1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7e7a0c518d50/
Changeset: 7e7a0c518d50
User: dannon
Date: 2014-12-17 16:00:29+00:00
Summary: Delete *ancient* cron/cleanup_datsets.py content, but leave a nice deprecation warning and pointer for those who might actually be using it in cron jobs.
Affected #: 1 file
diff -r 78597d2278e28ac962b80179d15eacd5849a4c79 -r 7e7a0c518d503cfc489dcb1fd8b1b9a113ed0e88 cron/cleanup_datasets.py
--- a/cron/cleanup_datasets.py
+++ b/cron/cleanup_datasets.py
@@ -1,63 +1,8 @@
#!/usr/bin/env python
-#This script removes deleted dataset files.
-#Takes 3 arguments:
-# 1: database directory to clean
-# 2: postgres database name
-# 3 (optional): number of days to allow as a buffer, defaults to 2
-#python cleanup_datasets.py /home/universe/server-home/wsgi-postgres/database/files/ galaxy_test 2
+import sys
-import sys, os, tempfile, time
-try:
- database_dir = sys.argv[1]
- database_name = sys.argv[2]
- num_days = 2
- try:
- num_days = int(sys.argv[3])
- except:
- print "Using Default of 2 days buffer on delete"
-except:
- print "Usage: python %s path_to_files:/home/universe/server-home/wsgi-postgres/database/files/ database_name:galaxy_test [num_days_buffer:2]" % sys.argv[0]
- sys.exit(0)
-id_file = tempfile.NamedTemporaryFile('w')
-id_filename = id_file.name
-id_file.close()
-ids = []
+print ("This script has been deprecated, replaced by the set of scripts in <galaxy_distribution>/scripts/cleanup_datsets/."
+ "See https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%2… for more information.")
-command = "psql -d %s -c \"select id from dataset;\" -o %s" % (database_name, id_filename)
-print "Getting IDs:", command
-id_file = os.popen(command)
-id_file.close()
-for line in open(id_filename,'r'):
- try:
- ids.append(int(line.strip()))
- except:
- print line.strip(),"is not a valid id, skipping."
-os.unlink(id_filename)
-if len(ids) < 1:
- print "Less than 1 IDs have been found! Deleting proccess has been canceled."
- sys.exit(0)
-print "-----%i IDs Retrieved -----" % len(ids)
-print "----- Checking database directory for deleted ids: %s -----" % database_dir
-file_size = 0
-num_delete = 0
-for result in os.walk(database_dir):
- this_base_dir,sub_dirs,files = result
- for file in files:
- if file.startswith("dataset_") and file.endswith(".dat"):
- id = int(file.replace("dataset_","").replace(".dat",""))
- file_name = os.path.join(this_base_dir,file)
- if id not in ids:
- file_time = os.path.getctime(file_name)
- if time.time() > file_time + (num_days*60*60*24): #num_days (default=2) days buffer room
- num_delete += 1
- size = os.path.getsize(file_name)
- file_size += size
- os.unlink(file_name)
-print file_size, "bytes"
-print float(file_size) / 1024, "kilobytes"
-print float(file_size) / 1024 / 1024, "Megabytes"
-print float(file_size) / 1024 / 1024 / 1024, "Gigabytes"
-print "%i files deleted" % num_delete
-
-sys.exit(0)
\ No newline at end of file
+sys.exit(1)
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/05604a5d31c1/
Changeset: 05604a5d31c1
Branch: next-stable
User: jmchilton
Date: 2014-12-17 15:57:44+00:00
Summary: Fix a74d320.
Affected #: 1 file
diff -r a74d32014b0512613042c2a44d0b946703a1fbcd -r 05604a5d31c1b150d4a04347e68c0f30f2d0a598 lib/galaxy/tools/test.py
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -195,8 +195,7 @@
if isinstance( value, basic.DataToolParameter ):
if not isinstance(param_value, list):
param_value = [ param_value ]
- map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ),
-param_value )
+ map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ), param_value )
processed_value = param_value
elif isinstance( value, basic.DataCollectionToolParameter ):
assert 'collection' in param_extra
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/a74d32014b05/
Changeset: a74d32014b05
Branch: next-stable
User: jmchilton
Date: 2014-12-17 14:38:49+00:00
Summary: Fix gz/zip upload of files to test framework.
With test case to ensure they don't break again. Problem was due to a small switch of an if to an elif in 7114d15a6d22 which had been sort of masking over an older bug.
Thanks to Peter Cock for reporting the issue.
Affected #: 3 files
diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd lib/galaxy/tools/test.py
--- a/lib/galaxy/tools/test.py
+++ b/lib/galaxy/tools/test.py
@@ -195,7 +195,9 @@
if isinstance( value, basic.DataToolParameter ):
if not isinstance(param_value, list):
param_value = [ param_value ]
- processed_value = [ self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ) for v in param_value ]
+ map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ),
+param_value )
+ processed_value = param_value
elif isinstance( value, basic.DataCollectionToolParameter ):
assert 'collection' in param_extra
collection_def = param_extra[ 'collection' ]
diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd test/functional/tools/gzipped_inputs.xml
--- /dev/null
+++ b/test/functional/tools/gzipped_inputs.xml
@@ -0,0 +1,19 @@
+<tool id="gzipped_inputs" name="Echo Dataset">
+ <command>
+ cat $input1 > $out_file1
+ </command>
+ <inputs>
+ <param name="input1" type="data" label="Concatenate Dataset"/>
+ </inputs>
+ <outputs>
+ <data name="out_file1" format="input" metadata_source="input1"/>
+ </outputs>
+ <tests>
+ <test>
+ <param name="input1" value="4.bed.gz" />
+ <output name="out_file1" file="4.bed" />
+ </test>
+ </tests>
+ <help>
+ </help>
+</tool>
diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd test/functional/tools/samples_tool_conf.xml
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -11,6 +11,7 @@
<tool file="multi_output_configured.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" />
+ <tool file="gzipped_inputs.xml" /><tool file="output_order.xml" /><tool file="output_format.xml" /><tool file="output_filter.xml" />
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/7197e949d3ab/
Changeset: 7197e949d3ab
Branch: stable
User: natefoo
Date: 2014-12-17 14:00:15+00:00
Summary: Update tag latest_2014.10.06 for changeset 5834b1066462
Affected #: 1 file
diff -r 5834b1066462dd219f67c1c3cbd77c78e7cf3a6c -r 7197e949d3ab990ceb76c193ebc940d90aa04cad .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06
+5834b1066462dd219f67c1c3cbd77c78e7cf3a6c latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d13f2b265dbf/
Changeset: d13f2b265dbf
User: Nitesh Turaga
Date: 2014-12-16 16:04:58+00:00
Summary: "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also.
Affected #: 1 file
diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r d13f2b265dbf58c60ce4f13bcc902c4848c65c7c config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -136,7 +136,7 @@
# Tools can be locally developed or installed from Galaxy tool sheds.
# (config/tool_conf.xml.sample will be used if left unset and
# config/tool_conf.xml does not exist).
-#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml
+#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
# Enable / disable checking if any tools defined in the above non-shed tool_config_files
# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool
https://bitbucket.org/galaxy/galaxy-central/commits/e614c7c1e0e9/
Changeset: e614c7c1e0e9
User: dannon
Date: 2014-12-16 20:48:44+00:00
Summary: Merged in nitesh1989/galaxy-central3 (pull request #615)
"shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also.
Affected #: 1 file
diff -r 1cf0af0a6324e24a0008f5ceff598573262f14ca -r e614c7c1e0e9648076759c06dc33ed48b1847b13 config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -136,7 +136,7 @@
# Tools can be locally developed or installed from Galaxy tool sheds.
# (config/tool_conf.xml.sample will be used if left unset and
# config/tool_conf.xml does not exist).
-#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml
+#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
# Enable / disable checking if any tools defined in the above non-shed tool_config_files
# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool
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/e614c7c1e0e9/
Changeset: e614c7c1e0e9
User: dannon
Date: 2014-12-16 20:48:44+00:00
Summary: Merged in nitesh1989/galaxy-central3 (pull request #615)
"shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also.
Affected #: 1 file
diff -r 1cf0af0a6324e24a0008f5ceff598573262f14ca -r e614c7c1e0e9648076759c06dc33ed48b1847b13 config/galaxy.ini.sample
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -136,7 +136,7 @@
# Tools can be locally developed or installed from Galaxy tool sheds.
# (config/tool_conf.xml.sample will be used if left unset and
# config/tool_conf.xml does not exist).
-#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml
+#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
# Enable / disable checking if any tools defined in the above non-shed tool_config_files
# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/31f0b0cbb4ef/
Changeset: 31f0b0cbb4ef
Branch: next-stable
User: davebgx
Date: 2014-12-16 20:15:57+00:00
Summary: Merge stable into next-stable.
Affected #: 2 files
diff -r d1f9d077c2288b25a35ae97e306cdf2924548d62 -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-e416697be38e66f18be89a4cfca70457c9784294 latest_2014.10.06
+7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06
diff -r d1f9d077c2288b25a35ae97e306cdf2924548d62 -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a lib/tool_shed/util/repository_util.py
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -322,8 +322,8 @@
return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name
else:
return "You already have a repository named <b>%s</b>, so choose a different name." % name
- if len( name ) < 4:
- return "Repository names must be at least 4 characters in length."
+ if len( name ) < 2:
+ return "Repository names must be at least 2 characters in length."
if len( name ) > 80:
return "Repository names cannot be more than 80 characters in length."
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
https://bitbucket.org/galaxy/galaxy-central/commits/1cf0af0a6324/
Changeset: 1cf0af0a6324
User: davebgx
Date: 2014-12-16 20:16:18+00:00
Summary: Merge next-stable into default.
Affected #: 2 files
diff -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 -r 1cf0af0a6324e24a0008f5ceff598573262f14ca .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-e416697be38e66f18be89a4cfca70457c9784294 latest_2014.10.06
+7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06
diff -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 -r 1cf0af0a6324e24a0008f5ceff598573262f14ca lib/tool_shed/util/repository_util.py
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -325,8 +325,8 @@
return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name
else:
return "You already have a repository named <b>%s</b>, so choose a different name." % name
- if len( name ) < 4:
- return "Repository names must be at least 4 characters in length."
+ if len( name ) < 2:
+ return "Repository names must be at least 2 characters in length."
if len( name ) > 80:
return "Repository names cannot be more than 80 characters in length."
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
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/5834b1066462/
Changeset: 5834b1066462
Branch: stable
User: davebgx
Date: 2014-12-16 20:00:50+00:00
Summary: Reduce minimum length of repository names from 4 characters to 2.
Affected #: 1 file
diff -r c265480083ecb81f1e968521932342137807601c -r 5834b1066462dd219f67c1c3cbd77c78e7cf3a6c lib/tool_shed/util/repository_util.py
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -322,8 +322,8 @@
return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name
else:
return "You already have a repository named <b>%s</b>, so choose a different name." % name
- if len( name ) < 4:
- return "Repository names must be at least 4 characters in length."
+ if len( name ) < 2:
+ return "Repository names must be at least 2 characters in length."
if len( name ) > 80:
return "Repository names cannot be more than 80 characters in length."
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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