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[galaxyproject/usegalaxy-playbook] 5171f8: Update Test.
by GitHub 28 Jan '15

28 Jan '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5171f8218643ed986a76281dd821a0000f605b87 https://github.com/galaxyproject/usegalaxy-playbook/commit/5171f8218643ed98… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-01-28 (Wed, 28 Jan 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test.

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commit/galaxy-central: natefoo: Merged in natefoo/galaxy-central/samtools1_bam_index (pull request #651)
by commits-noreply＠bitbucket.org 28 Jan '15

28 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f0a96002a553/ Changeset: f0a96002a553 User: natefoo Date: 2015-01-28 18:36:35+00:00 Summary: Merged in natefoo/galaxy-central/samtools1_bam_index (pull request #651) Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1. Affected #: 1 file diff -r c8ba5ce3b64af0fa6564744c0e45fc4c4ae1d450 -r f0a96002a5538b1b5e2ebafe8f80a64ed299b418 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -264,10 +264,23 @@ ##$ samtools index ##Usage: samtools index <in.bam> [<out.index>] stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name - command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name ) - proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) + command = [ 'samtools', 'index', dataset.file_name, index_file.file_name ] + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) exit_code = proc.wait() #Did index succeed? + if exit_code == -6: + # SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter. + dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ), + '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) + os.symlink( dataset.file_name, dataset_symlink ) + try: + command = [ 'samtools', 'index', dataset_symlink ] + exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) + shutil.move( dataset_symlink + '.bai', index_file.file_name ) + except Exception, e: + open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n' % e) + finally: + os.unlink( dataset_symlink ) stderr = open( stderr_name ).read().strip() if stderr: if exit_code != 0: 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: 4 new changesets
by commits-noreply＠bitbucket.org 28 Jan '15

28 Jan '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/402569731d73/ Changeset: 402569731d73 Branch: samtools1_bam_index User: natefoo Date: 2015-01-28 15:38:22+00:00 Summary: Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1. Affected #: 1 file diff -r 01c1ca281fba5d2fc38f7fcaec30c7c358bcf268 -r 402569731d731d794f07838388609ad859345fa2 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -264,10 +264,19 @@ ##$ samtools index ##Usage: samtools index <in.bam> [<out.index>] stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name - command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name ) - proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) + command = [ 'samtools', 'index', dataset.file_name, index_file.file_name ] + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) exit_code = proc.wait() #Did index succeed? + if exit_code == -6: + # SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter. + command = [ 'samtools', 'index', dataset.file_name ] + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) + exit_code = proc.wait() + if os.path.exists( os.path.join( dataset.file_name, '.bai' ) ): + shutil.move( os.path.join( dataset.file_name, '.bai' ), index_file.file_name ) + else: + open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed\n') stderr = open( stderr_name ).read().strip() if stderr: if exit_code != 0: https://bitbucket.org/galaxy/galaxy-central/commits/b3a163116fac/ Changeset: b3a163116fac Branch: samtools1_bam_index User: natefoo Date: 2015-01-28 16:58:23+00:00 Summary: Use a symlink to the dataset in the same directory as the MetadataTempFile as the input to samtools index so there's no clobber risk. Thanks Dan. Affected #: 1 file diff -r 402569731d731d794f07838388609ad859345fa2 -r b3a163116fac6b6b554524e70b3a2f4058fef1e8 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -270,13 +270,18 @@ #Did index succeed? if exit_code == -6: # SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter. - command = [ 'samtools', 'index', dataset.file_name ] - proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) - exit_code = proc.wait() - if os.path.exists( os.path.join( dataset.file_name, '.bai' ) ): - shutil.move( os.path.join( dataset.file_name, '.bai' ), index_file.file_name ) - else: - open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed\n') + dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ), + '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) + os.symlink( dataset.file_name, dataset_symlink ) + try: + command = [ 'samtools', 'index', dataset_symlink ] + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) + exit_code = proc.wait() + shutil.move( dataset_symlink + '.bai', index_file.file_name ) + except Exception, e: + open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n' % e) + finally: + os.unlink( dataset_symlink ) stderr = open( stderr_name ).read().strip() if stderr: if exit_code != 0: https://bitbucket.org/galaxy/galaxy-central/commits/8d9cbbb3374f/ Changeset: 8d9cbbb3374f Branch: samtools1_bam_index User: natefoo Date: 2015-01-28 18:25:11+00:00 Summary: Use subprocess.call() rather than Popen(), thanks Nicola. Affected #: 1 file diff -r b3a163116fac6b6b554524e70b3a2f4058fef1e8 -r 8d9cbbb3374f203a15f1c4e8c59e067c05b62cec lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -275,8 +275,7 @@ os.symlink( dataset.file_name, dataset_symlink ) try: command = [ 'samtools', 'index', dataset_symlink ] - proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) - exit_code = proc.wait() + exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) shutil.move( dataset_symlink + '.bai', index_file.file_name ) except Exception, e: open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n' % e) https://bitbucket.org/galaxy/galaxy-central/commits/f0a96002a553/ Changeset: f0a96002a553 User: natefoo Date: 2015-01-28 18:36:35+00:00 Summary: Merged in natefoo/galaxy-central/samtools1_bam_index (pull request #651) Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1. Affected #: 1 file diff -r c8ba5ce3b64af0fa6564744c0e45fc4c4ae1d450 -r f0a96002a5538b1b5e2ebafe8f80a64ed299b418 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -264,10 +264,23 @@ ##$ samtools index ##Usage: samtools index <in.bam> [<out.index>] stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name - command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name ) - proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) + command = [ 'samtools', 'index', dataset.file_name, index_file.file_name ] + proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) exit_code = proc.wait() #Did index succeed? + if exit_code == -6: + # SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter. + dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ), + '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) + os.symlink( dataset.file_name, dataset_symlink ) + try: + command = [ 'samtools', 'index', dataset_symlink ] + exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) + shutil.move( dataset_symlink + '.bai', index_file.file_name ) + except Exception, e: + open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n' % e) + finally: + os.unlink( dataset_symlink ) stderr = open( stderr_name ).read().strip() if stderr: if exit_code != 0: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for XmlToolSource.parse_command() to return None when a command element does not exist or text is empty.
by commits-noreply＠bitbucket.org 28 Jan '15

28 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8ba5ce3b64a/ Changeset: c8ba5ce3b64a User: dan Date: 2015-01-28 17:09:56+00:00 Summary: Fix for XmlToolSource.parse_command() to return None when a command element does not exist or text is empty. Affected #: 1 file diff -r 43c52ed25263e787f922c902590df41929edb0d8 -r c8ba5ce3b64af0fa6564744c0e45fc4c4ae1d450 lib/galaxy/tools/parser/xml.py --- a/lib/galaxy/tools/parser/xml.py +++ b/lib/galaxy/tools/parser/xml.py @@ -79,7 +79,7 @@ def parse_command(self): command_el = self._command_el - return (command_el is not None) and command_el.text + return ( ( command_el is not None ) and command_el.text ) or None def parse_interpreter(self): command_el = self._command_el 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: 6 new changesets
by commits-noreply＠bitbucket.org 28 Jan '15

28 Jan '15

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a2a8f96e7cb4/ Changeset: a2a8f96e7cb4 User: davebgx Date: 2015-01-28 16:49:48+00:00 Summary: Remove the alert popups from the repository and tool dependency installation status pages. Affected #: 2 files diff -r 01c1ca281fba5d2fc38f7fcaec30c7c358bcf268 -r a2a8f96e7cb49c4799d1ab9d86cc1e866d7e5cec templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -259,9 +259,6 @@ }); tool_dependency_status_updater( dependency_status_list ); }, - error: function() { - alert( "tool_dependency_status_updater_callback failed..." ); - } }); }; </script> @@ -317,9 +314,6 @@ }); tool_shed_repository_status_updater( repository_status_list ); }, - error: function() { - alert( "tool_shed_repository_status_updater_callback failed..." ); - } }); }; </script> diff -r 01c1ca281fba5d2fc38f7fcaec30c7c358bcf268 -r a2a8f96e7cb49c4799d1ab9d86cc1e866d7e5cec templates/admin/tool_shed_repository/initiate_repository_installation.mako --- a/templates/admin/tool_shed_repository/initiate_repository_installation.mako +++ b/templates/admin/tool_shed_repository/initiate_repository_installation.mako @@ -23,9 +23,6 @@ success : function ( data ) { //alert( "Initializing repository installation succeeded" ); }, - error: function() { - alert( "Initializing repository installation failed" ); - }, }); }; </script> https://bitbucket.org/galaxy/galaxy-central/commits/43c52ed25263/ Changeset: 43c52ed25263 User: davebgx Date: 2015-01-28 16:50:31+00:00 Summary: Allow a Galaxy admin to configure environment variables (e.g. $PATH) for their local Galaxy installation without altering the environment for their shell. Affected #: 1 file diff -r a2a8f96e7cb49c4799d1ab9d86cc1e866d7e5cec -r 43c52ed25263e787f922c902590df41929edb0d8 run.sh --- a/run.sh +++ b/run.sh @@ -10,6 +10,18 @@ . .venv/bin/activate fi +# If there is a file that defines a shell environment specific to this +# instance of Galaxy, source the file. +if [ -z "$GALAXY_LOCAL_ENV_FILE" ]; +then + GALAXY_LOCAL_ENV_FILE='./config/local_env.sh' +fi + +if [ -f $GALAXY_LOCAL_ENV_FILE ]; +then + . $GALAXY_LOCAL_ENV_FILE +fi + python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 https://bitbucket.org/galaxy/galaxy-central/commits/725252d2e51f/ Changeset: 725252d2e51f Branch: trevorw/add-template_cache_path-to-reports_wsgii-1422042129382 User: davebgx Date: 2015-01-28 16:53:07+00:00 Summary: Close merged branch trevorw/add-template_cache_path-to-reports_wsgii-1422042129382 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/f24d1447157e/ Changeset: f24d1447157e Branch: compressed_upload User: davebgx Date: 2015-01-28 16:53:35+00:00 Summary: Close merged branch compressed_upload Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/751a0bbe3363/ Changeset: 751a0bbe3363 Branch: snpeff_datatype User: davebgx Date: 2015-01-28 16:53:51+00:00 Summary: Close merged branch snpeff_datatype Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/0ead515a64b2/ Changeset: 0ead515a64b2 Branch: toolshed_blacklist_additions User: davebgx Date: 2015-01-28 16:54:03+00:00 Summary: Close merged branch toolshed_blacklist_additions Affected #: 0 files 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: Update tag latest_2015.01.13 for changeset 1b96d3a4ff28
by commits-noreply＠bitbucket.org 28 Jan '15

28 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/837baf8a92ad/ Changeset: 837baf8a92ad Branch: stable User: natefoo Date: 2015-01-28 14:00:26+00:00 Summary: Update tag latest_2015.01.13 for changeset 1b96d3a4ff28 Affected #: 1 file diff -r 1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 -r 837baf8a92add3084c7e230cf537016192a78b55 .hgtags --- a/.hgtags +++ b/.hgtags @@ -22,4 +22,4 @@ 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -4039bfd5584aac053f686197a76ac176253e6f3d latest_2015.01.13 +1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 latest_2015.01.13 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: ToolForm: Fix configuration flag
by commits-noreply＠bitbucket.org 27 Jan '15

27 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01c1ca281fba/ Changeset: 01c1ca281fba User: guerler Date: 2015-01-27 23:31:20+00:00 Summary: ToolForm: Fix configuration flag Affected #: 2 files diff -r 98fd2a336caa70166c26e005f7198369b97e1645 -r 01c1ca281fba5d2fc38f7fcaec30c7c358bcf268 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -759,7 +759,7 @@ # -- Beta features # Use new tool form -#toolform_upgrade = False +toolform_upgrade = True # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False diff -r 98fd2a336caa70166c26e005f7198369b97e1645 -r 01c1ca281fba5d2fc38f7fcaec30c7c358bcf268 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -4,7 +4,7 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')} ## skip new tool form code if disabled -##%if trans.app.config.get('toolform_upgrade', False): +##%if util.string_as_bool(trans.app.config.get('toolform_upgrade', False)): <% ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. ## This avoids making two separate requests since the classic form requires the mako anyway. 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 27 Jan '15

27 Jan '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d655c8a1633/ Changeset: 6d655c8a1633 User: martenson Date: 2015-01-27 23:13:50+00:00 Summary: add pretty_print_time_interval to make time intervals more readable Affected #: 1 file diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 6d655c8a163316b2af7f5fa9f49dbee5bf58073c lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -24,6 +24,7 @@ import threading from galaxy.util import json +from datetime import datetime from email.MIMEText import MIMEText @@ -336,6 +337,63 @@ return value +def pretty_print_time_interval( time = False, precise = False ): + """ + Get a datetime object or a int() Epoch timestamp and return a + pretty string like 'an hour ago', 'Yesterday', '3 months ago', + 'just now', etc + credit: http://stackoverflow.com/questions/1551382/user-friendly-time-format-in-pyt… + """ + now = datetime.now() + if type( time ) is int: + diff = now - datetime.fromtimestamp( time ) + elif isinstance( time, datetime ): + diff = now - time + elif not time: + diff = now - now + second_diff = diff.seconds + day_diff = diff.days + + if day_diff < 0: + return '' + + if precise: + if day_diff == 0: + if second_diff < 10: + return "just now" + if second_diff < 60: + return str(second_diff) + " seconds ago" + if second_diff < 120: + return "a minute ago" + if second_diff < 3600: + return str(second_diff / 60) + " minutes ago" + if second_diff < 7200: + return "an hour ago" + if second_diff < 86400: + return str(second_diff / 3600) + " hours ago" + if day_diff == 1: + return "Yesterday" + if day_diff < 7: + return str( day_diff ) + " days ago" + if day_diff < 31: + return str( day_diff / 7 ) + " weeks ago" + if day_diff < 365: + return str( day_diff / 30 ) + " months ago" + return str( day_diff / 365 ) + " years ago" + else: + if day_diff == 0: + return "Today" + if day_diff == 1: + return "Yesterday" + if day_diff < 7: + return "this week" + if day_diff < 31: + return "this month" + if day_diff < 365: + return "this year" + return str( day_diff / 365 ) + " years ago" + + def pretty_print_json(json_data, is_json_string=False): if is_json_string: json_data = json.loads(json_data) https://bitbucket.org/galaxy/galaxy-central/commits/39483e4a5cbf/ Changeset: 39483e4a5cbf User: martenson Date: 2015-01-27 23:14:27+00:00 Summary: use the new pretty_print_time_interval method from utils Affected #: 1 file diff -r 6d655c8a163316b2af7f5fa9f49dbee5bf58073c -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -1,8 +1,8 @@ """Module for searching the toolshed repositories""" import datetime -import dateutil.relativedelta from galaxy import exceptions from galaxy import eggs +from galaxy.util import pretty_print_time_interval from galaxy.web.base.controller import BaseAPIController from galaxy.webapps.tool_shed import model from tool_shed.util.shed_util_common import generate_sharable_link_for_repository_in_tool_shed @@ -117,18 +117,9 @@ hit_dict[ 'url'] = generate_sharable_link_for_repository_in_tool_shed( repo ) # Format the time since last update to be nicely readable. - dt1 = repo.update_time - dt2 = datetime.datetime.now() - rd = dateutil.relativedelta.relativedelta (dt2, dt1) - time_ago = '' - if rd.years > 0: - time_ago += str( rd.years ) + 'years' - if rd.months > 0: - time_ago += str( rd.months ) + ' months' - if rd.days > 0: - time_ago += str( rd.days ) + ' days ago' + time_ago = pretty_print_time_interval( repo.update_time ) hit_dict[ 'last_updated' ] = time_ago - + hit_dict[ 'full_last_updated' ] = repo.update_time.strftime( "%Y-%m-%d %I:%M %p" ) hit_dict[ 'times_downloaded' ] = repo.times_downloaded hit_dict[ 'approved' ] = approved results[ 'hits' ].append( {'repository': hit_dict, 'matched_terms': hit.matched_terms() } ) https://bitbucket.org/galaxy/galaxy-central/commits/98fd2a336caa/ Changeset: 98fd2a336caa User: martenson Date: 2015-01-27 23:15:10+00:00 Summary: Merge Affected #: 14 files diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -18,7 +18,9 @@ // shows form in compact view mode compact : false, // shows errors on start - initial_errors : false + initial_errors : false, + // use default value for disabled fields + use_defaults : false }; // configure options @@ -280,8 +282,7 @@ // create tool form section this.section = new ToolSection.View(self, { - inputs : options.inputs, - cls : 'ui-table-plain' + inputs : options.inputs }); // switch to classic tool form mako if the form definition is incompatible diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -21,6 +21,7 @@ // set labels this.options.text_enable = 'In Advance'; this.options.text_disable = 'At Runtime'; + this.options.use_defaults = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -14,10 +14,13 @@ // link inputs this.inputs = options.inputs; + // fix table style + options.cls = 'ui-table-plain'; + // add table class for tr tag // this assist in transforming the form into a json structure options.cls_tr = 'section-row'; - + // create table this.table = new Table.View(options); @@ -132,8 +135,7 @@ // create sub section var sub_section = new View(this.app, { - inputs : input_def.cases[i].inputs, - cls : 'ui-table-plain' + inputs : input_def.cases[i].inputs }); // displays as grouped subsection @@ -181,8 +183,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : inputs, - cls : 'ui-table-plain' + inputs : inputs }); // add tab @@ -255,8 +256,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' + inputs : input_def.inputs }); // delete button diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -123,8 +123,16 @@ } // validate value - if ((field.skip && input.optional) || (field.validate && !field.validate())) { - value = null; + var skipped = field.skip && input.optional; + var unvalidated = field.validate && !field.validate(); + if (!self.app.options.use_defaults) { + if (skipped || unvalidated) { + value = null; + } + } else { + if (!skipped && unvalidated) { + value = null; + } } // ignore certain values diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -18,7 +18,9 @@ // shows form in compact view mode compact : false, // shows errors on start - initial_errors : false + initial_errors : false, + // use default value for disabled fields + use_defaults : false }; // configure options @@ -280,8 +282,7 @@ // create tool form section this.section = new ToolSection.View(self, { - inputs : options.inputs, - cls : 'ui-table-plain' + inputs : options.inputs }); // switch to classic tool form mako if the form definition is incompatible diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -21,6 +21,7 @@ // set labels this.options.text_enable = 'In Advance'; this.options.text_disable = 'At Runtime'; + this.options.use_defaults = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -14,10 +14,13 @@ // link inputs this.inputs = options.inputs; + // fix table style + options.cls = 'ui-table-plain'; + // add table class for tr tag // this assist in transforming the form into a json structure options.cls_tr = 'section-row'; - + // create table this.table = new Table.View(options); @@ -132,8 +135,7 @@ // create sub section var sub_section = new View(this.app, { - inputs : input_def.cases[i].inputs, - cls : 'ui-table-plain' + inputs : input_def.cases[i].inputs }); // displays as grouped subsection @@ -181,8 +183,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : inputs, - cls : 'ui-table-plain' + inputs : inputs }); // add tab @@ -255,8 +256,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' + inputs : input_def.inputs }); // delete button diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -123,8 +123,16 @@ } // validate value - if ((field.skip && input.optional) || (field.validate && !field.validate())) { - value = null; + var skipped = field.skip && input.optional; + var unvalidated = field.validate && !field.validate(); + if (!self.app.options.use_defaults) { + if (skipped || unvalidated) { + value = null; + } + } else { + if (!skipped && unvalidated) { + value = null; + } } // ignore certain values diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,compact:false,initial_errors:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.compact&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.compact&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.compact&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.compact){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,compact:false,initial_errors:false,use_defaults:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.compact&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.compact&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.compact&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.compact){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.use_defaults=true;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs,cls:"ui-table-plain"});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i,cls:"ui-table-plain"});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs,cls:"ui-table-plain"});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if((t.skip&&u.optional)||(t.validate&&!t.validate())){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(l,n){for(var p in n){var w=n[p];if(w.input){var s=w.input;var t=l;if(l!=""){t+="|"}t+=s.name;switch(s.type){case"repeat":var k="section-";var q=[];var m=null;for(var r in w){var o=r.indexOf(k);if(o!=-1){o+=k.length;q.push(parseInt(r.substr(o)));if(!m){m=r.substr(0,o)}}}q.sort(function(A,i){return A-i});var p=0;for(var x in q){c(t+"_"+p++,w[m+q[x]])}break;case"conditional":var v=b.app.field_list[s.id].value();if(g[s.test_param.type]){v=g[s.test_param.type](v)}d(t+"|"+s.test_param.name,s.id,v);var u=b.matchCase(s,v);if(u!=-1){c(t,n[s.id+"-section-"+u])}break;case"section":c("",w);break;default:var j=b.app.field_list[s.id];if(j&&j.value){var v=j.value();if(g[s.type]){v=g[s.type](v)}var z=j.skip&&s.optional;var h=j.validate&&!j.validate();if(!b.app.options.use_defaults){if(z||h){v=null}}else{if(!z&&h){v=null}}if(s.ignore===undefined||(v!==null&&s.ignore!=v)){d(t,s.id,v);if(s.payload){for(var y in s.payload){d(y,s.id,s.payload[y])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1397,7 +1397,7 @@ .ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-table tbody{cursor:pointer} -.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important} +.ui-table-plain{table-layout:fixed}.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important} .ui-table-plain tbody{cursor:auto !important} .ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} .ui-table-form-element .ui-table-form-field{margin-top:5px} diff -r 39483e4a5cbfbec5d0603b3e910a315ed52768dd -r 98fd2a336caa70166c26e005f7198369b97e1645 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -33,6 +33,7 @@ .ui-table-plain { &:extend(.grid); + table-layout:fixed; tbody td { padding: 5px 0px 5px 0px !important; 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: ToolForm: Fix select2 width, adjust argument parsing
by commits-noreply＠bitbucket.org 27 Jan '15

27 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/08bacc9d402e/ Changeset: 08bacc9d402e User: guerler Date: 2015-01-27 23:02:09+00:00 Summary: ToolForm: Fix select2 width, adjust argument parsing Affected #: 14 files diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -18,7 +18,9 @@ // shows form in compact view mode compact : false, // shows errors on start - initial_errors : false + initial_errors : false, + // use default value for disabled fields + use_defaults : false }; // configure options @@ -280,8 +282,7 @@ // create tool form section this.section = new ToolSection.View(self, { - inputs : options.inputs, - cls : 'ui-table-plain' + inputs : options.inputs }); // switch to classic tool form mako if the form definition is incompatible diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -21,6 +21,7 @@ // set labels this.options.text_enable = 'In Advance'; this.options.text_disable = 'At Runtime'; + this.options.use_defaults = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -14,10 +14,13 @@ // link inputs this.inputs = options.inputs; + // fix table style + options.cls = 'ui-table-plain'; + // add table class for tr tag // this assist in transforming the form into a json structure options.cls_tr = 'section-row'; - + // create table this.table = new Table.View(options); @@ -132,8 +135,7 @@ // create sub section var sub_section = new View(this.app, { - inputs : input_def.cases[i].inputs, - cls : 'ui-table-plain' + inputs : input_def.cases[i].inputs }); // displays as grouped subsection @@ -181,8 +183,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : inputs, - cls : 'ui-table-plain' + inputs : inputs }); // add tab @@ -255,8 +256,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' + inputs : input_def.inputs }); // delete button diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -123,8 +123,16 @@ } // validate value - if ((field.skip && input.optional) || (field.validate && !field.validate())) { - value = null; + var skipped = field.skip && input.optional; + var unvalidated = field.validate && !field.validate(); + if (!self.app.options.use_defaults) { + if (skipped || unvalidated) { + value = null; + } + } else { + if (!skipped && unvalidated) { + value = null; + } } // ignore certain values diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -18,7 +18,9 @@ // shows form in compact view mode compact : false, // shows errors on start - initial_errors : false + initial_errors : false, + // use default value for disabled fields + use_defaults : false }; // configure options @@ -280,8 +282,7 @@ // create tool form section this.section = new ToolSection.View(self, { - inputs : options.inputs, - cls : 'ui-table-plain' + inputs : options.inputs }); // switch to classic tool form mako if the form definition is incompatible diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -21,6 +21,7 @@ // set labels this.options.text_enable = 'In Advance'; this.options.text_disable = 'At Runtime'; + this.options.use_defaults = true; // declare fields as optional Utils.deepeach(options.inputs, function(item) { diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -14,10 +14,13 @@ // link inputs this.inputs = options.inputs; + // fix table style + options.cls = 'ui-table-plain'; + // add table class for tr tag // this assist in transforming the form into a json structure options.cls_tr = 'section-row'; - + // create table this.table = new Table.View(options); @@ -132,8 +135,7 @@ // create sub section var sub_section = new View(this.app, { - inputs : input_def.cases[i].inputs, - cls : 'ui-table-plain' + inputs : input_def.cases[i].inputs }); // displays as grouped subsection @@ -181,8 +183,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : inputs, - cls : 'ui-table-plain' + inputs : inputs }); // add tab @@ -255,8 +256,7 @@ // create sub section var sub_section = new View(self.app, { - inputs : input_def.inputs, - cls : 'ui-table-plain' + inputs : input_def.inputs }); // delete button diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -123,8 +123,16 @@ } // validate value - if ((field.skip && input.optional) || (field.validate && !field.validate())) { - value = null; + var skipped = field.skip && input.optional; + var unvalidated = field.validate && !field.validate(); + if (!self.app.options.use_defaults) { + if (skipped || unvalidated) { + value = null; + } + } else { + if (!skipped && unvalidated) { + value = null; + } } // ignore certain values diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,compact:false,initial_errors:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.compact&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.compact&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.compact&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.compact){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,compact:false,initial_errors:false,use_defaults:false};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.compact&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.compact&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.compact&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(u.compact){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.use_defaults=true;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs,cls:"ui-table-plain"});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i,cls:"ui-table-plain"});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs,cls:"ui-table-plain"});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if((t.skip&&u.optional)||(t.validate&&!t.validate())){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(l,n){for(var p in n){var w=n[p];if(w.input){var s=w.input;var t=l;if(l!=""){t+="|"}t+=s.name;switch(s.type){case"repeat":var k="section-";var q=[];var m=null;for(var r in w){var o=r.indexOf(k);if(o!=-1){o+=k.length;q.push(parseInt(r.substr(o)));if(!m){m=r.substr(0,o)}}}q.sort(function(A,i){return A-i});var p=0;for(var x in q){c(t+"_"+p++,w[m+q[x]])}break;case"conditional":var v=b.app.field_list[s.id].value();if(g[s.test_param.type]){v=g[s.test_param.type](v)}d(t+"|"+s.test_param.name,s.id,v);var u=b.matchCase(s,v);if(u!=-1){c(t,n[s.id+"-section-"+u])}break;case"section":c("",w);break;default:var j=b.app.field_list[s.id];if(j&&j.value){var v=j.value();if(g[s.type]){v=g[s.type](v)}var z=j.skip&&s.optional;var h=j.validate&&!j.validate();if(!b.app.options.use_defaults){if(z||h){v=null}}else{if(!z&&h){v=null}}if(s.ignore===undefined||(v!==null&&s.ignore!=v)){d(t,s.id,v);if(s.payload){for(var y in s.payload){d(y,s.id,s.payload[y])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1397,7 +1397,7 @@ .ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-table tbody{cursor:pointer} -.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important} +.ui-table-plain{table-layout:fixed}.ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important} .ui-table-plain tbody{cursor:auto !important} .ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} .ui-table-form-element .ui-table-form-field{margin-top:5px} diff -r 73a261a75185704a35a05350a31a7d5169cbc9b0 -r 08bacc9d402e75a70ddc249c959ccac846e0512f static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -33,6 +33,7 @@ .ui-table-plain { &:extend(.grid); + table-layout:fixed; tbody td { padding: 5px 0px 5px 0px !important; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 27 Jan '15

27 Jan '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2228c58015cb/ Changeset: 2228c58015cb User: martenson Date: 2015-01-27 00:45:33+00:00 Summary: query parser experiments, better formatted time delta Affected #: 1 file diff -r 0733c87123cbc2f7009a125c5e57d630bb8296a6 -r 2228c58015cb928e8c2819614e2a69b70ea4f448 lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -1,11 +1,11 @@ """Module for searching the toolshed repositories""" +import datetime +import dateutil.relativedelta from galaxy import exceptions from galaxy import eggs from galaxy.web.base.controller import BaseAPIController from galaxy.webapps.tool_shed import model from tool_shed.util.shed_util_common import generate_sharable_link_for_repository_in_tool_shed - - import logging log = logging.getLogger( __name__ ) @@ -34,6 +34,7 @@ search_ready = False schema = None + class RepoSearch ( object ): def search( self, trans, search_term, **kwd ): @@ -72,9 +73,15 @@ 'remote_repository_url', 'repo_owner_username' ], schema=schema ) - hits = searcher.search( parser.parse( '*' + search_term + '*' ), terms = True ) + # user_query = parser.parse( search_term ) + user_query = parser.parse( '*' + search_term + '*' ) + + # hits = searcher.search( user_query, terms = True ) + hits = searcher.search_page( user_query, 1, pagelen = 1, terms = True ) + log.debug( 'total hits: ' + str( len( hits ) ) ) + log.debug( 'scored hits: ' + str( hits.scored_length() ) ) results = {} - results[ 'length'] = len( hits ) + results[ 'total_results'] = len( hits ) results[ 'hits' ] = [] for hit in hits: repo = trans.sa_session.query( model.Repository ).filter_by( id=hit[ 'id' ] ).one() @@ -85,7 +92,20 @@ break hit_dict = repo.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'user_id': trans.security.encode_id } ) hit_dict[ 'url'] = generate_sharable_link_for_repository_in_tool_shed( repo ) - hit_dict[ 'last_updated' ] = repo.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # Format the time since last update to be nicely readable. + dt1 = repo.update_time + dt2 = datetime.datetime.now() + rd = dateutil.relativedelta.relativedelta (dt2, dt1) + time_ago = '' + if rd.years > 0: + time_ago += str( rd.years ) + 'years' + if rd.months > 0: + time_ago += str( rd.months ) + ' months' + if rd.days > 0: + time_ago += str( rd.days ) + ' days ago' + hit_dict[ 'last_updated' ] = time_ago + hit_dict[ 'times_downloaded' ] = repo.times_downloaded hit_dict[ 'approved' ] = approved results[ 'hits' ].append( {'repository': hit_dict, 'matched_terms': hit.matched_terms() } ) https://bitbucket.org/galaxy/galaxy-central/commits/5877dc562874/ Changeset: 5877dc562874 User: martenson Date: 2015-01-27 22:15:18+00:00 Summary: adjust schema, start dynamic scoring Affected #: 2 files diff -r 2228c58015cb928e8c2819614e2a69b70ea4f448 -r 5877dc562874b894a83393bc54ba671d397909c9 lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -15,27 +15,47 @@ try: eggs.require( "Whoosh" ) import whoosh.index - from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT + from whoosh import scoring + from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT, STORED from whoosh.scoring import BM25F from whoosh.qparser import MultifieldParser from whoosh.index import Index search_ready = True schema = Schema( - id=STORED, - name=TEXT, - description=TEXT, - long_description=TEXT, - repo_type=TEXT, - homepage_url=TEXT, - remote_repository_url=TEXT, - repo_owner_username=TEXT ) + id = STORED, + name = TEXT( field_boost = 1.7 ), + description = TEXT( field_boost = 1.5 ), + long_description = TEXT, + repo_type = TEXT, + homepage_url = TEXT, + remote_repository_url = TEXT, + repo_owner_username = TEXT, + times_downloaded = STORED ) + except ImportError, e: search_ready = False schema = None + +class RepoWeighting( scoring.BM25F ): + """ + Affect the BM25G scoring model through the final method. + source: https://groups.google.com/forum/#!msg/whoosh/1AKNbW8R_l8/XySW0OecH6gJ + """ + use_final = True -class RepoSearch ( object ): + def final( self, searcher, docnum, score ): + + maxhits = 300 + hitcount = searcher.stored_fields( docnum )[ "times_downloaded" ] + log.debug( 'hitcount: ' + str( hitcount ) ) + + # Multiply the computed score for this document by the popularity + return score * ( hitcount / maxhits ) + + +class RepoSearch( object ): def search( self, trans, search_term, **kwd ): """ @@ -43,8 +63,7 @@ :param search_term: unicode encoded string with the search term(s) - :returns results: dictionary containing number of hits, - hits themselves and matched terms for each + :returns results: dictionary containing number of hits, hits themselves and matched terms for each """ if search_ready: toolshed_whoosh_index_dir = trans.app.config.toolshed_whoosh_index_dir @@ -55,42 +74,46 @@ # Some literature about BM25F: # http://trec.nist.gov/pubs/trec13/papers/microsoft-cambridge.web.hard.pdf # http://en.wikipedia.org/wiki/Okapi_BM25 - # Basically the higher number the bigger weight. - searcher = index.searcher( weighting=BM25F( field_B={ - 'name_B' : 0.9, - 'description_B' : 0.6, - 'long_description_B' : 0.5, - 'homepage_url_B' : 0.3, - 'remote_repository_url_B' : 0.2, - 'repo_owner_username' : 0.3, - 'repo_type_B' : 0.1 } ) ) + # __Basically__ the higher number the bigger weight. + repo_weighting = RepoWeighting( field_B = { 'name_B' : 0.9, + 'description_B' : 0.6, + 'long_description_B' : 0.5, + 'homepage_url_B' : 0.3, + 'remote_repository_url_B' : 0.2, + 'repo_owner_username' : 0.3, + 'repo_type_B' : 0.1 } ) + + # log.debug(repo_weighting.__dict__) + searcher = index.searcher( weighting = repo_weighting ) + parser = MultifieldParser( [ - 'name', - 'description', - 'long_description', - 'repo_type', - 'homepage_url', - 'remote_repository_url', - 'repo_owner_username' ], schema=schema ) + 'name', + 'description', + 'long_description', + 'repo_type', + 'homepage_url', + 'remote_repository_url', + 'repo_owner_username' ], schema = schema ) # user_query = parser.parse( search_term ) user_query = parser.parse( '*' + search_term + '*' ) - # hits = searcher.search( user_query, terms = True ) - hits = searcher.search_page( user_query, 1, pagelen = 1, terms = True ) + hits = searcher.search( user_query, terms = True ) + # hits = searcher.search_page( user_query, 1, pagelen = 1, terms = True ) + log.debug( 'searching for: #' + str( search_term ) ) log.debug( 'total hits: ' + str( len( hits ) ) ) log.debug( 'scored hits: ' + str( hits.scored_length() ) ) results = {} results[ 'total_results'] = len( hits ) results[ 'hits' ] = [] for hit in hits: - repo = trans.sa_session.query( model.Repository ).filter_by( id=hit[ 'id' ] ).one() + repo = trans.sa_session.query( model.Repository ).filter_by( id = hit[ 'id' ] ).one() approved = 'no' for review in repo.reviews: if review.approved == 'yes': approved = 'yes' break - hit_dict = repo.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'user_id': trans.security.encode_id } ) + hit_dict = repo.to_dict( view = 'element', value_mapper = { 'id': trans.security.encode_id, 'user_id': trans.security.encode_id } ) hit_dict[ 'url'] = generate_sharable_link_for_repository_in_tool_shed( repo ) # Format the time since last update to be nicely readable. diff -r 2228c58015cb928e8c2819614e2a69b70ea4f448 -r 5877dc562874b894a83393bc54ba671d397909c9 scripts/tool_shed/build_ts_whoosh_index.py --- a/scripts/tool_shed/build_ts_whoosh_index.py +++ b/scripts/tool_shed/build_ts_whoosh_index.py @@ -17,7 +17,7 @@ import whoosh.index import galaxy.webapps.tool_shed.model.mapping from whoosh.filedb.filestore import FileStorage - from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT + from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT, STORED from whoosh.scoring import BM25F from whoosh.qparser import MultifieldParser from whoosh.index import Index @@ -25,14 +25,15 @@ whoosh_ready = True schema = Schema( - id=STORED, - name=TEXT, - description=TEXT, - long_description=TEXT, - repo_type=TEXT, - homepage_url=TEXT, - remote_repository_url=TEXT, - repo_owner_username=TEXT ) + id = STORED, + name = TEXT( field_boost = 1.7 ), + description = TEXT( field_boost = 1.5 ), + long_description = TEXT, + repo_type = TEXT, + homepage_url = TEXT, + remote_repository_url = TEXT, + repo_owner_username = TEXT, + times_downloaded = STORED ) except ImportError, e: print 'import error' @@ -50,15 +51,16 @@ return a_basestr repos_indexed = 0 - for id, name, description, long_description, repo_type, homepage_url, remote_repository_url, repo_owner_username in get_repos( sa_session ): - writer.add_document( id=id, - name=to_unicode( name ), - description=to_unicode( description ), - long_description=to_unicode( long_description ), - repo_type=to_unicode( repo_type ), - homepage_url=to_unicode( homepage_url ), - remote_repository_url=to_unicode( remote_repository_url ), - repo_owner_username=to_unicode( repo_owner_username ) ) + for id, name, description, long_description, repo_type, homepage_url, remote_repository_url, repo_owner_username, times_downloaded in get_repos( sa_session ): + writer.add_document( id = id, + name = to_unicode( name ), + description = to_unicode( description ), + long_description = to_unicode( long_description ), + repo_type = to_unicode( repo_type ), + homepage_url = to_unicode( homepage_url ), + remote_repository_url = to_unicode( remote_repository_url ), + repo_owner_username = to_unicode( repo_owner_username ), + times_downloaded = times_downloaded ) repos_indexed += 1 writer.commit() print "Number of repos indexed: ", repos_indexed @@ -72,13 +74,14 @@ repo_type = repo.type homepage_url = repo.homepage_url remote_repository_url = repo.remote_repository_url + times_downloaded = repo.times_downloaded repo_owner_username = "" if repo.user_id is not None: user = sa_session.query( model.User ).filter( model.User.id == repo.user_id ).one() repo_owner_username = user.username - yield id, name, description, long_description, repo_type, homepage_url, remote_repository_url, repo_owner_username + yield id, name, description, long_description, repo_type, homepage_url, remote_repository_url, repo_owner_username, times_downloaded def get_sa_session_and_needed_config_settings( ini_file ): conf_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } ) https://bitbucket.org/galaxy/galaxy-central/commits/73a261a75185/ Changeset: 73a261a75185 User: martenson Date: 2015-01-27 22:19:07+00:00 Summary: Merge Affected #: 7 files diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -764,6 +764,25 @@ # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False + +# Enable beta workflow modules that should not yet be considered part of Galaxy's +# stable API. +#enable_beta_workflow_modules = False + +# Force usage of Galaxy's beta workflow scheduler under certain circumstances - +# this workflow scheduling forces Galaxy to schedule workflows in the background +# so initial submission of the workflows is signficantly sped up. This does +# however force the user to refresh their history manually to see newly scheduled +# steps (for "normal" workflows - steps are still scheduled far in advance of +# them being queued and scheduling here doesn't refer to actual cluster job +# scheduling). +# Workflows containing more than the specified number of steps will always use +# the Galaxy's beta workflow scheduling. +#force_beta_workflow_scheduled_min_steps=250 +# Switch to using Galaxy's beta workflow scheduling for all workflows involving +# ccollections. +#force_beta_workflow_scheduled_for_collections=False + # Enable authentication via OpenID. Allows users to log in to their Galaxy # account by authenticating with an OpenID provider. #enable_openid = False diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 config/tool_data_table_conf.xml.sample --- a/config/tool_data_table_conf.xml.sample +++ b/config/tool_data_table_conf.xml.sample @@ -60,4 +60,9 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/mosaik_index.loc" /></table> +  + <table name="twobit" comment_char="#"> + <columns>value, path</columns> + <file path="tool-data/twobit.loc" /> + </table></tables> diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -179,33 +179,59 @@ """ def __init__( self, app ): + self.app = app # Create list of genomes from app.genome_builds self.genomes = {} - for key, description in app.genome_builds.get_genome_build_names(): + # Store internal versions of data tables for twobit and __dbkey__ + self._table_versions = { 'twobit': None, '__dbkeys__': None } + self.reload_genomes() + + def reload_genomes( self ): + self.genomes = {} + # Store table versions for later + for table_name in self._table_versions.keys(): + table = self.app.tool_data_tables.get( table_name, None ) + if table is not None: + self._table_versions[ table_name ] = table._loaded_content_version + + twobit_table = self.app.tool_data_tables.get( 'twobit', None ) + twobit_fields = {} + if twobit_table is None: + # Add genome data (twobit files) to genomes, directly from twobit.loc + try: + for line in open( os.path.join( self.app.config.tool_data_path, "twobit.loc" ) ): + if line.startswith("#"): continue + val = line.split() + if len( val ) == 2: + key, path = val + twobit_fields[ key ] = path + except IOError, e: + # Thrown if twobit.loc does not exist. + log.exception( "Error reading twobit.loc: %s", e ) + for key, description in self.app.genome_builds.get_genome_build_names(): self.genomes[ key ] = Genome( key, description ) + # Add len files to genomes. + self.genomes[ key ].len_file = self.app.genome_builds.get_chrom_info( key )[0] + if self.genomes[ key ].len_file: + if not os.path.exists( self.genomes[ key ].len_file ): + self.genomes[ key ].len_file = None + # Add genome data (twobit files) to genomes. + if twobit_table is not None: + self.genomes[ key ].twobit_file = twobit_table.get_entry( 'value', key, 'path', default=None ) + elif key in twobit_fields: + self.genomes[ key ].twobit_file = twobit_fields[ key ] + - # Add len files to genomes. - len_files = glob.glob( os.path.join( app.config.len_file_path, "*.len" ) ) - for f in len_files: - key = os.path.split( f )[1].split( ".len" )[0] - if key in self.genomes: - self.genomes[ key ].len_file = f - - # Add genome data (twobit files) to genomes. - try: - for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ): - if line.startswith("#"): continue - val = line.split() - if len( val ) == 2: - key, path = val - if key in self.genomes: - self.genomes[ key ].twobit_file = path - except IOError, e: - # Thrown if twobit.loc does not exist. - log.exception( str( e ) ) + def check_and_reload( self ): + # Check if tables have been modified, if so reload + for table_name, table_version in self._table_versions.iteritems(): + table = self.app.tool_data_tables.get( table_name, None ) + if table is not None and not table.is_current_version( table_version ): + return self.reload_genomes() def get_build( self, dbkey ): """ Returns build for the given key. """ + self.check_and_reload() rval = None if dbkey in self.genomes: rval = self.genomes[ dbkey ] @@ -214,6 +240,7 @@ def get_dbkeys( self, trans, chrom_info=False, **kwd ): """ Returns all known dbkeys. If chrom_info is True, only dbkeys with chromosome lengths are returned. """ + self.check_and_reload() dbkeys = [] # Add user's custom keys to dbkeys. @@ -241,7 +268,7 @@ Returns a naturally sorted list of chroms/contigs for a given dbkey. Use either chrom or low to specify the starting chrom in the return list. """ - + self.check_and_reload() # If there is no dbkey owner, default to current user. dbkey_owner, dbkey = decode_dbkey( dbkey ) if dbkey_owner: @@ -303,6 +330,7 @@ Returns true if there is reference data for the specified dbkey. If dbkey is custom, dbkey_owner is needed to determine if there is reference data. """ + self.check_and_reload() # Look for key in built-in builds. if dbkey in self.genomes and self.genomes[ dbkey ].twobit_file: # There is built-in reference data. @@ -323,7 +351,7 @@ """ Return reference data for a build. """ - + self.check_and_reload() # If there is no dbkey owner, default to current user. dbkey_owner, dbkey = decode_dbkey( dbkey ) if dbkey_owner: diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -1351,31 +1351,46 @@ id = galaxy.util.listify( id ) name = galaxy.util.listify( name ) histories = [] - cur_names = [] + for history_id in id: history = self.history_manager.get_owned( trans, self.decode_id( history_id ), trans.user ) if history and history.user_id == user.id: histories.append( history ) - cur_names.append( history.get_display_name() ) if not name or len( histories ) != len( name ): return trans.fill_template( "/history/rename.mako", histories=histories ) - change_msg = "" - for i in range(len(histories)): - if histories[i].user_id == user.id: - if name[i] == histories[i].get_display_name(): - change_msg = change_msg + "<p>History: "+cur_names[i]+" is already named: "+name[i]+"</p>" - elif name[i] not in [None,'',' ']: - name[i] = escape(name[i]) - histories[i].name = sanitize_html( name[i] ) - trans.sa_session.add( histories[i] ) - trans.sa_session.flush() - change_msg = change_msg + "<p>History: "+cur_names[i]+" renamed to: "+name[i]+"</p>" - trans.log_event( "History renamed: id: %s, renamed to: '%s'" % (str(histories[i].id), name[i] ) ) - else: - change_msg = change_msg + "<p>You must specify a valid name for History: "+cur_names[i]+"</p>" - else: - change_msg = change_msg + "<p>History: "+cur_names[i]+" does not appear to belong to you.</p>" - return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) + + change_msgs = [] + for i in range( len( histories ) ): + cur_name = histories[i].get_display_name() + new_name = name[i] + + # skip if name is empty + if not isinstance( new_name, basestring ) or not new_name.strip(): + change_msgs.append( "You must specify a valid name for History: " + cur_name ) + continue + + # skip if not the owner + #??: isn't this already handled in get_history/if statement above? + if histories[i].user_id != user.id: + change_msgs.append( "History: " + cur_name + " does not appear to belong to you." ) + continue + + # skip if it wouldn't be a change + if new_name == cur_name: + change_msgs.append( "History: " + cur_name + " is already named: " + new_name ) + continue + + # escape, sanitize, set, and log the change + new_name = escape( new_name ) + histories[i].name = sanitize_html( new_name ) + trans.sa_session.add( histories[i] ) + trans.sa_session.flush() + + trans.log_event( "History renamed: id: %s, renamed to: '%s'" % ( str( histories[i].id ), new_name ) ) + change_msgs.append( "History: " + cur_name + " renamed to: " + new_name ) + + change_msg = '<br />'.join( change_msgs ) + return trans.show_message( change_msg, refresh_frames=['history'] ) @web.expose @web.require_login( "copy shared Galaxy history" ) diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 templates/admin/jobs.mako --- a/templates/admin/jobs.mako +++ b/templates/admin/jobs.mako @@ -55,11 +55,7 @@ </tr> %for job in jobs: <td> - %if job.state == 'upload': -   - %else: - <input type="checkbox" name="stop" value="${job.id}"/> - %endif + <input type="checkbox" name="stop" value="${job.id}"/></td><td>${job.id}</td> %if job.history and job.history.user: diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -17,7 +17,7 @@ ## An admin user may be creating a new user account, in which case we want to display the registration form. ## But if the current user is not an admin user, then don't display the registration form. -%if trans.user_is_admin() or not trans.user: +%if ( cntrller=='admin' and trans.user_is_admin() ) or not trans.user: ${render_registration_form()} %if trans.app.config.get( 'terms_url', None ) is not None: diff -r 5877dc562874b894a83393bc54ba671d397909c9 -r 73a261a75185704a35a05350a31a7d5169cbc9b0 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -201,6 +201,27 @@ response = self._run( "validation_default", history_id, inputs ) self._assert_status_code_is( response, 400 ) + @skip_without_tool( "multi_select" ) + def test_select_legal_values( self ): + history_id = self.dataset_populator.new_history() + inputs = { + 'select_ex': 'not_option', + } + response = self._run( "multi_select", history_id, inputs ) + self._assert_status_code_is( response, 400 ) + + @skip_without_tool( "column_param" ) + def test_column_legal_values( self ): + history_id = self.dataset_populator.new_history() + new_dataset1 = self.dataset_populator.new_dataset( history_id, content='#col1\tcol2' ) + inputs = { + 'input1': { "src": "hda", "id": new_dataset1["id"] }, + 'col': "' ; echo 'moo", + } + response = self._run( "column_param", history_id, inputs ) + # TODO: make this test pass... + self._assert_status_code_is( response, 400 ) + @skip_without_tool( "collection_paired_test" ) def test_collection_parameter( self ): history_id = self.dataset_populator.new_history() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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