galaxy-commits December 2014

galaxy-commits@lists.galaxyproject.org

2 participants
245 discussions

commit/galaxy-central: dannon: Merge next-stable.
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6d85572398e7/ Changeset: 6d85572398e7 User: dannon Date: 2014-12-15 16:18:20+00:00 Summary: Merge next-stable. 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.

1 0

commit/galaxy-central: nsoranzo: Fix variable name causing a NameError.
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fc799502f7a6/ Changeset: fc799502f7a6 Branch: next-stable User: nsoranzo Date: 2014-12-15 15:43:16+00:00 Summary: Fix variable name causing a NameError. Affected #: 1 file diff -r 6704c0ee9fec6b0624d739669cb7c66ea08d480a -r fc799502f7a6310f19230f58f11ab1fbe82b09ba 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.

1 0

commit/galaxy-central: nsoranzo: Fix variable name causing a NameError.
by commits-noreply＠bitbucket.org 16 Dec '14

16 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 16 Dec '14

16 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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galaxy-commits December 2014