September 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Bump version support for Cuffcompare, Cuffmerge to v2.0 and increase lines_diff to prevent Cuffmerge test from failing due to non-deterministic output.
by Bitbucket 26 Sep '12

26 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/199767a1714b/ changeset: 199767a1714b user: jgoecks date: 2012-09-26 16:30:59 summary: Bump version support for Cuffcompare, Cuffmerge to v2.0 and increase lines_diff to prevent Cuffmerge test from failing due to non-deterministic output. affected #: 4 files diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py +++ b/tools/ngs_rna/cuffcompare_wrapper.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +# Supports Cuffcompare versions v1.3.0 and newer. + import optparse, os, shutil, subprocess, sys, tempfile def stop_err( msg ): diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> -  + <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements><requirement type="package">cufflinks</requirement> diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +# Supports Cuffmerge versions 1.3 and newer. + import optparse, os, shutil, subprocess, sys, tempfile def stop_err( msg ): diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> -  + <description>merge together several Cufflinks assemblies</description><requirements><requirement type="package">cufflinks</requirement> @@ -88,7 +88,7 @@ <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="use_seq_data" value="No"/> - <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="8"/> + <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/></test></tests> 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: jgoecks: Cufflinks wrapper: add support for v2.0, add multiread correction parameter, and remove unused parameters.
by Bitbucket 26 Sep '12

26 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cfd6428269c8/ changeset: cfd6428269c8 user: jgoecks date: 2012-09-26 15:35:18 summary: Cufflinks wrapper: add support for v2.0, add multiread correction parameter, and remove unused parameters. affected #: 2 files diff -r 20144ac9ffa7d15a9738cee2a5c8cb2b4cf1c401 -r cfd6428269c88c4690d644929969e852af672f45 tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -1,5 +1,7 @@ #!/usr/bin/env python +# Supports Cufflinks versions 1.3 and newer. + import optparse, os, shutil, subprocess, sys, tempfile from galaxy import eggs from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str @@ -36,6 +38,7 @@ where each end is 50bp, you should set -r to be 200. The default is 45bp.') parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' ) parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' ) + parser.add_option( '-u', '--multi-read-correct', dest='multi_read_correct', action="store_true", help='Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome') # Normalization options. parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) @@ -116,7 +119,9 @@ if options.GTF: cmd += ( " -G %s" % options.GTF ) if options.GTFguide: - cmd += ( " -g %s" % options.GTFguide ) + cmd += ( " -g %s" % options.GTFguide ) + if options.multi_read_correct: + cmd += ( " -u" ) if options.num_importance_samples: cmd += ( " --num-importance-samples %i" % int ( options.num_importance_samples ) ) if options.max_mle_iterations: @@ -157,7 +162,7 @@ total_map_mass = -1 tmp_stderr = open( tmp_name, 'r' ) for line in tmp_stderr: - if line.lower().find( "total map mass" ) >= 0 or line.lower().find( "upper quartile" ) >= 0: + if line.lower().find( "map mass" ) >= 0 or line.lower().find( "upper quartile" ) >= 0: total_map_mass = float( line.split(":")[1].strip() ) break tmp_stderr.close() diff -r 20144ac9ffa7d15a9738cee2a5c8cb2b4cf1c401 -r cfd6428269c88c4690d644929969e852af672f45 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cufflinks" name="Cufflinks" version="0.0.5"> -  + <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements><requirement type="package">cufflinks</requirement> @@ -20,12 +20,6 @@ #if $reference_annotation.use_ref == "Use reference annotation guide": -g $reference_annotation.reference_annotation_guide_file #end if - - ## Set paired-end parameters? - #if $singlePaired.sPaired == "Yes": - -m $singlePaired.mean_inner_distance - -s $singlePaired.inner_distance_std_dev - #end if ## Normalization? #if str($do_normalization) == "Yes": @@ -34,7 +28,7 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: @@ -44,6 +38,11 @@ --index_dir=${GALAXY_DATA_INDEX_DIR} #end if + ## Multi-read correct? + #if str($multiread_correct) == "Yes": + -u + #end if + ## Include global model if available. #if $global_model: --global_model=$global_model @@ -55,12 +54,12 @@ <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help=""/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."> - <option value="No">No</option> + <option value="No" selected="true">No</option><option value="Yes">Yes</option></param><conditional name="reference_annotation"><param name="use_ref" type="select" label="Use Reference Annotation"> - <option value="No">No</option> + <option value="No" selected="true">No</option><option value="Use reference annotation">Use reference annotation</option><option value="Use reference annotation guide">Use reference annotation as guide</option></param> @@ -74,13 +73,13 @@ </conditional><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> - <option value="No">No</option> - <option value="Yes">Yes</option> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option></param><when value="Yes"><conditional name="seq_source"><param name="index_source" type="select" label="Reference sequence data"> - <option value="cached">Locally cached</option> + <option value="cached" selected="true">Locally cached</option><option value="history">History</option></param><when value="cached"></when> @@ -91,17 +90,12 @@ </when><when value="No"></when></conditional> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Set Parameters for Paired-end Reads? (not recommended)"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No"></when> - <when value="Yes"> - <param name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/> - <param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/> - </when> - </conditional> + + <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/></inputs> @@ -121,7 +115,6 @@ Simple test that uses test data included with cufflinks. --><test> - <param name="sPaired" value="No"/><param name="input" value="cufflinks_in.bam"/><param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/> @@ -129,6 +122,7 @@ <param name="use_ref" value="No"/><param name="do_normalization" value="No" /><param name="do_bias_correction" value="No"/> + <param name="multiread_correct" value="No"/><output name="genes_expression" format="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/><output name="transcripts_expression" format="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/><output name="assembled_isoforms" file="cufflinks_out1.gtf"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a required import to a tool shed controller.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/20144ac9ffa7/ changeset: 20144ac9ffa7 user: greg date: 2012-09-25 19:41:10 summary: Add a required import to a tool shed controller. affected #: 1 file diff -r 69f446023855cd7ed585ca6dde5ee581043e61f0 -r 20144ac9ffa7d15a9738cee2a5c8cb2b4cf1c401 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -5,7 +5,7 @@ from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * -from galaxy.util.shed_util import check_tool_input_params, clone_repository, copy_sample_file, generate_metadata_for_changeset_revision +from galaxy.util.shed_util import check_tool_input_params, clone_repository, concat_messages, copy_sample_file, generate_metadata_for_changeset_revision from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, load_tool_from_config, reset_tool_data_tables 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: Fixes for handling sample files in tool shed repositories.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/69f446023855/ changeset: 69f446023855 user: greg date: 2012-09-25 19:36:43 summary: Fixes for handling sample files in tool shed repositories. affected #: 4 files diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1469,7 +1469,7 @@ error, message = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) tool, valid, message2 = load_tool_from_config( trans.app, tool_config_filepath ) message = concat_messages( message, message2 ) - return tool, valid, message + return tool, valid, message, sample_files def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ): tool = None message = '' @@ -1490,7 +1490,7 @@ if manifest_ctx and ctx_file: tool, message2 = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) message = concat_messages( message, message2 ) - return tool, message + return tool, message, sample_files def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur) diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1010,9 +1010,8 @@ message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation ' message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' - message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool…" ' - message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' - message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.' + message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation of Galaxy tool shed repository tools ' + message += 'into a local Galaxy instance</a> section of the Galaxy tool shed wiki for all of the details.' return trans.show_error_message( message ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -620,7 +620,7 @@ can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir - tool, valid, message = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) if tool is not None: invalid_files_and_errors_tups = check_tool_input_params( trans.app, repo_files_dir, @@ -637,7 +637,7 @@ message = concat_messages( message, message2 ) status = 'error' else: - tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) try: shutil.rmtree( work_dir ) except: diff -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 -r 69f446023855cd7ed585ca6dde5ee581043e61f0 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -2301,11 +2301,18 @@ can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir - tool, valid, message = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, full_path_to_tool_config, work_dir ) + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, + repo_files_dir, + full_path_to_tool_config, + work_dir ) if message: status = 'error' else: - tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, + repo, + changeset_revision, + tool_config_filename, + work_dir ) if message: status = 'error' break Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Remove prefilled password/confirm/current fields from edit user info.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5f739cf9187b/ changeset: 5f739cf9187b user: dannon date: 2012-09-25 17:30:16 summary: Remove prefilled password/confirm/current fields from edit user info. affected #: 2 files diff -r e327eba84158eb62d0c5c76e77a62ae999fc3779 -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -694,6 +694,7 @@ else: widgets = user_type_form_definition.get_widgets( None, contents={}, **kwd ) return widgets + @web.expose def manage_user_info( self, trans, cntrller, **kwd ): '''Manage a user's login, password, public username, type, addresses, etc.''' @@ -707,11 +708,6 @@ raise AssertionError, "The user id (%s) is not valid" % str( user_id ) webapp = get_webapp( trans, **kwd ) email = util.restore_text( params.get( 'email', user.email ) ) - # Do not sanitize passwords, so take from kwd - # instead of params ( which were sanitized ) - current = kwd.get( 'current', '' ) - password = kwd.get( 'password', '' ) - confirm = kwd.get( 'confirm', '' ) username = util.restore_text( params.get( 'username', '' ) ) if not username: username = user.username @@ -721,7 +717,7 @@ user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) if user_type_fd_id == 'none' and user_type_form_definition is not None: - user_type_fd_id = trans.security.encode_id( user_type_form_definition.id ) + user_type_fd_id = trans.security.encode_id( user_type_form_definition.id ) user_type_fd_id_select_field = self.__build_user_type_fd_id_select_field( trans, selected_value=user_type_fd_id ) widgets = self.__get_widgets( trans, user_type_form_definition, user=user, **kwd ) # user's addresses @@ -739,14 +735,11 @@ cntrller=cntrller, user=user, email=email, - current=current, - password=password, - confirm=confirm, username=username, user_type_fd_id_select_field=user_type_fd_id_select_field, user_info_forms=user_info_forms, user_type_form_definition=user_type_form_definition, - widgets=widgets, + widgets=widgets, addresses=addresses, show_filter=show_filter, webapp=webapp, @@ -757,13 +750,11 @@ cntrller=cntrller, user=user, email=email, - current=current, - password=password, - confirm=confirm, username=username, webapp=webapp, message=message, status=status ) + # For REMOTE_USER, we need the ability to just edit the username @web.expose @web.require_login( "to manage the public name" ) diff -r e327eba84158eb62d0c5c76e77a62ae999fc3779 -r 5f739cf9187bde20a0b9d368bf83ffcac19eedc0 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -59,16 +59,16 @@ %if not is_admin: <div class="form-row"><label>Current password:</label> - <input type="password" name="current" value="${current}" size="40"/> + <input type="password" name="current" value="" size="40"/></div> %endif <div class="form-row"><label>New password:</label> - <input type="password" name="password" value="${password}" size="40"/> + <input type="password" name="password" value="" size="40"/></div><div class="form-row"><label>Confirm:</label> - <input type="password" name="confirm" value="${confirm}" size="40"/> + <input type="password" name="confirm" value="" size="40"/></div><div class="form-row"><input type="submit" name="change_password_button" value="Save"/> 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: dannon: Cleanup user controller imports, remove import *'s.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e327eba84158/ changeset: e327eba84158 user: dannon date: 2012-09-25 17:07:25 summary: Cleanup user controller imports, remove import *'s. affected #: 1 file diff -r b4e09ad8245967bc757c57f09a467bafd91ea370 -r e327eba84158eb62d0c5c76e77a62ae999fc3779 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -1,16 +1,22 @@ """ Contains the user interface in the Universe class """ + +import glob +import logging +import os +import socket +import string +import random +from galaxy import web +from galaxy import util, model +from galaxy.model.orm import and_ +from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password, transform_publicname +from galaxy.util.json import from_json_string, to_json_string +from galaxy.web import url_for +from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, get_webapp +from galaxy.web.form_builder import CheckboxField, build_select_field from galaxy.web.framework.helpers import time_ago, grids -from galaxy.web.base.controller import * -from galaxy.model.orm import * -from galaxy import util, model -import logging, os, string, re, socket, glob -from random import choice -from galaxy.web.form_builder import * -from galaxy.util.json import from_json_string, to_json_string -from galaxy.web.framework.helpers import iff -from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password, transform_publicname log = logging.getLogger( __name__ ) @@ -916,7 +922,7 @@ chars = string.letters + string.digits new_pass = "" for i in range(15): - new_pass = new_pass + choice(chars) + new_pass = new_pass + random.choice(chars) host = trans.request.host.split(':')[0] if host == 'localhost': host = socket.getfqdn() 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: jgoecks: Fixes for ReferenceTracks to make compatible with recent refactoring.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b4e09ad82459/ changeset: b4e09ad82459 user: jgoecks date: 2012-09-25 16:52:28 summary: Fixes for ReferenceTracks to make compatible with recent refactoring. affected #: 3 files diff -r cdd39c933d24e11b4f99b5d24e5d1b108fea41ea -r b4e09ad8245967bc757c57f09a467bafd91ea370 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -729,7 +729,7 @@ /** * Draw a single read. */ - draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) { + draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, ref_seq) { ctx.textAlign = "center"; var tile_region = [tile_low, tile_high], base_offset = 0, @@ -743,12 +743,12 @@ // Gap is needed so that read is offset and hence first base can be drawn on read. // TODO-FIX: using this gap offsets reads so that their start is not visually in sync with other tracks. - if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { + if ((mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { gap = Math.round(w_scale/2); } if (!cigar) { // If no cigar string, then assume all matches - cigar = [ [0, orig_seq.length] ]; + cigar = [ [0, ref_seq.length] ]; } for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) { var cig = cigar[cig_id], @@ -782,7 +782,8 @@ case "=": // Equals. if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { // Draw. - var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); + // -1 b/c sequence data is 1-based but painter is 0-based. + var seq = ref_seq.slice(seq_offset - 1, seq_offset + cig_len); if (gap > 0) { ctx.fillStyle = block_color; ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9); @@ -838,7 +839,8 @@ var insert_x_coord = s_start - gap; if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); + // -1 b/c sequence data is 1-based but painter is 0-based. + var seq = ref_seq.slice(seq_offset - 1, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. if (this.prefs.show_insertions) { @@ -849,7 +851,7 @@ // Draw sequence. // X center is offset + start - <half_sequence_length> var x_center = s_start - (s_end - s_start)/2; - if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { + if ( (mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { // Draw sequence container. ctx.fillStyle = "yellow"; ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); @@ -885,7 +887,7 @@ } } else { - if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { + if ( (mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } ); } diff -r cdd39c933d24e11b4f99b5d24e5d1b108fea41ea -r b4e09ad8245967bc757c57f09a467bafd91ea370 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3427,7 +3427,7 @@ 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 ReferenceTrackDataManager({ + this.data_manager = new visualization.ReferenceTrackDataManager({ data_url: this.data_url }); this.hide_contents(); diff -r cdd39c933d24e11b4f99b5d24e5d1b108fea41ea -r b4e09ad8245967bc757c57f09a467bafd91ea370 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -356,6 +356,13 @@ }); var ReferenceTrackDataManager = GenomeDataManager.extend({ + initialize: function(options) { + // Use generic object in place of dataset and set urlRoot to fetch data. + var dataset_placeholder = new Backbone.Model(); + dataset_placeholder.urlRoot = options.data_url; + this.set('dataset', dataset_placeholder); + }, + load_data: function(low, high, mode, resolution, extra_params) { if (resolution > 1) { // Now that data is pre-fetched before draw, we don't load reference tracks 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: dannon: HTML-escape registration fields. Remove prefilled password/confirm on create kickback.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cdd39c933d24/ changeset: cdd39c933d24 user: dannon date: 2012-09-25 16:35:45 summary: HTML-escape registration fields. Remove prefilled password/confirm on create kickback. affected #: 2 files diff -r d6d0c963712a9f85a6a2baede6ec402285088823 -r cdd39c933d24e11b4f99b5d24e5d1b108fea41ea lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -493,6 +493,7 @@ message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) success = True return ( message, status, user, success ) + @web.expose def logout( self, trans, webapp='galaxy', logout_all=False ): if webapp == 'galaxy': @@ -513,6 +514,7 @@ message=message, status='done', active_view="user" ) + @web.expose def create( self, trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd ): params = util.Params( kwd ) @@ -583,8 +585,6 @@ return trans.fill_template( '/user/register.mako', cntrller=cntrller, email=email, - password=password, - confirm=confirm, username=transform_publicname( trans, username ), subscribe_checked=subscribe_checked, user_type_fd_id_select_field=user_type_fd_id_select_field, @@ -597,6 +597,7 @@ refresh_frames=refresh_frames, message=message, status=status ) + def __register( self, trans, cntrller, subscribe_checked, **kwd ): email = util.restore_text( kwd.get( 'email', '' ) ) password = kwd.get( 'password', '' ) diff -r d6d0c963712a9f85a6a2baede6ec402285088823 -r cdd39c933d24e11b4f99b5d24e5d1b108fea41ea templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -3,7 +3,7 @@ %if redirect_url: <script type="text/javascript"> - top.location.href = '${redirect_url}'; + top.location.href = '${redirect_url | h}'; </script> %endif @@ -42,21 +42,21 @@ <div class="toolFormTitle">Create account</div><div class="form-row"><label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> - <input type="hidden" name="webapp" value="${webapp}" size="40"/> - <input type="hidden" name="redirect" value="${redirect}" size="40"/> + <input type="text" name="email" value="${email | h}" size="40"/> + <input type="hidden" name="webapp" value="${webapp | h}" size="40"/> + <input type="hidden" name="redirect" value="${redirect | h}" size="40"/></div><div class="form-row"><label>Password:</label> - <input type="password" name="password" value="${password}" size="40"/> + <input type="password" name="password" value="" size="40"/></div><div class="form-row"><label>Confirm password:</label> - <input type="password" name="confirm" value="${confirm}" size="40"/> + <input type="password" name="confirm" value="" size="40"/></div><div class="form-row"><label>Public name:</label> - <input type="text" name="username" size="40" value="${username}"/> + <input type="text" name="username" size="40" value="${username |h}"/> %if webapp == 'galaxy': <div class="toolParamHelp" style="clear: both;"> Your public name is an identifier that will be used to generate addresses for information 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: jgoecks: Viz framework: (a) improvements in setting dataset type when returning infomation; (b) transition Circster to use GenomeDataManager rather than custom data structures.
by Bitbucket 25 Sep '12

25 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d6d0c963712a/ changeset: d6d0c963712a user: jgoecks date: 2012-09-25 15:18:00 summary: Viz framework: (a) improvements in setting dataset type when returning infomation; (b) transition Circster to use GenomeDataManager rather than custom data structures. affected #: 7 files diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -113,7 +113,7 @@ class GenomeDataProvider( BaseDataProvider ): """ Base class for genome data providers. """ - data_type = None + dataset_type = None """ Mapping from column name to payload data; this mapping is used to create @@ -179,12 +179,21 @@ """ Returns data for complete genome. """ - dataset_summary = [] + genome_data = [] for chrom_info in chroms_info[ 'chrom_info' ]: - summary = self.get_data( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], **kwargs ) - dataset_summary.append( summary ) + chrom = chrom_info[ 'chrom' ] + chrom_len = chrom_info[ 'len' ] + chrom_data = self.get_data( chrom, 0, chrom_len, **kwargs ) + if chrom_data: + chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) + chrom_data[ 'dataset_type' ] = self.dataset_type + genome_data.append( chrom_data ) - return dataset_summary + return { + 'data': genome_data, + 'dataset_type': self.dataset_type + } + def get_filters( self ): """ @@ -316,7 +325,7 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): - data_type = 'tabix' + dataset_type = 'tabix' """ Tabix index data provider for the Galaxy track browser. @@ -358,7 +367,7 @@ # class IntervalDataProvider( GenomeDataProvider ): - data_type = 'interval_index' + dataset_type = 'interval_index' """ Processes interval data from native format to payload format. @@ -444,7 +453,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - data_type = 'interval_index' + dataset_type = 'interval_index' def get_iterator( self, chrom, start, end ): raise Exception( "Unimplemented Method" ) @@ -541,7 +550,7 @@ for large datasets. """ - data_type = 'interval_index' + dataset_type = 'interval_index' def get_iterator( self, chrom=None, start=None, end=None ): # Read first line in order to match chrom naming format. @@ -581,7 +590,7 @@ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - data_type = 'bai' + dataset_type = 'bai' def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ @@ -687,7 +696,7 @@ for large datasets. """ - data_type = 'tabix' + dataset_type = 'tabix' def get_iterator( self, chrom, start, end ): # Read first line in order to match chrom naming format. @@ -721,7 +730,7 @@ Summary tree data provider for the Galaxy track browser. """ - data_type = 'summary_tree' + dataset_type = 'summary_tree' CACHE = LRUCache( 20 ) # Store 20 recently accessed indices for performance @@ -765,7 +774,13 @@ if results == "detail" or results == "draw": return results else: - return results, stats[ level ][ "max" ], stats[ level ]["avg" ], stats[ level ][ "delta" ] + return { + 'dataset_type': self.dataset_type, + 'data': results, + 'max': stats[ level ][ "max" ], + 'avg': stats[ level ][ "avg" ], + 'delta': stats[ level ][ "delta" ] + } def has_data( self, chrom ): """ @@ -788,7 +803,7 @@ is reported in 1-based, closed format, i.e. SAM/BAM format. """ - data_type = 'bai' + dataset_type = 'bai' def get_filters( self ): """ @@ -970,7 +985,7 @@ class SamDataProvider( BamDataProvider ): - data_type = 'bai' + dataset_type = 'bai' def __init__( self, converted_dataset=None, original_dataset=None, dependencies=None ): """ Create SamDataProvider. """ @@ -987,7 +1002,7 @@ BBI data provider for the Galaxy track browser. """ - data_type = 'bigwig' + dataset_type = 'bigwig' def valid_chroms( self ): # No way to return this info as of now @@ -1122,7 +1137,7 @@ """ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - data_type = 'interval_index' + dataset_type = 'interval_index' def write_data_to_file( self, regions, filename ): source = open( self.original_dataset.file_name ) @@ -1201,7 +1216,7 @@ for large datasets. """ - data_type = 'interval_index' + dataset_type = 'interval_index' def get_iterator( self, chrom, start, end ): """ diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -139,12 +139,15 @@ if mode == "Coverage": # Get summary using minimal cutoffs. indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) - summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 ) + summary = indexer.get_data( chrom, low, high, + resolution=kwargs[ 'resolution' ], + level=kwargs.get( 'level', None ), + detail_cutoff=0, draw_cutoff=0 ) if summary == "detail": # Use maximum level of detail--2--to get summary data no matter the resolution. summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': indexer.data_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + return { 'dataset_type': indexer.dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": # Only check for summary_tree if it's Auto mode (which is the default) @@ -153,14 +156,13 @@ indexer = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ] ) if summary is None: - return { 'dataset_type': indexer.data_type, 'data': None } + return { 'dataset_type': indexer.dataset_type, 'data': None } if summary == "draw": kwargs["no_detail"] = True # meh extra_info = "no_detail" elif summary != "detail": - frequencies, max_v, avg_v, delta = summary - return { 'dataset_type': indexer.data_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } + return summary # Get data provider. data_provider = data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='data' ) @@ -171,7 +173,7 @@ # Get and return data from data_provider. result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs ) - result.update( { 'dataset_type': data_provider.data_type, 'extra_info': extra_info } ) + result.update( { 'dataset_type': data_provider.dataset_type, 'extra_info': extra_info } ) return result def _raw_data( self, trans, dataset, **kwargs ): diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -760,7 +760,7 @@ original_dataset=dataset, source='index' ) # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) } + track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,4 +1,4 @@ -define( ["libs/d3", "viz/visualization"], function( d3, visualization ) { +define( ["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) { // General backbone style inheritence var Base = function() { this.initialize && this.initialize.apply(this, arguments); }; Base.extend = Backbone.Model.extend; @@ -48,7 +48,8 @@ // Compute radius start based on model, will be centered // and fit entirely inside element by default. init_radius_start = ( Math.min(width, height)/2 - - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); + this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ), + tracks = this.model.get('tracks'); // Set up SVG element. var svg = d3.select(self.$el[0]) @@ -59,26 +60,37 @@ // Set up zooming, dragging. .append('svg:g') .call(d3.behavior.zoom().on('zoom', function() { + // Do zoom. svg.attr("transform", "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")"); - var utils = new SVGUtils(); - var visible_elts = d3.selectAll('path').filter(function(d, i) { + + // Update visible elements with more data. + var utils = new SVGUtils(), + tracks_and_chroms_to_update = {}; + + tracks.each(function(t) { + tracks_and_chroms_to_update[t.id] = []; + }); + + d3.selectAll('path.chrom-data').filter(function(d, i) { return utils.is_visible(this, svg); + }).each(function(d, i) { + var elt_data = $.data(this, "chrom_data"); + tracks_and_chroms_to_update[elt_data.track.id].push(elt_data.chrom); }); - visible_elts.each(function(d, i) { - // TODO: redraw visible elements. - }); + + // TODO: update tracks and chroms. + //console.log(tracks_and_chroms_to_update); })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g'); // -- Render each dataset in the visualization. -- - this.model.get('tracks').each(function(track, index) { - var dataset = track.get('genome_wide_data'), - radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), - track_renderer_class = (dataset instanceof visualization.GenomeWideBigWigData ? + tracks.each(function(track, index) { + var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), + track_renderer_class = (track.get('track_type') === 'LineTrack' ? CircsterBigWigTrackRenderer : CircsterSummaryTreeTrackRenderer ); @@ -160,12 +172,17 @@ render_data: function(svg) { var self = this, chrom_arcs = this.chroms_layout(), - dataset = this.options.track.get('genome_wide_data'), + track = this.options.track, r_start = this.options.radius_start, r_end = this.options.radius_end, + + genome_wide_data = track.get_genome_wide_data(this.options.genome), // Merge chroms layout with data. - layout_and_data = _.zip(chrom_arcs, dataset.get('data')), + layout_and_data = _.zip(chrom_arcs, genome_wide_data), + + // Get min, max in data. + bounds = this.get_bounds(genome_wide_data), // Do dataset layout for each chromosome's data using pie layout. chroms_data_layout = _.map(layout_and_data, function(chrom_info) { @@ -173,7 +190,7 @@ data = chrom_info[1]; return self.render_chrom_data(svg, chrom_arc, data, r_start, r_end, - dataset.get('min'), dataset.get('max')); + bounds.min, bounds.max); }); return chroms_data_layout; @@ -187,7 +204,7 @@ /** * Renders quantitative data with the form [x, value] and assumes data is equally spaced across - * chromosome. + * chromosome. Attachs a dict with track and chrom name information to DOM element. */ render_quantitative_data: function(svg, chrom_arc, data, inner_radius, outer_radius, min, max) { // Radius scaler. @@ -212,14 +229,25 @@ .angle(line.angle()); // Render data. - var parent = svg.datum(data); - - parent.append("path") - .attr("class", "chrom-data") - .attr("d", area); - } + var parent = svg.datum(data), + path = parent.append("path") + .attr("class", "chrom-data") + .attr("d", area); -}) + // Attach dict with track and chrom info for path. + $.data(path[0][0], "chrom_data", { + track: this.options.track, + chrom: chrom_arc.data.chrom + }); + }, + + /** + * Returns an object with min, max attributes denoting the minimum and maximum + * values for the track. + */ + get_bounds: function() {} + +}); /** * Layout for summary tree data in a circster visualization. @@ -235,7 +263,19 @@ return null; } - return this.render_quantitative_data(svg, chrom_arc, chrom_data[0], inner_radius, outer_radius, min, max); + return this.render_quantitative_data(svg, chrom_arc, chrom_data.data, inner_radius, outer_radius, min, max); + }, + + get_bounds: function(data) { + // Get max across data. + var max_data = _.map(data, function(d) { + if (!d || typeof d === 'string') { return 0; } + return d.max; + }); + return { + min: 0, + max: (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) + }; } }); @@ -252,6 +292,27 @@ if (data.length === 0) { return; } return this.render_quantitative_data(svg, chrom_arc, data, inner_radius, outer_radius, min, max); + }, + + get_bounds: function(data) { + // Set max across dataset by extracting all values, flattening them into a + // single array, and getting the min and max. + var values = _.flatten( _.map(data, function(d) { + if (d) { + // Each data point has the form [position, value], so return all values. + return _.map(d.data, function(p) { + return p[1]; + }); + } + else { + return 0; + } + }) ); + + return { + min: _.min(values), + max: _.max(values) + }; } }); diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3550,8 +3550,7 @@ track.vertical_range = undefined; return $.getJSON( track.dataset.url(), { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, - high: track.view.max_high, hda_ldda: track.hda_ldda, dataset_id: - track.dataset_id }, function(result) { + high: track.view.max_high, hda_ldda: track.hda_ldda }, function(result) { track.container_div.addClass( "line-track" ); var data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,4 +1,4 @@ -define( ["mvc/data", "viz/trackster/util" ], function(data, util) { +define( ["mvc/data", "viz/trackster/util" ], function(data_mod, util_mod) { /** * Model, view, and controller objects for Galaxy visualization framework. @@ -138,7 +138,6 @@ dataset: null, filters_manager: null, data_type: "data", - genome_wide_summary_data: null, data_mode_compatible: function(entry, mode) { return true; }, can_subset: function(entry) { return false; } }), @@ -150,7 +149,7 @@ data_is_ready: function() { var dataset = this.get('dataset'), ready_deferred = $.Deferred(), - ss_deferred = new util.ServerStateDeferred({ + ss_deferred = new util_mod.ServerStateDeferred({ ajax_settings: { url: this.get('dataset').url(), data: { @@ -176,7 +175,6 @@ var dataset = this.get('dataset'), params = { query: query, - dataset_id: dataset.id, hda_ldda: dataset.get('hda_ldda'), data_type: 'features' }; @@ -188,22 +186,17 @@ */ load_data: function(region, mode, resolution, extra_params) { // Setup data request params. - var params = { + var dataset = this.get('dataset'), + params = { "data_type": this.get('data_type'), "chrom": region.get('chrom'), "low": region.get('start'), "high": region.get('end'), "mode": mode, - "resolution": resolution - }, - dataset = this.get('dataset'); - - // ReferenceDataManager does not have dataset. - if (dataset) { - params.dataset_id = dataset.id; - params.hda_ldda = dataset.get('hda_ldda'); - } - + "resolution": resolution, + "hda_ldda": dataset.get('hda_ldda') + }; + $.extend(params, extra_params); // Add track filters to params. @@ -533,69 +526,53 @@ model: BrowserBookmark }); -var GenomeWideBigWigData = Backbone.Model.extend({ - defaults: { - data: null, - min: 0, - max: 0 - }, - - initialize: function(options) { - // Set max across dataset by extracting all values, flattening them into a - // single array, and getting the min and max. - var values = _.flatten( _.map(this.get('data'), function(d) { - if (d.data.length !== 0) { - // Each data point has the form [position, value], so return all values. - return _.map(d.data, function(p) { - return p[1]; - }); - } - else { - return 0; - } - }) ); - this.set('max', _.max(values)); - this.set('min', _.min(values)); - } -}); - -/** - * Genome-wide summary tree dataset. - */ -var GenomeWideSummaryTreeData = Backbone.RelationalModel.extend({ - defaults: { - data: null, - min: 0, - max: 0 - }, - - initialize: function(options) { - // Set max across dataset. - var max_data = _.max(this.get('data'), function(d) { - if (!d || typeof d === 'string') { return 0; } - return d[1]; - }); - this.attributes.max = (max_data && typeof max_data !== 'string' ? max_data[1] : 0); - } -}); - /** * A track of data in a genome visualization. */ // TODO: rename to Track and merge with Trackster's Track object. -var BackboneTrack = data.Dataset.extend({ +var BackboneTrack = data_mod.Dataset.extend({ initialize: function(options) { // Dataset id is unique ID for now. this.set('id', options.dataset_id); - // Create genome-wide dataset if available. - var genome_wide_data = this.get('genome_wide_data'); - if (genome_wide_data) { - var gwd_class = (this.get('track_type') === 'LineTrack' ? - GenomeWideBigWigData : GenomeWideSummaryTreeData); - this.set('genome_wide_data', new gwd_class(genome_wide_data)); + // Set up data manager. + var data_manager = new GenomeDataManager({ + dataset: this + }); + this.set('data_manager', data_manager); + + // If there's preloaded data, add it to data manager. + var preloaded_data = this.get('preloaded_data'); + if (preloaded_data) { + // Increase size to accomodate all preloaded data. + data_manager.set('num_elements', preloaded_data.data.length); + + // Put data into manager. + _.each(preloaded_data.data, function(entry) { + data_manager.set_data(entry.region, entry); + }); } + }, + + /** + * Returns an array of data with each entry representing one chromosome/contig + * of data. + */ + get_genome_wide_data: function(genome) { + var self = this, + data_manager = this.get('data_manager'); + + // Map chromosome data into track data. + return _.map(genome.get('chroms_info').chrom_info, function(chrom_info) { + return data_manager.get_elt( + new GenomeRegion({ + chrom: chrom_info.chrom, + start: 0, + end: chrom_info.len + }) + ); + }); } }); @@ -716,7 +693,7 @@ }, id = $(this).val(); if ($(this).attr("name") !== "id") { - data['hda_ldda'] = 'ldda'; + data.hda_ldda = 'ldda'; } requests[requests.length] = $.ajax({ url: add_track_async_url + "/" + id, @@ -754,8 +731,6 @@ GenomeRegion: GenomeRegion, GenomeRegionCollection: GenomeRegionCollection, GenomeVisualization: GenomeVisualization, - GenomeWideBigWigData: GenomeWideBigWigData, - GenomeWideSummaryTreeData: GenomeWideSummaryTreeData, ReferenceTrackDataManager: ReferenceTrackDataManager, TrackBrowserRouter: TrackBrowserRouter, TrackConfig: TrackConfig, diff -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a -r d6d0c963712a9f85a6a2baede6ec402285088823 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -23,6 +23,7 @@ require.config({ baseUrl: "${h.url_for('/static/scripts')}", shim: { + "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" } } }); 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: dannon: Prevent potential login XSS.
by Bitbucket 24 Sep '12

24 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36ca2ecd42fd/ changeset: 36ca2ecd42fd user: dannon date: 2012-09-24 19:55:35 summary: Prevent potential login XSS. affected #: 2 files diff -r 327632b4f9992b2c3f4b9c6f705bed1f4e05914d -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -395,6 +395,7 @@ use_panels=use_panels, message=message, status=status ) ) + @web.expose @web.require_login( 'manage OpenIDs' ) def openid_manage( self, trans, webapp='galaxy', **kwd ): @@ -409,10 +410,10 @@ action='openid_disassociate', use_panels=use_panels, id=kwd['id'] ) ) - kwd['redirect'] = kwd.get( 'redirect', url_for( controller='user', action='openid_manage', use_panels=True ) ).strip() kwd['openid_providers'] = trans.app.openid_providers return self.user_openid_grid( trans, **kwd ) + @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): '''Handle Galaxy Log in''' @@ -423,6 +424,9 @@ header = '' user = None email = kwd.get( 'email', '' ) + #Sanitize webapp login here, once, since it can be reflected to the user in messages/etc. + #Only text is valid. + webapp = util.sanitize_text(webapp) if kwd.get( 'login_button', False ): if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: diff -r 327632b4f9992b2c3f4b9c6f705bed1f4e05914d -r 36ca2ecd42fdbc581b0caa253b66a136aa0f848a templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -30,7 +30,7 @@ %if redirect_url: <script type="text/javascript"> - top.location.href = '${redirect_url}'; + top.location.href = '${redirect_url | h}'; </script> %endif @@ -81,9 +81,9 @@ <form name="login" id="login" action="${form_action}" method="post" ><div class="form-row"><label>Email address:</label> - <input type="text" name="email" value="${email}" size="40"/> - <input type="hidden" name="webapp" value="${webapp}" size="40"/> - <input type="hidden" name="redirect" value="${redirect}" size="40"/> + <input type="text" name="email" value="${email | h}" size="40"/> + <input type="hidden" name="webapp" value="${webapp | h}" size="40"/> + <input type="hidden" name="redirect" value="${redirect | h}" size="40"/></div><div class="form-row"><label>Password:</label> @@ -107,8 +107,8 @@ <div class="form-row"><label>OpenID URL:</label><input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/> - <input type="hidden" name="webapp" value="${webapp}" size="40"/> - <input type="hidden" name="redirect" value="${redirect}" size="40"/> + <input type="hidden" name="webapp" value="${webapp | h}" size="40"/> + <input type="hidden" name="redirect" value="${redirect | h}" size="40"/></div><div class="form-row"> Or, authenticate with your <select name="openid_provider"> 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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