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commit/galaxy-central: nsoranzo: Fix variable name causing a NameError.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/733696644b89/ Changeset: 733696644b89 User: nsoranzo Date: 2014-12-15 15:43:16+00:00 Summary: Fix variable name causing a NameError. Affected #: 1 file diff -r 3c0acd32969bc282603607037522a2e16d70d074 -r 733696644b89ba39bbeeaf5908b97f4698d6868c lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -195,7 +195,7 @@ if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): cut_id = encoded_folder_id[ 1: ] else: - raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) ) + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) return cut_id def decode_folder_id( self, trans, encoded_folder_id ): 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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[galaxyproject/usegalaxy-playbook] fdfbf4: added ga_code for google analytics purposes
by GitHub 15 Dec '14

15 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fdfbf4b48b6f86f9a524772c11a0f41a95fdad76 https://github.com/galaxyproject/usegalaxy-playbook/commit/fdfbf4b48b6f86f9… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- added ga_code for google analytics purposes Commit: 9485f82f52b57445b6e45d63845bc162c7ab155b https://github.com/galaxyproject/usegalaxy-playbook/commit/9485f82f52b57445… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- add ga_code for google analytics purposes Commit: 8f1785c81d7ee068b564f079dd02f4eaa33c49de https://github.com/galaxyproject/usegalaxy-playbook/commit/8f1785c81d7ee068… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- add ga script and onclick event sending to track whether the cycle thing is used Commit: 33e106b5e2f13eeb88b5c5356b4c49a87a615c62 https://github.com/galaxyproject/usegalaxy-playbook/commit/33e106b5e2f13eeb… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-12 (Fri, 12 Dec 2014) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- do not init ga twice use the one in top.window instead Commit: 1bbaae7a09fa230a97337d42d5b4cd754d377ba1 https://github.com/galaxyproject/usegalaxy-playbook/commit/1bbaae7a09fa230a… Author: Marten <emulatorer(a)gmail.com> Date: 2014-12-15 (Mon, 15 Dec 2014) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Merge pull request #2 from martenson/master track how people click on the carousel links Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/15b2fa183d58...…

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commit/galaxy-central: dannon: Retab, whitespace in base.less
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c0acd32969b/ Changeset: 3c0acd32969b User: dannon Date: 2014-12-15 14:56:25+00:00 Summary: Retab, whitespace in base.less Affected #: 1 file diff -r 36457cc1ec26c440e7a996ce51eb87ed7c58cc4d -r 3c0acd32969bc282603607037522a2e16d70d074 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1,7 +1,7 @@ // bootstrap.less modified for Galaxy @import "bootstrap.less"; -// Galaxy specific variables +// Galaxy specific variables @import "galaxy_variables.less"; @white: #fff; @@ -92,23 +92,23 @@ } #messagebox { - position:absolute; + position:absolute; top: @navbar-height + @layout_top_padding + 1; - left:0; - width:100%; + left:0; + width:100%; height: @panel-message-height !important; - overflow: hidden; + overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; } #inactivebox { - position:absolute; + position:absolute; top: @navbar-height + @layout_top_padding + 1; - left:0; - width:100%; + left:0; + width:100%; height: @panel-message-height !important; - overflow: hidden; + overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; } @@ -116,10 +116,10 @@ // Panels #left, #left-border, #center, #right-border, #right { - position: absolute; + position: absolute; top: @navbar-height + @layout_top_padding + 1; bottom: 0px; - overflow: hidden; + overflow: hidden; background: #fff; } #left, #center, #right, #left-border, #right-border { @@ -145,7 +145,7 @@ } #right { width: 250px; - right: 0px; + right: 0px; z-index: 200; border-left: solid @layout-border-color 1px; } @@ -277,11 +277,11 @@ } } } - + .menu-bg { background: whiteSmoke top repeat-x; } - + div.unified-panel-body { position: absolute; top: @panel_header_height; @@ -326,10 +326,10 @@ z-index: 900; // Bootstrap elements start at 1000 position: absolute; top: 0; - left: 0; + left: 0; width: 100%; height: 100%; -} +} // Messages for message box, slightly different style @@ -345,19 +345,19 @@ background-position: 6px 50%; } -.panel-warning-message +.panel-warning-message { background-image: url(warn_small.png); background-color: @state-warning-bg; } -.panel-done-message +.panel-done-message { background-image: url(ok_small.png); background-color: @state-success-bg; } -.panel-info-message +.panel-info-message { background-image: url(info_small.png); background-color: @state-info-bg; @@ -367,9 +367,9 @@ #masthead { - position:absolute; - top:0; - left:0; + position:absolute; + top:0; + left:0; width:100%; min-width:990px; padding: 0; @@ -385,7 +385,7 @@ color: gold; } } - + //.dropdown-menu { // z-index: 15002; //} @@ -412,8 +412,8 @@ z-index: 2000; img { - display: inline; - width: 26px; + display: inline; + width: 26px; vertical-align: top; } a { @@ -421,7 +421,7 @@ text-decoration: none; } } - + .iconbar { position : absolute; @@ -448,7 +448,7 @@ left : 23px; top : -12px; } - + .toggle { color : gold; @@ -542,7 +542,7 @@ border-color:#999; } -div.metadataHelpBody { +div.metadataHelpBody { width:100%;overflow:auto; } @@ -553,7 +553,7 @@ padding-bottom: 0.25em; } -// Forms +// Forms div.toolFormBody div.toolFormTitle { background: transparent; @@ -602,7 +602,7 @@ .border-radius(@panel-border-radius); } -div.form-title, div.toolFormTitle { +div.form-title, div.toolFormTitle { // font-size: @font-size-base * 1.25; // line-height: @line-height-base * 1.5; padding: 5px 10px; @@ -610,7 +610,7 @@ border-bottom: solid @form-border 1px; } -div.form-body { +div.form-body { padding: 5px 0; } @@ -687,7 +687,7 @@ font: inherit; } -.form-row { +.form-row { select, textarea, input[type="text"], input[type="file"], input[type="password"] { // -webkit-box-sizing: border-box; max-width: 90%; @@ -733,15 +733,15 @@ } .search-spinner { - position: absolute; - display: none; - right: 6px; + position: absolute; + display: none; + right: 6px; top: 9px; } #search-clear-btn { - position: absolute; - right: 6px; + position: absolute; + right: 6px; top: 9px; display: block; font-size: 1.4em !important; @@ -753,7 +753,7 @@ } } -// Messages +// Messages .errormessagelarge, .warningmessagelarge, .donemessagelarge, .infomessagelarge { .alert(); @@ -786,7 +786,7 @@ background-image: url(info_large.png); } -.screencastBox { +.screencastBox { padding-left: 10px; border-color: #AAAA66; background-color: #FFFFCC; @@ -891,7 +891,7 @@ line-height: @line-height-base; } -table.colored tr.header { +table.colored tr.header { background: @table-heading-bg; color: contrast(@complement-color-3); background-repeat: repeat-x; @@ -900,11 +900,11 @@ font-weight: bold; } -table.colored tr { +table.colored tr { background: @white; } -table.colored tr.odd_row { +table.colored tr.odd_row { background: @table-bg-accent; } @@ -1018,7 +1018,7 @@ height: 18px; vertical-align: middle; margin-left: 2px; - + } .search-box-input { border: 0; @@ -1051,7 +1051,7 @@ div.odd_row { background: @table-bg-accent; } - + #footer { display: none; } @@ -1199,15 +1199,15 @@ cursor: pointer; position: relative; .unselectable; - + // border: solid transparent 1px; // -moz-border-radius: 0.25em; // -webkit-border-radius: 0.25em; // border-radius: 0.25em; - + // padding: 1px 0.25em; // margin: -1px -0.25em; - + a { text-decoration: none; } @@ -1335,28 +1335,28 @@ background:#aaa; color:#aaa; } - + table { border-collapse:collapse; border-top:1px solid #ccc; border-left:1px solid #ccc; } - + blockquote { color:#666; } - + fieldset { border-color:#ccc; border:1px solid #ccc; } - + th,td { border-bottom:1px solid #ddd; border-right:1px solid #ccc; } - + th,td { padding:.8em; } @@ -1438,7 +1438,7 @@ margin:10px 0; padding-left:5px; } - + // ============================================================================ History @import "sprite-history-states.less"; @import "sprite-history-buttons.less"; @@ -1457,7 +1457,7 @@ @import "ui/pagination.less"; -// ==== Tool menu styles +// ==== Tool menu styles .toolMenuContainer { @@ -1480,7 +1480,7 @@ } div.toolSectionDetailsInner -{ +{ margin-left: 5px; margin-right: 5px; } @@ -1565,9 +1565,9 @@ .toolMenuAndView .toolForm { - float: left; - background-color: white; - margin: 10px; + float: left; + background-color: white; + margin: 10px; } // @import "base_sprites"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

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commit/galaxy-central: dannon: Organize and deduplicate imports, pep8 in lib/galaxy/config.py
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e68aa3d8d16/ Changeset: 7e68aa3d8d16 User: dannon Date: 2014-12-15 13:28:21+00:00 Summary: Organize and deduplicate imports, pep8 in lib/galaxy/config.py Affected #: 1 file diff -r 5223de4eacea84dc2f39ec1ecec33ce45fa84739 -r 7e68aa3d8d161ff2a0526101aedebc026b4d71cc lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -4,23 +4,22 @@ # absolute_import needed for tool_shed package. from __future__ import absolute_import +import ConfigParser +import logging +import logging.config import os import re import socket import string import sys import tempfile -import logging -import logging.config -import ConfigParser from datetime import timedelta +from galaxy import eggs +from galaxy.util import listify +from galaxy.util import string_as_bool +from galaxy.util.dbkeys import GenomeBuilds from galaxy.web.formatting import expand_pretty_datetime_format -from galaxy.util import string_as_bool -from galaxy.util import listify -from galaxy.util.dbkeys import GenomeBuilds -from galaxy import eggs -import ConfigParser log = logging.getLogger( __name__ ) @@ -442,23 +441,23 @@ Backwards compatibility for config files moved to the config/ dir. """ defaults = dict( - data_manager_config_file = [ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], - datatypes_config_file = [ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], - external_service_type_config_file = [ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], - job_config_file = [ 'config/job_conf.xml', 'job_conf.xml' ], - job_metrics_config_file = [ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], - dependency_resolvers_config_file = [ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], - job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], - migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], - object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], - openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], - shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], - shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], - tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], + data_manager_config_file=[ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ], + datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], + external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], + job_config_file=[ 'config/job_conf.xml', 'job_conf.xml' ], + job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], + dependency_resolvers_config_file=[ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], + job_resource_params_file=[ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], + migrated_tools_config=[ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], + object_store_config_file=[ 'config/object_store_conf.xml', 'object_store_conf.xml' ], + openid_config_file=[ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], + shed_data_manager_config_file=[ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], + shed_tool_data_table_config=[ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], + tool_sheds_config_file=[ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], ) listify_defaults = dict( - tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path=[ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], # rationale: # [0]: user has explicitly created config/tool_conf.xml but did not # move their existing shed_tool_conf.xml, don't use @@ -469,7 +468,7 @@ # [0], probably moved their shed_tool_conf.xml as well # [2]: user has done nothing, use the old files # [3]: fresh install - tool_config_file = [ 'config/tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] + tool_config_file=[ 'config/tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml,config/shed_tool_conf.xml', 'tool_conf.xml,shed_tool_conf.xml', 'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ] ) for var, defaults in defaults.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merge.
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5223de4eacea/ Changeset: 5223de4eacea User: dannon Date: 2014-12-15 13:25:15+00:00 Summary: Merge. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6704c0ee9fec/ Changeset: 6704c0ee9fec Branch: next-stable User: dannon Date: 2014-12-15 13:23:47+00:00 Summary: Bugfix for openid configuration locations, pointed out by Jelle in https://trello.com/c/AwZwAx4l/2289-lib-galaxy-config-py-missing-comma-on-op… Affected #: 1 file diff -r 7a027f285f3b441f8ff1fe48dfc5841d8bc41bfa -r 6704c0ee9fec6b0624d739669cb7c66ea08d480a lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -445,7 +445,7 @@ job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], - openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml' 'config/openid_conf.xml.sample' ], + openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], https://bitbucket.org/galaxy/galaxy-central/commits/6fee59d63b7e/ Changeset: 6fee59d63b7e User: dannon Date: 2014-12-15 13:23:47+00:00 Summary: Bugfix for openid configuration locations, pointed out by Jelle in https://trello.com/c/AwZwAx4l/2289-lib-galaxy-config-py-missing-comma-on-op… Affected #: 1 file diff -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 -r 6fee59d63b7e042851b2a63e4d66ad6dde630e3b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -451,7 +451,7 @@ job_resource_params_file = [ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config = [ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], object_store_config_file = [ 'config/object_store_conf.xml', 'object_store_conf.xml' ], - openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml' 'config/openid_conf.xml.sample' ], + openid_config_file = [ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ], shed_data_manager_config_file = [ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ], shed_tool_data_table_config = [ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ], tool_sheds_config_file = [ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in jjohnson/galaxy-central-7 (pull request #609)
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad28e42a8af3/ Changeset: ad28e42a8af3 User: dannon Date: 2014-12-15 12:43:42+00:00 Summary: Merged in jjohnson/galaxy-central-7 (pull request #609) Add dataproviders for SQlite datatype Affected #: 2 files diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -620,6 +620,16 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + @dataproviders.decorators.dataprovider_factory( 'sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings ) + def sqlite_datatableprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataTableProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings ) + def sqlite_datadictprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -13,6 +13,7 @@ import external from galaxy.util import sqlite import re +import sys from galaxy import eggs eggs.require( 'bx-python' ) @@ -726,3 +727,55 @@ else: yield +class SQliteDataTableProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of arrays + """ + settings = { + 'query': 'str', + 'headers': 'bool', + 'limit': 'int' + } + + def __init__( self, source, query=None, headers=False, limit=sys.maxint, **kwargs ): + self.query = query + self.headers = headers + self.limit = limit + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataTableProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + results = cur.execute(self.query) + if self.headers: + yield [col[0] for col in cur.description] + for i,row in enumerate(results): + if i >= self.limit: + break + yield [val for val in row] + else: + yield + +class SQliteDataDictProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of dicts + """ + settings = { + 'query': 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataDictProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + for row in cur.execute(self.query): + yield [dict((cur.description[i][0], value) for i, value in enumerate(row))] + else: + yield 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 15 Dec '14

15 Dec '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e6035e53de5/ Changeset: 1e6035e53de5 User: jjohnson Date: 2014-12-12 19:35:40+00:00 Summary: Add SQlite dataproviders: SQliteDataTableProvider - Allows any query to be run and returns the resulting rows as arrays of arrays, SQliteDataDictProvider - Allows any query to be run and returns the resulting rows as arrays of dicts Affected #: 1 file diff -r efd0286e7629289c4c583898ebecb32646834c64 -r 1e6035e53de58ce4fe1687ab74512da711d99989 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -13,6 +13,7 @@ import external from galaxy.util import sqlite import re +import sys from galaxy import eggs eggs.require( 'bx-python' ) @@ -726,3 +727,55 @@ else: yield +class SQliteDataTableProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of arrays + """ + settings = { + 'query': 'str', + 'headers': 'bool', + 'limit': 'int' + } + + def __init__( self, source, query=None, headers=False, limit=sys.maxint, **kwargs ): + self.query = query + self.headers = headers + self.limit = limit + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataTableProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + results = cur.execute(self.query) + if self.headers: + yield [col[0] for col in cur.description] + for i,row in enumerate(results): + if i >= self.limit: + break + yield [val for val in row] + else: + yield + +class SQliteDataDictProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of dicts + """ + settings = { + 'query': 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataDictProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + for row in cur.execute(self.query): + yield [dict((cur.description[i][0], value) for i, value in enumerate(row))] + else: + yield https://bitbucket.org/galaxy/galaxy-central/commits/c207054ea196/ Changeset: c207054ea196 User: jjohnson Date: 2014-12-12 19:41:35+00:00 Summary: Add dataproviders to the SQlite dataype Affected #: 1 file diff -r 1e6035e53de58ce4fe1687ab74512da711d99989 -r c207054ea1966bc9d4640a6215192414e8071739 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -620,6 +620,16 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + @dataproviders.decorators.dataprovider_factory( 'sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings ) + def sqlite_datatableprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataTableProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings ) + def sqlite_datadictprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) https://bitbucket.org/galaxy/galaxy-central/commits/ad28e42a8af3/ Changeset: ad28e42a8af3 User: dannon Date: 2014-12-15 12:43:42+00:00 Summary: Merged in jjohnson/galaxy-central-7 (pull request #609) Add dataproviders for SQlite datatype Affected #: 2 files diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -620,6 +620,16 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + @dataproviders.decorators.dataprovider_factory( 'sqlite-table', dataproviders.dataset.SQliteDataTableProvider.settings ) + def sqlite_datatableprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataTableProvider( dataset_source, **settings ) + + @dataproviders.decorators.dataprovider_factory( 'sqlite-dict', dataproviders.dataset.SQliteDataDictProvider.settings ) + def sqlite_datadictprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataDictProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite) diff -r ecac8a8679612d419347dcbedc398319418b077e -r ad28e42a8af34c81f0ebcbe6f3baef9bdcf80ae8 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -13,6 +13,7 @@ import external from galaxy.util import sqlite import re +import sys from galaxy import eggs eggs.require( 'bx-python' ) @@ -726,3 +727,55 @@ else: yield +class SQliteDataTableProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of arrays + """ + settings = { + 'query': 'str', + 'headers': 'bool', + 'limit': 'int' + } + + def __init__( self, source, query=None, headers=False, limit=sys.maxint, **kwargs ): + self.query = query + self.headers = headers + self.limit = limit + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataTableProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + results = cur.execute(self.query) + if self.headers: + yield [col[0] for col in cur.description] + for i,row in enumerate(results): + if i >= self.limit: + break + yield [val for val in row] + else: + yield + +class SQliteDataDictProvider( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + Allows any query to be run and returns the resulting rows as arrays of dicts + """ + settings = { + 'query': 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) + super( SQliteDataDictProvider, self ).__init__( source, **kwargs ) + + def __iter__( self ): + if (self.query is not None) and sqlite.is_read_only_query(self.query): + cur = self.connection.cursor() + for row in cur.execute(self.query): + yield [dict((cur.description[i][0], value) for i, value in enumerate(row))] + else: + yield 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: 7 new changesets
by commits-noreply＠bitbucket.org 15 Dec '14

15 Dec '14

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/563a28409672/ Changeset: 563a28409672 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Allow multiple tool data table config files... ... use this functionality to implement tests for tool data API. Affected #: 5 files diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -31,8 +31,10 @@ # at server startup. If tool shed repositories are installed that contain a valid file named tool_data_table_conf.xml.sample, entries # from that file are inserted into this dict at the time of installation. self.data_tables = {} - if config_filename: - self.load_from_config_file( config_filename, self.tool_data_path, from_shed_config=False ) + for single_config_filename in util.listify( config_filename ): + if not single_config_filename: + continue + self.load_from_config_file( single_config_filename, self.tool_data_path, from_shed_config=False ) def __getitem__( self, key ): return self.data_tables.__getitem__( key ) diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -231,7 +231,16 @@ start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ tool_data_table_config_path = None if os.path.exists( 'tool_data_table_conf.test.xml' ): + # If explicitly defined tables for test, use those. tool_data_table_config_path = 'tool_data_table_conf.test.xml' + else: + # ... otherise find whatever Galaxy would use as the default and + # the sample data for fucntional tests to that. + default_tool_data_config = 'config/tool_data_table_conf.xml.sample' + for tool_data_config in ['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml' ]: + if os.path.exists( tool_data_config ): + default_tool_data_config = tool_data_config + tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c test/api/test_tool_data.py --- /dev/null +++ b/test/api/test_tool_data.py @@ -0,0 +1,30 @@ +""" Tests for the tool data API. +""" +from base import api + +import operator + + +class ToolDataApiTestCase( api.ApiTestCase ): + + def test_admin_only( self ): + index_response = self._get( "tool_data", admin=False ) + self._assert_status_code_is( index_response, 403 ) + + def test_list(self): + index_response = self._get( "tool_data", admin=True ) + self._assert_status_code_is( index_response, 200 ) + print index_response.content + index = index_response.json() + assert "testalpha" in map(operator.itemgetter("name"), index) + + def test_show(self): + show_response = self._get( "tool_data/testalpha", admin=True ) + self._assert_status_code_is( show_response, 200 ) + print show_response.content + data_table = show_response.json() + assert data_table["columns"] == ["value", "name", "path"] + first_entry = data_table["fields"][0] + assert first_entry[0] == "data1" + assert first_entry[1] == "data1name" + assert first_entry[2].endswith("test/functional/tool-data/data1/entry.txt") diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c test/functional/tool-data/sample_tool_data_tables.xml --- /dev/null +++ b/test/functional/tool-data/sample_tool_data_tables.xml @@ -0,0 +1,12 @@ +<tables> + <table name="testalpha" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/testalpha.loc" /> + </table> +  +</tables> diff -r 6363c839528ca8bbbbc60c1b3784c788468d9445 -r 563a28409672988f6b30545ba987017e7da2e14c test/functional/tool-data/testalpha.loc --- /dev/null +++ b/test/functional/tool-data/testalpha.loc @@ -0,0 +1,2 @@ +data1 data1name ${__HERE__}/data1/entry.txt +data2 data2name ${__HERE__}/data2/entry.txt https://bitbucket.org/galaxy/galaxy-central/commits/8795d0fe13c4/ Changeset: 8795d0fe13c4 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: PEP-8 fixes for lib/galaxy/tools/data/__init__.py. Affected #: 1 file diff -r 563a28409672988f6b30545ba987017e7da2e14c -r 8795d0fe13c45804ea53f4543c71ee7ca6f41a0c lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -9,9 +9,7 @@ import logging import os import os.path -import shutil import string -import tempfile from galaxy import util from galaxy.util.odict import odict @@ -22,6 +20,7 @@ DEFAULT_TABLE_TYPE = 'tabular' + class ToolDataTableManager( object ): """Manages a collection of tool data tables""" @@ -81,7 +80,7 @@ log.debug( "Loaded tool data table '%s'", table.name ) else: log.debug( "Loading another instance of data table '%s', attempting to merge content.", table.name ) - self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) #only merge content, do not persist to disk, do not allow duplicate rows when merging + self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) # only merge content, do not persist to disk, do not allow duplicate rows when merging # FIXME: This does not account for an entry with the same unique build ID, but a different path. return table_elems @@ -128,7 +127,7 @@ """ if not ( new_elems or remove_elems ): log.debug( 'ToolDataTableManager.to_xml_file called without any elements to add or remove.' ) - return #no changes provided, no need to persist any changes + return # no changes provided, no need to persist any changes if not new_elems: new_elems = [] if not remove_elems: @@ -175,7 +174,7 @@ assert table_type in tool_data_table_types, "Unknown data table type '%s'" % type return tool_data_table_types[ table_type ]( table_elem, tool_data_path, from_shed_config=from_shed_config, filename=filename ) - def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + def __init__( self, config_element, tool_data_path, from_shed_config=False, filename=None ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) self.empty_field_value = config_element.get( 'empty_field_value', '' ) @@ -187,7 +186,7 @@ # increment this variable any time a new entry is added, or when the table is totally reloaded # This value has no external meaning, and does not represent an abstract version of the underlying data self._loaded_content_version = 1 - self._load_info = ( [ config_element, tool_data_path ], { 'from_shed_config':from_shed_config } ) + self._load_info = ( [ config_element, tool_data_path ], { 'from_shed_config': from_shed_config } ) self._merged_load_info = [] def _update_version( self, version=None ): @@ -252,13 +251,13 @@ type_key = 'tabular' - def __init__( self, config_element, tool_data_path, from_shed_config = False, filename=None ): + def __init__( self, config_element, tool_data_path, from_shed_config=False, filename=None ): super( TabularToolDataTable, self ).__init__( config_element, tool_data_path, from_shed_config, filename) self.config_element = config_element self.data = [] self.configure_and_load( config_element, tool_data_path, from_shed_config) - def configure_and_load( self, config_element, tool_data_path, from_shed_config = False): + def configure_and_load( self, config_element, tool_data_path, from_shed_config=False): """ Configure and load table from an XML element. """ @@ -323,7 +322,6 @@ else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) - def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): assert self.columns == other_table.columns, "Merging tabular data tables with non matching columns is not allowed: %s:%s != %s:%s" % ( self.name, self.columns, other_table.name, other_table.columns ) #merge filename info @@ -350,7 +348,7 @@ for i, field in enumerate( fields ): field_name = named_colums[i] if field_name is None: - field_name = i #check that this is supposed to be 0 based. + field_name = i # check that this is supposed to be 0 based. field_dict[ field_name ] = field rval.append( field_dict ) return rval @@ -508,7 +506,7 @@ data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line - data_table_fh.seek( -1, 2 ) #last char in file + data_table_fh.seek( -1, 2 ) # last char in file last_char = data_table_fh.read( 1 ) if last_char not in [ '\n', '\r' ]: data_table_fh.write( '\n' ) @@ -577,7 +575,7 @@ def to_dict(self, view='collection'): rval = super(TabularToolDataTable, self).to_dict() if view == 'element': - rval['columns'] = sorted(self.columns.keys(), key=lambda x:self.columns[x]) + rval['columns'] = sorted(self.columns.keys(), key=lambda x: self.columns[x]) rval['fields'] = self.get_fields() return rval https://bitbucket.org/galaxy/galaxy-central/commits/6d54a7fd1fe9/ Changeset: 6d54a7fd1fe9 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Small improvements to tool data API. Update tool data API to use newer API decorator for better error handling, create some abstractions for reuse down stream, etc... Affected #: 1 file diff -r 8795d0fe13c45804ea53f4543c71ee7ca6f41a0c -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,4 +1,6 @@ +from galaxy import exceptions from galaxy import web +from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController @@ -8,21 +10,21 @@ """ @web.require_admin - @web.expose_api + @expose_api def index( self, trans, **kwds ): """ GET /api/tool_data: returns a list tool_data tables:: """ - return list( a.to_dict() for a in trans.app.tool_data_tables.data_tables.values() ) + return list( a.to_dict() for a in self._data_tables.values() ) @web.require_admin - @web.expose_api + @expose_api def show( self, trans, id, **kwds ): - return trans.app.tool_data_tables.data_tables[id].to_dict(view='element') + return self._data_table(id).to_dict(view='element') @web.require_admin - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/tool_data/{id} @@ -61,3 +63,13 @@ return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) return data_table.remove_entry(split_values) + + def _data_table( self, id ): + try: + return self._data_tables[id] + except IndexError: + raise exceptions.ObjectNotFound("No such data table %s" % id) + + @property + def _data_tables( self ): + return self.app.tool_data_tables.data_tables https://bitbucket.org/galaxy/galaxy-central/commits/edbe286564de/ Changeset: edbe286564de User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Implement a detailed break down of data table fields via API. Originally this approach was laid out by Kyle Ellrott in this pull request (https://bitbucket.org/galaxy/galaxy-central/pull-request/531/add-downloads-…) The changes to galaxy.tools.data are entirely his contribution, I only reworked the API and endpoint slightly and did some stylistic fixes and refactoring. Affected #: 4 files diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -9,7 +9,11 @@ import logging import os import os.path +import re import string +import hashlib + +from glob import glob from galaxy import util from galaxy.util.odict import odict @@ -340,6 +344,13 @@ def get_fields( self ): return self.data + def get_field(self, value): + rval = None + for i in self.get_named_fields_list(): + if i['value'] == value: + rval = TabularToolDataField(i) + return rval + def get_named_fields_list( self ): rval = [] named_colums = self.get_column_name_list() @@ -580,6 +591,58 @@ return rval +class TabularToolDataField(Dictifiable, object): + + dict_collection_visible_keys = [] + + def __init__(self, data): + self.data = data + + def __getitem__(self, key): + return self.data[key] + + def get_base_path(self): + return os.path.normpath(os.path.abspath( self.data['path'] )) + + def get_base_dir(self): + path = self.get_base_path() + if not os.path.isdir(path): + path = os.path.dirname(path) + return path + + def clean_base_dir(self, path): + return re.sub( "^" + self.get_base_dir() + r"/*", "", path ) + + def get_files(self): + return glob( self.get_base_path() + "*" ) + + def get_filesize_map(self, rm_base_dir=False): + out = {} + for path in self.get_files(): + if rm_base_dir: + out[self.clean_base_dir(path)] = os.path.getsize(path) + else: + out[path] = os.path.getsize(path) + return out + + def get_fingerprint(self): + sha1 = hashlib.sha1() + fmap = self.get_filesize_map(True) + for k in sorted(fmap.keys()): + sha1.update(k) + sha1.update(str(fmap[k])) + return sha1.hexdigest() + + def to_dict(self): + rval = super(TabularToolDataField, self).to_dict() + rval['name'] = self.data['value'] + rval['fields'] = self.data + rval['base_dir'] = self.get_base_dir(), + rval['files'] = self.get_filesize_map(True) + rval['fingerprint'] = self.get_fingerprint() + return rval + + def expand_here_template(content, here=None): if here and content: content = string.Template(content).safe_substitute( { "__HERE__": here }) diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -64,6 +64,22 @@ return data_table.remove_entry(split_values) + @web.require_admin + @expose_api + def show_field( self, trans, id, value, **kwds ): + """ + GET /api/tool_data/<id>/fields/<value> + + Get information about a partiular field in a tool_data table + """ + return self._data_table_field( id, value ).to_dict() + + def _data_table_field( self, id, value ): + out = self._data_table(id).get_field(value) + if out is None: + raise exceptions.ObjectNotFound("No such field %s in data table %s." % (value, id)) + return out + def _data_table( self, id ): try: return self._data_tables[id] diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -171,6 +171,7 @@ webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) + webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) diff -r 6d54a7fd1fe9edfdf2f5c2fdb1b5ddb7eebdf59a -r edbe286564de14b2d51656c03443b3e4aa99e3ab test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -28,3 +28,11 @@ assert first_entry[0] == "data1" assert first_entry[1] == "data1name" assert first_entry[2].endswith("test/functional/tool-data/data1/entry.txt") + + def test_show_field(self): + show_field_response = self._get( "tool_data/testalpha/fields/data1", admin=True ) + self._assert_status_code_is( show_field_response, 200 ) + field = show_field_response.json() + self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" ) + files = field[ "files" ] + assert len( files ) == 2 https://bitbucket.org/galaxy/galaxy-central/commits/e416c3a2f956/ Changeset: e416c3a2f956 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Allow downloading index files via tool data API. This provides direct access to the files to admins - probably still wise to provide some mechanism to download a copressed archive of these files. Affected #: 3 files diff -r edbe286564de14b2d51656c03443b3e4aa99e3ab -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -1,6 +1,9 @@ +import os + from galaxy import exceptions from galaxy import web from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_raw as expose_api_raw from galaxy.web.base.controller import BaseAPIController @@ -74,6 +77,16 @@ """ return self._data_table_field( id, value ).to_dict() + @web.require_admin + @expose_api_raw + def download_field_file( self, trans, id, value, path, **kwds ): + field_value = self._data_table_field( id, value ) + base_dir = field_value.get_base_dir() + full_path = os.path.join( base_dir, path ) + if full_path not in field_value.get_files(): + raise exceptions.ObjectNotFound("No such path in data table field.") + return open(full_path, "r") + def _data_table_field( self, id, value ): out = self._data_table(id).get_field(value) if out is None: diff -r edbe286564de14b2d51656c03443b3e4aa99e3ab -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -171,6 +171,7 @@ webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' ) + webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data" ) webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" ) webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/') webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) diff -r edbe286564de14b2d51656c03443b3e4aa99e3ab -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -36,3 +36,9 @@ self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" ) files = field[ "files" ] assert len( files ) == 2 + + def test_download_field_file(self): + show_field_response = self._get( "tool_data/testalpha/fields/data1/files/entry.txt", admin=True ) + self._assert_status_code_is( show_field_response, 200 ) + content = show_field_response.content + assert content == "This is data 1.", content https://bitbucket.org/galaxy/galaxy-central/commits/66fbbbd58209/ Changeset: 66fbbbd58209 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Allow specification of multiple data manager configuration files... ... use this to create API functional tests for data managers. Affected #: 7 files diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -25,7 +25,10 @@ self.managed_data_tables = odict() self.tool_path = None self.filename = xml_filename or self.app.config.data_manager_config_file - self.load_from_xml( self.filename ) + for filename in util.listify( self.filename ): + if not filename: + continue + self.load_from_xml( filename ) if self.app.config.shed_data_manager_config_file: self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True ) diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -241,6 +241,12 @@ if os.path.exists( tool_data_config ): default_tool_data_config = tool_data_config tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config + + default_data_manager_config = 'config/data_manager_conf.xml.sample' + for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml' ]: + if os.path.exists( data_manager_config ): + default_data_manager_config = data_manager_config + data_manager_config_file = "%s,test/functional/tools/sample_data_manager_conf.xml" % default_data_manager_config shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) @@ -329,6 +335,7 @@ master_api_key=master_api_key, use_tasked_jobs=True, enable_beta_tool_formats=True, + data_manager_config_file=data_manager_config_file, ) if install_database_connection is not None: kwargs[ 'install_database_connection' ] = install_database_connection diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -1,6 +1,9 @@ """ Tests for the tool data API. """ +import json + from base import api +from .helpers import DatasetPopulator import operator @@ -42,3 +45,19 @@ self._assert_status_code_is( show_field_response, 200 ) content = show_field_response.content assert content == "This is data 1.", content + + def test_create_data_with_manager(self): + dataset_populator = DatasetPopulator( self.galaxy_interactor ) + history_id = dataset_populator.new_history() + payload = dataset_populator.run_tool_payload( + tool_id="data_manager", + inputs={"ignored_value": "moo"}, + history_id=history_id, + ) + create_response = self._post( "tools", data=payload ) + self._assert_status_code_is( create_response, 200 ) + dataset_populator.wait_for_history( history_id, assert_ok=True ) + show_response = self._get( "tool_data/testbeta", admin=True ) + print show_response.content + assert False + diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/functional/tool-data/sample_tool_data_tables.xml --- a/test/functional/tool-data/sample_tool_data_tables.xml +++ b/test/functional/tool-data/sample_tool_data_tables.xml @@ -3,10 +3,8 @@ <columns>value, name, path</columns><file path="${__HERE__}/testalpha.loc" /></table> - </tables> diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/functional/tools/data_manager.xml --- /dev/null +++ b/test/functional/tools/data_manager.xml @@ -0,0 +1,16 @@ +<tool id="data_manager" name="Test Data Manager" tool_type="manage_data" version="0.0.1"> + <configfiles> + <configfile name="static_test_data">{"data_tables": {"testbeta": [{"value": "newvalue", "path": "newvalue.txt"}]}}</configfile> + </configfiles> + <command> + mkdir $out_file.files_path ; + echo "A new value" > $out_file.files_path/newvalue.txt; + cp $static_test_data $out_file + </command> + <inputs> + <param type="text" name="ignored_value" value="" label="Ignored" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> +</tool> diff -r e416c3a2f956a28127eb730076f37ad6ee4b1d8b -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 test/functional/tools/sample_data_manager_conf.xml --- /dev/null +++ b/test/functional/tools/sample_data_manager_conf.xml @@ -0,0 +1,16 @@ +<data_managers tool_path="test/functional/tools"> + <data_manager tool_file="data_manager.xml" id="test_data_manager" version="1.0"> + <data_table name="testbeta"> + <output> + <column name="value" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">testbeta/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/testbeta/${value}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> https://bitbucket.org/galaxy/galaxy-central/commits/ecac8a867961/ Changeset: ecac8a867961 User: jmchilton Date: 2014-12-15 05:20:35+00:00 Summary: Implement test case for Pull Request #577. Affected #: 1 file diff -r 66fbbbd58209dba224f95c2aaf973ec7c64b7c11 -r ecac8a8679612d419347dcbedc398319418b077e test/api/test_tool_data.py --- a/test/api/test_tool_data.py +++ b/test/api/test_tool_data.py @@ -5,6 +5,8 @@ from base import api from .helpers import DatasetPopulator +from requests import delete + import operator @@ -46,7 +48,10 @@ content = show_field_response.content assert content == "This is data 1.", content - def test_create_data_with_manager(self): + def test_delete_entry(self): + show_response = self._get( "tool_data/testbeta", admin=True ) + original_count = len(show_response.json()["fields"]) + dataset_populator = DatasetPopulator( self.galaxy_interactor ) history_id = dataset_populator.new_history() payload = dataset_populator.run_tool_payload( @@ -58,6 +63,12 @@ self._assert_status_code_is( create_response, 200 ) dataset_populator.wait_for_history( history_id, assert_ok=True ) show_response = self._get( "tool_data/testbeta", admin=True ) - print show_response.content - assert False + updated_fields = show_response.json()["fields"] + assert len(updated_fields) == original_count + 1 + field0 = updated_fields[0] + url = self._api_url( "tool_data/testbeta?key=%s" % self.galaxy_interactor.master_api_key ) + delete( url, data=json.dumps({"values": "\t".join(field0)}) ) + show_response = self._get( "tool_data/testbeta", admin=True ) + updated_fields = show_response.json()["fields"] + assert len(updated_fields) == original_count Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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