From 7d378792cc697ded34a40c2ed6783cc27d534e81 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Thu, 31 Mar 2016 10:59:16 -0400 Subject: [PATCH 1/3] Replace common_util.url_join with util.build_url. --- lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 2219afd4ba6..7c54e151a56 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -205,10 +205,10 @@ class AdminToolshed( AdminGalaxy ): def browse_toolshed( self, trans, **kwd ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) - url = common_util.url_join( tool_shed_url, pathspec=[ 'api', 'categories' ] ) + url = util.build_url( tool_shed_url, pathspec=[ 'api', 'categories' ] ) categories = json.loads( common_util.tool_shed_get( trans.app, url ) ) repositories = [] - url = common_util.url_join( tool_shed_url, pathspec=[ 'api', 'repositories' ] ) + url = util.build_url( tool_shed_url, pathspec=[ 'api', 'repositories' ] ) for repo in json.loads( common_util.tool_shed_get( trans.app, url ) ): repositories.append( dict( value=repo[ 'id' ], label='%s/%s' % ( repo[ 'owner' ], repo[ 'name' ] ) ) ) return trans.fill_template( '/admin/tool_shed_repository/browse_categories.mako', @@ -221,7 +221,7 @@ class AdminToolshed( AdminGalaxy ): def browse_tool_shed_category( self, trans, **kwd ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) category_id = kwd.get( 'category_id', '' ) - url = common_util.url_join( tool_shed_url ) + url = util.build_url( tool_shed_url ) json_data = json.loads( common_util.tool_shed_get( trans.app, url, pathspec=[ 'api', 'categories', category_id, 'repositories' ] ) ) for idx, repository in enumerate( json_data[ 'repositories' ] ): try: @@ -234,7 +234,7 @@ class AdminToolshed( AdminGalaxy ): json_data[ 'repositories' ][ idx ][ 'metadata' ] = { 'tools_functionally_correct': True } repositories = [] - url = common_util.url_join( tool_shed_url, pathspec=[ 'api', 'repositories' ] ) + url = util.build_url( tool_shed_url, pathspec=[ 'api', 'repositories' ] ) for repo in json.loads( common_util.tool_shed_get( trans.app, url ) ): repositories.append( dict( value=repo[ 'id' ], label='%s/%s' % ( repo[ 'owner' ], repo[ 'name' ] ) ) ) return trans.fill_template( '/admin/tool_shed_repository/browse_category.mako', From 494384171f260a924517844f4ff30db40a7dddbc Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Thu, 31 Mar 2016 11:05:31 -0400 Subject: [PATCH 2/3] Do the same for tool_shed_get. --- .../webapps/galaxy/controllers/admin_toolshed.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 7c54e151a56..cfbc5c3fc2f 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -206,10 +206,10 @@ class AdminToolshed( AdminGalaxy ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) url = util.build_url( tool_shed_url, pathspec=[ 'api', 'categories' ] ) - categories = json.loads( common_util.tool_shed_get( trans.app, url ) ) + categories = json.loads( util.url_get( url ) ) repositories = [] url = util.build_url( tool_shed_url, pathspec=[ 'api', 'repositories' ] ) - for repo in json.loads( common_util.tool_shed_get( trans.app, url ) ): + for repo in json.loads( util.url_get( url ) ): repositories.append( dict( value=repo[ 'id' ], label='%s/%s' % ( repo[ 'owner' ], repo[ 'name' ] ) ) ) return trans.fill_template( '/admin/tool_shed_repository/browse_categories.mako', tool_shed_url=tool_shed_url, @@ -222,10 +222,10 @@ class AdminToolshed( AdminGalaxy ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) category_id = kwd.get( 'category_id', '' ) url = util.build_url( tool_shed_url ) - json_data = json.loads( common_util.tool_shed_get( trans.app, url, pathspec=[ 'api', 'categories', category_id, 'repositories' ] ) ) + json_data = json.loads( util.url_get( url, pathspec=[ 'api', 'categories', category_id, 'repositories' ] ) ) for idx, repository in enumerate( json_data[ 'repositories' ] ): try: - metadata = json.loads( common_util.tool_shed_get( trans.app, + metadata = json.loads( util.url_get( url, pathspec=[ 'api', 'repositories', repository[ 'id' ], 'metadata' ], params=dict( recursive=False ) ) ) @@ -235,7 +235,7 @@ class AdminToolshed( AdminGalaxy ): repositories = [] url = util.build_url( tool_shed_url, pathspec=[ 'api', 'repositories' ] ) - for repo in json.loads( common_util.tool_shed_get( trans.app, url ) ): + for repo in json.loads( util.url_get( url ) ): repositories.append( dict( value=repo[ 'id' ], label='%s/%s' % ( repo[ 'owner' ], repo[ 'name' ] ) ) ) return trans.fill_template( '/admin/tool_shed_repository/browse_category.mako', tool_shed_url=tool_shed_url, @@ -1277,8 +1277,8 @@ class AdminToolshed( AdminGalaxy ): def preview_repository( self, trans, **kwd ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) tsr_id = kwd.get( 'tsr_id', '' ) - toolshed_data = json.loads( common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=[ 'api', 'repositories', tsr_id ] ) ) - toolshed_data[ 'metadata' ] = json.loads( common_util.tool_shed_get( trans.app, tool_shed_url, pathspec=[ 'api', 'repositories', tsr_id, 'metadata' ] ) ) + toolshed_data = json.loads( util.url_get( tool_shed_url, pathspec=[ 'api', 'repositories', tsr_id ] ) ) + toolshed_data[ 'metadata' ] = json.loads( util.url_get( tool_shed_url, pathspec=[ 'api', 'repositories', tsr_id, 'metadata' ] ) ) shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) return trans.fill_template( '/admin/tool_shed_repository/preview_repository.mako', From d885367955a0aa1a6a389ae7d67a6829002f8254 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Thu, 31 Mar 2016 13:52:43 -0400 Subject: [PATCH 3/3] Fix indent broken with search/replace. --- lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index cfbc5c3fc2f..048ffa19cff 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -225,10 +225,9 @@ class AdminToolshed( AdminGalaxy ): json_data = json.loads( util.url_get( url, pathspec=[ 'api', 'categories', category_id, 'repositories' ] ) ) for idx, repository in enumerate( json_data[ 'repositories' ] ): try: - metadata = json.loads( util.url_get( - url, - pathspec=[ 'api', 'repositories', repository[ 'id' ], 'metadata' ], - params=dict( recursive=False ) ) ) + metadata = json.loads( util.url_get( url, + pathspec=[ 'api', 'repositories', repository[ 'id' ], 'metadata' ], + params=dict( recursive=False ) ) ) json_data[ 'repositories' ][ idx ][ 'metadata' ] = metadata except: json_data[ 'repositories' ][ idx ][ 'metadata' ] = { 'tools_functionally_correct': True }