans ): - if trans.workflow_building_mode: + if not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False converter_safe = [True] def visitor( prefix, input, value, parent = None ):

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Galaxy with web services
by Praveen Agrawal 29 Sep '08

29 Sep '08

Hi, I am trying to use Galaxy at my site and cann't figure out Galaxy with web services. I understand that it's possible to integrate a data source using WSDL/SOAP. Is the same possible for a remote tool as well? Regards, Praveen ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ http://www.scfbio-iitd.res.in ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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[hg] galaxy 1532: Fix for interval to bed converter.
by Greg Von Kuster 26 Sep '08

26 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/3b6771227a43 changeset: 1532:3b6771227a43 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Sep 26 09:10:04 2008 -0400 description: Fix for interval to bed converter. 1 file(s) affected in this change: lib/galaxy/datatypes/converters/interval_to_bed_converter.py diffs (11 lines): diff -r aa1088e4c6c6 -r 3b6771227a43 lib/galaxy/datatypes/converters/interval_to_bed_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Thu Sep 25 15:03:05 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Fri Sep 26 09:10:04 2008 -0400 @@ -38,6 +38,7 @@ skipped_lines = 0 first_skipped_line = 0 out = open( output_name,'w' ) + count = 0 for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ): try: if nameCol >= 0:

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