From 8a15acb8a8d2cffa3c0435f5c20bcdaf2fa09ec8 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Thu, 23 May 2013 11:11:37 -0400 Subject: [PATCH 1/9] Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. --- lib/galaxy/tools/data/__init__.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py index 92103823898..7f5938a51ec 100644 --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -273,9 +273,12 @@ class TabularToolDataTable( ToolDataTable ): found_column = False for name, index in self.columns.iteritems(): if index == i: - rval.append( name ) + if not found_column: + rval.append( name ) + elif name == 'value': + #the column named 'value' always has priority over other named columns + rval[ -1 ] = name found_column = True - break if not found_column: rval.append( None ) return rval From c04ccc33d48c572360b392352bff633ad114f1c7 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 3 Jun 2013 15:43:31 -0400 Subject: [PATCH 2/9] Close the next-stable branch. From b8ed2c1207d8ac4be4371d6e0d4ba3dfae22b28d Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 3 Jun 2013 15:45:31 -0400 Subject: [PATCH 3/9] Added tag release_2013.06.03 for changeset 58811a78af8a --- .hgtags | 1 + 1 file changed, 1 insertion(+) diff --git a/.hgtags b/.hgtags index 4b94f4612d6..23ec599b629 100644 --- a/.hgtags +++ b/.hgtags @@ -2,3 +2,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +58811a78af8a09b77405dc343a5b2795f4cc6e88 release_2013.06.03 From 7ff56bfc60703af37e6f063d97fe5a309453fc67 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Mon, 3 Jun 2013 16:12:24 -0400 Subject: [PATCH 4/9] Cleanup after merge conflict. --- templates/webapps/tool_shed/index.mako | 39 ++++---------------------- 1 file changed, 5 insertions(+), 34 deletions(-) diff --git a/templates/webapps/tool_shed/index.mako b/templates/webapps/tool_shed/index.mako index be93640cc12..63d1335d948 100644 --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -92,14 +92,11 @@ Browse by category %if trans.user: -
-
- Repositories I Can Change -
-
- Repositories I own -
- %if has_reviewed_repositories: + %if trans.user.active_repositories: +
+
+ Repositories I Can Change +
Repositories I own
@@ -138,32 +135,6 @@ Latest revision: invalid tools %endif - %if has_deprecated_repositories: -
- Deprecated repositories I own -
- %endif -
- My writable repositories -
-
- Latest revision: missing tool tests -
-
- Latest revision: installation errors -
-
- Latest revision: failing tool tests -
-
- Latest revision: skip tool tests -
-
- Latest revision: all tool tests pass -
-
- Latest revision: invalid tools -
Available Actions From 64f08d4f028f075bbc8c7d6ef77cc4105981d3e2 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 3 Jun 2013 16:17:31 -0400 Subject: [PATCH 5/9] Update tag for stable_2013.06.03 --- .hgtags | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.hgtags b/.hgtags index 23ec599b629..843ac397c4d 100644 --- a/.hgtags +++ b/.hgtags @@ -2,4 +2,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 -58811a78af8a09b77405dc343a5b2795f4cc6e88 release_2013.06.03 +524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 From 6334bd05e3221ff2955bbe1788289e7327ac908b Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Tue, 4 Jun 2013 11:05:17 -0400 Subject: [PATCH 6/9] Fix server error when displaying a tool dependency installation status when the tool dependency contains certain unicode characters in the displayed error message. --- lib/tool_shed/util/shed_util_common.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py index 7ae9e9dcd81..658ab6a014a 100644 --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1214,7 +1214,7 @@ def to_safe_string( text, to_html=True ): if text: if to_html: try: - escaped_text = text.decode( 'utf-8' ) + escaped_text = unicodify( text ) escaped_text = escaped_text.encode( 'ascii', 'ignore' ) escaped_text = str( markupsafe.escape( escaped_text ) ) except UnicodeDecodeError, e: From 10a01ffa7ccd74741f9d99e10b6050d8bbc6290f Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Tue, 4 Jun 2013 12:02:55 -0400 Subject: [PATCH 7/9] Fix missing import. --- lib/tool_shed/util/shed_util_common.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py index 658ab6a014a..2aab8cf19aa 100644 --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -8,6 +8,7 @@ from time import gmtime from time import strftime from galaxy import util from galaxy.util import json +from galaxy.util import unicodify from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.datatypes import checkers From bf6ad2c0668ec9f52ed42beb9da3541a9f2afa71 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Wed, 5 Jun 2013 09:58:11 -0400 Subject: [PATCH 8/9] Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories. --- lib/tool_shed/util/common_install_util.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/tool_shed/util/common_install_util.py b/lib/tool_shed/util/common_install_util.py index 39b40721835..83c86eefe75 100644 --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -252,6 +252,8 @@ def get_required_repo_info_dicts( trans, tool_shed_url, repo_info_dicts ): # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. required_repository_tups = [] for repo_info_dict in repo_info_dicts: + if repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( repo_info_dict ) for repository_name, repo_info_tup in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) From 2fd2b094a8fe55a86485cd00ea3a8ac34fa609ca Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 5 Jun 2013 10:13:40 -0400 Subject: [PATCH 9/9] Strip select2 behavior from quota, role, and group creation in the admin panel --- templates/admin/dataset_security/group/group_create.mako | 2 ++ templates/admin/dataset_security/role/role_create.mako | 2 ++ templates/admin/quota/quota_create.mako | 2 ++ 3 files changed, 6 insertions(+) diff --git a/templates/admin/dataset_security/group/group_create.mako b/templates/admin/dataset_security/group/group_create.mako index bc474623efc..126c8a33fac 100644 --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -40,6 +40,8 @@ $().ready(function() { $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); diff --git a/templates/admin/dataset_security/role/role_create.mako b/templates/admin/dataset_security/role/role_create.mako index fb7ea562449..02f3d7a37ca 100644 --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); diff --git a/templates/admin/quota/quota_create.mako b/templates/admin/quota/quota_create.mako index f1192f466bd..77da81f894f 100644 --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); });