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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Mar '13

21 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55a425f1f2f3/ changeset: 55a425f1f2f3 branch: next-stable user: jgoecks date: 2013-03-21 17:19:14 summary: Add support for column ranges to Cut tool. Thank to John Chilton for this code. affected #: 2 files diff -r b76683ec3daaf3058a93b4aff00aee4e1c5f9331 -r 55a425f1f2f363f6e9fe94ab539bb58daeb8d136 tools/filters/cutWrapper.pl --- a/tools/filters/cutWrapper.pl +++ b/tools/filters/cutWrapper.pl @@ -9,6 +9,9 @@ my @out = (); my $command = ""; my $field = 0; +my $start = 0; +my $end = 0; +my $i = 0; # a wrapper for cut for use in galaxy # cutWrapper.pl [filename] [columns] [delim] [output] @@ -20,6 +23,13 @@ if (m/^c\d{1,}$/i) { push (@columns, $_); $columns[@columns-1] =~s/c//ig; + } elsif (m/^c\d{1,}-c\d{1,}$/i) { + ($start, $end) = split(/-/, $_); + $start =~ s/c//ig; + $end =~ s/c//ig; + for $i ($start .. $end) { + push (@columns, $i); + } } } diff -r b76683ec3daaf3058a93b4aff00aee4e1c5f9331 -r 55a425f1f2f363f6e9fe94ab539bb58daeb8d136 tools/filters/cutWrapper.xml --- a/tools/filters/cutWrapper.xml +++ b/tools/filters/cutWrapper.xml @@ -1,4 +1,4 @@ -<tool id="Cut1" name="Cut" version="1.0.1"> +<tool id="Cut1" name="Cut" version="1.0.2"><description>columns from a table</description><command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command><inputs> @@ -141,6 +141,12 @@ <param name="input" value="1.bed"/><output name="out_file1" file="eq-cut.dat"/></test> + <test> + <param name="columnList" value="c1,c4,c2-c3" /> + <param name="delimiter" value="T" /> + <param name="input" value="1.bed" /> + <output name="out_file1" file="eq-cut.dat" /> + </test></tests><help> @@ -191,6 +197,11 @@ + 0 gene1 chr1 + 0 gene2 chr2 +**cut** on columns "**c1-c3**" will return:: + + chr1 10 1000 + chr2 100 1500 + **cut** on columns "**c8,c7,c4**" will return:: https://bitbucket.org/galaxy/galaxy-central/commits/0ce683ac64b9/ changeset: 0ce683ac64b9 user: jgoecks date: 2013-03-21 17:19:45 summary: Merge in next-stable affected #: 2 files diff -r 3e43e8c42bc19eca2532989f83adbc8811062f62 -r 0ce683ac64b95a2d6f6738407e8f69c7087a6b30 tools/filters/cutWrapper.pl --- a/tools/filters/cutWrapper.pl +++ b/tools/filters/cutWrapper.pl @@ -9,6 +9,9 @@ my @out = (); my $command = ""; my $field = 0; +my $start = 0; +my $end = 0; +my $i = 0; # a wrapper for cut for use in galaxy # cutWrapper.pl [filename] [columns] [delim] [output] @@ -20,6 +23,13 @@ if (m/^c\d{1,}$/i) { push (@columns, $_); $columns[@columns-1] =~s/c//ig; + } elsif (m/^c\d{1,}-c\d{1,}$/i) { + ($start, $end) = split(/-/, $_); + $start =~ s/c//ig; + $end =~ s/c//ig; + for $i ($start .. $end) { + push (@columns, $i); + } } } diff -r 3e43e8c42bc19eca2532989f83adbc8811062f62 -r 0ce683ac64b95a2d6f6738407e8f69c7087a6b30 tools/filters/cutWrapper.xml --- a/tools/filters/cutWrapper.xml +++ b/tools/filters/cutWrapper.xml @@ -1,4 +1,4 @@ -<tool id="Cut1" name="Cut" version="1.0.1"> +<tool id="Cut1" name="Cut" version="1.0.2"><description>columns from a table</description><command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command><inputs> @@ -141,6 +141,12 @@ <param name="input" value="1.bed"/><output name="out_file1" file="eq-cut.dat"/></test> + <test> + <param name="columnList" value="c1,c4,c2-c3" /> + <param name="delimiter" value="T" /> + <param name="input" value="1.bed" /> + <output name="out_file1" file="eq-cut.dat" /> + </test></tests><help> @@ -191,6 +197,11 @@ + 0 gene1 chr1 + 0 gene2 chr2 +**cut** on columns "**c1-c3**" will return:: + + chr1 10 1000 + chr2 100 1500 + **cut** on columns "**c8,c7,c4**" will return:: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Move the tool_shed_repository_revision_update.py api example script to ~/lib/tool_shed/scripts/api
by commits-noreply＠bitbucket.org 21 Mar '13

21 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e43e8c42bc1/ changeset: 3e43e8c42bc1 user: greg date: 2013-03-21 15:58:11 summary: Move the tool_shed_repository_revision_update.py api example script to ~/lib/tool_shed/scripts/api affected #: 1 file diff -r cd766b6391448acae0574fcf240b4cf5c55d340e -r 3e43e8c42bc19eca2532989f83adbc8811062f62 lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py --- /dev/null +++ b/lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py @@ -0,0 +1,37 @@ +#!/usr/bin/env python +""" +PUT/update script to update appropriate values in a repository_metadata table record in the Tool Shed. + +usage: tool_shed_repository_revision_update.py key url key1=value1 key2=value2 ... +""" + +import os, sys +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import update + +import pkg_resources +pkg_resources.require( "simplejson" ) + +import simplejson + +to_json_string = simplejson.dumps +from_json_string = simplejson.loads + +data = {} +for key, value in [ kwarg.split( '=', 1 ) for kwarg in sys.argv[ 3: ] ]: + """ + This example script will properly handle updating the value of one or more of the following RepositoryMetadata attributes: + tools_functionally_correct, do_not_test, tool_test_errors + """ + if key in [ 'tools_functionally_correct', 'do_not_test' ]: + if str( value ).lower() in [ 'true', 'yes', 'on' ]: + new_value = True + else: + new_value = False + elif key in [ 'tool_test_errors' ]: + new_value = from_json_string( value ) + else: + new_value = str( value ) + data[ key ] = new_value + +update( sys.argv[ 1 ], sys.argv[ 2 ], data ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Mar '13

21 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b76683ec3daa/ changeset: b76683ec3daa branch: next-stable user: inithello date: 2013-03-21 15:01:49 summary: Make approved column blank if None. affected #: 1 file diff -r c5d124552c0b00b39f519ae491d4c64ed4472c08 -r b76683ec3daaf3058a93b4aff00aee4e1c5f9331 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -123,7 +123,8 @@ def get_value( self, trans, grid, repository ): rval = '' for review in repository.reviews: - rval += '%s<br/>' % review.approved + if review.approved: + rval += '%s<br/>' % review.approved return rval title = "All reviewed repositories" https://bitbucket.org/galaxy/galaxy-central/commits/cd766b639144/ changeset: cd766b639144 user: inithello date: 2013-03-21 15:02:13 summary: Merged in changes from next-stable. affected #: 1 file diff -r deb9b395f110750fa8e069a7b0ac5c494b67e985 -r cd766b6391448acae0574fcf240b4cf5c55d340e lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -123,7 +123,8 @@ def get_value( self, trans, grid, repository ): rval = '' for review in repository.reviews: - rval += '%s<br/>' % review.approved + if review.approved: + rval += '%s<br/>' % review.approved return rval title = "All reviewed repositories" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Mar '13

21 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5d124552c0b/ changeset: c5d124552c0b branch: next-stable user: inithello date: 2013-03-21 14:51:51 summary: Add columns for rating and approval status to repositories with reviews grid. affected #: 3 files diff -r 8910b01b8addcc3967b46206be1d0518629dbdf9 -r c5d124552c0b00b39f519ae491d4c64ed4472c08 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -3,6 +3,7 @@ from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import SelectField, CheckboxField from sqlalchemy.sql.expression import func +from galaxy.model.orm import and_ from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP import tool_shed.util.shed_util_common as suc @@ -315,7 +316,9 @@ if flushed: # Update the repository rating value to be the average of all component review ratings. average_rating = trans.sa_session.query( func.avg( trans.model.ComponentReview.table.c.rating ) ) \ - .filter( trans.model.ComponentReview.table.c.repository_review_id == review.id ) \ + .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == review.id, + trans.model.ComponentReview.table.c.deleted == False, + trans.model.ComponentReview.table.c.approved != trans.model.ComponentReview.approved_states.NA ) ) \ .scalar() review.rating = int( average_rating ) trans.sa_session.add( review ) diff -r 8910b01b8addcc3967b46206be1d0518629dbdf9 -r c5d124552c0b00b39f519ae491d4c64ed4472c08 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -71,6 +71,7 @@ class WithoutReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): # Restrict the options to revisions that have not yet been reviewed. repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review( repository, reviewed=False ) @@ -96,6 +97,35 @@ rval += '%s</a> | ' % user.username rval = rval.rstrip( ' | ' ) return rval + + + class RatingColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository ): + rval = '' + for review in repository.reviews: + if review.rating: + for index in range( 1, 6 ): + rval += '<input ' + rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) + rval += 'type="radio" ' + rval += 'class="community_rating_star star" ' + rval += 'disabled="disabled" ' + rval += 'value="%s" ' % str( review.rating ) + if review.rating > ( index - 0.5 ) and review.rating < ( index + 0.5 ): + rval += 'checked="checked" ' + rval += '/>' + rval += '<br/>' + return rval + + class ApprovedColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository ): + rval = '' + for review in repository.reviews: + rval += '%s<br/>' % review.approved + return rval + title = "All reviewed repositories" model_class = model.Repository template='/webapps/tool_shed/repository_review/grid.mako' @@ -105,10 +135,11 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), + RepositoryGrid.UserColumn( "Owner", attach_popup=False ), WithReviewsRevisionColumn( "Reviewed revisions" ), - WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoryGrid.UserColumn( "Owner", attach_popup=False ), - ReviewersColumn( "Reviewers", attach_popup=False ) + ReviewersColumn( "Reviewers", attach_popup=False ), + RatingColumn( "Rating", attach_popup=False ), + ApprovedColumn( "Approved", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[ 0 ] ], @@ -253,13 +284,16 @@ def get_value( self, trans, grid, review ): if review.rating: - rval = '<input ' - rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) - rval += 'type="radio" ' - rval += 'class="community_rating_star star" ' - rval += 'disabled="disabled" ' - rval += 'value="%s"' % str( review.rating ) - rval += '/>' + for index in range( 1, 6 ): + rval = '<input ' + rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) + rval += 'type="radio" ' + rval += 'class="community_rating_star star" ' + rval += 'disabled="disabled" ' + rval += 'value="%s" ' % str( review.rating ) + if review.rating > ( index - 0.5 ) and review.rating < ( index + 0.5 ): + rval += 'checked="checked" ' + rval += '/>' return rval return '' diff -r 8910b01b8addcc3967b46206be1d0518629dbdf9 -r c5d124552c0b00b39f519ae491d4c64ed4472c08 lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -8,6 +8,8 @@ ( 'Yes', trans.model.ComponentReview.approved_states.YES ) ] if for_component: options.append( ( 'Not applicable', trans.model.ComponentReview.approved_states.NA ) ) + if selected_value is None: + selected_value = trans.model.ComponentReview.approved_states.NA select_field = SelectField( name=name ) for option_tup in options: selected = selected_value and option_tup[ 1 ] == selected_value https://bitbucket.org/galaxy/galaxy-central/commits/deb9b395f110/ changeset: deb9b395f110 user: inithello date: 2013-03-21 14:52:57 summary: Merge in changes from next-stable affected #: 3 files diff -r 2a19abf0f450adbae1cc119abe3e50edbf05a18d -r deb9b395f110750fa8e069a7b0ac5c494b67e985 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -3,6 +3,7 @@ from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import SelectField, CheckboxField from sqlalchemy.sql.expression import func +from galaxy.model.orm import and_ from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP import tool_shed.util.shed_util_common as suc @@ -315,7 +316,9 @@ if flushed: # Update the repository rating value to be the average of all component review ratings. average_rating = trans.sa_session.query( func.avg( trans.model.ComponentReview.table.c.rating ) ) \ - .filter( trans.model.ComponentReview.table.c.repository_review_id == review.id ) \ + .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == review.id, + trans.model.ComponentReview.table.c.deleted == False, + trans.model.ComponentReview.table.c.approved != trans.model.ComponentReview.approved_states.NA ) ) \ .scalar() review.rating = int( average_rating ) trans.sa_session.add( review ) diff -r 2a19abf0f450adbae1cc119abe3e50edbf05a18d -r deb9b395f110750fa8e069a7b0ac5c494b67e985 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -71,6 +71,7 @@ class WithoutReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): # Restrict the options to revisions that have not yet been reviewed. repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review( repository, reviewed=False ) @@ -96,6 +97,35 @@ rval += '%s</a> | ' % user.username rval = rval.rstrip( ' | ' ) return rval + + + class RatingColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository ): + rval = '' + for review in repository.reviews: + if review.rating: + for index in range( 1, 6 ): + rval += '<input ' + rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) + rval += 'type="radio" ' + rval += 'class="community_rating_star star" ' + rval += 'disabled="disabled" ' + rval += 'value="%s" ' % str( review.rating ) + if review.rating > ( index - 0.5 ) and review.rating < ( index + 0.5 ): + rval += 'checked="checked" ' + rval += '/>' + rval += '<br/>' + return rval + + class ApprovedColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository ): + rval = '' + for review in repository.reviews: + rval += '%s<br/>' % review.approved + return rval + title = "All reviewed repositories" model_class = model.Repository template='/webapps/tool_shed/repository_review/grid.mako' @@ -105,10 +135,11 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), + RepositoryGrid.UserColumn( "Owner", attach_popup=False ), WithReviewsRevisionColumn( "Reviewed revisions" ), - WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoryGrid.UserColumn( "Owner", attach_popup=False ), - ReviewersColumn( "Reviewers", attach_popup=False ) + ReviewersColumn( "Reviewers", attach_popup=False ), + RatingColumn( "Rating", attach_popup=False ), + ApprovedColumn( "Approved", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[ 0 ] ], @@ -253,13 +284,16 @@ def get_value( self, trans, grid, review ): if review.rating: - rval = '<input ' - rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) - rval += 'type="radio" ' - rval += 'class="community_rating_star star" ' - rval += 'disabled="disabled" ' - rval += 'value="%s"' % str( review.rating ) - rval += '/>' + for index in range( 1, 6 ): + rval = '<input ' + rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) + rval += 'type="radio" ' + rval += 'class="community_rating_star star" ' + rval += 'disabled="disabled" ' + rval += 'value="%s" ' % str( review.rating ) + if review.rating > ( index - 0.5 ) and review.rating < ( index + 0.5 ): + rval += 'checked="checked" ' + rval += '/>' return rval return '' diff -r 2a19abf0f450adbae1cc119abe3e50edbf05a18d -r deb9b395f110750fa8e069a7b0ac5c494b67e985 lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -8,6 +8,8 @@ ( 'Yes', trans.model.ComponentReview.approved_states.YES ) ] if for_component: options.append( ( 'Not applicable', trans.model.ComponentReview.approved_states.NA ) ) + if selected_value is None: + selected_value = trans.model.ComponentReview.approved_states.NA select_field = SelectField( name=name ) for option_tup in options: selected = selected_value and option_tup[ 1 ] == selected_value Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 21 Mar '13

21 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8910b01b8add/ changeset: 8910b01b8add branch: next-stable user: jgoecks date: 2013-03-21 13:50:38 summary: Update Cuffdiff wrapper to use working directory rather than a temporary directory. affected #: 1 file diff -r 765739078002bc1ea5b1384a605b810e9a0bc640 -r 8910b01b8addcc3967b46206be1d0518629dbdf9 tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -118,16 +118,13 @@ raise Exception except: sys.stdout.write( 'Could not determine Cuffdiff version\n' ) - - # Make temp directory for output. - tmp_output_dir = tempfile.mkdtemp() # If doing bias correction, set/link to sequence file. if options.do_bias_correction: if options.ref_file != 'None': # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. - seq_path = os.path.join( tmp_output_dir, "ref.fa" ) + seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. @@ -189,9 +186,9 @@ # Run command. try: - tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() tmp_stderr.close() @@ -213,31 +210,26 @@ raise Exception, stderr # check that there are results in the output file - if len( open( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), 'rb' ).read().strip() ) == 0: + if len( open( "isoforms.fpkm_tracking", 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cuffdiff. ' + str( e ) ) - # Copy output files from tmp directory to specified files. + # Copy output files to specified files. try: - try: - shutil.copyfile( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), options.isoforms_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) - except Exception, e: - stop_err( 'Error in cuffdiff:\n' + str( e ) ) - finally: - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + shutil.copyfile( "isoforms.fpkm_tracking", options.isoforms_fpkm_tracking_output ) + shutil.copyfile( "genes.fpkm_tracking", options.genes_fpkm_tracking_output ) + shutil.copyfile( "cds.fpkm_tracking", options.cds_fpkm_tracking_output ) + shutil.copyfile( "tss_groups.fpkm_tracking", options.tss_groups_fpkm_tracking_output ) + shutil.copyfile( "isoform_exp.diff", options.isoforms_exp_output ) + shutil.copyfile( "gene_exp.diff", options.genes_exp_output ) + shutil.copyfile( "tss_group_exp.diff", options.tss_groups_exp_output ) + shutil.copyfile( "splicing.diff", options.splicing_diff_output ) + shutil.copyfile( "cds.diff", options.cds_diff_output ) + shutil.copyfile( "cds_exp.diff", options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( "promoters.diff", options.promoters_diff_output ) + except Exception, e: + stop_err( 'Error in cuffdiff:\n' + str( e ) ) if __name__=="__main__": __main__() https://bitbucket.org/galaxy/galaxy-central/commits/2a19abf0f450/ changeset: 2a19abf0f450 user: jgoecks date: 2013-03-21 13:51:10 summary: Merge in next-stable affected #: 1 file diff -r 353a42c6aa216db1603d565ec7565d1cae68c050 -r 2a19abf0f450adbae1cc119abe3e50edbf05a18d tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -118,16 +118,13 @@ raise Exception except: sys.stdout.write( 'Could not determine Cuffdiff version\n' ) - - # Make temp directory for output. - tmp_output_dir = tempfile.mkdtemp() # If doing bias correction, set/link to sequence file. if options.do_bias_correction: if options.ref_file != 'None': # Sequence data from history. # Create symbolic link to ref_file so that index will be created in working directory. - seq_path = os.path.join( tmp_output_dir, "ref.fa" ) + seq_path = "ref.fa" os.symlink( options.ref_file, seq_path ) else: # Sequence data from loc file. @@ -189,9 +186,9 @@ # Run command. try: - tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_name = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_name, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() tmp_stderr.close() @@ -213,31 +210,26 @@ raise Exception, stderr # check that there are results in the output file - if len( open( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), 'rb' ).read().strip() ) == 0: + if len( open( "isoforms.fpkm_tracking", 'rb' ).read().strip() ) == 0: raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' except Exception, e: stop_err( 'Error running cuffdiff. ' + str( e ) ) - # Copy output files from tmp directory to specified files. + # Copy output files to specified files. try: - try: - shutil.copyfile( os.path.join( tmp_output_dir, "isoforms.fpkm_tracking" ), options.isoforms_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) - except Exception, e: - stop_err( 'Error in cuffdiff:\n' + str( e ) ) - finally: - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + shutil.copyfile( "isoforms.fpkm_tracking", options.isoforms_fpkm_tracking_output ) + shutil.copyfile( "genes.fpkm_tracking", options.genes_fpkm_tracking_output ) + shutil.copyfile( "cds.fpkm_tracking", options.cds_fpkm_tracking_output ) + shutil.copyfile( "tss_groups.fpkm_tracking", options.tss_groups_fpkm_tracking_output ) + shutil.copyfile( "isoform_exp.diff", options.isoforms_exp_output ) + shutil.copyfile( "gene_exp.diff", options.genes_exp_output ) + shutil.copyfile( "tss_group_exp.diff", options.tss_groups_exp_output ) + shutil.copyfile( "splicing.diff", options.splicing_diff_output ) + shutil.copyfile( "cds.diff", options.cds_diff_output ) + shutil.copyfile( "cds_exp.diff", options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( "promoters.diff", options.promoters_diff_output ) + except Exception, e: + stop_err( 'Error in cuffdiff:\n' + str( e ) ) if __name__=="__main__": __main__() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Clean up the tool shed api methods.
by commits-noreply＠bitbucket.org 20 Mar '13

20 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/353a42c6aa21/ changeset: 353a42c6aa21 user: greg date: 2013-03-20 20:09:43 summary: Clean up the tool shed api methods. affected #: 4 files diff -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab -r 353a42c6aa216db1603d565ec7565d1cae68c050 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -1,24 +1,21 @@ +import logging import tool_shed.util.shed_util_common as suc from galaxy import web, util from galaxy.web.base.controller import BaseAPIController -from galaxy.web.framework.helpers import is_true - -import pkg_resources -pkg_resources.require( "Routes" ) -import routes -import logging log = logging.getLogger( __name__ ) + class RepositoriesController( BaseAPIController ): """RESTful controller for interactions with repositories in the Tool Shed.""" + @web.expose_api def index( self, trans, deleted=False, **kwd ): """ - GET /api/repository_revisions + GET /api/repositories Displays a collection (list) of repositories. """ - rval = [] + repository_dicts = [] deleted = util.string_as_bool( deleted ) try: query = trans.sa_session.query( trans.app.model.Repository ) \ @@ -28,30 +25,37 @@ for repository in query: value_mapper={ 'id' : trans.security.encode_id( repository.id ), 'user_id' : trans.security.encode_id( repository.user_id ) } - item = repository.get_api_value( view='collection', value_mapper=value_mapper ) - item[ 'url' ] = web.url_for( 'repository_contents', repository_id=trans.security.encode_id( repository.id ) ) - rval.append( item ) + repository_dict = repository.get_api_value( view='collection', value_mapper=value_mapper ) + repository_dict[ 'url' ] = web.url_for( controller='repository_contents', + action='index', + repository_id=trans.security.encode_id( repository.id ) ) + repository_dicts.append( repository_dict ) + return repository_dicts except Exception, e: message = "Error in the Tool Shed repositories API in index: %s" % str( e ) log.error( message, exc_info=True ) trans.response.status = 500 return message - return rval + @web.expose_api def show( self, trans, id, **kwd ): """ GET /api/repositories/{encoded_repository_id} Displays information about a repository in the Tool Shed. + + :param id: the encoded id of the `Repository` object """ try: repository = suc.get_repository_in_tool_shed( trans, id ) value_mapper={ 'id' : trans.security.encode_id( repository.id ), 'user_id' : trans.security.encode_id( repository.user_id ) } - repository_data = repository.get_api_value( view='element', value_mapper=value_mapper ) - repository_data[ 'contents_url' ] = web.url_for( 'repository_contents', repository_id=id ) + repository_dict = repository.get_api_value( view='element', value_mapper=value_mapper ) + repository_dict[ 'url' ] = web.url_for( controller='repository_contents', + action='index', + repository_id=trans.security.encode_id( repository.id ) ) + return repository_dict except Exception, e: message = "Error in the Tool Shed repositories API in show: %s" % str( e ) log.error( message, exc_info=True ) trans.response.status = 500 return message - return repository_data diff -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab -r 353a42c6aa216db1603d565ec7565d1cae68c050 lib/galaxy/webapps/tool_shed/api/repository_contents.py --- a/lib/galaxy/webapps/tool_shed/api/repository_contents.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_contents.py @@ -3,33 +3,31 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController -import pkg_resources -pkg_resources.require( "Routes" ) -import routes - log = logging.getLogger( __name__ ) + class RepositoryContentsController( BaseAPIController ): + @web.expose_api def index( self, trans, **kwd ): """ - GET /api/repositories/{encoded_repository_id}/contents + GET /api/repositories/{encoded_repository_id} Displays a collection (dictionary) of repository contents. - :param repository_id: an encoded id string of the `Repository` to inspect + :param repository_id: the encoded id of the `Repository` object """ - rval = [] - repository_id = kwd.get( 'repository_id', None ) try: + repository_id = kwd[ 'repository_id' ] repository = suc.get_repository_in_tool_shed( trans, repository_id ) - value_mapper={ 'id' : repository_id, + value_mapper={ 'id' : trans.security.encode_id( repository.id ), 'user_id' : trans.security.encode_id( repository.user_id ) } repository_dict = repository.as_dict( value_mapper ) - repository_dict[ 'url' ] = web.url_for( 'repository_contents', repository_id=repository_id ) - rval.append( repository_dict ) + repository_dict[ 'url' ] = web.url_for( controller='repository_contents', + action='index', + repository_id=repository_id ) + return repository_dict except Exception, e: message = "Error in the Tool Shed repository_contents API in index: %s" % str( e ) log.error( message, exc_info=True ) trans.response.status = 500 return message - return rval diff -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab -r 353a42c6aa216db1603d565ec7565d1cae68c050 lib/galaxy/webapps/tool_shed/api/repository_revision_contents.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revision_contents.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revision_contents.py @@ -1,14 +1,9 @@ import logging +from galaxy import web from galaxy.web.framework.helpers import time_ago -import tool_shed.util.shed_util_common as suc from tool_shed.util import metadata_util -from galaxy import web from galaxy.web.base.controller import BaseAPIController -import pkg_resources -pkg_resources.require( "Routes" ) -import routes - log = logging.getLogger( __name__ ) def default_value_mapper( trans, repository_metadata ): @@ -18,25 +13,27 @@ value_mapper[ 'time_last_tested' ] = time_ago( repository_metadata.time_last_tested ) return value_mapper + class RepositoryRevisionContentsController( BaseAPIController ): + @web.expose_api def index( self, trans, **kwd ): """ - GET /api/repository_revisions/{encoded_repository_metadata_id}/contents + GET /api/repository_revisions/{encoded_repository_metadata_id} Displays a collection (dictionary) of repository_metadata contents. - :param repository_metadata_id: an encoded id string of the `RepositoryMetadata` to inspect + :param repository_metadata_id: the encoded id of the `RepositoryMetadata` object """ - rval = [] - repository_metadata_id = kwd.get( 'repository_metadata_id', None ) try: + repository_metadata_id = kwd.get( 'repository_metadata_id', None ) repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_dict = repository_metadata.as_dict( value_mapper=default_value_mapper( trans, repository_metadata ) ) - repository_dict[ 'url' ] = web.url_for( 'repository_revision_contents', repository_metadata_id=repository_metadata_id ) - rval.append( repository_dict ) + repository_dict[ 'url' ] = web.url_for( controller='repository_revision_contents', + action='index', + repository_metadata_id=repository_metadata_id ) + return repository_dict except Exception, e: - message = "Error in the Tool Shed repository_revision_contents API in index: %s" % str( e ) + message = "Error in the Tool Shed repository_revision_contents API in index: %s" % str( e ) log.error( message, exc_info=True ) trans.response.status = 500 return message - return rval diff -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab -r 353a42c6aa216db1603d565ec7565d1cae68c050 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -1,16 +1,9 @@ -import datetime +import datetime, logging from galaxy.web.framework.helpers import time_ago -import tool_shed.util.shed_util_common as suc from tool_shed.util import metadata_util from galaxy import web, util -from galaxy.model.orm import and_, or_ +from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController -from galaxy.web.framework.helpers import is_true - -import pkg_resources -pkg_resources.require( "Routes" ) -import routes -import logging log = logging.getLogger( __name__ ) @@ -21,15 +14,17 @@ value_mapper[ 'time_last_tested' ] = time_ago( repository_metadata.time_last_tested ) return value_mapper + class RepositoryRevisionsController( BaseAPIController ): """RESTful controller for interactions with tool shed repository revisions.""" + @web.expose_api def index( self, trans, **kwd ): """ GET /api/repository_revisions Displays a collection (list) of repository revisions. """ - rval = [] + repository_metadata_dicts = [] # Build up an anded clause list of filters. clause_list = [] # Filter by downloadable if received. @@ -58,32 +53,40 @@ .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ .all() for repository_metadata in query: - item = repository_metadata.get_api_value( view='collection', - value_mapper=default_value_mapper( trans, repository_metadata ) ) - item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) - rval.append( item ) + repository_metadata_dict = repository_metadata.get_api_value( view='collection', + value_mapper=default_value_mapper( trans, repository_metadata ) ) + repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revision_contents', + action='index', + repository_metadata_id=trans.security.encode_id( repository_metadata.id ) ) + repository_metadata_dicts.append( repository_metadata_dict ) + return repository_metadata_dicts except Exception, e: - rval = "Error in the Tool Shed repository_revisions API in index: " + str( e ) - log.error( rval + ": %s" % str( e ) ) + message = "Error in the Tool Shed repository_revisions API in index: " + str( e ) + log.error( message, exc_info=True ) trans.response.status = 500 - return rval + return message + @web.expose_api def show( self, trans, id, **kwd ): """ GET /api/repository_revisions/{encoded_repository_metadata_id} Displays information about a repository_metadata record in the Tool Shed. + + :param id: the encoded id of the `RepositoryMetadata` object """ try: repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) - repository_data = repository_metadata.get_api_value( view='element', - value_mapper=default_value_mapper( trans, repository_metadata ) ) - repository_data[ 'contents_url' ] = web.url_for( 'repository_revision_contents', repository_metadata_id=id ) + repository_metadata_dict = repository_metadata.as_dict( value_mapper=default_value_mapper( trans, repository_metadata ) ) + repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revision_contents', + action='index', + repository_metadata_id=trans.security.encode_id( repository_metadata.id ) ) + return repository_metadata_dict except Exception, e: message = "Error in the Tool Shed repository_revisions API in show: %s" % str( e ) log.error( message, exc_info=True ) trans.response.status = 500 return message - return repository_data + @web.expose_api def update( self, trans, payload, **kwd ): """ @@ -110,6 +113,8 @@ log.error( message, exc_info=True ) trans.response.status = 500 return message - item = repository_metadata.as_dict( value_mapper=default_value_mapper( trans, repository_metadata ) ) - item[ 'url' ] = web.url_for( 'repository_revision', id=repository_metadata_id ) - return [ item ] + repository_metadata_dict = repository_metadata.as_dict( value_mapper=default_value_mapper( trans, repository_metadata ) ) + repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revision_contents', + action='index', + repository_metadata_id=trans.security.encode_id( repository_metadata.id ) ) + return repository_metadata_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Mar '13

20 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/765739078002/ changeset: 765739078002 branch: next-stable user: jgoecks date: 2013-03-20 18:18:13 summary: Simplify help text for eye icon. affected #: 4 files diff -r 6a80f6558febba87a6e32b9533256543597e8d30 -r 765739078002bc1ea5b1384a605b810e9a0bc640 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -219,7 +219,7 @@ displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); } else { - displayBtnData.title = _l( 'Display data in browser' ); + displayBtnData.title = _l( 'View data' ); displayBtnData.href = this.urls.display; } diff -r 6a80f6558febba87a6e32b9533256543597e8d30 -r 765739078002bc1ea5b1384a605b810e9a0bc640 templates/webapps/galaxy/root/alternate_history.mako --- a/templates/webapps/galaxy/root/alternate_history.mako +++ b/templates/webapps/galaxy/root/alternate_history.mako @@ -28,7 +28,7 @@ ## "You are over your disk ...w your allocated quota.", ## "Show deleted", ## "Show hidden", - ## "Display data in browser", + ## "View data", ## "Edit Attributes", ## "Download", ## "View details", @@ -60,7 +60,7 @@ # from history_common.mako 'Download', 'Display Data', - 'Display data in browser', + 'View data', 'Edit attributes', 'Delete', 'Job is waiting to run', diff -r 6a80f6558febba87a6e32b9533256543597e8d30 -r 765739078002bc1ea5b1384a605b810e9a0bc640 templates/webapps/galaxy/root/history_common.mako --- a/templates/webapps/galaxy/root/history_common.mako +++ b/templates/webapps/galaxy/root/history_common.mako @@ -98,7 +98,7 @@ %if data.purged: <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span> %else: - <a class="icon-button display tooltip" dataset_id="${dataset_id}" title='${_("Display data in browser")}' href="${display_url}" + <a class="icon-button display tooltip" dataset_id="${dataset_id}" title='${_("View data")}' href="${display_url}" %if for_editing: target="galaxy_main" %endif diff -r 6a80f6558febba87a6e32b9533256543597e8d30 -r 765739078002bc1ea5b1384a605b810e9a0bc640 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -305,7 +305,7 @@ hda : { ok: { tooltips : { - displayButton : 'Display data in browser', + displayButton : 'View data', editAttrButton : 'Edit Attributes', deleteButton : 'Delete' }, https://bitbucket.org/galaxy/galaxy-central/commits/fde3df1cfee9/ changeset: fde3df1cfee9 user: jgoecks date: 2013-03-20 18:22:43 summary: Merge in next-stable. affected #: 4 files diff -r 3b437901dab6efd84478a74c856206dfb96a7f81 -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -219,7 +219,7 @@ displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); } else { - displayBtnData.title = _l( 'Display data in browser' ); + displayBtnData.title = _l( 'View data' ); displayBtnData.href = this.urls.display; } diff -r 3b437901dab6efd84478a74c856206dfb96a7f81 -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab templates/webapps/galaxy/root/alternate_history.mako --- a/templates/webapps/galaxy/root/alternate_history.mako +++ b/templates/webapps/galaxy/root/alternate_history.mako @@ -28,7 +28,7 @@ ## "You are over your disk ...w your allocated quota.", ## "Show deleted", ## "Show hidden", - ## "Display data in browser", + ## "View data", ## "Edit Attributes", ## "Download", ## "View details", @@ -60,7 +60,7 @@ # from history_common.mako 'Download', 'Display Data', - 'Display data in browser', + 'View data', 'Edit attributes', 'Delete', 'Job is waiting to run', diff -r 3b437901dab6efd84478a74c856206dfb96a7f81 -r fde3df1cfee9e7fdf09ac4ad5e02e47623fb3eab templates/webapps/galaxy/root/history_common.mako --- a/templates/webapps/galaxy/root/history_common.mako +++ b/templates/webapps/galaxy/root/history_common.mako @@ -98,7 +98,7 @@ %if data.purged: <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span> %else: - <a class="icon-button display tooltip" dataset_id="${dataset_id}" title='${_("Display data in browser")}' href="${display_url}" + <a class="icon-button display tooltip" dataset_id="${dataset_id}" title='${_("View data")}' href="${display_url}" %if for_editing: target="galaxy_main" %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Mar '13

20 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6a80f6558feb/ changeset: 6a80f6558feb branch: next-stable user: jgoecks date: 2013-03-20 15:55:24 summary: Trackster fixes: (a) render bases/colors in Firefox; (b) make deletions black to avoid color conflicts with colored bases; (c) use group name for composite track. Modal fix: set maximum body height so that it does not overflow the bottom of the page. Pack scripts. affected #: 6 files diff -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 -r 6a80f6558febba87a6e32b9533256543597e8d30 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -173,6 +173,13 @@ // Fix min-width so that modal cannot shrink considerably if // new content is loaded. this.$body.css( "min-width", this.$body.width() ); + // Set max-height so that modal does not exceed window size. + // FIXME: this could perhaps be handled better using a container for the modal + // header-body-footer and setting max-height for the container. + this.$body.css( "max-height", + // 2* to provide buffer between bottom of modal and bottom of page. + $(window).height() - 2 * this.$dialog.offset().top - + this.$footer.outerHeight() - this.$header.outerHeight()); } // Callback on init if ( callback ) { diff -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 -r 6a80f6558febba87a6e32b9533256543597e8d30 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_paths.attributes.image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-2*this.$dialog.offset().top-this.$footer.outerHeight()-this.$header.outerHeight())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_paths.attributes.image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 -r 6a80f6558febba87a6e32b9533256543597e8d30 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 -r 6a80f6558febba87a6e32b9533256543597e8d30 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"FF00FF"}],saved_values:ac.prefs,onchange:function(){track.request_redraw(false,true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter 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class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. 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ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}else{aj=view.reference_track.data_manager.subset_entry(aj,af)}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var af=[];for(var ad=0;ad<this.drawables.length;ad++){af.push(this.drawables[ad].name)}var ae=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"}],saved_values:ac.prefs,onchange:function(){track.request_redraw(false,true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}else{aj=view.reference_track.data_manager.subset_entry(aj,af)}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 -r 6a80f6558febba87a6e32b9533256543597e8d30 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -845,7 +845,7 @@ base_offset += cig_len; break; case "D": // Deletion. - ctx.fillStyle = "red"; + ctx.fillStyle = "black"; ctx.fillRect(s_start, y_center + 4, s_end - s_start, 3); // TODO: is this true? No change in seq_offset because sequence not used when skipping. base_offset += cig_len; diff -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 -r 6a80f6558febba87a6e32b9533256543597e8d30 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -813,11 +813,10 @@ for (var i = 0; i < this.drawables.length; i++) { drawables_names.push(this.drawables[i].name); } - var new_track_name = "Composite Track of " + this.drawables.length + " tracks (" + drawables_names.join(", ") + ")"; // Replace this group with composite track. var composite_track = new CompositeTrack(this.view, this.view, { - name: new_track_name, + name: this.name, drawables: this.drawables }); var index = this.container.replace_drawable(this, composite_track, true); @@ -885,10 +884,10 @@ this.config = new DrawableConfig( { track: this, params: [ - { key: 'a_color', label: 'A Color', type: 'color', default_value: "FF0000" }, - { key: 'c_color', label: 'C Color', type: 'color', default_value: "00FF00" }, - { key: 'g_color', label: 'G Color', type: 'color', default_value: "0000FF" }, - { key: 't_color', label: 'T Color', type: 'color', default_value: "FF00FF" } + { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, + { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" }, + { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" }, + { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" } ], saved_values: obj_dict.prefs, onchange: function() { https://bitbucket.org/galaxy/galaxy-central/commits/3b437901dab6/ changeset: 3b437901dab6 user: jgoecks date: 2013-03-20 15:55:46 summary: Merge in next-stable affected #: 6 files diff -r c6503a2cc9a477f28337de575ce77e24ccb781d9 -r 3b437901dab6efd84478a74c856206dfb96a7f81 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -173,6 +173,13 @@ // Fix min-width so that modal cannot shrink considerably if // new content is loaded. this.$body.css( "min-width", this.$body.width() ); + // Set max-height so that modal does not exceed window size. + // FIXME: this could perhaps be handled better using a container for the modal + // header-body-footer and setting max-height for the container. + this.$body.css( "max-height", + // 2* to provide buffer between bottom of modal and bottom of page. + $(window).height() - 2 * this.$dialog.offset().top - + this.$footer.outerHeight() - this.$header.outerHeight()); } // Callback on init if ( callback ) { diff -r c6503a2cc9a477f28337de575ce77e24ccb781d9 -r 3b437901dab6efd84478a74c856206dfb96a7f81 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_paths.attributes.image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-2*this.$dialog.offset().top-this.$footer.outerHeight()-this.$header.outerHeight())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_paths.attributes.image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r c6503a2cc9a477f28337de575ce77e24ccb781d9 -r 3b437901dab6efd84478a74c856206dfb96a7f81 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r c6503a2cc9a477f28337de575ce77e24ccb781d9 -r 3b437901dab6efd84478a74c856206dfb96a7f81 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"FF00FF"}],saved_values:ac.prefs,onchange:function(){track.request_redraw(false,true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}else{aj=view.reference_track.data_manager.subset_entry(aj,af)}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var af=[];for(var ad=0;ad<this.drawables.length;ad++){af.push(this.drawables[ad].name)}var ae=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"}],saved_values:ac.prefs,onchange:function(){track.request_redraw(false,true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: 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ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running 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C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}else{aj=view.reference_track.data_manager.subset_entry(aj,af)}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r c6503a2cc9a477f28337de575ce77e24ccb781d9 -r 3b437901dab6efd84478a74c856206dfb96a7f81 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -845,7 +845,7 @@ base_offset += cig_len; break; case "D": // Deletion. - ctx.fillStyle = "red"; + ctx.fillStyle = "black"; ctx.fillRect(s_start, y_center + 4, s_end - s_start, 3); // TODO: is this true? No change in seq_offset because sequence not used when skipping. base_offset += cig_len; diff -r c6503a2cc9a477f28337de575ce77e24ccb781d9 -r 3b437901dab6efd84478a74c856206dfb96a7f81 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -813,11 +813,10 @@ for (var i = 0; i < this.drawables.length; i++) { drawables_names.push(this.drawables[i].name); } - var new_track_name = "Composite Track of " + this.drawables.length + " tracks (" + drawables_names.join(", ") + ")"; // Replace this group with composite track. var composite_track = new CompositeTrack(this.view, this.view, { - name: new_track_name, + name: this.name, drawables: this.drawables }); var index = this.container.replace_drawable(this, composite_track, true); @@ -885,10 +884,10 @@ this.config = new DrawableConfig( { track: this, params: [ - { key: 'a_color', label: 'A Color', type: 'color', default_value: "FF0000" }, - { key: 'c_color', label: 'C Color', type: 'color', default_value: "00FF00" }, - { key: 'g_color', label: 'G Color', type: 'color', default_value: "0000FF" }, - { key: 't_color', label: 'T Color', type: 'color', default_value: "FF00FF" } + { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, + { key: 'c_color', label: 'C Color', type: 'color', default_value: "#00FF00" }, + { key: 'g_color', label: 'G Color', type: 'color', default_value: "#0000FF" }, + { key: 't_color', label: 'T Color', type: 'color', default_value: "#FF00FF" } ], saved_values: obj_dict.prefs, onchange: function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Display an error message when cookies are blocked between the tool shed and galaxy.
by commits-noreply＠bitbucket.org 20 Mar '13

20 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8607202c00cc/ changeset: 8607202c00cc branch: next-stable user: inithello date: 2013-03-20 14:33:34 summary: Display an error message when cookies are blocked between the tool shed and galaxy. affected #: 2 files diff -r c92d41cb71440de8564112e6e89a75598388268c -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -317,9 +317,9 @@ @web.expose def browse_valid_categories( self, trans, **kwd ): # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions. - galaxy_url = kwd.get( 'galaxy_url', None ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + kwd[ 'galaxy_url' ] = galaxy_url if 'f-free-text-search' in kwd: if kwd[ 'f-free-text-search' ] == 'All': # The user performed a search, then clicked the "x" to eliminate the search criteria. @@ -346,11 +346,14 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_repositories', **kwd ) ) + log.debug("CCC In browse_valid_categories, just before returning valid_category_grid, kwd: %s" % str( kwd )) return self.valid_category_grid( trans, **kwd ) @web.expose def browse_valid_repositories( self, trans, **kwd ): - galaxy_url = kwd.get( 'galaxy_url', None ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url: + kwd[ 'galaxy_url' ] = galaxy_url repository_id = kwd.get( 'id', None ) if 'f-free-text-search' in kwd: if 'f-Category.name' in kwd: @@ -359,8 +362,6 @@ category = suc.get_category_by_name( trans, category_name ) # Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method. kwd[ 'id' ] = trans.security.encode_id( category.id ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": @@ -423,7 +424,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -437,11 +438,14 @@ if from_update_manager: update = 'true' no_update = 'false' - else: + elif galaxy_url: # Start building up the url to redirect back to the calling Galaxy instance. url = suc.url_join( galaxy_url, 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) + else: + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: @@ -746,9 +750,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) if item_id: @@ -833,9 +835,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) if item_id: @@ -952,7 +952,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -1443,18 +1442,23 @@ changeset_revisions = kwd.get( 'changeset_revisions', None ) name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) - galaxy_url = kwd.get( 'galaxy_url', None ) if not repository_ids: repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_ids = trans.security.encode_id( repository.id ) - if not galaxy_url: - # If galaxy_url is not in the request, it had to have been stored in a cookie by the tool shed. - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - # Redirect back to local Galaxy to perform install. - url = suc.url_join( galaxy_url, - 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ - ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) - return trans.response.send_redirect( url ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url: + # Redirect back to local Galaxy to perform install. + url = suc.url_join( galaxy_url, + 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) + return trans.response.send_redirect( url ) + else: + message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + status = 'error' + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_valid_categories', + message=message, + status=status ) ) @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): @@ -1854,8 +1858,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) diff -r c92d41cb71440de8564112e6e89a75598388268c -r 8607202c00ccd5ecf6852a348e354b4d77f68d54 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -116,6 +116,7 @@ return False def changeset_is_valid( app, repository, changeset_revision ): + """Make sure a changeset hash is valid for a specified repository.""" repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) @@ -124,6 +125,7 @@ return False def clean_repository_clone_url( repository_clone_url ): + """Return a URL that can be used to clone a tool shed repository, eliminating the protocol and user if either exists.""" if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: # http://test@bx.psu.edu:9009/repos/some_username/column @@ -139,6 +141,7 @@ return tmp_url def clean_tool_shed_url( tool_shed_url ): + """Return a tool shed URL, eliminating the port if it exists.""" if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. return tool_shed_url.split( ':' )[ 0 ] @@ -186,6 +189,10 @@ def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ): + """ + Update a tool shed repository record i the Galaxy database with the new information received. If a record defined by the received tool shed, repository name + and owner does not exists, create a new record with the received information. + """ # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used # to be in the Galaxy distribution, but have been moved to the main Galaxy tool shed. log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) @@ -272,6 +279,7 @@ return sharable_url def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): + """Create and return an ElementTree tool Element.""" if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) else: @@ -429,6 +437,7 @@ return _ui def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): + """Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the combination of a name, owner and changeset revision.""" url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() @@ -448,6 +457,7 @@ return None, None def get_file_context_from_ctx( ctx, filename ): + """Return the mercurial file context for a specified file.""" # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario @@ -473,6 +483,7 @@ return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_named_tmpfile_from_ctx( ctx, filename, dir ): + """Return a named temporary file created from a specified file with a given name included in a repository changeset revision.""" filename = strip_path( filename ) for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) @@ -958,6 +969,14 @@ except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def handle_galaxy_url( trans, **kwd ): + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + else: + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + return galaxy_url + def open_repository_files_folder( trans, folder_path ): """Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy.""" try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Display an error message when cookies are blocked between the tool shed and galaxy.
by commits-noreply＠bitbucket.org 20 Mar '13

20 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c6503a2cc9a4/ changeset: c6503a2cc9a4 user: inithello date: 2013-03-20 14:33:34 summary: Display an error message when cookies are blocked between the tool shed and galaxy. affected #: 2 files diff -r 254f3e344235d8446adf5902d2e90567f5c34d6b -r c6503a2cc9a477f28337de575ce77e24ccb781d9 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -317,9 +317,9 @@ @web.expose def browse_valid_categories( self, trans, **kwd ): # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions. - galaxy_url = kwd.get( 'galaxy_url', None ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + kwd[ 'galaxy_url' ] = galaxy_url if 'f-free-text-search' in kwd: if kwd[ 'f-free-text-search' ] == 'All': # The user performed a search, then clicked the "x" to eliminate the search criteria. @@ -346,11 +346,14 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_repositories', **kwd ) ) + log.debug("CCC In browse_valid_categories, just before returning valid_category_grid, kwd: %s" % str( kwd )) return self.valid_category_grid( trans, **kwd ) @web.expose def browse_valid_repositories( self, trans, **kwd ): - galaxy_url = kwd.get( 'galaxy_url', None ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url: + kwd[ 'galaxy_url' ] = galaxy_url repository_id = kwd.get( 'id', None ) if 'f-free-text-search' in kwd: if 'f-Category.name' in kwd: @@ -359,8 +362,6 @@ category = suc.get_category_by_name( trans, category_name ) # Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method. kwd[ 'id' ] = trans.security.encode_id( category.id ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": @@ -423,7 +424,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -437,11 +438,14 @@ if from_update_manager: update = 'true' no_update = 'false' - else: + elif galaxy_url: # Start building up the url to redirect back to the calling Galaxy instance. url = suc.url_join( galaxy_url, 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) + else: + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: @@ -746,9 +750,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) if item_id: @@ -833,9 +835,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) if item_id: @@ -952,7 +952,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -1443,18 +1442,23 @@ changeset_revisions = kwd.get( 'changeset_revisions', None ) name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) - galaxy_url = kwd.get( 'galaxy_url', None ) if not repository_ids: repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_ids = trans.security.encode_id( repository.id ) - if not galaxy_url: - # If galaxy_url is not in the request, it had to have been stored in a cookie by the tool shed. - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - # Redirect back to local Galaxy to perform install. - url = suc.url_join( galaxy_url, - 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ - ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) - return trans.response.send_redirect( url ) + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url: + # Redirect back to local Galaxy to perform install. + url = suc.url_join( galaxy_url, + 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) + return trans.response.send_redirect( url ) + else: + message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + status = 'error' + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_valid_categories', + message=message, + status=status ) ) @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): @@ -1854,8 +1858,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) diff -r 254f3e344235d8446adf5902d2e90567f5c34d6b -r c6503a2cc9a477f28337de575ce77e24ccb781d9 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -116,6 +116,7 @@ return False def changeset_is_valid( app, repository, changeset_revision ): + """Make sure a changeset hash is valid for a specified repository.""" repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) @@ -124,6 +125,7 @@ return False def clean_repository_clone_url( repository_clone_url ): + """Return a URL that can be used to clone a tool shed repository, eliminating the protocol and user if either exists.""" if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: # http://test@bx.psu.edu:9009/repos/some_username/column @@ -139,6 +141,7 @@ return tmp_url def clean_tool_shed_url( tool_shed_url ): + """Return a tool shed URL, eliminating the port if it exists.""" if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. return tool_shed_url.split( ':' )[ 0 ] @@ -186,6 +189,10 @@ def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ): + """ + Update a tool shed repository record i the Galaxy database with the new information received. If a record defined by the received tool shed, repository name + and owner does not exists, create a new record with the received information. + """ # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used # to be in the Galaxy distribution, but have been moved to the main Galaxy tool shed. log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) @@ -272,6 +279,7 @@ return sharable_url def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): + """Create and return an ElementTree tool Element.""" if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) else: @@ -429,6 +437,7 @@ return _ui def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): + """Send a request to the tool shed to retrieve the ctx_rev for a repository defined by the combination of a name, owner and changeset revision.""" url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() @@ -448,6 +457,7 @@ return None, None def get_file_context_from_ctx( ctx, filename ): + """Return the mercurial file context for a specified file.""" # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario @@ -473,6 +483,7 @@ return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) def get_named_tmpfile_from_ctx( ctx, filename, dir ): + """Return a named temporary file created from a specified file with a given name included in a repository changeset revision.""" filename = strip_path( filename ) for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) @@ -958,6 +969,14 @@ except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def handle_galaxy_url( trans, **kwd ): + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + else: + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + return galaxy_url + def open_repository_files_folder( trans, folder_path ): """Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy.""" try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Add option to specify extra tool data for the automated install and test framework.
by commits-noreply＠bitbucket.org 19 Mar '13

19 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/254f3e344235/ changeset: 254f3e344235 user: inithello date: 2013-03-19 21:59:27 summary: Add option to specify extra tool data for the automated install and test framework. affected #: 1 file diff -r 2d8fcb2f456caaee4ff804ea4a01893a8a3accae -r 254f3e344235d8446adf5902d2e90567f5c34d6b test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -98,6 +98,15 @@ </toolbox> ''' +# If we have a tool_data_table_conf.test.xml, set it up to be loaded when the UniverseApplication is started. +# This allows one to specify a set of tool data that is used exclusively for testing, and not loaded into any +# Galaxy instance. By default, this will be in the test-data-repo/location directory generated by buildbot_setup.sh. +if os.path.exists( 'tool_data_table_conf.test.xml' ): + additional_tool_data_tables = 'tool_data_table_conf.test.xml' + additional_tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_EXTRA_TOOL_DATA_PATH', os.path.join( 'test-data-repo', 'location' ) ) +else: + additional_tool_data_tables = None + additional_tool_data_path = None # And set up a blank tool_data_table_conf.xml and shed_tool_data_table_conf.xml. tool_data_table_conf_xml_template = '''<?xml version="1.0"?><tables> @@ -463,6 +472,12 @@ log.info( "The embedded Galaxy application is running on %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) log.info( "Repositories will be installed from the tool shed at %s" % galaxy_tool_shed_url ) success = False + # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. + if additional_tool_data_tables: + app.tool_data_tables.add_new_entries_from_config_file( config_filename=additional_tool_data_tables, + tool_data_path=additional_tool_data_path, + shed_tool_data_table_config=None, + persist=False ) # Initialize some variables for the summary that will be printed to stdout. repositories_tested = 0 repositories_passed = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Add missing import in upload controller.
by commits-noreply＠bitbucket.org 19 Mar '13

19 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c92d41cb7144/ changeset: c92d41cb7144 branch: next-stable user: inithello date: 2013-03-19 17:26:33 summary: Add missing import in upload controller. affected #: 1 file diff -r 6d5efc862967ffe5b520a3c6eccdb7549ca01171 -r c92d41cb71440de8564112e6e89a75598388268c lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -2,6 +2,8 @@ from galaxy.web.base.controller import BaseUIController from galaxy import web, util from galaxy.datatypes import checkers +from galaxy.util import json + import tool_shed.util.shed_util_common as suc from tool_shed.util import metadata_util, repository_dependency_util, tool_dependency_util, tool_util Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Add missing import in upload controller.
by commits-noreply＠bitbucket.org 19 Mar '13

19 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d8fcb2f456c/ changeset: 2d8fcb2f456c user: inithello date: 2013-03-19 17:26:33 summary: Add missing import in upload controller. affected #: 1 file diff -r e409e7af84be829a91e630d983ec7009b20907bc -r 2d8fcb2f456caaee4ff804ea4a01893a8a3accae lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -2,6 +2,8 @@ from galaxy.web.base.controller import BaseUIController from galaxy import web, util from galaxy.datatypes import checkers +from galaxy.util import json + import tool_shed.util.shed_util_common as suc from tool_shed.util import metadata_util, repository_dependency_util, tool_dependency_util, tool_util Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix tool tip for compute quality statistics
by commits-noreply＠bitbucket.org 19 Mar '13

19 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e409e7af84be/ changeset: e409e7af84be user: guerler date: 2013-03-19 17:04:24 summary: Fix tool tip for compute quality statistics affected #: 1 file diff -r 9b74ad2ccd683258bd1e0f6ed282118f6f55bb15 -r e409e7af84be829a91e630d983ec7009b20907bc tools/solid_tools/solid_qual_stats.xml --- a/tools/solid_tools/solid_qual_stats.xml +++ b/tools/solid_tools/solid_qual_stats.xml @@ -23,7 +23,7 @@ .. class:: infomark -**TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** tool. +**TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** and **Nucleotides Distribution** tool. ----- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: tool tip fix for fastq summary and sorter
by commits-noreply＠bitbucket.org 19 Mar '13

19 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b74ad2ccd68/ changeset: 9b74ad2ccd68 user: guerler date: 2013-03-19 16:50:03 summary: tool tip fix for fastq summary and sorter affected #: 2 files diff -r a9cd08b97ec0e4a65f5d2ab62f6bff2599765cfb -r 9b74ad2ccd683258bd1e0f6ed282118f6f55bb15 tools/fastq/fastq_stats.xml --- a/tools/fastq/fastq_stats.xml +++ b/tools/fastq/fastq_stats.xml @@ -18,7 +18,7 @@ .. class:: infomark -**TIP:** This statistics report can be used as input for the **Boxplot** and **Nucleotides Distribution** tools. +**TIP:** This statistics report can be used as input for the **Boxplot** tools. ----- diff -r a9cd08b97ec0e4a65f5d2ab62f6bff2599765cfb -r 9b74ad2ccd683258bd1e0f6ed282118f6f55bb15 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -65,69 +65,67 @@ </test></tests><help> +.. class:: infomark - .. class:: infomark +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* - **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* +----- + +**Syntax** + +This tool sorts the dataset on any number of columns in either ascending or descending order. + +* Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. +* Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). - ----- - - **Syntax** - - This tool sorts the dataset on any number of columns in either ascending or descending order. - - * Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. - * Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). - - ----- - - **Examples** - - The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting. - - Sorting the following:: - - Q d 7 II jhu 45 - A kk 4 I h 111 - Pd p 1 ktY WS 113 - A g 10 H ZZ 856 - A edf 4 tw b 234 - BBB rt 10 H ZZ 100 - A rew 10 d b 1111 - C sd 19 YH aa 10 - Hah c 23 ver bb 467 - MN gtr 1 a X 32 - N j 9 a T 205 - BBB rrf 10 b Z 134 - odfr ws 6 Weg dew 201 - C f 3 WW SW 34 - A jhg 4 I b 345 - Pd gf 7 Gthe de 567 - rS hty 90 YY LOp 89 - A g 10 H h 43 - A g 4 I h 500 - - on columns 1 (alpha), 3 (num), and 6 (num) in ascending order will yield:: - - A kk 4 I h 111 - A edf 4 tw b 234 - A jhg 4 I b 345 - A g 4 I h 500 - A g 10 H h 43 - A g 10 H ZZ 856 - A rew 10 d b 1111 - BBB rt 10 H ZZ 100 - BBB rrf 10 b Z 134 - C f 3 WW SW 34 - C sd 19 YH aa 10 - Hah c 23 ver bb 467 - MN gtr 1 a X 32 - N j 9 a T 205 - odfr ws 6 Weg dew 201 - Pd p 1 ktY WS 113 - Pd gf 7 Gthe de 567 - Q d 7 II jhu 45 - rS hty 90 YY LOp 89 - +----- + +**Examples** + +The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting. + +Sorting the following:: + + Q d 7 II jhu 45 + A kk 4 I h 111 + Pd p 1 ktY WS 113 + A g 10 H ZZ 856 + A edf 4 tw b 234 + BBB rt 10 H ZZ 100 + A rew 10 d b 1111 + C sd 19 YH aa 10 + Hah c 23 ver bb 467 + MN gtr 1 a X 32 + N j 9 a T 205 + BBB rrf 10 b Z 134 + odfr ws 6 Weg dew 201 + C f 3 WW SW 34 + A jhg 4 I b 345 + Pd gf 7 Gthe de 567 + rS hty 90 YY LOp 89 + A g 10 H h 43 + A g 4 I h 500 + +on columns 1 (alpha), 3 (num), and 6 (num) in ascending order will yield:: + + A kk 4 I h 111 + A edf 4 tw b 234 + A jhg 4 I b 345 + A g 4 I h 500 + A g 10 H h 43 + A g 10 H ZZ 856 + A rew 10 d b 1111 + BBB rt 10 H ZZ 100 + BBB rrf 10 b Z 134 + C f 3 WW SW 34 + C sd 19 YH aa 10 + Hah c 23 ver bb 467 + MN gtr 1 a X 32 + N j 9 a T 205 + odfr ws 6 Weg dew 201 + Pd p 1 ktY WS 113 + Pd gf 7 Gthe de 567 + Q d 7 II jhu 45 + rS hty 90 YY LOp 89 </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Mar '13

19 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a9cd08b97ec0/ changeset: a9cd08b97ec0 user: inithello date: 2013-03-19 15:56:35 summary: Remove reference to shed_util_common in remove_tool_dependency method. affected #: 1 file diff -r 5bfe49c7983310e13f0cc8bc5857ff39da6936a5 -r a9cd08b97ec0e4a65f5d2ab62f6bff2599765cfb lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -319,7 +319,7 @@ def remove_tool_dependency( trans, tool_dependency ): dependency_install_dir = tool_dependency.installation_directory( trans.app ) - removed, error_message = suc.remove_tool_dependency_installation_directory( dependency_install_dir ) + removed, error_message = remove_tool_dependency_installation_directory( dependency_install_dir ) if removed: tool_dependency.status = trans.model.ToolDependency.installation_status.UNINSTALLED tool_dependency.error_message = None https://bitbucket.org/galaxy/galaxy-central/commits/6d5efc862967/ changeset: 6d5efc862967 branch: next-stable user: inithello date: 2013-03-19 15:56:35 summary: Remove reference to shed_util_common in remove_tool_dependency method. affected #: 1 file diff -r f1f1d36479082ab77ac5cf67832f09cbbf70c65a -r 6d5efc862967ffe5b520a3c6eccdb7549ca01171 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -319,7 +319,7 @@ def remove_tool_dependency( trans, tool_dependency ): dependency_install_dir = tool_dependency.installation_directory( trans.app ) - removed, error_message = suc.remove_tool_dependency_installation_directory( dependency_install_dir ) + removed, error_message = remove_tool_dependency_installation_directory( dependency_install_dir ) if removed: tool_dependency.status = trans.model.ToolDependency.installation_status.UNINSTALLED tool_dependency.error_message = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: upload: dont refresh history panel from upload_async_message as tool_executed.mako will already do this.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5bfe49c79833/ changeset: 5bfe49c79833 user: carlfeberhard date: 2013-03-18 22:46:21 summary: upload: dont refresh history panel from upload_async_message as tool_executed.mako will already do this. affected #: 1 file diff -r ef7f32032b55995657d15af8b173613461dd49af -r 5bfe49c7983310e13f0cc8bc5857ff39da6936a5 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -312,4 +312,4 @@ <p><b>Please do not use your browser\'s "stop" or "reload" buttons until the upload is complete, or it may be interrupted.</b></p><p>You may safely continue to use Galaxy while the upload is in progress. Using "stop" and "reload" on pages other than Galaxy is also safe.</p> """ - return trans.show_message( msg, refresh_frames='history' ) + return trans.show_message( msg ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/579c0b64e463/ changeset: 579c0b64e463 user: jgoecks date: 2013-03-18 22:17:14 summary: When possible, move HDA attribute addition from controller method down to model. affected #: 2 files diff -r a7bd59964f5053133897e6e7b89065a608e11d03 -r 579c0b64e463918691bb38e718af8d70dd6f9fa7 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1516,6 +1516,11 @@ # other model classes. hda = self rval = dict( id = hda.id, + uuid = ( lambda uuid: str( uuid ) if uuid else None )( hda.dataset.uuid ), + history_id = hda.history.id, + hid = hda.hid, + file_ext = hda.ext, + peek = ( lambda hda: hda.display_peek() if hda.peek and hda.peek != 'no peek' else None )( hda ), model_class = self.__class__.__name__, name = hda.name, deleted = hda.deleted, diff -r a7bd59964f5053133897e6e7b89065a608e11d03 -r 579c0b64e463918691bb38e718af8d70dd6f9fa7 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -195,20 +195,16 @@ return "Not implemented." -#TODO: move these into model def get_hda_dict( trans, history, hda, for_editing ): hda_dict = hda.get_api_value( view='element' ) - hda_dict[ 'id' ] = trans.security.encode_id( hda.id ) - hda_dict[ 'history_id' ] = trans.security.encode_id( history.id ) - hda_dict[ 'hid' ] = hda.hid - - hda_dict[ 'file_ext' ] = hda.ext + # Add additional attributes that depend on trans can hence must be added here rather than at the model level. if trans.user_is_admin() or trans.app.config.expose_dataset_path: hda_dict[ 'file_name' ] = hda.file_name if not hda_dict[ 'deleted' ]: - hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), history_content_id = trans.security.encode_id( hda.id ) ) + hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), + history_content_id = trans.security.encode_id( hda.id ) ) can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) @@ -224,22 +220,14 @@ hda_dict[ 'display_apps' ] = get_display_apps( trans, hda ) hda_dict[ 'display_types' ] = get_old_display_applications( trans, hda ) - - if hda.dataset.uuid is None: - hda_dict['uuid'] = None - else: - hda_dict['uuid'] = str(hda.dataset.uuid) - hda_dict[ 'visualizations' ] = hda.get_visualizations() - if hda.peek and hda.peek != 'no peek': - hda_dict[ 'peek' ] = to_unicode( hda.display_peek() ) if hda.creating_job and hda.creating_job.tool_id: tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) if tool_used and tool_used.force_history_refresh: hda_dict[ 'force_history_refresh' ] = True - return hda_dict + return trans.security.encode_dict_ids( hda_dict ) def get_display_apps( trans, hda ): #TODO: make more straightforward (somehow) https://bitbucket.org/galaxy/galaxy-central/commits/c39687f63b9a/ changeset: c39687f63b9a user: jgoecks date: 2013-03-18 22:18:31 summary: Remove unused parameter. affected #: 1 file diff -r 579c0b64e463918691bb38e718af8d70dd6f9fa7 -r c39687f63b9afb75c56102ec89431997a586a656 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -67,7 +67,7 @@ if encoded_hda_id in ids: #TODO: share code with show try: - rval.append( get_hda_dict( trans, history, hda, for_editing=True ) ) + rval.append( get_hda_dict( trans, history, hda ) ) except Exception, exc: # don't fail entire list if hda err's, record and move on @@ -149,7 +149,7 @@ hda = self.get_history_dataset_association( trans, history, id, check_ownership=True, check_accessible=True ) - hda_dict = get_hda_dict( trans, history, hda, for_editing=True ) + hda_dict = get_hda_dict( trans, history, hda ) except Exception, e: msg = "Error in history API at listing dataset: %s" % ( str(e) ) @@ -195,7 +195,7 @@ return "Not implemented." -def get_hda_dict( trans, history, hda, for_editing ): +def get_hda_dict( trans, history, hda ): hda_dict = hda.get_api_value( view='element' ) # Add additional attributes that depend on trans can hence must be added here rather than at the model level. https://bitbucket.org/galaxy/galaxy-central/commits/ef7f32032b55/ changeset: ef7f32032b55 user: jgoecks date: 2013-03-18 22:38:31 summary: Move get_hda_dict and associated methods from history_contents controller to HDA mixin. Use get_hda_dict in datasets controller; this unifies the dataset dictionary returns by API controllers. affected #: 3 files diff -r c39687f63b9afb75c56102ec89431997a586a656 -r ef7f32032b55995657d15af8b173613461dd49af lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -6,12 +6,16 @@ import os import re import pkg_resources +import urllib pkg_resources.require("SQLAlchemy >= 0.4") +pkg_resources.require( "Routes" ) +import routes from sqlalchemy import func, and_, select from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError, HTTPNotImplemented, HTTPRequestRangeNotSatisfiable from galaxy import util, web +from gettext import gettext from galaxy.datatypes.interval import ChromatinInteractions from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException, MessageException from galaxy.security.validate_user_input import validate_publicname @@ -25,6 +29,11 @@ from galaxy.datatypes.data import Text +from galaxy.datatypes.display_applications import util as da_util +from galaxy.datatypes.metadata import FileParameter + +from galaxy.datatypes.display_applications.link_generator import get_display_app_link_generator + log = logging.getLogger( __name__ ) # States for passing messages @@ -322,6 +331,85 @@ return dataset.conversion_messages.PENDING return None + def get_hda_dict( self, trans, hda ): + hda_dict = hda.get_api_value( view='element' ) + history = hda.history + + # Add additional attributes that depend on trans can hence must be added here rather than at the model level. + if trans.user_is_admin() or trans.app.config.expose_dataset_path: + hda_dict[ 'file_name' ] = hda.file_name + + if not hda_dict[ 'deleted' ]: + hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), + history_content_id = trans.security.encode_id( hda.id ) ) + + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) + hda_dict[ 'api_type' ] = "file" + + if not( hda.purged or hda.deleted or hda.dataset.purged ): + meta_files = [] + for meta_type in hda.metadata.spec.keys(): + if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): + meta_files.append( dict( file_type=meta_type ) ) + if meta_files: + hda_dict[ 'meta_files' ] = meta_files + + hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) + hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + hda_dict[ 'visualizations' ] = hda.get_visualizations() + + if hda.creating_job and hda.creating_job.tool_id: + tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) + if tool_used and tool_used.force_history_refresh: + hda_dict[ 'force_history_refresh' ] = True + + return trans.security.encode_dict_ids( hda_dict ) + + def get_display_apps( self, trans, hda ): + #TODO: make more straightforward (somehow) + display_apps = [] + + def get_display_app_url( display_app_link, hda, trans ): + web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) + dataset_hash, user_hash = da_util.encode_dataset_user( trans, hda, None ) + return web_url_for( controller='dataset', + action="display_application", + dataset_id=dataset_hash, + user_id=user_hash, + app_name=urllib.quote_plus( display_app_link.display_application.id ), + link_name=urllib.quote_plus( display_app_link.id ) ) + + for display_app in hda.get_display_applications( trans ).itervalues(): + app_links = [] + for display_app_link in display_app.links.itervalues(): + app_links.append({ + 'target' : display_app_link.url.get( 'target_frame', '_blank' ), + 'href' : get_display_app_url( display_app_link, hda, trans ), + 'text' : gettext( display_app_link.name ) + }) + display_apps.append( dict( label=display_app.name, links=app_links ) ) + + return display_apps + + def get_old_display_applications( self, trans, hda ): + display_apps = [] + for display_app_name in hda.datatype.get_display_types(): + link_generator = get_display_app_link_generator( display_app_name ) + display_links = link_generator.generate_links( trans, hda ) + + app_links = [] + for display_name, display_link in display_links: + app_links.append({ + 'target' : '_blank', + 'href' : display_link, + 'text' : display_name + }) + if app_links: + display_apps.append( dict( label=hda.datatype.get_display_label( display_app_name ), links=app_links ) ) + + return display_apps + class UsesLibraryMixin: diff -r c39687f63b9afb75c56102ec89431997a586a656 -r ef7f32032b55995657d15af8b173613461dd49af lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -50,8 +50,11 @@ elif data_type == 'genome_data': rval = self._get_genome_data( trans, dataset, kwd.get('dbkey', None) ) else: - # Default: return dataset as API value. - rval = dataset.get_api_value() + # Default: return dataset as dict. + if hda_ldda == 'hda': + rval = self.get_hda_dict( trans, dataset ) + else: + rval = dataset.get_api_value() except Exception, e: rval = "Error in dataset API at listing contents: " + str( e ) diff -r c39687f63b9afb75c56102ec89431997a586a656 -r ef7f32032b55995657d15af8b173613461dd49af lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -2,24 +2,12 @@ API operations on the contents of a history. """ import logging -import urllib -from gettext import gettext from galaxy import web from galaxy.web.base.controller import BaseAPIController, url_for from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin, UsesHistoryMixin from galaxy.web.base.controller import UsesLibraryMixin, UsesLibraryMixinItems -from galaxy.web.framework.helpers import to_unicode -from galaxy.datatypes.display_applications import util -from galaxy.datatypes.metadata import FileParameter - -from galaxy.datatypes.display_applications.link_generator import get_display_app_link_generator - -import pkg_resources -pkg_resources.require( "Routes" ) -import routes - log = logging.getLogger( __name__ ) class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, @@ -67,7 +55,7 @@ if encoded_hda_id in ids: #TODO: share code with show try: - rval.append( get_hda_dict( trans, history, hda ) ) + rval.append( self.get_hda_dict( trans, hda ) ) except Exception, exc: # don't fail entire list if hda err's, record and move on @@ -149,7 +137,7 @@ hda = self.get_history_dataset_association( trans, history, id, check_ownership=True, check_accessible=True ) - hda_dict = get_hda_dict( trans, history, hda ) + hda_dict = self.get_hda_dict( trans, hda ) except Exception, e: msg = "Error in history API at listing dataset: %s" % ( str(e) ) @@ -194,81 +182,3 @@ trans.response.status = 403 return "Not implemented." - -def get_hda_dict( trans, history, hda ): - hda_dict = hda.get_api_value( view='element' ) - - # Add additional attributes that depend on trans can hence must be added here rather than at the model level. - if trans.user_is_admin() or trans.app.config.expose_dataset_path: - hda_dict[ 'file_name' ] = hda.file_name - - if not hda_dict[ 'deleted' ]: - hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), - history_content_id = trans.security.encode_id( hda.id ) ) - - can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) - hda_dict[ 'api_type' ] = "file" - - if not( hda.purged or hda.deleted or hda.dataset.purged ): - meta_files = [] - for meta_type in hda.metadata.spec.keys(): - if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): - meta_files.append( dict( file_type=meta_type ) ) - if meta_files: - hda_dict[ 'meta_files' ] = meta_files - - hda_dict[ 'display_apps' ] = get_display_apps( trans, hda ) - hda_dict[ 'display_types' ] = get_old_display_applications( trans, hda ) - hda_dict[ 'visualizations' ] = hda.get_visualizations() - - if hda.creating_job and hda.creating_job.tool_id: - tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) - if tool_used and tool_used.force_history_refresh: - hda_dict[ 'force_history_refresh' ] = True - - return trans.security.encode_dict_ids( hda_dict ) - -def get_display_apps( trans, hda ): - #TODO: make more straightforward (somehow) - display_apps = [] - - def get_display_app_url( display_app_link, hda, trans ): - web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) - dataset_hash, user_hash = util.encode_dataset_user( trans, hda, None ) - return web_url_for( controller='dataset', - action="display_application", - dataset_id=dataset_hash, - user_id=user_hash, - app_name=urllib.quote_plus( display_app_link.display_application.id ), - link_name=urllib.quote_plus( display_app_link.id ) ) - - for display_app in hda.get_display_applications( trans ).itervalues(): - app_links = [] - for display_app_link in display_app.links.itervalues(): - app_links.append({ - 'target' : display_app_link.url.get( 'target_frame', '_blank' ), - 'href' : get_display_app_url( display_app_link, hda, trans ), - 'text' : gettext( display_app_link.name ) - }) - display_apps.append( dict( label=display_app.name, links=app_links ) ) - - return display_apps - -def get_old_display_applications( trans, hda ): - display_apps = [] - for display_app_name in hda.datatype.get_display_types(): - link_generator = get_display_app_link_generator( display_app_name ) - display_links = link_generator.generate_links( trans, hda ) - - app_links = [] - for display_name, display_link in display_links: - app_links.append({ - 'target' : '_blank', - 'href' : display_link, - 'text' : display_name - }) - if app_links: - display_apps.append( dict( label=hda.datatype.get_display_label( display_app_name ), links=app_links ) ) - - return display_apps Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Reference the right app.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1f1d3647908/ changeset: f1f1d3647908 branch: next-stable user: inithello date: 2013-03-18 20:51:04 summary: Reference the right app. affected #: 1 file diff -r 7b5f97700fdc8286db3e5ed6b6425127694ca42f -r f1f1d36479082ab77ac5cf67832f09cbbf70c65a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -399,7 +399,7 @@ tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) - tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) + tool_util.copy_sample_files( trans.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Reference the right app.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7bd59964f50/ changeset: a7bd59964f50 user: inithello date: 2013-03-18 20:51:04 summary: Reference the right app. affected #: 1 file diff -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda -r a7bd59964f5053133897e6e7b89065a608e11d03 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -399,7 +399,7 @@ tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) - tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) + tool_util.copy_sample_files( trans.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: browser tests: refactoring, add api module
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f19741fdb9a6/ changeset: f19741fdb9a6 user: carlfeberhard date: 2013-03-18 20:14:22 summary: browser tests: refactoring, add api module affected #: 14 files diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -175,15 +175,20 @@ if from_ld_id: try: ld = self.get_library_dataset( trans, from_ld_id, check_ownership=False, check_accessible=False ) - assert type( ld ) is trans.app.model.LibraryDataset, "Library content id ( %s ) is not a dataset" % from_ld_id + assert type( ld ) is trans.app.model.LibraryDataset, ( + "Library content id ( %s ) is not a dataset" % from_ld_id ) + except AssertionError, e: trans.response.status = 400 return str( e ) + except Exception, e: return str( e ) + hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) trans.sa_session.flush() return hda.get_api_value() + else: # TODO: implement other "upload" methods here. trans.response.status = 403 diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -68,15 +68,10 @@ }); // ------------------------------------------------------------------- check the empty history for well formedness -// grab the history frame bounds for mouse later tests -spaceghost.then( function(){ - historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); - //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); -}); - spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ this.test.comment( 'history panel for anonymous user, new history' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ + + this.withHistoryPanel( function(){ this.test.comment( "frame should have proper url and title: 'History'" ); this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); @@ -103,15 +98,12 @@ 'Message contains "' + emptyMsgStr + '"' ); this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); - // mouse over to find tooltip - this.historypanel.hoverOver( nameSelector, function testingHover(){ - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); - }, historyFrameInfo ); + this.historypanel.hoverOver( nameSelector ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); this.test.comment( 'name should NOT be editable when clicked by anon-user' ); - this.assertDoesntHaveClass( nameSelector, editableTextClass, - "Name field is not classed as editable text" ); + this.assertDoesntHaveClass( nameSelector, editableTextClass, "Name field is not classed as editable text" ); this.click( nameSelector ); this.test.assertDoesntExist( editableTextInput, "Clicking on name does not create an input" ); }); @@ -120,12 +112,13 @@ // ------------------------------------------------------------------- anon user can upload file spaceghost.then( function testAnonUpload(){ this.test.comment( 'anon-user should be able to upload files' ); + spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + this.debug( 'uploaded HDA info: ' + this.jsonStr( this.quickInfo( _uploadInfo.hdaElement ) ) ); var hasHda = _uploadInfo.hdaElement, hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.hdaElement.text ); testUploadInfo = _uploadInfo; }); }); @@ -134,19 +127,18 @@ this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is not visible' ); }); - // ------------------------------------------------------------------- anon user can run tool on file // ------------------------------------------------------------------- anon user registers/logs in -> same history spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.test.comment( 'anon-user should login and be associated with previous history' ); - this.test.comment( 'anon-user should login and be associated with previous history' ); var loggedInAs = spaceghost.user.loggedInAs(); this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.name, testUploadInfo.hid ); + this.historypanel.waitForHdas( function(){ + var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.hdaElement.text ); this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); if( hdaInfo ){ this.test.assert( testUploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, @@ -155,17 +147,18 @@ }); }); +// ------------------------------------------------------------------- logs out -> new history spaceghost.user.logout(); spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.test.comment( 'logging out should create a new, anonymous history' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ + + this.historypanel.waitForHdas( function(){ this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, 'Message contains "' + emptyMsgStr + '"' ); }); }); - // =================================================================== spaceghost.run( function(){ this.test.done(); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -73,7 +73,7 @@ debug = False # bit of a hack - this is the beginning of the last string when capserjs --verbose=true --logLevel=debug # use this to get subprocess to stop waiting for output - casper_done_str = '# Tests complete' + casper_done_str = '# Stopping' # convert js test results to unittest.TestResults results_adapter = None #CasperJsonToUnittestResultsConverter() @@ -209,7 +209,8 @@ js_test_results = json.loads( results ) failures = js_test_results[ 'testResults' ][ 'failures' ] assert len( failures ) == 0, ( - "Some assertions failed in the headless browser tests (see the log for details)" ) + "%d assertions failed in the headless browser tests" %( len( failures ) ) + + " (see the log for details)" ) # ---------------------------------------------------------------- TestCase overrides def setUp( self ): @@ -299,10 +300,12 @@ # ==================================================================== TESTCASE EXAMPLE # these could be broken out into other py files - shouldn't be necc. ATM class Test_01_User( CasperJSTestCase ): - """TestCase that uses javascript and a headless browser to test dynamic pages. + """Tests for the Galaxy user centered functionality: + registration, login, etc. """ def test_10_registration( self ): - """User registration tests: register new user, logout, attempt bad registrations. + """User registration tests: + register new user, logout, attempt bad registrations. """ # all keywords will be compiled into a single JSON obj and passed to the server #self.run_js_script( 'registration-tests.js', @@ -331,7 +334,7 @@ class Test_03_HistoryPanel( CasperJSTestCase ): - """(Minimal) casperjs tests for tools. + """Tests for History fetching, rendering, and modeling. """ def test_00_history_panel( self ): """Test history panel basics (controls, structure, refresh, history options menu, etc.). @@ -339,13 +342,18 @@ self.run_js_script( 'history-panel-tests.js' ) def test_10_anonymous_histories( self ): + """Test history options button. + """ + self.run_js_script( 'history-options-tests.js' ) + + def test_20_anonymous_histories( self ): """Test history panel basics with an anonymous user. """ self.run_js_script( 'anon-history-tests.js' ) class Test_04_HDAs( CasperJSTestCase ): - """(Minimal) casperjs tests for tools. + """Tests for HistoryDatasetAssociation fetching, rendering, and modeling. """ def test_00_HDA_states( self ): """Test structure rendering of HDAs in all the possible HDA states diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -55,17 +55,10 @@ // start a new user spaceghost.user.loginOrRegisterUser( email, password ); -// grab the history frame bounds for later mouse tests -spaceghost.then( function(){ - historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); - //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); -}); - // upload a file spaceghost.then( function upload(){ spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ testUploadInfo = _uploadInfo; - this.info( 'testUploadInfo:' + this.jsonStr( testUploadInfo ) ); }); }); @@ -73,13 +66,12 @@ // =================================================================== TEST HELPERS //NOTE: to be called with fn.call( spaceghost, ... ) -function testTitle( hdaSelector, hid, name ){ - var titleSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.title, - titleShouldBe = hid + ': ' + name; +function testTitle( hdaSelector, name ){ + var titleSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.title; this.test.assertVisible( titleSelector, 'HDA title is visible' ); - this.test.assertSelectorHasText( titleSelector, titleShouldBe, - 'HDA has proper hid and title' ); + this.test.assertSelectorHasText( titleSelector, name, + 'HDA contains name (' + name + '): ' + this.fetchText( titleSelector ) ); } function testTitleButtonStructure( hdaSelector, shouldHaveTheseButtons ){ @@ -87,28 +79,9 @@ shouldHaveTheseButtons = shouldHaveTheseButtons || [ 'display', 'edit', 'delete' ]; var hdaDbId = this.getElementAttribute( hdaSelector, 'id' ).split( '-' )[1], - buttonsArea = hdaSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons, - buttons = { - // this seems backwards -> TODO: move buttonsArea concat into loop below, move this data to historypanel.data - display : { - nodeName : this.historypanel.data.text.hda.ok.nodeNames.displayButton, - selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.displayButton, - tooltip : this.historypanel.data.text.hda.ok.tooltips.displayButton, - hrefTpl : this.historypanel.data.text.hda.ok.hrefs.displayButton - }, - edit : { - nodeName : this.historypanel.data.text.hda.ok.nodeNames.editAttrButton, - selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.editAttrButton, - tooltip : this.historypanel.data.text.hda.ok.tooltips.editAttrButton, - hrefTpl : this.historypanel.data.text.hda.ok.hrefs.editAttrButton - }, - 'delete' : { - nodeName : this.historypanel.data.text.hda.ok.nodeNames.deleteButton, - selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.deleteButton, - tooltip : this.historypanel.data.text.hda.ok.tooltips.deleteButton, - hrefTpl : this.historypanel.data.text.hda.ok.hrefs.deleteButton - } - }; + buttonsArea = hdaSelector + ' ' + this.historypanel.data.selectors.hda.titleButtonArea, + buttons = this.historypanel.data.hdaTitleButtons; + this.test.assertVisible( buttonsArea, 'Button area is visible' ); for( var i=0; i<shouldHaveTheseButtons.length; i++ ){ @@ -123,7 +96,7 @@ this.test.assertVisible( button.selector, buttonName + ' button is visible' ); var buttonElement = this.getElementInfo( button.selector ); - this.debug( 'buttonElement:' + this.jsonStr( buttonElement ) ); + this.debug( 'buttonElement:' + this.jsonStr( this.quickInfo( buttonElement ) ) ); // should be an anchor this.test.assert( buttonElement.nodeName === button.nodeName, @@ -135,12 +108,13 @@ this.assertTextContains( href, hrefShouldBe, buttonName + ' has proper href (' + hrefShouldBe + '): ' + href ); - this.historypanel.hoverOver( button.selector, function testingHover(){ - var tooltipText = button.tooltip; - this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); - this.test.assertSelectorHasText( tooltipSelector, tooltipText, - buttonName + ' button has tooltip text: "' + tooltipText + '"' ); - }, historyFrameInfo ); + this.historypanel.hoverOver( button.selector ); + var tooltipText = button.tooltip; + this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); + this.test.assertSelectorHasText( tooltipSelector, tooltipText, + buttonName + ' button has tooltip text: "' + tooltipText + '"' ); + // clear the tooltip + this.page.sendEvent( 'mouseover', 0, 0 ); } } @@ -185,6 +159,7 @@ this.test.comment( 'Primary action buttons div should exist and be visible' ); this.test.assertExists( buttonsSelector, 'Primary action buttons div exists' ); this.test.assertVisible( buttonsSelector, 'Primary action buttons div is visible' ); + //TODO: ... } function testSecondaryActionButtons( hdaSelector ){ @@ -193,6 +168,7 @@ this.test.comment( 'Secondary action buttons div should exist and be visible' ); this.test.assertExists( buttonsSelector, 'Secondary action buttons div exists' ); this.test.assertVisible( buttonsSelector, 'Secondary action buttons div is visible' ); + //TODO: ... } function testPeek( hdaSelector, expectedPeekArray ){ @@ -239,112 +215,97 @@ // =================================================================== TESTS // ------------------------------------------------------------------- ok state -spaceghost.then( function checkOkState(){ +spaceghost.withHistoryPanel( function(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.test.assertVisible( uploadSelector, 'HDA is visible' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.test.assertVisible( uploadSelector, 'HDA is visible' ); - this.test.comment( 'should have the proper state class' ); - this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, - 'HDA has ok state class' ); + this.test.comment( 'should have the proper state class' ); + this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, + 'HDA has ok state class' ); - // since we're using css there's no great way to test state icon (.state-icon is empty) + // since we're using css there's no great way to test state icon (.state-icon is empty) - this.test.comment( 'should have proper title and hid' ); - testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); + this.test.comment( 'should have proper title and hid' ); + testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); - this.test.comment( 'should have all of the three, main buttons' ); - testTitleButtonStructure.call( spaceghost, uploadSelector ); + this.test.comment( 'should have all of the three, main buttons' ); + testTitleButtonStructure.call( spaceghost, uploadSelector ); - this.test.comment( 'body is not visible before clicking the hda title' ); - var body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; - this.test.assertNotVisible( body, 'body is not visible' ); + this.test.comment( 'body is not visible before clicking the hda title' ); + var body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; + this.test.assertNotVisible( body, 'body is not visible' ); - this.test.comment( 'clicking the hda title should expand its body' ); - var hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; - this.click( hdaTitle ); - this.wait( 500, function(){ + this.test.comment( 'clicking the hda title should expand its body' ); + this.historypanel.thenExpandHda( uploadSelector, function(){ + // ugh. + this.jumpToHistory( function(){ testExpandedBody.call( spaceghost, uploadSelector, summaryShouldBeArray, infoShouldBe, false ); }); }); }); +// restore to collapsed +spaceghost.then( function(){ + this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; -// restore to collapsed -spaceghost.then( function collapseOkState(){ - this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id, - hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; - body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; - - this.click( hdaTitle ); - this.wait( 500, function(){ - this.test.assertNotVisible( body, 'body is not visible' ); - }); + spaceghost.historypanel.thenCollapseHda( uploadSelector, function collapseOkState(){ + this.test.assertNotVisible( uploadSelector + ' ' + this.historypanel.data.selectors.hda.body, + 'body is not visible' ); }); }); +// ------------------------------------------------------------------- new state +spaceghost.withHistoryPanel( function(){ + // set state directly through model, wait for re-render + //TODO: not ideal to test this + this.evaluate( function(){ + return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'new' ); + }); + this.wait( 1000, function(){ + this.test.comment( 'HDAs in the "new" state should be well formed' ); -// ------------------------------------------------------------------- new state -spaceghost.then( function checkNewState(){ - this.test.comment( 'HDAs in the "new" state should be well formed' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.test.assertVisible( uploadSelector, 'HDA is visible' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - // set state directly through model - //TODO: not ideal - this.evaluate( function(){ - return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'new' ); - }); - // wait for re-render - this.wait( 500, function(){ - var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.test.assertVisible( uploadSelector, 'HDA is visible' ); + // should have proper title and hid + testTitle.call( spaceghost, uploadSelector, testUploadInfo.filename ); - // should have proper title and hid - testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); + this.test.comment( 'new HDA should have the new state class' ); + this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], + 'HDA has new state class' ); - this.test.comment( 'new HDA should have the new state class' ); - this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], - 'HDA has new state class' ); + this.test.comment( 'new HDA should NOT have any of the three, main buttons' ); + var buttonSelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons + ' a'; + this.test.assertDoesntExist( buttonSelector, 'No display, edit, or delete buttons' ); - this.test.comment( 'new HDA should NOT have any of the three, main buttons' ); - var buttonSelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons + ' a'; - this.test.assertDoesntExist( buttonSelector, 'No display, edit, or delete buttons' ); + this.test.comment( 'clicking the title of the new HDA will expand the body' ); - this.test.comment( 'clicking the title of the new HDA will expand the body' ); - var hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; - this.click( hdaTitle ); - this.wait( 500, function(){ - var bodySelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; - this.test.assertVisible( bodySelector, 'HDA body is visible (after expanding)' ); + this.historypanel.thenExpandHda( uploadSelector, function(){ + var bodySelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; + this.test.assertVisible( bodySelector, 'HDA body is visible (after expanding)' ); - var expectedBodyText = 'This is a new dataset'; - this.test.comment( 'the body should have the text: ' + expectedBodyText ); - this.test.assertSelectorHasText( bodySelector, expectedBodyText, - 'HDA body has text: ' + expectedBodyText ); - - // restore to collapsed - this.click( hdaTitle ); - }); + var expectedBodyText = 'This is a new dataset'; + this.test.comment( 'the body should have the text: ' + expectedBodyText ); + this.test.assertSelectorHasText( bodySelector, expectedBodyText, + 'HDA body has text: ' + expectedBodyText ); }); }); }); // restore state, collapse -spaceghost.then( function revertStateAndCollapse(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ +spaceghost.withHistoryPanel( function revertStateAndCollapse(){ + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + + this.historypanel.thenCollapseHda( uploadSelector, function(){ this.evaluate( function(){ return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'ok' ); }); - this.wait( 500, function(){ - var hdaTitle = '#' + testUploadInfo.hdaElement.attributes.id - + ' ' + this.historypanel.data.selectors.hda.title; - this.click( hdaTitle ); - }); }); + this.wait( 1000 ); }); - +/* +*/ // =================================================================== spaceghost.run( function(){ diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/history-options-tests.js --- /dev/null +++ b/test/casperjs/history-options-tests.js @@ -0,0 +1,145 @@ +// have to handle errors here - or phantom/casper won't bail but _HANG_ +try { + var utils = require( 'utils' ), + xpath = require( 'casper' ).selectXPath, + format = utils.format, + + //...if there's a better way - please let me know, universe + scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + spaceghost.start(); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + +// =================================================================== +/* TODO: + possibly break this file up +*/ +// =================================================================== globals and helpers +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; + spaceghost.info( 'Will use fixtureData.testUser: ' + email ); +} + +// selectors and labels +var includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; + +// local +var filepathToUpload = '../../test-data/1.txt', + testUploadInfo = {}; + + +// =================================================================== TESTS +// ------------------------------------------------------------------- set up +// start a new user +spaceghost.user.loginOrRegisterUser( email, password ); + +spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ + testUploadInfo = _uploadInfo; +}); + +// ------------------------------------------------------------------- history options menu structure +//NOTE: options menu should be functionally tested elsewhere +spaceghost.historypanel.waitForHdas().then( function checkHistoryOptions(){ + this.test.comment( 'History options icon should be in place and menu should have the proper structure' ); + + // check the button and icon + this.test.assertExists( this.historyoptions.data.selectors.button, "Found history options button" ); + this.test.assertVisible( this.historyoptions.data.selectors.button, "History options button is visible" ); + this.test.assertVisible( this.historyoptions.data.selectors.buttonIcon, "History options icon is visible" ); + + // open the menu + this.click( this.historyoptions.data.selectors.button ); + this.test.assertVisible( this.historyoptions.data.selectors.menu, + "Menu is visible when options button is clicked" ); + + // check the options + var historyOptions = this.historyoptions.data.labels.options; + for( var optionKey in historyOptions ){ + if( historyOptions.hasOwnProperty( optionKey ) ){ + var optionLabel = historyOptions[ optionKey ]; + this.test.assertVisible( this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ), + 'Option label is visible: ' + optionLabel ); + } + } + + // clear the menu + this.click( 'body' ); + this.test.assertNotVisible( this.historyoptions.data.selectors.menu, + "Clicking away from the menu closes it" ); +}); + +// ------------------------------------------------------------------- options allow showing/hiding deleted hdas +spaceghost.then( function(){ + this.test.comment( 'Deleting HDA' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + + this.historypanel.deleteHda( uploadSelector, function(){ + this.test.assertNotExists( uploadSelector, "Deleted HDA is NOT in the DOM" ); + }); +}); + +spaceghost.then( function(){ + this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + + this.historyoptions.includeDeleted( function(){ + this.test.assertExists( uploadSelector, + "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); + this.test.assertVisible( uploadSelector, + "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); + }); +}); + +spaceghost.then( function(){ + this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); + + this.historyoptions.excludeDeleted( function(){ + this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, + "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); + }); + // undelete the uploaded file + this.historypanel.undeleteHda( '#' + testUploadInfo.hdaElement.attributes.id ); +}); + +// ------------------------------------------------------------------- hidden hdas aren't shown +// ------------------------------------------------------------------- history options allows showing hidden hdas +// can't test this yet w/o a way to make hdas hidden thru the ui or api + + +// ------------------------------------------------------------------- history options collapses all expanded hdas +spaceghost.then( function(){ + this.historypanel.thenExpandHda( '#' + testUploadInfo.hdaElement.attributes.id ); +}); +spaceghost.then( function(){ + this.test.comment( 'History option collapses all expanded hdas' ); + + this.historyoptions.collapseExpanded( function(){ + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.withHistoryPanel( function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); + }); + }); +}); + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -72,177 +72,164 @@ // ------------------------------------------------------------------- set up // start a new user spaceghost.user.loginOrRegisterUser( email, password ); -//??: why is a reload needed here? If we don't, loggedInAs === '' ... -spaceghost.thenOpen( spaceghost.baseUrl, function(){ - var loggedInAs = spaceghost.user.loggedInAs(); - this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); + +// ------------------------------------------------------------------- check structure of empty history +spaceghost.thenOpen( spaceghost.baseUrl ).historypanel.waitForHdas( function(){ + this.test.comment( 'history panel with a new, empty history should be well formed' ); + this.test.comment( "frame should have proper url and title: 'History'" ); + this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); + this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + + this.test.comment( "history subtitle should display size and size should be: " + initialSizeStr ); + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, + 'History subtitle has "' + initialSizeStr + '"' ); + + this.test.comment( "tags and annotation icons should be available" ); + this.test.assertExists( tagIconSelector, 'Tag icon button found' ); + this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); + + this.test.comment( "A message about the current history being empty should be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); + this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, + 'Message contains "' + emptyMsgStr + '"' ); }); -// grab the history frame bounds for later mouse tests -spaceghost.then( function(){ - historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); - //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); -}); +// ------------------------------------------------------------------- name editing +spaceghost.withHistoryPanel( function(){ + this.test.comment( 'history panel, editing the history name' ); -// ------------------------------------------------------------------- check structure of empty history -spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ - this.test.comment( 'history panel, new history' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( "frame should have proper url and title: 'History'" ); - this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); - this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + this.test.comment( 'name should have a tooltip with proper info on name editing' ); + this.historypanel.hoverOver( nameSelector ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); + // clear the tooltip + this.page.sendEvent( 'mousemove', -1, -1 ); - this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); - this.test.assertExists( nameSelector, nameSelector + ' exists' ); - this.test.assertVisible( nameSelector, 'History name is visible' ); - this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + this.test.comment( 'name should be create an input when clicked' ); + this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); + this.click( nameSelector ); + this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); - this.test.comment( "history subtitle should display size and size should be: " + initialSizeStr ); - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, - 'History subtitle has "' + initialSizeStr + '"' ); - - this.test.comment( "tags and annotation icons should be available" ); - this.test.assertExists( tagIconSelector, 'Tag icon button found' ); - this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); - - this.test.comment( "A message about the current history being empty should be displayed" ); - this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); - this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); - this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, - 'Message contains "' + emptyMsgStr + '"' ); + this.test.comment( 'name should be editable by entering keys and pressing enter' ); + //NOTE: casperjs.sendKeys adds a click before and a selector.blur after sending - won't work here + this.page.sendEvent( 'keypress', newHistoryName ); + this.page.sendEvent( 'keypress', this.page.event.key.Enter ); + // wait for send and re-render name + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after pressing enter" ); }); }); -// ------------------------------------------------------------------- name editing -spaceghost.then( function(){ - this.test.comment( 'history panel, editing the history name' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( 'name should have a tooltip with proper info on name editing' ); - var nameInfo = this.getElementInfo( nameSelector ); - this.page.sendEvent( 'mousemove', historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); +spaceghost.withHistoryPanel( function(){ + this.test.comment( 'name should revert if user clicks away while editing' ); - this.test.comment( 'name should be create an input when clicked' ); - this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); - this.click( nameSelector ); - this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); + this.click( nameSelector ); + this.page.sendEvent( 'keypress', "Woodchipper metagenomics, Fargo, ND" ); - this.test.comment( 'name should be editable by entering keys and pressing enter' ); - //NOTE: casperjs.sendKeys adds a click before and a selector.blur after sending - won't work here - this.page.sendEvent( 'keypress', newHistoryName ); - this.page.sendEvent( 'keypress', this.page.event.key.Enter ); - this.wait( 1000, function(){ - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInput, "Input disappears after pressing enter" ); - }); + this.page.sendEvent( 'mousedown', -1, -1 ); + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after clicking away" ); }); }); -spaceghost.then( function(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( 'name should revert if user clicks away while editing' ); - this.click( nameSelector ); - this.page.sendEvent( 'keypress', "Woodchipper metagenomics, Fargo, ND" ); - // click above the name input element - var inputInfo = this.getElementInfo( editableTextInput ); - this.page.sendEvent( 'mousedown', historyFrameInfo.x + inputInfo.x + 1, historyFrameInfo.y + inputInfo.y - 5 ); +spaceghost.withHistoryPanel( function(){ + this.test.comment( 'name should revert if user hits ESC while editing' ); - this.wait( 1000, function(){ - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInput, "Input disappears after clicking away" ); - }); - }); -}); -spaceghost.then( function(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( 'name should revert if user hits ESC while editing' ); - this.click( nameSelector ); - this.page.sendEvent( 'keypress', "Arsenic Bacteria" ); + this.click( nameSelector ); + this.page.sendEvent( 'keypress', "Arsenic Bacteria" ); - this.page.sendEvent( 'keypress', this.page.event.key.Escape ); - this.wait( 1000, function(){ - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInput, "Input disappears after hitting ESC" ); - }); + this.page.sendEvent( 'keypress', this.page.event.key.Escape ); + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after hitting ESC" ); }); }); // ------------------------------------------------------------------- check structure of NON empty history // upload file: 1.txt -spaceghost.then( function upload(){ +spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ this.test.comment( 'uploaded file should appear in history' ); - spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ - this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); - var hasHda = _uploadInfo.hdaElement, - hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; - this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); - testUploadInfo = _uploadInfo; - }); + + this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + var hasHda = _uploadInfo.hdaElement, + hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], + hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); + testUploadInfo = _uploadInfo; }); -spaceghost.then( function checkPanelStructure(){ +spaceghost.withHistoryPanel( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); - this.test.assertExists( nameSelector, nameSelector + ' exists' ); - this.test.assertVisible( nameSelector, 'History name is visible' ); - this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); - var onetxtFilesize = require( 'fs' ).size( this.options.scriptDir + filepathToUpload ), - expectedSubtitle = onetxtFilesize + ' bytes'; - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, - 'History subtitle has "' + expectedSubtitle + '"' ); + this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); + var onetxtFilesize = require( 'fs' ).size( this.options.scriptDir + filepathToUpload ), + expectedSubtitle = onetxtFilesize + ' bytes'; + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, + 'History subtitle has "' + expectedSubtitle + '": ' + this.fetchText( subtitleSelector ).trim() ); - this.test.comment( "tags and annotation icons should be available" ); - this.test.assertExists( tagIconSelector, 'Tag icon button found' ); - this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); + this.test.comment( "tags and annotation icons should be available" ); + this.test.assertExists( tagIconSelector, 'Tag icon button found' ); + this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); - this.test.comment( "A message about the current history being empty should NOT be displayed" ); - this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); - this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is NOT visible' ); - }); + this.test.comment( "A message about the current history being empty should NOT be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is NOT visible' ); }); // ------------------------------------------------------------------- tags // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.then( function openTags(){ +spaceghost.withHistoryPanel( function openTags(){ this.test.comment( 'tag area should open when the history panel tag icon is clicked' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.mouseEvent( 'click', tagIconSelector ); - this.wait( 1000, function(){ - this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); - }); + + this.click( tagIconSelector ); + this.wait( 1000, function(){ + this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); + }); +}); +spaceghost.withHistoryPanel( function closeAnnotation(){ + this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); + + this.click( tagIconSelector ); + this.wait( 1000, function(){ + this.test.assertNotVisible( tagAreaSelector, 'Tag area is now hidden' ); }); }); // ------------------------------------------------------------------- annotation // keeping this light here - better for it's own test file //TODO: check tooltips -spaceghost.then( function openAnnotation(){ +spaceghost.withHistoryPanel( function openAnnotation(){ this.test.comment( 'annotation area should open when the history panel annotation icon is clicked' ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.mouseEvent( 'click', annoIconSelector ); - this.wait( 1000, function(){ - this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); - }); + + this.click( annoIconSelector ); + this.wait( 1000, function(){ + this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); }); }); -spaceghost.then( function closeAnnotation(){ +spaceghost.withHistoryPanel( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); - this.withFrame( spaceghost.data.selectors.frames.history, function bler(){ - this.mouseEvent( 'click', annoIconSelector ); - this.wait( 1000, function(){ - this.test.assertNotVisible( annoAreaSelector, 'Tag area is now hidden' ); - }); + + this.click( annoIconSelector ); + this.wait( 1000, function(){ + this.test.assertNotVisible( annoAreaSelector, 'Annotation area is now hidden' ); }); }); @@ -261,96 +248,16 @@ }); }); -// ------------------------------------------------------------------- history options menu structure -//NOTE: options menu should be functionally tested elsewhere -spaceghost.then( function historyOptions(){ - this.test.comment( 'History options icon should be in place and menu should have the proper structure' ); - - // check the button and icon - this.test.assertExists( this.historyoptions.data.selectors.button, "Found history options button" ); - this.test.assertVisible( this.historyoptions.data.selectors.button, "History options button is visible" ); - this.test.assertVisible( this.historyoptions.data.selectors.buttonIcon, "History options icon is visible" ); - - // open the menu - this.click( this.historyoptions.data.selectors.button ); - this.test.assertVisible( this.historyoptions.data.selectors.menu, - "Menu is visible when options button is clicked" ); - - // check the options - for( var optionKey in this.historyoptions.data.labels.options ){ - if( this.historyoptions.data.labels.options.hasOwnProperty( optionKey ) ){ - var optionLabel = this.historyoptions.data.labels.options[ optionKey ], - optionXpath = this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ); - this.test.assertVisible( optionXpath, 'Option label is visible: ' + optionLabel ); - } - } -}); - -// ------------------------------------------------------------------- deleted hdas aren't in the dom -spaceghost.then( function(){ - this.test.comment( 'deleted hdas shouldn\'t be in the history panel DOM' ); - - this.historypanel.deleteHda( '#' + testUploadInfo.hdaElement.attributes.id, function(){ - this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is not in the DOM" ); - }); -}); - -// ------------------------------------------------------------------- options allow showing/hiding deleted hdas -spaceghost.then( function(){ - this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); - - this.historyoptions.includeDeleted(); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertExists( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - this.test.assertVisible( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); - }); - }); -}); - -spaceghost.then( function(){ - this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); - - this.historyoptions.includeDeleted(); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, - "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - }); - }); -}); - -// undelete the uploaded file -spaceghost.then( function(){ - this.historyoptions.includeDeleted(); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - //TODO: to conv. fn - this.click( '#' + testUploadInfo.hdaElement.attributes.id - + ' ' + this.historypanel.data.selectors.history.undeleteLink ); - }); - }); -}); - -// ------------------------------------------------------------------- hidden hdas aren't shown -// ------------------------------------------------------------------- history options allows showing hidden hdas -// can't test this yet w/o a way to make hdas hidden thru the ui or api - // ------------------------------------------------------------------- hdas can be expanded by clicking on the hda name // broken in webkit w/ jq 1.7 -spaceghost.then( function(){ +spaceghost.historypanel.waitForHdas( function(){ this.test.comment( 'HDAs can be expanded by clicking on the name' ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.click( uploadedSelector + ' .historyItemTitle' ); - this.wait( 1000, function(){ - this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is visible" ); - }); + this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); + this.wait( 1000, function(){ + this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is visible" ); }); }); @@ -360,26 +267,22 @@ var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( refreshButtonSelector ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is visible" ); - }); + this.historypanel.waitForHdas( function(){ + this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is visible" ); }); // this will break: webkit + jq 1.7 }); // ------------------------------------------------------------------- expanded hdas collapse by clicking name again -spaceghost.then( function(){ +spaceghost.withHistoryPanel( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); - this.wait( 500, function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); + this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); + this.wait( 500, function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); @@ -389,32 +292,9 @@ var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( refreshButtonSelector ); - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.waitForSelector( nameSelector, function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); - }); -}); - -// ------------------------------------------------------------------- history options collapses all expanded hdas -spaceghost.then( function(){ - // expand again - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.click( '#' + testUploadInfo.hdaElement.attributes.id + ' ' + this.historypanel.data.selectors.hda.title ); - this.wait( 500, function(){}); - }); -}); -spaceghost.then( function(){ - this.test.comment( 'History option collapses all expanded hdas' ); - var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - - this.historyoptions.collapseExpanded(); - this.wait( 500, function(){ - this.withFrame( spaceghost.data.selectors.frames.history, function(){ - this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, - "Body for uploaded file is not visible" ); - }); + this.historypanel.waitForHdas( function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/login-tests.js --- a/test/casperjs/login-tests.js +++ b/test/casperjs/login-tests.js @@ -39,6 +39,8 @@ password = spaceghost.fixtureData.testUser.password; } +var userEmailSelector = '//a[contains(text(),"Logged in as")]/span["id=#user-email"]'; + // =================================================================== TESTS // register a user (again...) spaceghost.thenOpen( spaceghost.baseUrl, function(){ @@ -52,8 +54,7 @@ spaceghost.user.logout(); }); spaceghost.then( function(){ - this.test.assertSelectorDoesntHaveText( - xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), /\w/ ); + this.test.assertSelectorDoesntHaveText( xpath( userEmailSelector ), /\w/ ); this.test.assert( spaceghost.user.loggedInAs() === '', 'loggedInAs() is empty string' ); }); @@ -63,8 +64,7 @@ spaceghost.user._submitLogin( email, password ); //No such user }); spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.test.assertSelectorHasText( - xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), email ); + this.test.assertSelectorHasText( xpath( userEmailSelector ), email ); this.test.assert( spaceghost.user.loggedInAs() === email, 'loggedInAs() matches email' ); }); diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/modules/api.js --- /dev/null +++ b/test/casperjs/modules/api.js @@ -0,0 +1,231 @@ +// =================================================================== module object, exports +/** Creates a new api module object. + * @param {SpaceGhost} spaceghost a spaceghost instance + * @exported + */ +exports.create = function createAPI( spaceghost, apikey ){ + return new API( spaceghost ); +}; + +/** User object constructor. + * @param {SpaceGhost} spaceghost a spaceghost instance + * @param {String} apikey apikey for use when not using session authentication + */ +var API = function API( spaceghost, apikey ){ + this.spaceghost = spaceghost; + this.apikey = apikey; + + this.encodedIdExpectedLength = 16; + this.jQueryLocation = '../../static/scripts/libs/jquery/jquery.js'; + + this.histories = new HistoriesAPI( this ); + this.hdas = new HDAAPI( this ); +}; +exports.API = API; + +API.prototype.toString = function toString(){ + return ( this.spaceghost + '.API:' + + (( this.apikey )?( this.apikey ):( '(session)' )) ); +}; + +// ------------------------------------------------------------------- APIError +APIError.prototype = new Error(); +APIError.prototype.constructor = Error; +/** @class Thrown when Galaxy the API returns an error from a request */ +function APIError( msg ){ + Error.apply( this, arguments ); + this.name = "APIError"; + this.message = msg; +} +exports.APIError = APIError; + +/* ------------------------------------------------------------------- TODO: + can we component-ize this to become the basis for js-based api binding/resource + +*/ +// =================================================================== INTERNAL +var utils = require( 'utils' ); + +API.prototype._ajax = function _ajax( url, options ){ + options = options || {}; + options.async = false; + + this.ensureJQuery( '../../static/scripts/libs/jquery/jquery.js' ); + var resp = this.spaceghost.evaluate( function( url, options ){ + return jQuery.ajax( url, options ); + }, url, options ); + //this.spaceghost.debug( 'resp: ' + this.spaceghost.jsonStr( resp ) ); + + if( resp.status !== 200 ){ + // grrr... this doesn't lose the \n\r\t + throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) ); + } + return JSON.parse( resp.responseText ); +}; + +// =================================================================== MISC +API.prototype.isEncodedId = function isEncodedId( id ){ + if( typeof id !== 'string' ){ return false; } + if( id.match( /[g-zG-Z]/ ) ){ return false; } + return ( id.length === this.encodedIdExpectedLength ); +}; + +// ------------------------------------------------------------------- is type or throw err +API.prototype.ensureId = function ensureId( id ){ + if( !this.isEncodedId( id ) ){ + throw new APIError( 'ID is not a valid encoded id: ' + id ); + } + return id; +}; + +API.prototype.ensureObject = function ensureObject( obj ){ + if( !utils.isObject( obj ) ){ + throw new APIError( 'Not a valid object: ' + obj ); + } + return obj; +}; + +// ------------------------------------------------------------------- jquery +// using jq for the ajax in this module - that's why these are here +//TODO:?? could go in spaceghost +API.prototype.hasJQuery = function hasJQuery(){ + return this.spaceghost.evaluate( function pageHasJQuery(){ + var has = false; + try { + has = typeof ( jQuery + '' ) === 'string'; + } catch( err ){} + return has; + }); +}; + +API.prototype.ensureJQuery = function ensureJQuery(){ + if( !this.hasJQuery() ){ + var absLoc = this.spaceghost.options.scriptDir + this.jQueryLocation, + injected = this.spaceghost.page.injectJs( absLoc ); + if( !injected ){ + throw new APIError( 'Could not inject jQuery' ); + } + } +}; + + +// =================================================================== HISTORIES +var HistoriesAPI = function HistoriesAPI( api ){ + this.api = api; +}; +HistoriesAPI.prototype.toString = function toString(){ + return this.api + '.HistoriesAPI'; +}; + +// ------------------------------------------------------------------- +HistoriesAPI.prototype.urlTpls = { + index : 'api/histories', + show : 'api/histories/%s', + create : 'api/histories', + delete_ : 'api/histories/%s', + undelete: 'api/histories/deleted/%s/undelete' +}; + +HistoriesAPI.prototype.index = function index( deleted ){ + this.api.spaceghost.info( 'history.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); + + deleted = deleted || false; + return this.api._ajax( this.urlTpls.index, { + data : { deleted: deleted } + }); +}; + +HistoriesAPI.prototype.show = function show( id, deleted ){ + this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + deleted = deleted || false; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : { deleted: deleted } + }); +}; + +HistoriesAPI.prototype.create = function create( payload ){ + this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; + +HistoriesAPI.prototype.delete_ = function delete_( id, purge ){ + this.api.spaceghost.info( 'history.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); + + // py.payload <-> ajax.data + var payload = ( purge )?({ purge: true }):({}); + return this.api._ajax( utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ), { + type : 'DELETE', + data : payload + }); +}; + +HistoriesAPI.prototype.undelete = function undelete( id ){ + //throw ( 'unimplemented' ); + this.api.spaceghost.info( 'history.undelete: ' + id ); + + return this.api._ajax( utils.format( this.urlTpls.undelete, this.api.ensureId( id ) ), { + type : 'POST' + }); +}; + + +// =================================================================== HDAS +var HDAAPI = function HDAAPI( api ){ + this.api = api; +}; +HDAAPI.prototype.toString = function toString(){ + return this.api + '.HDAAPI'; +}; + +// ------------------------------------------------------------------- +HDAAPI.prototype.urlTpls = { + index : 'api/histories/%s/contents', + show : 'api/histories/%s/contents/%s', + create : 'api/histories/%s/contents'//, + // not implemented + //delete_ : 'api/histories/%s', + //undelete: 'api/histories/deleted/%s/undelete' +}; + +HDAAPI.prototype.index = function index( historyId, ids ){ + this.api.spaceghost.info( 'history.index: ' + [ historyId, ids ] ); + var data = {}; + if( ids ){ + ids = ( utils.isArray( ids ) )?( ids.join( ',' ) ):( ids ); + data.ids = ids; + } + + return this.api._ajax( utils.format( this.urlTpls.index, this.api.ensureId( historyId ) ), { + data : data + }); +}; + +HDAAPI.prototype.show = function show( historyId, id, deleted ){ + this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + deleted = deleted || false; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : { deleted: deleted } + }); +}; + +HDAAPI.prototype.create = function create( historyId, payload ){ + this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; + diff -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 -r f19741fdb9a6b6f15f3e9b983d4a8228b205ffda test/casperjs/modules/historyoptions.js --- a/test/casperjs/modules/historyoptions.js +++ b/test/casperjs/modules/historyoptions.js @@ -21,23 +21,65 @@ // ------------------------------------------------------------------- /* TODO: + some of the fns below can be applied to any popup */ +// =================================================================== internal +var xpath = require( 'casper' ).selectXPath; + // =================================================================== API (external) /** Just open the menu + * @param {Function} fn function to call when the menu opens + * @returns {Any} the return value of fn */ -HistoryOptions.prototype.openMenu = function openMenu(){ - this.spaceghost.click( this.data.selectors.button ); +HistoryOptions.prototype.openMenu = function openMenu( fn ){ + return this.spaceghost.jumpToTop( function(){ + this.click( this.historyoptions.data.selectors.button ); + return fn.call( this ); + }); }; /** Click an option by Label + * @param {String} optionLabel the label of the option to click (can be partial?) + * @returns {SpaceGhost} for chaining */ HistoryOptions.prototype.clickOption = function clickOption( optionLabel ){ - this.openMenu(); - // casperjs clickLabel - var optionXpath = this.data.selectors.optionXpathByLabelFn( optionLabel ); - this.spaceghost.click( optionXpath ); + this.openMenu( function(){ + this.click( this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ) ); + // shouldnt need to clear - clicking an option will do that + }); + return this.spaceghost; +}; + +/** Is the history option with the given label showing as toggled? + * @param {String} optionLabel the label of the option to check (can be partial?) + * @returns {Boolean} true if the option is on, false if off OR not a toggle + */ +HistoryOptions.prototype.isOn = function isOn( optionLabel ){ + return this.openMenu( function(){ + var toggleIconInfo = this.elementInfoOrNull( + this.historyoptions.data.selectors.optionIsOnXpathByLabelFn( optionLabel ) ); + // have to clear manually + this.click( 'body' ); + return !!toggleIconInfo; + }); +}; + +/** Toggle the option - optionally forcing to on or off. + * @param {String} optionLabel the label of the option to check (can be partial?) + * @param {Boolean} force if true ensure option is on, if false ensure it's off, + * if undefined simply toggle + * @returns {Boolean} true if the option is now on, false if now off or not a toggle + */ +HistoryOptions.prototype.toggle = function toggle( optionLabel, force ){ + var isOn = this.isOn( optionLabel ); + if( ( force === false && isOn ) + || ( force === true && !isOn ) + || ( force === undefined ) ){ + return this.clickOption( optionLabel ); + } + return force; }; // ------------------------------------------------------------------- @@ -101,22 +143,68 @@ //}; -// ------------------------------------------------------------------- +// ------------------------------------------------------------------- check the togglable options // these are easy, one click options (they don't open a new page) +/** Is 'Include Deleted Datasets' on (accrd. to the menu)? + */ +HistoryOptions.prototype.deletedAreIncluded = function deletedAreIncluded(){ + return this.isOn( this.data.labels.options.includeDeleted ); +}; +/** Is 'Include Deleted Datasets' on (accrd. to the menu)? + */ +HistoryOptions.prototype.hiddenAreIncluded = function hiddenAreIncluded(){ + return this.isOn( this.data.labels.options.includeHidden ); +}; + +// ------------------------------------------------------------------- options that control the hpanel /** corresponds to history options menu: 'Collapse Expanded Datasets' */ -HistoryOptions.prototype.collapseExpanded = function collapseExpanded(){ - this.clickOption( this.data.labels.options.collapseExpanded ); +HistoryOptions.prototype.collapseExpanded = function collapseExpanded( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.clickOption( this.historyoptions.data.labels.options.collapseExpanded ); + this.wait( 500, then ); + }); }; -/** corresponds to history options menu: 'Include Deleted Datasets' + +/** set 'Include Deleted Datasets' to on + * @param {Function} then casper step to run when option is set */ -HistoryOptions.prototype.includeDeleted = function includeDeleted(){ - this.clickOption( this.data.labels.options.includeDeleted ); +HistoryOptions.prototype.includeDeleted = function includeDeleted( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, true ); + this.historypanel.waitForHdas( then ); + }); }; -/** corresponds to history options menu: 'Include Hidden Datasets' + +/** set 'Include Deleted Datasets' to off + * @param {Function} then casper step to run when option is set */ -HistoryOptions.prototype.includeHidden = function includeHidden(){ - this.clickOption( this.data.labels.options.includeHidden ); +HistoryOptions.prototype.excludeDeleted = function excludeDeleted( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeDeleted, false ); + //TODO:?? this puts in the history frame. Is that what we want? + this.historypanel.waitForHdas( then ); + }); +}; + +/** set 'Include Hidden Datasets' to on + * @param {Function} then casper step to run when option is set + */ +HistoryOptions.prototype.includeHidden = function includeHidden( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, true ); + this.historypanel.waitForHdas( then ); + }); +}; + +/** set 'Include Hidden Datasets' to off + * @param {Function} then casper step to run when option is set + */ +HistoryOptions.prototype.excludeHidden = function excludeHidden( then ){ + return this.spaceghost.then( function(){ + this.historyoptions.toggle( this.historyoptions.data.labels.options.includeHidden, false ); + this.historypanel.waitForHdas( then ); + }); }; @@ -129,6 +217,10 @@ menu : '#history-options-button-menu', optionXpathByLabelFn : function optionXpathByLabelFn( label ){ return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' ); + }, + optionIsOnXpathByLabelFn : function optionIsOnXpathByLabelFn( label ){ + return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' + + '/span[@class="fa-icon-ok"]' ); } }, labels : { This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b5f97700fdc/ changeset: 7b5f97700fdc branch: next-stable user: inithello date: 2013-03-18 19:32:06 summary: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors. affected #: 1 file diff -r e0607a09d9fa9eb690e9b410d9c167072db0b55a -r 7b5f97700fdc8286db3e5ed6b6425127694ca42f lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1059,7 +1059,12 @@ """Translates the characters in text to an html string""" if text: if to_html: - escaped_text = str( markupsafe.escape( text ) ) + try: + escaped_text = text.decode( 'utf-8' ) + escaped_text = escaped_text.encode( 'ascii', 'ignore' ) + escaped_text = str( markupsafe.escape( escaped_text ) ) + except UnicodeDecodeError, e: + escaped_text = "Error decoding string: %s" % str( e ) else: escaped_text = str( text ) translated = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/51d3a88f45ee/ changeset: 51d3a88f45ee user: inithello date: 2013-03-18 19:32:06 summary: Fix unicode decoding error when displaying the contents of certain files. Catch any future errors. affected #: 1 file diff -r 7a4dd13dac9be2b3c9233b7a60e61d30d283744f -r 51d3a88f45ee2e3aa89395d2df13b5452d463274 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1059,7 +1059,12 @@ """Translates the characters in text to an html string""" if text: if to_html: - escaped_text = str( markupsafe.escape( text ) ) + try: + escaped_text = text.decode( 'utf-8' ) + escaped_text = escaped_text.encode( 'ascii', 'ignore' ) + escaped_text = str( markupsafe.escape( escaped_text ) ) + except UnicodeDecodeError, e: + escaped_text = "Error decoding string: %s" % str( e ) else: escaped_text = str( text ) translated = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Include LWR and job running fixes from John Chilton in next-stable.
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e0607a09d9fa/ changeset: e0607a09d9fa branch: next-stable user: natefoo date: 2013-03-18 16:38:34 summary: Include LWR and job running fixes from John Chilton in next-stable. affected #: 10 files diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -7,6 +7,7 @@ <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/><plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> + <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /></plugins><handlers default="handlers"> + <param id="private_token">123456789changeme</param> + </destination></destinations><tools><!-- Tools can be configured to use specific destinations or handlers, diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -126,7 +126,12 @@ for plugin in self.__findall_with_required(plugins, 'plugin', ('id', 'type', 'load')): if plugin.get('type') == 'runner': workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS)) - self.runner_plugins.append(dict(id=plugin.get('id'), load=plugin.get('load'), workers=int(workers))) + runner_kwds = self.__get_params(plugin) + runner_info = dict(id=plugin.get('id'), + load=plugin.get('load'), + workers=int(workers), + kwds=runner_kwds) + self.runner_plugins.append(runner_info) else: log.error('Unknown plugin type: %s' % plugin.get('type')) # Load tasks if configured @@ -480,7 +485,7 @@ log.warning("Job runner classes must be subclassed from BaseJobRunner, %s has bases: %s" % (id, runner_class.__bases__)) continue try: - rval[id] = runner_class( self.app, runner['workers'] ) + rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) ) except TypeError: log.warning( "Job runner '%s:%s' has not been converted to a new-style runner" % ( module_name, class_name ) ) rval[id] = runner_class( self.app ) @@ -833,7 +838,7 @@ log.warning('set_runner() is deprecated, use set_job_destination()') self.set_job_destination(self.job_destination, external_id) - def set_job_destination(self, job_destination, external_id): + def set_job_destination(self, job_destination, external_id=None ): """ Persist job destination params in the database for recovery. diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -3,11 +3,12 @@ from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import JobDestination import errno from time import sleep -from lwr_client import FileStager, Client +from lwr_client import FileStager, Client, url_to_destination_params log = logging.getLogger( __name__ ) @@ -19,11 +20,16 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers ): + def __init__( self, app, nworkers, transport=None ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self._init_monitor_thread() self._init_worker_threads() + self.transport_type = transport + + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="lwr", params=url_to_destination_params( url ) ) def check_watched_item(self, job_state): try: @@ -42,7 +48,7 @@ def queue_job(self, job_wrapper): stderr = stdout = command_line = '' - runner_url = job_wrapper.get_job_runner_url() + job_destination = job_wrapper.job_destination try: job_wrapper.prepare() @@ -74,7 +80,7 @@ rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id client.launch( rebuilt_command_line ) - job_wrapper.set_runner( runner_url, job_id ) + job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.RUNNING ) except Exception, exc: @@ -87,32 +93,26 @@ lwr_job_state.job_id = job_id lwr_job_state.old_state = True lwr_job_state.running = True - lwr_job_state.runner_url = runner_url + lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) def get_output_files(self, job_wrapper): output_fnames = job_wrapper.get_output_fnames() return [ str( o ) for o in output_fnames ] - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - def get_client_from_wrapper(self, job_wrapper): job_id = job_wrapper.job_id if hasattr(job_wrapper, 'task_id'): job_id = "%s_%s" % (job_id, job_wrapper.task_id) - return self.get_client( job_wrapper.get_job_runner_url(), job_id ) + return self.get_client( job_wrapper.job_destination.params, job_id ) def get_client_from_state(self, job_state): - job_runner = job_state.runner_url + job_destination_params = job_state.job_destination.params job_id = job_state.job_id - return self.get_client(job_runner, job_id) + return self.get_client( job_destination_params, job_id ) - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) + def get_client( self, job_destination_params, job_id ): + return Client( job_destination_params, job_id, transport_type=self.transport_type ) def finish_job( self, job_state ): stderr = stdout = command_line = '' @@ -210,7 +210,7 @@ lwr_url = job.job_runner_name job_id = job.job_runner_external_id log.debug("Attempt remote lwr kill of job with url %s and id %s" % (lwr_url, job_id)) - client = self.get_client(lwr_url, job_id) + client = self.get_client(job.destination_params, job_id) client.kill() @@ -219,6 +219,7 @@ job_state = AsynchronousJobState() job_state.job_id = str( job.get_job_runner_external_id() ) job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper if job.get_state() == model.Job.states.RUNNING: diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -5,502 +5,9 @@ This module contains logic for interfacing with an external LWR server. """ -import os -import re -import time -import urllib -import simplejson +from .stager import FileStager +from .client import Client +from .destination import url_to_destination_params -from transport import get_transport - - -class JobInputs(object): - """ - Abstractions over dynamic inputs created for a given job (namely the command to - execute and created configfiles). - - **Parameters** - - command_line : str - Local command to execute for this job. (To be rewritten.) - config_files : str - Config files created for this job. (To be rewritten.) - - - >>> import tempfile - >>> tf = tempfile.NamedTemporaryFile() - >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) - ... return inputs - >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' - >>> tf.close() - >>> tf = tempfile.NamedTemporaryFile() - >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] - >>> inputs.path_referenced('/path/to') - True - >>> inputs.path_referenced('/path/to/input') - True - >>> inputs.path_referenced('/path/to/notinput') - False - >>> tf.close() - """ - - def __init__(self, command_line, config_files): - self.rewritten_command_line = command_line - self.rewritten_config_files = {} - for config_file in config_files or []: - config_contents = _read(config_file) - self.rewritten_config_files[config_file] = config_contents - - def find_referenced_subfiles(self, directory): - """ - Return list of files below specified `directory` in job inputs. Could - use more sophisticated logic (match quotes to handle spaces, handle - subdirectories, etc...). - - **Parameters** - - directory : str - Full path to directory to search. - - """ - pattern = r"(%s%s\S+)" % (directory, os.sep) - referenced_files = set() - for input_contents in self.__items(): - referenced_files.update(re.findall(pattern, input_contents)) - return list(referenced_files) - - def path_referenced(self, path): - pattern = r"%s" % path - found = False - for input_contents in self.__items(): - if re.findall(pattern, input_contents): - found = True - break - return found - - def rewrite_paths(self, local_path, remote_path): - """ - Rewrite references to `local_path` with `remote_path` in job inputs. - """ - self.__rewrite_command_line(local_path, remote_path) - self.__rewrite_config_files(local_path, remote_path) - - def __rewrite_command_line(self, local_path, remote_path): - self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) - - def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): - self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) - - def __items(self): - items = [self.rewritten_command_line] - items.extend(self.rewritten_config_files.values()) - return items - - -class FileStager(object): - """ - Objects of the FileStager class interact with an LWR client object to - stage the files required to run jobs on a remote LWR server. - - **Parameters** - - client : Client - LWR client object. - command_line : str - The local command line to execute, this will be rewritten for the remote server. - config_files : list - List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. - input_files : list - List of input files used by job. These will be transferred and references rewritten. - output_files : list - List of output_files produced by job. - tool_dir : str - Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). - working_directory : str - Local path created by Galaxy for running this job. - - """ - - def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): - """ - """ - self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_id = tool.id - self.tool_version = tool.version - self.tool_dir = os.path.abspath(tool.tool_dir) - self.working_directory = working_directory - - # Setup job inputs, these will need to be rewritten before - # shipping off to remote LWR server. - self.job_inputs = JobInputs(self.command_line, self.config_files) - - self.file_renames = {} - - self.__handle_setup() - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__upload_working_directory_files() - self.__initialize_output_file_renames() - self.__initialize_task_output_file_renames() - self.__initialize_config_file_renames() - self.__handle_rewrites() - self.__upload_rewritten_config_files() - - def __handle_setup(self): - job_config = self.client.setup(self.tool_id, self.tool_version) - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - # If remote LWR server assigned job id, use that otherwise - # just use local job_id assigned. - galaxy_job_id = self.client.job_id - self.job_id = job_config.get('job_id', galaxy_job_id) - if self.job_id != galaxy_job_id: - # Remote LWR server assigned an id different than the - # Galaxy job id, update client to reflect this. - self.client.job_id = self.job_id - - def __initialize_referenced_tool_files(self): - self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - self.__upload_input_file(input_file) - self.__upload_input_extra_files(input_file) - - def __upload_input_file(self, input_file): - if self.job_inputs.path_referenced(input_file): - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - - def __upload_input_extra_files(self, input_file): - # TODO: Determine if this is object store safe and what needs to be - # done if it is not. - files_path = "%s_files" % input_file[0:-len(".dat")] - if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): - for extra_file in os.listdir(files_path): - extra_file_path = os.path.join(files_path, extra_file) - relative_path = os.path.basename(files_path) - extra_file_relative_path = os.path.join(relative_path, extra_file) - response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) - self.file_renames[extra_file_path] = response['path'] - - def __upload_working_directory_files(self): - # Task manager stages files into working directory, these need to be - # uploaded if present. - for working_directory_file in os.listdir(self.working_directory): - path = os.path.join(self.working_directory, working_directory_file) - working_file_response = self.client.upload_working_directory_file(path) - self.file_renames[path] = working_file_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_task_output_file_renames(self): - for output_file in self.output_files: - name = os.path.basename(output_file) - self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - name) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __handle_rewrites(self): - for local_path, remote_path in self.file_renames.iteritems(): - self.job_inputs.rewrite_paths(local_path, remote_path) - - def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): - self.client.upload_config_file(config_file, new_config_contents) - - def get_rewritten_command_line(self): - """ - Returns the rewritten version of the command line to execute suitable - for remote host. - """ - return self.job_inputs.rewritten_command_line - - -class parseJson(object): - - def __init__(self): - pass - - def __call__(self, func): - def replacement(*args, **kwargs): - response = func(*args, **kwargs) - return simplejson.loads(response) - return replacement - - -class Client(object): - """ - Objects of this client class perform low-level communication with a remote LWR server. - - **Parameters** - - remote_host : str - Remote URL of the LWR server. - job_id : str - Galaxy job/task id. - private_key : str (optional) - Secret key the remote LWR server is configured with. - """ - - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match = re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - self.transport = get_transport() - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): - url = self.__build_url(command, args) - response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) - return response - - @parseJson() - def __upload_file(self, action, path, name=None, contents=None): - if not name: - name = os.path.basename(path) - args = {"job_id": self.job_id, "name": name} - input_path = path - if contents: - input_path = None - return self.__raw_execute(action, args, contents, input_path) - - def upload_tool_file(self, path): - """ - Upload a tool related file (e.g. wrapper) required to run job. - - **Parameters** - - path : str - Local path tool. - """ - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - """ - Upload input dataset to remote server. - - **Parameters** - - path : str - Local path of input dataset. - """ - return self.__upload_file("upload_input", path) - - def upload_extra_input(self, path, relative_name): - """ - Upload extra input file to remote server. - - **Parameters** - - path : str - Extra files path of input dataset corresponding to this input. - relative_name : str - Relative path of extra file to upload relative to inputs extra files path. - """ - return self.__upload_file("upload_extra_input", path, name=relative_name) - - def upload_config_file(self, path, contents): - """ - Upload a job's config file to the remote server. - - **Parameters** - - path : str - Local path to the original config file. - contents : str - Rewritten contents of the config file to upload. - """ - return self.__upload_file("upload_config_file", path, contents=contents) - - def upload_working_directory_file(self, path): - """ - Upload the supplied file (path) from a job's working directory - to remote server. - - **Parameters** - - path : str - Path to file to upload. - """ - return self.__upload_file("upload_working_directory_file", path) - - @parseJson() - def _get_output_type(self, name): - return self.__raw_execute("get_output_type", {"name": name, - "job_id": self.job_id}) - - def download_work_dir_output(self, source, working_directory, output_path): - """ - Download an output dataset specified with from_work_dir from the - remote server. - - **Parameters** - - source : str - Path in job's working_directory to find output in. - working_directory : str - Local working_directory for the job. - output_path : str - Full path to output dataset. - """ - output = open(output_path, "wb") - name = os.path.basename(source) - self.__raw_download_output(name, self.job_id, "work_dir", output) - - def download_output(self, path, working_directory): - """ - Download an output dataset from the remote server. - - **Parameters** - - path : str - Local path of the dataset. - working_directory : str - Local working_directory for the job. - """ - name = os.path.basename(path) - output_type = self._get_output_type(name) - if output_type == "direct": - output_path = path - elif output_type == "task": - output_path = os.path.join(working_directory, name) - else: - raise Exception("No remote output found for dataset with path %s" % path) - self.__raw_download_output(name, self.job_id, output_type, output_path) - - def __raw_download_output(self, name, job_id, output_type, output_path): - self.__raw_execute("download_output", - {"name": name, - "job_id": self.job_id, - "output_type": output_type}, - output_path=output_path) - - def launch(self, command_line): - """ - Run or queue up the execution of the supplied - `command_line` on the remote server. - - **Parameters** - - command_line : str - Command to execute. - """ - return self.__raw_execute("launch", {"command_line": command_line, - "job_id": self.job_id}) - - def kill(self): - """ - Cancel remote job, either removing from the queue or killing it. - """ - return self.__raw_execute("kill", {"job_id": self.job_id}) - - def wait(self): - """ - Wait for job to finish. - """ - while True: - complete_response = self.raw_check_complete() - if complete_response["complete"] == "true": - return complete_response - time.sleep(1) - - @parseJson() - def raw_check_complete(self): - """ - Get check_complete response from the remote server. - """ - check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) - return check_complete_response - - def check_complete(self): - """ - Return boolean indicating whether the job is complete. - """ - return self.raw_check_complete()["complete"] == "true" - - def clean(self): - """ - Cleanup the remote job. - """ - self.__raw_execute("clean", {"job_id": self.job_id}) - - @parseJson() - def setup(self, tool_id=None, tool_version=None): - """ - Setup remote LWR server to run this job. - """ - setup_args = {"job_id": self.job_id} - if tool_id: - setup_args["tool_id"] = tool_id - if tool_version: - setup_args["tool_version"] = tool_version - return self.__raw_execute("setup", setup_args) - - -def _read(path): - """ - Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. - """ - input = open(path, "r") - try: - return input.read() - finally: - input.close() +__all__ = [Client, FileStager, url_to_destination_params] diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/client.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -0,0 +1,235 @@ +import os +import time +import urllib +import simplejson + +from .transport import get_transport +from .destination import url_to_destination_params + + +class parseJson(object): + + def __init__(self): + pass + + def __call__(self, func): + def replacement(*args, **kwargs): + response = func(*args, **kwargs) + return simplejson.loads(response) + return replacement + + +class Client(object): + """ + Objects of this client class perform low-level communication with a remote LWR server. + + **Parameters** + + destination_params : dict or str + connection parameters, either url with dict containing url (and optionally `private_token`). + job_id : str + Galaxy job/task id. + """ + + def __init__(self, destination_params, job_id, transport_type=None): + if isinstance(destination_params, str) or isinstance(destination_params, unicode): + destination_params = url_to_destination_params(destination_params) + self.remote_host = destination_params.get("url") + assert self.remote_host != None, "Failed to determine url for LWR client." + self.private_key = destination_params.get("private_token", None) + self.job_id = job_id + self.transport = get_transport(transport_type) + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + data = urllib.urlencode(args) + url = self.remote_host + command + "?" + data + return url + + def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): + url = self.__build_url(command, args) + response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) + return response + + @parseJson() + def __upload_file(self, action, path, name=None, contents=None): + if not name: + name = os.path.basename(path) + args = {"job_id": self.job_id, "name": name} + input_path = path + if contents: + input_path = None + return self.__raw_execute(action, args, contents, input_path) + + def upload_tool_file(self, path): + """ + Upload a tool related file (e.g. wrapper) required to run job. + + **Parameters** + + path : str + Local path tool. + """ + return self.__upload_file("upload_tool_file", path) + + def upload_input(self, path): + """ + Upload input dataset to remote server. + + **Parameters** + + path : str + Local path of input dataset. + """ + return self.__upload_file("upload_input", path) + + def upload_extra_input(self, path, relative_name): + """ + Upload extra input file to remote server. + + **Parameters** + + path : str + Extra files path of input dataset corresponding to this input. + relative_name : str + Relative path of extra file to upload relative to inputs extra files path. + """ + return self.__upload_file("upload_extra_input", path, name=relative_name) + + def upload_config_file(self, path, contents): + """ + Upload a job's config file to the remote server. + + **Parameters** + + path : str + Local path to the original config file. + contents : str + Rewritten contents of the config file to upload. + """ + return self.__upload_file("upload_config_file", path, contents=contents) + + def upload_working_directory_file(self, path): + """ + Upload the supplied file (path) from a job's working directory + to remote server. + + **Parameters** + + path : str + Path to file to upload. + """ + return self.__upload_file("upload_working_directory_file", path) + + @parseJson() + def _get_output_type(self, name): + return self.__raw_execute("get_output_type", {"name": name, + "job_id": self.job_id}) + + def download_work_dir_output(self, source, working_directory, output_path): + """ + Download an output dataset specified with from_work_dir from the + remote server. + + **Parameters** + + source : str + Path in job's working_directory to find output in. + working_directory : str + Local working_directory for the job. + output_path : str + Full path to output dataset. + """ + output = open(output_path, "wb") + name = os.path.basename(source) + self.__raw_download_output(name, self.job_id, "work_dir", output) + + def download_output(self, path, working_directory): + """ + Download an output dataset from the remote server. + + **Parameters** + + path : str + Local path of the dataset. + working_directory : str + Local working_directory for the job. + """ + name = os.path.basename(path) + output_type = self._get_output_type(name) + if output_type == "direct": + output_path = path + elif output_type == "task": + output_path = os.path.join(working_directory, name) + else: + raise Exception("No remote output found for dataset with path %s" % path) + self.__raw_download_output(name, self.job_id, output_type, output_path) + + def __raw_download_output(self, name, job_id, output_type, output_path): + self.__raw_execute("download_output", + {"name": name, + "job_id": self.job_id, + "output_type": output_type}, + output_path=output_path) + + def launch(self, command_line): + """ + Run or queue up the execution of the supplied + `command_line` on the remote server. + + **Parameters** + + command_line : str + Command to execute. + """ + return self.__raw_execute("launch", {"command_line": command_line, + "job_id": self.job_id}) + + def kill(self): + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self.__raw_execute("kill", {"job_id": self.job_id}) + + def wait(self): + """ + Wait for job to finish. + """ + while True: + complete_response = self.raw_check_complete() + if complete_response["complete"] == "true": + return complete_response + time.sleep(1) + + @parseJson() + def raw_check_complete(self): + """ + Get check_complete response from the remote server. + """ + check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) + return check_complete_response + + def check_complete(self): + """ + Return boolean indicating whether the job is complete. + """ + return self.raw_check_complete()["complete"] == "true" + + def clean(self): + """ + Cleanup the remote job. + """ + self.__raw_execute("clean", {"job_id": self.job_id}) + + @parseJson() + def setup(self, tool_id=None, tool_version=None): + """ + Setup remote LWR server to run this job. + """ + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.__raw_execute("setup", setup_args) diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/destination.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -0,0 +1,44 @@ + +from re import match + + +def url_to_destination_params(url): + """Convert a legacy runner URL to a job destination + + >>> params_simple = url_to_destination_params("http://localhost:8913/") + >>> params_simple["url"] + 'http://localhost:8913/' + >>> params_simple["private_token"] is None + True + >>> advanced_url = "https://1234x@example.com:8914/managers/longqueue" + >>> params_advanced = url_to_destination_params(advanced_url) + >>> params_advanced["url"] + 'https://example.com:8914/managers/longqueue/' + >>> params_advanced["private_token"] + '1234x' + >>> runner_url = "lwr://http://localhost:8913/" + >>> runner_params = url_to_destination_params(runner_url) + >>> runner_params['url'] + 'http://localhost:8913/' + """ + + if url.startswith("lwr://"): + url = url[len("lwr://"):] + + if not url.endswith("/"): + url += "/" + + ## Check for private token embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_token_format = "https?://(.*)@.*/?" + private_token_match = match(private_token_format, url) + private_token = None + if private_token_match: + private_token = private_token_match.group(1) + url = url.replace("%s@" % private_token, '', 1) + + destination_args = {"url": url, + "private_token": private_token} + + return destination_args diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/stager.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -0,0 +1,256 @@ + +import os +from re import findall + + +class JobInputs(object): + """ + Abstractions over dynamic inputs created for a given job (namely the command to + execute and created configfiles). + + **Parameters** + + command_line : str + Local command to execute for this job. (To be rewritten.) + config_files : str + Config files created for this job. (To be rewritten.) + + + >>> import tempfile + >>> tf = tempfile.NamedTemporaryFile() + >>> def setup_inputs(tf): + ... open(tf.name, "w").write("world /path/to/input the rest") + ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... return inputs + >>> inputs = setup_inputs(tf) + >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') + >>> inputs.rewritten_command_line + 'hello C:\\\\input' + >>> inputs.rewritten_config_files[tf.name] + 'world C:\\\\input the rest' + >>> tf.close() + >>> tf = tempfile.NamedTemporaryFile() + >>> inputs = setup_inputs(tf) + >>> inputs.find_referenced_subfiles('/path/to') + ['/path/to/input'] + >>> inputs.path_referenced('/path/to') + True + >>> inputs.path_referenced('/path/to/input') + True + >>> inputs.path_referenced('/path/to/notinput') + False + >>> tf.close() + """ + + def __init__(self, command_line, config_files): + self.rewritten_command_line = command_line + self.rewritten_config_files = {} + for config_file in config_files or []: + config_contents = _read(config_file) + self.rewritten_config_files[config_file] = config_contents + + def find_referenced_subfiles(self, directory): + """ + Return list of files below specified `directory` in job inputs. Could + use more sophisticated logic (match quotes to handle spaces, handle + subdirectories, etc...). + + **Parameters** + + directory : str + Full path to directory to search. + + """ + pattern = r"(%s%s\S+)" % (directory, os.sep) + referenced_files = set() + for input_contents in self.__items(): + referenced_files.update(findall(pattern, input_contents)) + return list(referenced_files) + + def path_referenced(self, path): + pattern = r"%s" % path + found = False + for input_contents in self.__items(): + if findall(pattern, input_contents): + found = True + break + return found + + def rewrite_paths(self, local_path, remote_path): + """ + Rewrite references to `local_path` with `remote_path` in job inputs. + """ + self.__rewrite_command_line(local_path, remote_path) + self.__rewrite_config_files(local_path, remote_path) + + def __rewrite_command_line(self, local_path, remote_path): + self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) + + def __rewrite_config_files(self, local_path, remote_path): + for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) + + def __items(self): + items = [self.rewritten_command_line] + items.extend(self.rewritten_config_files.values()) + return items + + +class FileStager(object): + """ + Objects of the FileStager class interact with an LWR client object to + stage the files required to run jobs on a remote LWR server. + + **Parameters** + + client : Client + LWR client object. + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + + """ + + def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): + """ + """ + self.client = client + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.tool_id = tool.id + self.tool_version = tool.version + self.tool_dir = os.path.abspath(tool.tool_dir) + self.working_directory = working_directory + + # Setup job inputs, these will need to be rewritten before + # shipping off to remote LWR server. + self.job_inputs = JobInputs(self.command_line, self.config_files) + + self.file_renames = {} + + self.__handle_setup() + self.__initialize_referenced_tool_files() + self.__upload_tool_files() + self.__upload_input_files() + self.__upload_working_directory_files() + self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() + self.__initialize_config_file_renames() + self.__handle_rewrites() + self.__upload_rewritten_config_files() + + def __handle_setup(self): + job_config = self.client.setup(self.tool_id, self.tool_version) + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + # If remote LWR server assigned job id, use that otherwise + # just use local job_id assigned. + galaxy_job_id = self.client.job_id + self.job_id = job_config.get('job_id', galaxy_job_id) + if self.job_id != galaxy_job_id: + # Remote LWR server assigned an id different than the + # Galaxy job id, update client to reflect this. + self.client.job_id = self.job_id + + def __initialize_referenced_tool_files(self): + self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) + + def __upload_tool_files(self): + for referenced_tool_file in self.referenced_tool_files: + tool_upload_response = self.client.upload_tool_file(referenced_tool_file) + self.file_renames[referenced_tool_file] = tool_upload_response['path'] + + def __upload_input_files(self): + for input_file in self.input_files: + self.__upload_input_file(input_file) + self.__upload_input_extra_files(input_file) + + def __upload_input_file(self, input_file): + if self.job_inputs.path_referenced(input_file): + input_upload_response = self.client.upload_input(input_file) + self.file_renames[input_file] = input_upload_response['path'] + + def __upload_input_extra_files(self, input_file): + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be + # uploaded if present. + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + + def __initialize_output_file_renames(self): + for output_file in self.output_files: + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, + os.path.basename(output_file)) + + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + + def __initialize_config_file_renames(self): + for config_file in self.config_files: + self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + os.path.basename(config_file)) + + def __rewrite_paths(self, contents): + new_contents = contents + for local_path, remote_path in self.file_renames.iteritems(): + new_contents = new_contents.replace(local_path, remote_path) + return new_contents + + def __handle_rewrites(self): + for local_path, remote_path in self.file_renames.iteritems(): + self.job_inputs.rewrite_paths(local_path, remote_path) + + def __upload_rewritten_config_files(self): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + self.client.upload_config_file(config_file, new_config_contents) + + def get_rewritten_command_line(self): + """ + Returns the rewritten version of the command line to execute suitable + for remote host. + """ + return self.job_inputs.rewritten_command_line + + +def _read(path): + """ + Utility method to quickly read small files (config files and tool + wrappers) into memory as strings. + """ + input = open(path, "r") + try: + return input.read() + finally: + input.close() diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/lwr_client/transport/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/transport/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/transport/__init__.py @@ -3,14 +3,24 @@ import os -def get_transport(os_module=os): - use_curl = os_module.getenv('LWR_CURL_TRANSPORT', "0") - ## If LWR_CURL_TRANSPORT is unset or set to 0, use default, - ## else use curl. - if use_curl.isdigit() and not int(use_curl): - return Urllib2Transport() +def get_transport(transport_type=None, os_module=os): + transport_type = __get_transport_type(transport_type, os_module) + if transport_type == 'urllib': + transport = Urllib2Transport() else: - return PycurlTransport() + transport = PycurlTransport() + return transport +def __get_transport_type(transport_type, os_module): + if not transport_type: + use_curl = os_module.getenv('LWR_CURL_TRANSPORT', "0") + ## If LWR_CURL_TRANSPORT is unset or set to 0, use default, + ## else use curl. + if use_curl.isdigit() and not int(use_curl): + transport_type = 'urllib' + else: + transport_type = 'curl' + return transport_type + __all__ = [get_transport] diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -173,7 +173,9 @@ return JobDestination(runner='pbs', params=params) def parse_destination_params(self, params): - """A wrapper method around __args_to_attrs() that allow administrators to define PBS params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" args (as in ``pbs_submit(3B)``). + """A wrapper method around __args_to_attrs() that allow administrators to define PBS + params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" + args (as in ``pbs_submit(3B)``). :returns: list of dicts -- The dicts map directly to pbs attropl structs (see ``pbs_submit(3B)``) """ @@ -185,7 +187,7 @@ arg = arg.lstrip('-') args[arg] = value except: - log.warning('Unrecognized long argument in destination params: %s' % k) + log.warning('Unrecognized long argument in destination params: %s' % arg) return self.__args_to_attrs(args) # Internal stuff diff -r e58bb74b6afe3ebac548a2b2d124c24bf149a24a -r e0607a09d9fa9eb690e9b410d9c167072db0b55a lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -9,12 +9,13 @@ from time import sleep from galaxy.jobs import TaskWrapper +from galaxy.jobs.runners import BaseJobRunner log = logging.getLogger( __name__ ) __all__ = [ 'TaskedJobRunner' ] -class TaskedJobRunner( object ): +class TaskedJobRunner( BaseJobRunner ): """ Job runner backed by a finite pool of worker threads. FIFO scheduling """ @@ -25,7 +26,7 @@ self._init_worker_threads() def queue_job( self, job_wrapper ): - super( LocalJobRunner, self ).queue_job( job_wrapper ) + super( TaskedJobRunner, self ).queue_job( job_wrapper ) if not job_wrapper.is_ready: return Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 8 new changesets
by commits-noreply＠bitbucket.org 18 Mar '13

18 Mar '13

8 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/547d6844325a/ changeset: 547d6844325a user: jmchilton date: 2013-03-10 06:51:59 summary: Update LWR infrastructure for new destination based configuration of Galaxy runners. Implement legacy mapping functionality. Break lwr_client/__init__.py into separate smaller modules. Updates LWR client to LWR changeset https://bitbucket.org/jmchilton/lwr/commits/b0fbc1a299baa470b9346127767fcbe…. affected #: 5 files diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -3,11 +3,12 @@ from galaxy import model from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner +from galaxy.jobs import JobDestination import errno from time import sleep -from lwr_client import FileStager, Client +from lwr_client import FileStager, Client, url_to_destination_params log = logging.getLogger( __name__ ) @@ -25,6 +26,10 @@ self._init_monitor_thread() self._init_worker_threads() + def url_to_destination( self, url ): + """Convert a legacy URL to a job destination""" + return JobDestination( runner="lwr", params=url_to_destination_params( url ) ) + def check_watched_item(self, job_state): try: client = self.get_client_from_state(job_state) @@ -42,7 +47,7 @@ def queue_job(self, job_wrapper): stderr = stdout = command_line = '' - runner_url = job_wrapper.get_job_runner_url() + job_destination = job_wrapper.job_destination try: job_wrapper.prepare() @@ -74,7 +79,7 @@ rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id client.launch( rebuilt_command_line ) - job_wrapper.set_runner( runner_url, job_id ) + job_wrapper.set_job_destination( job_destination, job_id ) job_wrapper.change_state( model.Job.states.RUNNING ) except Exception, exc: @@ -87,32 +92,26 @@ lwr_job_state.job_id = job_id lwr_job_state.old_state = True lwr_job_state.running = True - lwr_job_state.runner_url = runner_url + lwr_job_state.job_destination = job_destination self.monitor_job(lwr_job_state) def get_output_files(self, job_wrapper): output_fnames = job_wrapper.get_output_fnames() return [ str( o ) for o in output_fnames ] - - def determine_lwr_url(self, url): - lwr_url = url[ len( 'lwr://' ) : ] - return lwr_url - def get_client_from_wrapper(self, job_wrapper): job_id = job_wrapper.job_id if hasattr(job_wrapper, 'task_id'): job_id = "%s_%s" % (job_id, job_wrapper.task_id) - return self.get_client( job_wrapper.get_job_runner_url(), job_id ) + return self.get_client( job_wrapper.job_destination.params, job_id ) def get_client_from_state(self, job_state): - job_runner = job_state.runner_url + job_destination_params = job_state.job_destination.params job_id = job_state.job_id - return self.get_client(job_runner, job_id) + return self.get_client( job_destination_params, job_id ) - def get_client(self, job_runner, job_id): - lwr_url = self.determine_lwr_url( job_runner ) - return Client(lwr_url, job_id) + def get_client( self, job_destination_params, job_id ): + return Client( job_destination_params, job_id ) def finish_job( self, job_state ): stderr = stdout = command_line = '' @@ -210,7 +209,7 @@ lwr_url = job.job_runner_name job_id = job.job_runner_external_id log.debug("Attempt remote lwr kill of job with url %s and id %s" % (lwr_url, job_id)) - client = self.get_client(lwr_url, job_id) + client = self.get_client(job.destination_params, job_id) client.kill() @@ -219,6 +218,7 @@ job_state = AsynchronousJobState() job_state.job_id = str( job.get_job_runner_external_id() ) job_state.runner_url = job_wrapper.get_job_runner_url() + job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper if job.get_state() == model.Job.states.RUNNING: diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -5,502 +5,9 @@ This module contains logic for interfacing with an external LWR server. """ -import os -import re -import time -import urllib -import simplejson +from .stager import FileStager +from .client import Client +from .destination import url_to_destination_params -from transport import get_transport - - -class JobInputs(object): - """ - Abstractions over dynamic inputs created for a given job (namely the command to - execute and created configfiles). - - **Parameters** - - command_line : str - Local command to execute for this job. (To be rewritten.) - config_files : str - Config files created for this job. (To be rewritten.) - - - >>> import tempfile - >>> tf = tempfile.NamedTemporaryFile() - >>> def setup_inputs(tf): - ... open(tf.name, "w").write("world /path/to/input the rest") - ... inputs = JobInputs("hello /path/to/input", [tf.name]) - ... return inputs - >>> inputs = setup_inputs(tf) - >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') - >>> inputs.rewritten_command_line - 'hello C:\\\\input' - >>> inputs.rewritten_config_files[tf.name] - 'world C:\\\\input the rest' - >>> tf.close() - >>> tf = tempfile.NamedTemporaryFile() - >>> inputs = setup_inputs(tf) - >>> inputs.find_referenced_subfiles('/path/to') - ['/path/to/input'] - >>> inputs.path_referenced('/path/to') - True - >>> inputs.path_referenced('/path/to/input') - True - >>> inputs.path_referenced('/path/to/notinput') - False - >>> tf.close() - """ - - def __init__(self, command_line, config_files): - self.rewritten_command_line = command_line - self.rewritten_config_files = {} - for config_file in config_files or []: - config_contents = _read(config_file) - self.rewritten_config_files[config_file] = config_contents - - def find_referenced_subfiles(self, directory): - """ - Return list of files below specified `directory` in job inputs. Could - use more sophisticated logic (match quotes to handle spaces, handle - subdirectories, etc...). - - **Parameters** - - directory : str - Full path to directory to search. - - """ - pattern = r"(%s%s\S+)" % (directory, os.sep) - referenced_files = set() - for input_contents in self.__items(): - referenced_files.update(re.findall(pattern, input_contents)) - return list(referenced_files) - - def path_referenced(self, path): - pattern = r"%s" % path - found = False - for input_contents in self.__items(): - if re.findall(pattern, input_contents): - found = True - break - return found - - def rewrite_paths(self, local_path, remote_path): - """ - Rewrite references to `local_path` with `remote_path` in job inputs. - """ - self.__rewrite_command_line(local_path, remote_path) - self.__rewrite_config_files(local_path, remote_path) - - def __rewrite_command_line(self, local_path, remote_path): - self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) - - def __rewrite_config_files(self, local_path, remote_path): - for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): - self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) - - def __items(self): - items = [self.rewritten_command_line] - items.extend(self.rewritten_config_files.values()) - return items - - -class FileStager(object): - """ - Objects of the FileStager class interact with an LWR client object to - stage the files required to run jobs on a remote LWR server. - - **Parameters** - - client : Client - LWR client object. - command_line : str - The local command line to execute, this will be rewritten for the remote server. - config_files : list - List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. - input_files : list - List of input files used by job. These will be transferred and references rewritten. - output_files : list - List of output_files produced by job. - tool_dir : str - Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). - working_directory : str - Local path created by Galaxy for running this job. - - """ - - def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): - """ - """ - self.client = client - self.command_line = command_line - self.config_files = config_files - self.input_files = input_files - self.output_files = output_files - self.tool_id = tool.id - self.tool_version = tool.version - self.tool_dir = os.path.abspath(tool.tool_dir) - self.working_directory = working_directory - - # Setup job inputs, these will need to be rewritten before - # shipping off to remote LWR server. - self.job_inputs = JobInputs(self.command_line, self.config_files) - - self.file_renames = {} - - self.__handle_setup() - self.__initialize_referenced_tool_files() - self.__upload_tool_files() - self.__upload_input_files() - self.__upload_working_directory_files() - self.__initialize_output_file_renames() - self.__initialize_task_output_file_renames() - self.__initialize_config_file_renames() - self.__handle_rewrites() - self.__upload_rewritten_config_files() - - def __handle_setup(self): - job_config = self.client.setup(self.tool_id, self.tool_version) - - self.new_working_directory = job_config['working_directory'] - self.new_outputs_directory = job_config['outputs_directory'] - self.remote_path_separator = job_config['path_separator'] - # If remote LWR server assigned job id, use that otherwise - # just use local job_id assigned. - galaxy_job_id = self.client.job_id - self.job_id = job_config.get('job_id', galaxy_job_id) - if self.job_id != galaxy_job_id: - # Remote LWR server assigned an id different than the - # Galaxy job id, update client to reflect this. - self.client.job_id = self.job_id - - def __initialize_referenced_tool_files(self): - self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) - - def __upload_tool_files(self): - for referenced_tool_file in self.referenced_tool_files: - tool_upload_response = self.client.upload_tool_file(referenced_tool_file) - self.file_renames[referenced_tool_file] = tool_upload_response['path'] - - def __upload_input_files(self): - for input_file in self.input_files: - self.__upload_input_file(input_file) - self.__upload_input_extra_files(input_file) - - def __upload_input_file(self, input_file): - if self.job_inputs.path_referenced(input_file): - input_upload_response = self.client.upload_input(input_file) - self.file_renames[input_file] = input_upload_response['path'] - - def __upload_input_extra_files(self, input_file): - # TODO: Determine if this is object store safe and what needs to be - # done if it is not. - files_path = "%s_files" % input_file[0:-len(".dat")] - if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): - for extra_file in os.listdir(files_path): - extra_file_path = os.path.join(files_path, extra_file) - relative_path = os.path.basename(files_path) - extra_file_relative_path = os.path.join(relative_path, extra_file) - response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) - self.file_renames[extra_file_path] = response['path'] - - def __upload_working_directory_files(self): - # Task manager stages files into working directory, these need to be - # uploaded if present. - for working_directory_file in os.listdir(self.working_directory): - path = os.path.join(self.working_directory, working_directory_file) - working_file_response = self.client.upload_working_directory_file(path) - self.file_renames[path] = working_file_response['path'] - - def __initialize_output_file_renames(self): - for output_file in self.output_files: - self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, - self.remote_path_separator, - os.path.basename(output_file)) - - def __initialize_task_output_file_renames(self): - for output_file in self.output_files: - name = os.path.basename(output_file) - self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - name) - - def __initialize_config_file_renames(self): - for config_file in self.config_files: - self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, - self.remote_path_separator, - os.path.basename(config_file)) - - def __rewrite_paths(self, contents): - new_contents = contents - for local_path, remote_path in self.file_renames.iteritems(): - new_contents = new_contents.replace(local_path, remote_path) - return new_contents - - def __handle_rewrites(self): - for local_path, remote_path in self.file_renames.iteritems(): - self.job_inputs.rewrite_paths(local_path, remote_path) - - def __upload_rewritten_config_files(self): - for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): - self.client.upload_config_file(config_file, new_config_contents) - - def get_rewritten_command_line(self): - """ - Returns the rewritten version of the command line to execute suitable - for remote host. - """ - return self.job_inputs.rewritten_command_line - - -class parseJson(object): - - def __init__(self): - pass - - def __call__(self, func): - def replacement(*args, **kwargs): - response = func(*args, **kwargs) - return simplejson.loads(response) - return replacement - - -class Client(object): - """ - Objects of this client class perform low-level communication with a remote LWR server. - - **Parameters** - - remote_host : str - Remote URL of the LWR server. - job_id : str - Galaxy job/task id. - private_key : str (optional) - Secret key the remote LWR server is configured with. - """ - - def __init__(self, remote_host, job_id, private_key=None): - if not remote_host.endswith("/"): - remote_host = remote_host + "/" - ## If we don't have an explicit private_key defined, check for - ## one embedded in the URL. A URL of the form - ## https://moo@cow:8913 will try to contact https://cow:8913 - ## with a private key of moo - private_key_format = "https?://(.*)@.*/?" - private_key_match = re.match(private_key_format, remote_host) - if not private_key and private_key_match: - private_key = private_key_match.group(1) - remote_host = remote_host.replace("%s@" % private_key, '', 1) - self.remote_host = remote_host - self.job_id = job_id - self.private_key = private_key - self.transport = get_transport() - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - data = urllib.urlencode(args) - url = self.remote_host + command + "?" + data - return url - - def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): - url = self.__build_url(command, args) - response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) - return response - - @parseJson() - def __upload_file(self, action, path, name=None, contents=None): - if not name: - name = os.path.basename(path) - args = {"job_id": self.job_id, "name": name} - input_path = path - if contents: - input_path = None - return self.__raw_execute(action, args, contents, input_path) - - def upload_tool_file(self, path): - """ - Upload a tool related file (e.g. wrapper) required to run job. - - **Parameters** - - path : str - Local path tool. - """ - return self.__upload_file("upload_tool_file", path) - - def upload_input(self, path): - """ - Upload input dataset to remote server. - - **Parameters** - - path : str - Local path of input dataset. - """ - return self.__upload_file("upload_input", path) - - def upload_extra_input(self, path, relative_name): - """ - Upload extra input file to remote server. - - **Parameters** - - path : str - Extra files path of input dataset corresponding to this input. - relative_name : str - Relative path of extra file to upload relative to inputs extra files path. - """ - return self.__upload_file("upload_extra_input", path, name=relative_name) - - def upload_config_file(self, path, contents): - """ - Upload a job's config file to the remote server. - - **Parameters** - - path : str - Local path to the original config file. - contents : str - Rewritten contents of the config file to upload. - """ - return self.__upload_file("upload_config_file", path, contents=contents) - - def upload_working_directory_file(self, path): - """ - Upload the supplied file (path) from a job's working directory - to remote server. - - **Parameters** - - path : str - Path to file to upload. - """ - return self.__upload_file("upload_working_directory_file", path) - - @parseJson() - def _get_output_type(self, name): - return self.__raw_execute("get_output_type", {"name": name, - "job_id": self.job_id}) - - def download_work_dir_output(self, source, working_directory, output_path): - """ - Download an output dataset specified with from_work_dir from the - remote server. - - **Parameters** - - source : str - Path in job's working_directory to find output in. - working_directory : str - Local working_directory for the job. - output_path : str - Full path to output dataset. - """ - output = open(output_path, "wb") - name = os.path.basename(source) - self.__raw_download_output(name, self.job_id, "work_dir", output) - - def download_output(self, path, working_directory): - """ - Download an output dataset from the remote server. - - **Parameters** - - path : str - Local path of the dataset. - working_directory : str - Local working_directory for the job. - """ - name = os.path.basename(path) - output_type = self._get_output_type(name) - if output_type == "direct": - output_path = path - elif output_type == "task": - output_path = os.path.join(working_directory, name) - else: - raise Exception("No remote output found for dataset with path %s" % path) - self.__raw_download_output(name, self.job_id, output_type, output_path) - - def __raw_download_output(self, name, job_id, output_type, output_path): - self.__raw_execute("download_output", - {"name": name, - "job_id": self.job_id, - "output_type": output_type}, - output_path=output_path) - - def launch(self, command_line): - """ - Run or queue up the execution of the supplied - `command_line` on the remote server. - - **Parameters** - - command_line : str - Command to execute. - """ - return self.__raw_execute("launch", {"command_line": command_line, - "job_id": self.job_id}) - - def kill(self): - """ - Cancel remote job, either removing from the queue or killing it. - """ - return self.__raw_execute("kill", {"job_id": self.job_id}) - - def wait(self): - """ - Wait for job to finish. - """ - while True: - complete_response = self.raw_check_complete() - if complete_response["complete"] == "true": - return complete_response - time.sleep(1) - - @parseJson() - def raw_check_complete(self): - """ - Get check_complete response from the remote server. - """ - check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) - return check_complete_response - - def check_complete(self): - """ - Return boolean indicating whether the job is complete. - """ - return self.raw_check_complete()["complete"] == "true" - - def clean(self): - """ - Cleanup the remote job. - """ - self.__raw_execute("clean", {"job_id": self.job_id}) - - @parseJson() - def setup(self, tool_id=None, tool_version=None): - """ - Setup remote LWR server to run this job. - """ - setup_args = {"job_id": self.job_id} - if tool_id: - setup_args["tool_id"] = tool_id - if tool_version: - setup_args["tool_version"] = tool_version - return self.__raw_execute("setup", setup_args) - - -def _read(path): - """ - Utility method to quickly read small files (config files and tool - wrappers) into memory as strings. - """ - input = open(path, "r") - try: - return input.read() - finally: - input.close() +__all__ = [Client, FileStager, url_to_destination_params] diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/client.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -0,0 +1,235 @@ +import os +import time +import urllib +import simplejson + +from .transport import get_transport +from .destination import url_to_destination_params + + +class parseJson(object): + + def __init__(self): + pass + + def __call__(self, func): + def replacement(*args, **kwargs): + response = func(*args, **kwargs) + return simplejson.loads(response) + return replacement + + +class Client(object): + """ + Objects of this client class perform low-level communication with a remote LWR server. + + **Parameters** + + destination_params : dict or str + connection parameters, either url with dict containing url (and optionally `private_token`). + job_id : str + Galaxy job/task id. + """ + + def __init__(self, destination_params, job_id): + if isinstance(destination_params, str) or isinstance(destination_params, unicode): + destination_params = url_to_destination_params(destination_params) + self.remote_host = destination_params.get("url") + assert self.remote_host != None, "Failed to determine url for LWR client." + self.private_key = destination_params.get("private_token", None) + self.job_id = job_id + self.transport = get_transport() + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + data = urllib.urlencode(args) + url = self.remote_host + command + "?" + data + return url + + def __raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): + url = self.__build_url(command, args) + response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) + return response + + @parseJson() + def __upload_file(self, action, path, name=None, contents=None): + if not name: + name = os.path.basename(path) + args = {"job_id": self.job_id, "name": name} + input_path = path + if contents: + input_path = None + return self.__raw_execute(action, args, contents, input_path) + + def upload_tool_file(self, path): + """ + Upload a tool related file (e.g. wrapper) required to run job. + + **Parameters** + + path : str + Local path tool. + """ + return self.__upload_file("upload_tool_file", path) + + def upload_input(self, path): + """ + Upload input dataset to remote server. + + **Parameters** + + path : str + Local path of input dataset. + """ + return self.__upload_file("upload_input", path) + + def upload_extra_input(self, path, relative_name): + """ + Upload extra input file to remote server. + + **Parameters** + + path : str + Extra files path of input dataset corresponding to this input. + relative_name : str + Relative path of extra file to upload relative to inputs extra files path. + """ + return self.__upload_file("upload_extra_input", path, name=relative_name) + + def upload_config_file(self, path, contents): + """ + Upload a job's config file to the remote server. + + **Parameters** + + path : str + Local path to the original config file. + contents : str + Rewritten contents of the config file to upload. + """ + return self.__upload_file("upload_config_file", path, contents=contents) + + def upload_working_directory_file(self, path): + """ + Upload the supplied file (path) from a job's working directory + to remote server. + + **Parameters** + + path : str + Path to file to upload. + """ + return self.__upload_file("upload_working_directory_file", path) + + @parseJson() + def _get_output_type(self, name): + return self.__raw_execute("get_output_type", {"name": name, + "job_id": self.job_id}) + + def download_work_dir_output(self, source, working_directory, output_path): + """ + Download an output dataset specified with from_work_dir from the + remote server. + + **Parameters** + + source : str + Path in job's working_directory to find output in. + working_directory : str + Local working_directory for the job. + output_path : str + Full path to output dataset. + """ + output = open(output_path, "wb") + name = os.path.basename(source) + self.__raw_download_output(name, self.job_id, "work_dir", output) + + def download_output(self, path, working_directory): + """ + Download an output dataset from the remote server. + + **Parameters** + + path : str + Local path of the dataset. + working_directory : str + Local working_directory for the job. + """ + name = os.path.basename(path) + output_type = self._get_output_type(name) + if output_type == "direct": + output_path = path + elif output_type == "task": + output_path = os.path.join(working_directory, name) + else: + raise Exception("No remote output found for dataset with path %s" % path) + self.__raw_download_output(name, self.job_id, output_type, output_path) + + def __raw_download_output(self, name, job_id, output_type, output_path): + self.__raw_execute("download_output", + {"name": name, + "job_id": self.job_id, + "output_type": output_type}, + output_path=output_path) + + def launch(self, command_line): + """ + Run or queue up the execution of the supplied + `command_line` on the remote server. + + **Parameters** + + command_line : str + Command to execute. + """ + return self.__raw_execute("launch", {"command_line": command_line, + "job_id": self.job_id}) + + def kill(self): + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self.__raw_execute("kill", {"job_id": self.job_id}) + + def wait(self): + """ + Wait for job to finish. + """ + while True: + complete_response = self.raw_check_complete() + if complete_response["complete"] == "true": + return complete_response + time.sleep(1) + + @parseJson() + def raw_check_complete(self): + """ + Get check_complete response from the remote server. + """ + check_complete_response = self.__raw_execute("check_complete", {"job_id": self.job_id}) + return check_complete_response + + def check_complete(self): + """ + Return boolean indicating whether the job is complete. + """ + return self.raw_check_complete()["complete"] == "true" + + def clean(self): + """ + Cleanup the remote job. + """ + self.__raw_execute("clean", {"job_id": self.job_id}) + + @parseJson() + def setup(self, tool_id=None, tool_version=None): + """ + Setup remote LWR server to run this job. + """ + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.__raw_execute("setup", setup_args) diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/destination.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -0,0 +1,40 @@ + +from re import match + + +def url_to_destination_params(url): + """Convert a legacy runner URL to a job destination + + >>> params_simple = url_to_destination_params("http://localhost:8913/") + >>> params_simple["url"] + 'http://localhost:8913/' + >>> params_simple["private_token"] is None + True + >>> advanced_url = "https://1234x@example.com:8914/managers/longqueue" + >>> params_advanced = url_to_destination_params(advanced_url) + >>> params_advanced["url"] + 'https://example.com:8914/managers/longqueue/' + >>> params_advanced["private_token"] + '1234x' + """ + + if url.startswith("lwr://"): + url = url[len("lwr://"):] + + if not url.endswith("/"): + url += "/" + + ## Check for private token embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_token_format = "https?://(.*)@.*/?" + private_token_match = match(private_token_format, url) + private_token = None + if private_token_match: + private_token = private_token_match.group(1) + url = url.replace("%s@" % private_token, '', 1) + + destination_args = {"url": url, + "private_token": private_token} + + return destination_args diff -r 2b4d6af45a04ddb49c2c87a0ead3874503d35832 -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 lib/galaxy/jobs/runners/lwr_client/stager.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/stager.py @@ -0,0 +1,256 @@ + +import os +from re import findall + + +class JobInputs(object): + """ + Abstractions over dynamic inputs created for a given job (namely the command to + execute and created configfiles). + + **Parameters** + + command_line : str + Local command to execute for this job. (To be rewritten.) + config_files : str + Config files created for this job. (To be rewritten.) + + + >>> import tempfile + >>> tf = tempfile.NamedTemporaryFile() + >>> def setup_inputs(tf): + ... open(tf.name, "w").write("world /path/to/input the rest") + ... inputs = JobInputs("hello /path/to/input", [tf.name]) + ... return inputs + >>> inputs = setup_inputs(tf) + >>> inputs.rewrite_paths("/path/to/input", 'C:\\input') + >>> inputs.rewritten_command_line + 'hello C:\\\\input' + >>> inputs.rewritten_config_files[tf.name] + 'world C:\\\\input the rest' + >>> tf.close() + >>> tf = tempfile.NamedTemporaryFile() + >>> inputs = setup_inputs(tf) + >>> inputs.find_referenced_subfiles('/path/to') + ['/path/to/input'] + >>> inputs.path_referenced('/path/to') + True + >>> inputs.path_referenced('/path/to/input') + True + >>> inputs.path_referenced('/path/to/notinput') + False + >>> tf.close() + """ + + def __init__(self, command_line, config_files): + self.rewritten_command_line = command_line + self.rewritten_config_files = {} + for config_file in config_files or []: + config_contents = _read(config_file) + self.rewritten_config_files[config_file] = config_contents + + def find_referenced_subfiles(self, directory): + """ + Return list of files below specified `directory` in job inputs. Could + use more sophisticated logic (match quotes to handle spaces, handle + subdirectories, etc...). + + **Parameters** + + directory : str + Full path to directory to search. + + """ + pattern = r"(%s%s\S+)" % (directory, os.sep) + referenced_files = set() + for input_contents in self.__items(): + referenced_files.update(findall(pattern, input_contents)) + return list(referenced_files) + + def path_referenced(self, path): + pattern = r"%s" % path + found = False + for input_contents in self.__items(): + if findall(pattern, input_contents): + found = True + break + return found + + def rewrite_paths(self, local_path, remote_path): + """ + Rewrite references to `local_path` with `remote_path` in job inputs. + """ + self.__rewrite_command_line(local_path, remote_path) + self.__rewrite_config_files(local_path, remote_path) + + def __rewrite_command_line(self, local_path, remote_path): + self.rewritten_command_line = self.rewritten_command_line.replace(local_path, remote_path) + + def __rewrite_config_files(self, local_path, remote_path): + for config_file, rewritten_contents in self.rewritten_config_files.iteritems(): + self.rewritten_config_files[config_file] = rewritten_contents.replace(local_path, remote_path) + + def __items(self): + items = [self.rewritten_command_line] + items.extend(self.rewritten_config_files.values()) + return items + + +class FileStager(object): + """ + Objects of the FileStager class interact with an LWR client object to + stage the files required to run jobs on a remote LWR server. + + **Parameters** + + client : Client + LWR client object. + command_line : str + The local command line to execute, this will be rewritten for the remote server. + config_files : list + List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + input_files : list + List of input files used by job. These will be transferred and references rewritten. + output_files : list + List of output_files produced by job. + tool_dir : str + Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + working_directory : str + Local path created by Galaxy for running this job. + + """ + + def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): + """ + """ + self.client = client + self.command_line = command_line + self.config_files = config_files + self.input_files = input_files + self.output_files = output_files + self.tool_id = tool.id + self.tool_version = tool.version + self.tool_dir = os.path.abspath(tool.tool_dir) + self.working_directory = working_directory + + # Setup job inputs, these will need to be rewritten before + # shipping off to remote LWR server. + self.job_inputs = JobInputs(self.command_line, self.config_files) + + self.file_renames = {} + + self.__handle_setup() + self.__initialize_referenced_tool_files() + self.__upload_tool_files() + self.__upload_input_files() + self.__upload_working_directory_files() + self.__initialize_output_file_renames() + self.__initialize_task_output_file_renames() + self.__initialize_config_file_renames() + self.__handle_rewrites() + self.__upload_rewritten_config_files() + + def __handle_setup(self): + job_config = self.client.setup(self.tool_id, self.tool_version) + + self.new_working_directory = job_config['working_directory'] + self.new_outputs_directory = job_config['outputs_directory'] + self.remote_path_separator = job_config['path_separator'] + # If remote LWR server assigned job id, use that otherwise + # just use local job_id assigned. + galaxy_job_id = self.client.job_id + self.job_id = job_config.get('job_id', galaxy_job_id) + if self.job_id != galaxy_job_id: + # Remote LWR server assigned an id different than the + # Galaxy job id, update client to reflect this. + self.client.job_id = self.job_id + + def __initialize_referenced_tool_files(self): + self.referenced_tool_files = self.job_inputs.find_referenced_subfiles(self.tool_dir) + + def __upload_tool_files(self): + for referenced_tool_file in self.referenced_tool_files: + tool_upload_response = self.client.upload_tool_file(referenced_tool_file) + self.file_renames[referenced_tool_file] = tool_upload_response['path'] + + def __upload_input_files(self): + for input_file in self.input_files: + self.__upload_input_file(input_file) + self.__upload_input_extra_files(input_file) + + def __upload_input_file(self, input_file): + if self.job_inputs.path_referenced(input_file): + input_upload_response = self.client.upload_input(input_file) + self.file_renames[input_file] = input_upload_response['path'] + + def __upload_input_extra_files(self, input_file): + # TODO: Determine if this is object store safe and what needs to be + # done if it is not. + files_path = "%s_files" % input_file[0:-len(".dat")] + if os.path.exists(files_path) and self.job_inputs.path_referenced(files_path): + for extra_file in os.listdir(files_path): + extra_file_path = os.path.join(files_path, extra_file) + relative_path = os.path.basename(files_path) + extra_file_relative_path = os.path.join(relative_path, extra_file) + response = self.client.upload_extra_input(extra_file_path, extra_file_relative_path) + self.file_renames[extra_file_path] = response['path'] + + def __upload_working_directory_files(self): + # Task manager stages files into working directory, these need to be + # uploaded if present. + for working_directory_file in os.listdir(self.working_directory): + path = os.path.join(self.working_directory, working_directory_file) + working_file_response = self.client.upload_working_directory_file(path) + self.file_renames[path] = working_file_response['path'] + + def __initialize_output_file_renames(self): + for output_file in self.output_files: + self.file_renames[output_file] = r'%s%s%s' % (self.new_outputs_directory, + self.remote_path_separator, + os.path.basename(output_file)) + + def __initialize_task_output_file_renames(self): + for output_file in self.output_files: + name = os.path.basename(output_file) + self.file_renames[os.path.join(self.working_directory, name)] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + name) + + def __initialize_config_file_renames(self): + for config_file in self.config_files: + self.file_renames[config_file] = r'%s%s%s' % (self.new_working_directory, + self.remote_path_separator, + os.path.basename(config_file)) + + def __rewrite_paths(self, contents): + new_contents = contents + for local_path, remote_path in self.file_renames.iteritems(): + new_contents = new_contents.replace(local_path, remote_path) + return new_contents + + def __handle_rewrites(self): + for local_path, remote_path in self.file_renames.iteritems(): + self.job_inputs.rewrite_paths(local_path, remote_path) + + def __upload_rewritten_config_files(self): + for config_file, new_config_contents in self.job_inputs.rewritten_config_files.iteritems(): + self.client.upload_config_file(config_file, new_config_contents) + + def get_rewritten_command_line(self): + """ + Returns the rewritten version of the command line to execute suitable + for remote host. + """ + return self.job_inputs.rewritten_command_line + + +def _read(path): + """ + Utility method to quickly read small files (config files and tool + wrappers) into memory as strings. + """ + input = open(path, "r") + try: + return input.read() + finally: + input.close() https://bitbucket.org/galaxy/galaxy-central/commits/89fa5f5873e4/ changeset: 89fa5f5873e4 user: jmchilton date: 2013-03-10 06:51:59 summary: Update job_conf.xml.sample_advanced with LWR usage examples. affected #: 1 file diff -r 547d6844325ad305cc5d713365e3d66d75bbb5c1 -r 89fa5f5873e45f4e1ef5eabbf226d1dd528ff4d1 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -7,6 +7,7 @@ <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/><plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/><plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAARunner"/> + <plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr.LwrJobRunner" /></plugins><handlers default="handlers"> + <param id="private_token">123456789changeme</param> + </destination></destinations><tools><!-- Tools can be configured to use specific destinations or handlers, https://bitbucket.org/galaxy/galaxy-central/commits/d0dd203bdaaf/ changeset: d0dd203bdaaf user: jmchilton date: 2013-03-10 06:51:59 summary: Small pbs runner fixes. affected #: 1 file diff -r 89fa5f5873e45f4e1ef5eabbf226d1dd528ff4d1 -r d0dd203bdaafd5507998241cdd096430e4f21f1f lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -173,7 +173,9 @@ return JobDestination(runner='pbs', params=params) def parse_destination_params(self, params): - """A wrapper method around __args_to_attrs() that allow administrators to define PBS params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" args (as in ``pbs_submit(3B)``). + """A wrapper method around __args_to_attrs() that allow administrators to define PBS + params as either command-line options (as in ``qsub(1B)``) or more human-readable "long" + args (as in ``pbs_submit(3B)``). :returns: list of dicts -- The dicts map directly to pbs attropl structs (see ``pbs_submit(3B)``) """ @@ -185,7 +187,7 @@ arg = arg.lstrip('-') args[arg] = value except: - log.warning('Unrecognized long argument in destination params: %s' % k) + log.warning('Unrecognized long argument in destination params: %s' % arg) return self.__args_to_attrs(args) # Internal stuff https://bitbucket.org/galaxy/galaxy-central/commits/4e0659495eb2/ changeset: 4e0659495eb2 user: jmchilton date: 2013-03-10 06:51:59 summary: Allow child param elements to appear in plugin elements of job_conf.xml. Pass these as keyword arguments into job runner constructor. affected #: 1 file diff -r d0dd203bdaafd5507998241cdd096430e4f21f1f -r 4e0659495eb2ad674bcc0a08cc1a9d211f691104 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -126,7 +126,12 @@ for plugin in self.__findall_with_required(plugins, 'plugin', ('id', 'type', 'load')): if plugin.get('type') == 'runner': workers = plugin.get('workers', plugins.get('workers', JobConfiguration.DEFAULT_NWORKERS)) - self.runner_plugins.append(dict(id=plugin.get('id'), load=plugin.get('load'), workers=int(workers))) + runner_kwds = self.__get_params(plugin) + runner_info = dict(id=plugin.get('id'), + load=plugin.get('load'), + workers=int(workers), + kwds=runner_kwds) + self.runner_plugins.append(runner_info) else: log.error('Unknown plugin type: %s' % plugin.get('type')) # Load tasks if configured @@ -480,7 +485,7 @@ log.warning("Job runner classes must be subclassed from BaseJobRunner, %s has bases: %s" % (id, runner_class.__bases__)) continue try: - rval[id] = runner_class( self.app, runner['workers'] ) + rval[id] = runner_class( self.app, runner['workers'], **runner['kwds'] ) except TypeError: log.warning( "Job runner '%s:%s' has not been converted to a new-style runner" % ( module_name, class_name ) ) rval[id] = runner_class( self.app ) https://bitbucket.org/galaxy/galaxy-central/commits/71da862d92ab/ changeset: 71da862d92ab user: jmchilton date: 2013-03-10 06:51:59 summary: Use new plugin param passing from previous changeset to provide a much cleaner mechanism for specifing LWR transport type. To enable pycurl based transport for the LWR client, now one just needs to add <param id="transport">curl</param> to the plugin definition in job_conf.xml. Updates LWR client through LWR changeset: https://bitbucket.org/jmchilton/lwr/commits/b09da65bd2ffe12b28cf6c545c7d052…. affected #: 4 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/3b6c209d2d07/ changeset: 3b6c209d2d07 user: jmchilton date: 2013-03-17 18:39:17 summary: Task job runner fixes. affected #: 2 files Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/67b37b0c11e7/ changeset: 67b37b0c11e7 user: jmchilton date: 2013-03-17 20:14:22 summary: Fix for job runner configuration dicts without new kwds pair present. affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/7a4dd13dac9b/ changeset: 7a4dd13dac9b user: natefoo date: 2013-03-18 16:21:22 summary: Merged in jmchilton/galaxy-central-lwr (pull request #138) LWR Updates and Other Small Job Destination Tweaks affected #: 10 files Diff not available. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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