1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2accb50ef103/
Changeset: 2accb50ef103
User: greg
Date: 2013-07-08 18:03:22
Summary: Fix for checking the Galaxy environment for missing migrated tools at server startup.
Affected #: 1 file
diff -r afec613d77fa58ad0de7066a2d9b18daad8cdb88 -r 2accb50ef103b083f053c9550518d75c7527f706 lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -19,6 +19,7 @@
tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed )
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
+ missing_tool_configs_dict = odict()
if tool_shed_url:
for elem in root:
if elem.tag == 'repository':
@@ -48,7 +49,6 @@
migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies
if tool_shed_accessible:
# Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names.
- missing_tool_configs_dict = odict()
for tool_panel_config in tool_panel_configs:
tree, error_message = xml_util.parse_xml( tool_panel_config )
if tree:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a691d69caa99/
Changeset: a691d69caa99
User: greg
Date: 2013-07-07 01:41:10
Summary: Allow public usernames in the tool shed to be a minimum of 3 characters.
Affected #: 2 files
diff -r a13a9bce1c09319b0c18f287d17cbc2a7cd544ed -r a691d69caa99ec771062d5dd5312a516af5ff6c1 lib/galaxy/security/validate_user_input.py
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -23,8 +23,12 @@
return ''
if user and user.username == publicname:
return ''
- if len( publicname ) < 4:
- return "Public name must be at least 4 characters in length"
+ if trans.webapp.name == 'tool_shed':
+ if len( publicname ) < 3:
+ return "Public name must be at least 3 characters in length"
+ else:
+ if len( publicname ) < 4:
+ return "Public name must be at least 4 characters in length"
if len( publicname ) > 255:
return "Public name cannot be more than 255 characters in length"
if not( VALID_PUBLICNAME_RE.match( publicname ) ):
diff -r a13a9bce1c09319b0c18f287d17cbc2a7cd544ed -r a691d69caa99ec771062d5dd5312a516af5ff6c1 tools/data_source/upload.xml
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -33,7 +33,7 @@
</param><param name="async_datasets" type="hidden" value="None"/><upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
- <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator).">
+ <param name="file_data" type="file" size="30" label="File" ajax-upload="false" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."><validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator><!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs --></param><param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a13a9bce1c09/
Changeset: a13a9bce1c09
User: jgoecks
Date: 2013-07-03 16:39:02
Summary: Make BAM_to_SAM tool write temporary files to job working directory rather than generic temp space.
Affected #: 1 file
diff -r ebe87051fadff5750ec226490b31e49bdd68b070 -r a13a9bce1c09319b0c18f287d17cbc2a7cd544ed tools/samtools/bam_to_sam.py
--- a/tools/samtools/bam_to_sam.py
+++ b/tools/samtools/bam_to_sam.py
@@ -43,7 +43,7 @@
except:
sys.stdout.write( 'Could not determine Samtools version\n' )
- tmp_dir = tempfile.mkdtemp()
+ tmp_dir = tempfile.mkdtemp( dir='.' )
try:
# exit if input file empty
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c7a07f350887/
Changeset: c7a07f350887
User: jgoecks
Date: 2013-07-02 15:25:55
Summary: Make SAM_to_BAM tool write temporary files to job working directory rather than generic temp space.
Affected #: 1 file
diff -r a600d1f3f9009f383d8f4667f48592450b9154cf -r c7a07f350887fe3b4e822ba6b26b63ac3ac14bdf tools/samtools/sam_to_bam.py
--- a/tools/samtools/sam_to_bam.py
+++ b/tools/samtools/sam_to_bam.py
@@ -42,7 +42,7 @@
except:
sys.stdout.write( 'Could not determine Samtools version\n' )
- tmp_dir = tempfile.mkdtemp()
+ tmp_dir = tempfile.mkdtemp( dir='.' )
if not options.ref_file or options.ref_file == 'None':
# We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
# The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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