commit/galaxy-central: jgoecks: Trackster: fix syntax error.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dfb77de2aff5/
Changeset: dfb77de2aff5
User: jgoecks
Date: 2013-05-30 18:24:17
Summary: Trackster: fix syntax error.
Affected #: 1 file
diff -r b9af82c027e7d720214f12f212adc592e6841ce9 -r dfb77de2aff56137a6f7bf8efc7761f03fcabf6f static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1577,7 +1577,7 @@
view.overview_drawable.request_draw();
this.changed();
},
- view
+
/** Close and reset overview. */
reset_overview: function() {
// Update UI.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Add specific ami functionality (via GET param) to cloudlaunch. Prevent existing instance selection when using a share string.
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b9af82c027e7/
Changeset: b9af82c027e7
User: dannon
Date: 2013-05-30 17:23:29
Summary: Add specific ami functionality (via GET param) to cloudlaunch. Prevent existing instance selection when using a share string.
Affected #: 2 files
diff -r b37711ed16fe64bc96ec8eacc6e6ce7026643bab -r b9af82c027e7d720214f12f212adc592e6841ce9 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
--- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
+++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
@@ -35,8 +35,8 @@
BaseUIController.__init__(self, app)
@web.expose
- def index(self, trans, share_string=None):
- return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string)
+ def index(self, trans, share_string=None, ami=None):
+ return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string, ami=ami)
@web.expose
def get_account_info(self, trans, key_id, secret, **kwargs):
@@ -92,7 +92,7 @@
return to_json_string(account_info)
@web.expose
- def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, zone=None, **kwargs):
+ def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, **kwargs):
ec2_error = None
try:
# Create security group & key pair used when starting an instance
@@ -113,11 +113,14 @@
user_provided_data['password'] = password
if share_string:
user_provided_data['share_string'] = share_string
+
rs = run_instance(ec2_conn=ec2_conn,
+ image_id = ami,
user_provided_data=user_provided_data,
key_name=kp_name,
security_groups=[sg_name],
- placement=zone)
+ placement=zone
+ )
if rs:
instance = rs.instances[0]
ct = 0
@@ -266,7 +269,7 @@
return None, None
return kp.name, kp.material
-def run_instance(ec2_conn, user_provided_data, image_id=DEFAULT_AMI,
+def run_instance(ec2_conn, user_provided_data, image_id=None,
kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR,
placement=None, security_groups=['CloudMan']):
""" Start an instance. If instance start was OK, return the ResultSet object
diff -r b37711ed16fe64bc96ec8eacc6e6ce7026643bab -r b9af82c027e7d720214f12f212adc592e6841ce9 templates/webapps/galaxy/cloud/index.mako
--- a/templates/webapps/galaxy/cloud/index.mako
+++ b/templates/webapps/galaxy/cloud/index.mako
@@ -202,12 +202,14 @@
</div><div id="hidden_options">
+ %if not share_string:
<div id='existing_instance_wrapper' style="display:none;" class="form-row"><label for="id_existing_instance">Instances in your account</label><select name="existing_instance" id="id_existing_instance"></select><input id='id_zone' type='hidden' name='zone' value=''/></div>
+ %endif
<div id='cluster_name_wrapper' class="form-row"><label for="id_cluster_name">Cluster Name</label><input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/>
@@ -244,6 +246,10 @@
</div>
%endif
+ %if ami:
+ <input type='hidden' name='ami' value='${ami}'/>
+ %endif
+
<div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7be69524cfaa/
Changeset: 7be69524cfaa
Branch: next-stable
User: Dave Bouvier
Date: 2013-05-30 16:36:40
Summary: Fix error reporting in the tool dependency installation process.
Affected #: 2 files
diff -r 7b2c4fff40c0682bdb64a5fe8049df15cf836541 -r 7be69524cfaae9c56f1eb9cd77a857a9b912108c lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
@@ -1,7 +1,9 @@
import logging
import os
import shutil
+import sys
import tarfile
+import traceback
import urllib2
import zipfile
import tool_shed.util.shed_util_common as suc
@@ -78,6 +80,10 @@
tar.extractall( path=file_path )
tar.close()
+def format_traceback():
+ ex_type, ex, tb = sys.exc_info()
+ return ''.join( traceback.format_tb( tb ) )
+
def extract_zip( archive_path, extraction_path ):
# TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5.
if not zipfile_ok( archive_path ):
@@ -220,6 +226,8 @@
dst = open( file_path,'wb' )
dst.write( data )
except:
+ raise
+ finally:
if src:
src.close()
if dst:
diff -r 7b2c4fff40c0682bdb64a5fe8049df15cf836541 -r 7be69524cfaae9c56f1eb9cd77a857a9b912108c lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -165,8 +165,9 @@
# There is currently only one fabric method.
fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
except Exception, e:
+ log.exception( 'Error installing tool dependency %s version %s.', str( tool_dependency.name ), str( tool_dependency.version ) )
tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
- tool_dependency.error_message = str( e )
+ tool_dependency.error_message = '%s\n%s' % ( common_util.format_traceback(), str( e ) )
sa_session.add( tool_dependency )
sa_session.flush()
if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
https://bitbucket.org/galaxy/galaxy-central/commits/b37711ed16fe/
Changeset: b37711ed16fe
User: Dave Bouvier
Date: 2013-05-30 16:37:11
Summary: Merge in next-stable.
Affected #: 2 files
diff -r e47d4ab261370d174641e0db1f5b7dd2adc96365 -r b37711ed16fe64bc96ec8eacc6e6ce7026643bab lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
@@ -1,7 +1,9 @@
import logging
import os
import shutil
+import sys
import tarfile
+import traceback
import urllib2
import zipfile
import tool_shed.util.shed_util_common as suc
@@ -78,6 +80,10 @@
tar.extractall( path=file_path )
tar.close()
+def format_traceback():
+ ex_type, ex, tb = sys.exc_info()
+ return ''.join( traceback.format_tb( tb ) )
+
def extract_zip( archive_path, extraction_path ):
# TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5.
if not zipfile_ok( archive_path ):
@@ -220,6 +226,8 @@
dst = open( file_path,'wb' )
dst.write( data )
except:
+ raise
+ finally:
if src:
src.close()
if dst:
diff -r e47d4ab261370d174641e0db1f5b7dd2adc96365 -r b37711ed16fe64bc96ec8eacc6e6ce7026643bab lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -165,8 +165,9 @@
# There is currently only one fabric method.
fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
except Exception, e:
+ log.exception( 'Error installing tool dependency %s version %s.', str( tool_dependency.name ), str( tool_dependency.version ) )
tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
- tool_dependency.error_message = str( e )
+ tool_dependency.error_message = '%s\n%s' % ( common_util.format_traceback(), str( e ) )
sa_session.add( tool_dependency )
sa_session.flush()
if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: fubar: clean up fastqc updates a tiny bit
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e47d4ab26137/
Changeset: e47d4ab26137
User: fubar
Date: 2013-05-30 07:01:29
Summary: clean up fastqc updates a tiny bit
Affected #: 1 file
diff -r 34b03e0f3182af0601d747b7988308ddc2931149 -r e47d4ab261370d174641e0db1f5b7dd2adc96365 tools/rgenetics/rgFastQC.py
--- a/tools/rgenetics/rgFastQC.py
+++ b/tools/rgenetics/rgFastQC.py
@@ -62,10 +62,9 @@
infname = self.opts.inputfilename
linf = infname.lower()
trimext = False
- isgz = linf.endswith('.gz') or linf.endswith('.gzip')
# decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
# patched may 29 2013 until this is fixed properly
- if isgz:
+ if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
f = gzip.open(self.opts.input)
try:
testrow = f.readline()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: fubar: Starting the Rgenetics deprecation process - removing all rgenetics sections from tool_conf.xml.sample and fastqc update to dance around EBI_SRA download bogus file extensions
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/34b03e0f3182/
Changeset: 34b03e0f3182
User: fubar
Date: 2013-05-30 06:57:13
Summary: Starting the Rgenetics deprecation process - removing all rgenetics sections from tool_conf.xml.sample and fastqc update to dance around EBI_SRA download bogus file extensions
Affected #: 3 files
diff -r cc25fdb717ebde12121948a318bb9d141eb6710a -r 34b03e0f3182af0601d747b7988308ddc2931149 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -397,38 +397,6 @@
<section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /></section>
- <section name="SNP/WGA: Data; Filters" id="rgdat">
-
- <label text="Data: Import and upload" id="rgimport" />
- <tool file="data_source/upload.xml"/>
- <tool file="data_source/access_libraries.xml" />
-
- <label text="Data: Filter and Clean" id="rgfilter" />
- <tool file="rgenetics/rgClean.xml"/>
- <tool file="rgenetics/rgPedSub.xml"/>
- <tool file="rgenetics/rgLDIndep.xml"/>
-
- <label text="Simulate" id="rgsim" />
- <tool file="rgenetics/rgfakePhe.xml"/>
- <tool file="rgenetics/rgfakePed.xml"/>
- </section>
- <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
-
- <label text="QC; Eigenstrat" id="rgvisual" />
- <tool file="rgenetics/rgQC.xml"/>
- <tool file="rgenetics/rgEigPCA.xml"/>
-
- <label text="LD; Manhattan/QQ; GRR" id="rgld" />
- <tool file="rgenetics/rgHaploView.xml"/>
- <tool file="rgenetics/rgManQQ.xml"/>
- <tool file="rgenetics/rgGRR.xml"/>
- </section>
- <section name="SNP/WGA: Statistical Models" id="rgmodel">
- <tool file="rgenetics/rgCaCo.xml"/>
- <tool file="rgenetics/rgTDT.xml"/>
- <tool file="rgenetics/rgGLM.xml"/>
- <tool file="rgenetics/rgManQQ.xml"/>
- </section><section name="Phenotype Association" id="hgv"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" />
diff -r cc25fdb717ebde12121948a318bb9d141eb6710a -r 34b03e0f3182af0601d747b7988308ddc2931149 tools/rgenetics/rgFastQC.py
--- a/tools/rgenetics/rgFastQC.py
+++ b/tools/rgenetics/rgFastQC.py
@@ -1,4 +1,5 @@
"""
+# May 2013 ross added check for bogus gz extension - fastqc gets confused
# added sanitizer for user supplied name
# removed shell and make cl a sequence for Popen call
# ross lazarus August 10 2012 in response to anon insecurity report
@@ -24,6 +25,8 @@
import shutil
import tempfile
from rgutils import getFileString
+import zipfile
+import gzip
class FastQC():
"""wrapper
@@ -56,7 +59,32 @@
cl.append('--contaminants=%s' % self.opts.contaminants)
# patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30
# use a symlink in a temporary directory so that the FastQC report reflects the history input file name
- fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename))
+ infname = self.opts.inputfilename
+ linf = infname.lower()
+ trimext = False
+ isgz = linf.endswith('.gz') or linf.endswith('.gzip')
+ # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
+ # patched may 29 2013 until this is fixed properly
+ if isgz:
+ f = gzip.open(self.opts.input)
+ try:
+ testrow = f.readline()
+ except:
+ trimext = True
+ f.close()
+ elif linf.endswith('bz2'):
+ f = bz2.open(self.opts.input,'rb')
+ try:
+ f.readline()
+ except:
+ trimext = True
+ f.close()
+ elif linf.endswith('.zip'):
+ if not zipfile.is_zipfile(self.opts.input):
+ trimext = True
+ if trimext:
+ infname = os.path.splitext(infname)[0]
+ fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
link_name = os.path.join(self.opts.outputdir, fastqinfilename)
os.symlink(self.opts.input, link_name)
cl.append(link_name)
diff -r cc25fdb717ebde12121948a318bb9d141eb6710a -r 34b03e0f3182af0601d747b7988308ddc2931149 tools/rgenetics/rgFastQC.xml
--- a/tools/rgenetics/rgFastQC.xml
+++ b/tools/rgenetics/rgFastQC.xml
@@ -1,4 +1,4 @@
-<tool name="FastQC:Read QC" id="fastqc" version="0.51">
+<tool name="FastQC:Read QC" id="fastqc" version="0.52"><description>reports using FastQC</description><command interpreter="python">
rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Tools API: better error handling in create, encode ids returned; Scripts: add history_upload script to api
by commits-noreply＠bitbucket.org
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cc25fdb717eb/
Changeset: cc25fdb717eb
User: carlfeberhard
Date: 2013-05-29 23:28:47
Summary: Tools API: better error handling in create, encode ids returned; Scripts: add history_upload script to api
Affected #: 2 files
diff -r 93f6e07db8549411be10ba5385ba4cf9fab0c046 -r cc25fdb717ebde12121948a318bb9d141eb6710a lib/galaxy/webapps/galaxy/api/tools.py
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -66,9 +66,9 @@
# -- Execute tool. --
# Get tool.
- tool_id = payload[ 'tool_id' ]
- tool = trans.app.toolbox.get_tool( tool_id )
+ tool = trans.app.toolbox.get_tool( payload[ 'tool_id' ] ) if 'tool_id' in payload else None
if not tool:
+ trans.response.status = 404
return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } }
# Set running history from payload parameters.
@@ -82,7 +82,7 @@
target_history = None
# Set up inputs.
- inputs = payload[ 'inputs' ]
+ inputs = payload.get( 'inputs', {} )
# Find files coming in as multipart file data and add to inputs.
for k, v in payload.iteritems():
if k.startswith("files_"):
@@ -91,17 +91,23 @@
# HACK: add run button so that tool.handle_input will run tool.
inputs['runtool_btn'] = 'Execute'
# TODO: encode data ids and decode ids.
+ # TODO: handle dbkeys
params = util.Params( inputs, sanitize = False )
- template, vars = tool.handle_input( trans, params.__dict__, history=target_history)
+ template, vars = tool.handle_input( trans, params.__dict__, history=target_history )
+ if 'errors' in vars:
+ trans.response.status = 400
+ return { "message": { "type": "error", "data" : vars[ 'errors' ] } }
# TODO: check for errors and ensure that output dataset(s) are available.
- output_datasets = vars.get('out_data', {}).values()
+ output_datasets = vars.get( 'out_data', {} ).values()
rval = {
"outputs": []
}
outputs = rval[ "outputs" ]
+ #TODO:?? poss. only return ids?
for output in output_datasets:
- outputs.append( output.get_api_value() )
+ output_dict = output.get_api_value()
+ outputs.append( trans.security.encode_dict_ids( output_dict ) )
return rval
#
diff -r 93f6e07db8549411be10ba5385ba4cf9fab0c046 -r cc25fdb717ebde12121948a318bb9d141eb6710a scripts/api/history_upload.py
--- /dev/null
+++ b/scripts/api/history_upload.py
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+"""
+Upload a file to the desired history.
+"""
+_USAGE = ( "history_upload.py <api key><galaxy base url><history id><filepath to upload>\n"
+ + " (where galaxy base url is just the root url where your Galaxy is served; e.g. 'localhost:8080')" )
+
+import os, sys, json, pprint
+#sys.path.insert( 0, os.path.dirname( __file__ ) )
+
+try:
+ import requests
+except ImportError, imp_err:
+ log.error( "Could not import the requests module. See http://docs.python-requests.org/en/latest/ or "
+ + "install with 'pip install requests'" )
+ raise
+
+def upload_file( full_url, api_key, history_id, filepath, **kwargs ):
+
+ payload = {
+ 'key' : api_key,
+ 'tool_id' : 'upload1',
+ 'history_id' : history_id,
+ }
+ inputs = {
+ 'files_0|NAME' : kwargs.get( 'filename', os.path.basename( filepath ) ),
+ 'files_0|type' : 'upload_dataset',
+ #TODO: the following doesn't work with tools.py
+ #'dbkey' : kwargs.get( 'dbkey', '?' ),
+ 'dbkey' : '?',
+ 'file_type' : kwargs.get( 'file_type', 'auto' ),
+ 'ajax_upload' : u'true',
+ 'async_datasets': '1',
+ }
+ payload[ 'inputs' ] = json.dumps( inputs )
+
+ response = None
+ with open( filepath, 'rb' ) as file_to_upload:
+ files = { 'files_0|file_data' : file_to_upload }
+ response = requests.post( full_url, data=payload, files=files )
+ return response
+
+if __name__ == '__main__':
+
+ if len( sys.argv ) < 5:
+ print _USAGE
+ sys.exit( 1 )
+
+ api_key, base_url, history_id, filepath = sys.argv[1:5]
+ full_url = base_url + '/api/tools'
+ kwargs = dict([ kwarg.split('=', 1) for kwarg in sys.argv[5:]])
+
+ response = upload_file( full_url, api_key, history_id, filepath, **kwargs )
+ print >> sys.stderr, response
+ print response.content
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 1 month
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7b2c4fff40c0/
Changeset: 7b2c4fff40c0
Branch: next-stable
User: carlfeberhard
Date: 2013-05-29 22:25:01
Summary: HDA.get_api_value: remove history_id as tuple
Affected #: 1 file
diff -r 05674ed7665cbd7a1012d8b31b728cdbf52a3dbd -r 7b2c4fff40c0682bdb64a5fe8049df15cf836541 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1684,7 +1684,7 @@
misc_blurb = hda.blurb )
if hda.history is not None:
- rval['history_id'] = hda.history.id,
+ rval['history_id'] = hda.history.id
rval[ 'peek' ] = to_unicode( hda.display_peek() )
for name, spec in hda.metadata.spec.items():
https://bitbucket.org/galaxy/galaxy-central/commits/93f6e07db854/
Changeset: 93f6e07db854
User: carlfeberhard
Date: 2013-05-29 22:26:01
Summary: merge next-stable
Affected #: 1 file
diff -r 13797aac2667307106edeaba3076f04abd96e60d -r 93f6e07db8549411be10ba5385ba4cf9fab0c046 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1684,7 +1684,7 @@
misc_blurb = hda.blurb )
if hda.history is not None:
- rval['history_id'] = hda.history.id,
+ rval['history_id'] = hda.history.id
rval[ 'peek' ] = to_unicode( hda.display_peek() )
for name, spec in hda.metadata.spec.items():
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/05674ed7665c/
Changeset: 05674ed7665c
Branch: next-stable
User: greg
Date: 2013-05-29 22:18:27
Summary: Fix styles for automated tool test results containers in the tool shed.
Affected #: 2 files
diff -r eb524e42fc65eb69274857bcaf85030f0edd32f0 -r 05674ed7665cbd7a1012d8b31b728cdbf52a3dbd lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -33,7 +33,7 @@
@web.expose_api_anonymous
def get_ordered_installable_revisions( self, trans, name, owner, **kwd ):
"""
- GET /api/repository/get_ordered_installable_revisions
+ GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
@@ -59,7 +59,7 @@
@web.expose_api_anonymous
def get_repository_revision_install_info( self, trans, name, owner, changeset_revision, **kwd ):
"""
- GET /api/repository/get_repository_revision_install_info
+ GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
diff -r eb524e42fc65eb69274857bcaf85030f0edd32f0 -r 05674ed7665cbd7a1012d8b31b728cdbf52a3dbd templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -395,13 +395,23 @@
<%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( failed_test.id ) %>
+ <style type="text/css">
+ #failed_test_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="readme_table">
+ <table id="failed_test_table"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr>
@@ -485,14 +495,14 @@
encoded_id = trans.security.encode_id( invalid_tool_dependency.id )
%><style type="text/css">
- #readme_table{ table-layout:fixed;
- width:100%;
- overflow-wrap:normal;
- overflow:hidden;
- border:0px;
- word-break:keep-all;
- word-wrap:break-word;
- line-break:strict; }
+ #invalid_td_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
</style><tr class="datasetRow"
%if parent is not None:
@@ -500,7 +510,9 @@
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- ${ invalid_tool_dependency.error | h }
+ <table id="invalid_td_table">
+ <tr><td>${ invalid_tool_dependency.error | h }</td></tr>
+ </table></td></tr><%
@@ -511,13 +523,23 @@
<%def name="render_missing_test_component( missing_test_component, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( missing_test_component.id ) %>
+ <style type="text/css">
+ #missing_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="readme_table">
+ <table id="missing_table"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr>
@@ -632,13 +654,23 @@
<%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %>
+ <style type="text/css">
+ #td_install_error_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="td_installation_errors">
+ <table id="td_install_error_table"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr>
@@ -660,13 +692,23 @@
<%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %>
+ <style type="text/css">
+ #rd_install_error_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="repository_installation_errors">
+ <table id="rd_install_error_table">
%if not is_current_repository:
<tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th>
@@ -691,13 +733,23 @@
<%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( passed_test.id ) %>
+ <style type="text/css">
+ #passed_tests_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="readme_table">
+ <table id="passed_tests_table"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr>
https://bitbucket.org/galaxy/galaxy-central/commits/13797aac2667/
Changeset: 13797aac2667
User: greg
Date: 2013-05-29 22:18:54
Summary: Merged from next-stable
Affected #: 2 files
diff -r 49cc4a899f2ff5853d6c4f4c70ef9063df2f5b1b -r 13797aac2667307106edeaba3076f04abd96e60d lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -33,7 +33,7 @@
@web.expose_api_anonymous
def get_ordered_installable_revisions( self, trans, name, owner, **kwd ):
"""
- GET /api/repository/get_ordered_installable_revisions
+ GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
@@ -59,7 +59,7 @@
@web.expose_api_anonymous
def get_repository_revision_install_info( self, trans, name, owner, changeset_revision, **kwd ):
"""
- GET /api/repository/get_repository_revision_install_info
+ GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
diff -r 49cc4a899f2ff5853d6c4f4c70ef9063df2f5b1b -r 13797aac2667307106edeaba3076f04abd96e60d templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -395,13 +395,23 @@
<%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( failed_test.id ) %>
+ <style type="text/css">
+ #failed_test_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="readme_table">
+ <table id="failed_test_table"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr>
@@ -485,14 +495,14 @@
encoded_id = trans.security.encode_id( invalid_tool_dependency.id )
%><style type="text/css">
- #readme_table{ table-layout:fixed;
- width:100%;
- overflow-wrap:normal;
- overflow:hidden;
- border:0px;
- word-break:keep-all;
- word-wrap:break-word;
- line-break:strict; }
+ #invalid_td_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
</style><tr class="datasetRow"
%if parent is not None:
@@ -500,7 +510,9 @@
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- ${ invalid_tool_dependency.error | h }
+ <table id="invalid_td_table">
+ <tr><td>${ invalid_tool_dependency.error | h }</td></tr>
+ </table></td></tr><%
@@ -511,13 +523,23 @@
<%def name="render_missing_test_component( missing_test_component, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( missing_test_component.id ) %>
+ <style type="text/css">
+ #missing_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="readme_table">
+ <table id="missing_table"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr>
@@ -632,13 +654,23 @@
<%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %>
+ <style type="text/css">
+ #td_install_error_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="td_installation_errors">
+ <table id="td_install_error_table"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr>
@@ -660,13 +692,23 @@
<%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %>
+ <style type="text/css">
+ #rd_install_error_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="repository_installation_errors">
+ <table id="rd_install_error_table">
%if not is_current_repository:
<tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th>
@@ -691,13 +733,23 @@
<%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( passed_test.id ) %>
+ <style type="text/css">
+ #passed_tests_table{ table-layout:fixed;
+ width:100%;
+ overflow-wrap:normal;
+ overflow:hidden;
+ border:0px;
+ word-break:keep-all;
+ word-wrap:break-word;
+ line-break:strict; }
+ </style><tr class="datasetRow"
%if parent is not None:
parent="${parent}"
%endif
id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;">
- <table class="grid" id="readme_table">
+ <table id="passed_tests_table"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/eb524e42fc65/
Changeset: eb524e42fc65
Branch: next-stable
User: natefoo
Date: 2013-05-29 22:16:11
Summary: Update pgcleanup.py for dialect name change.
Affected #: 1 file
diff -r f3bb3c093851c7b07b8d24bfcfa30e986298fb89 -r eb524e42fc65eb69274857bcaf85030f0edd32f0 scripts/cleanup_datasets/pgcleanup.py
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -108,7 +108,7 @@
args = url.translate_connect_args()
args.update(url.query)
- assert url.get_dialect().name == 'postgres', 'This script can only be used with PostgreSQL.'
+ assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
self.conn = psycopg2.connect(**args)
https://bitbucket.org/galaxy/galaxy-central/commits/49cc4a899f2f/
Changeset: 49cc4a899f2f
User: natefoo
Date: 2013-05-29 22:16:24
Summary: merge next-stable.
Affected #: 1 file
diff -r 07a135ce18a7e40009fe93654ce46030ff213799 -r 49cc4a899f2ff5853d6c4f4c70ef9063df2f5b1b scripts/cleanup_datasets/pgcleanup.py
--- a/scripts/cleanup_datasets/pgcleanup.py
+++ b/scripts/cleanup_datasets/pgcleanup.py
@@ -108,7 +108,7 @@
args = url.translate_connect_args()
args.update(url.query)
- assert url.get_dialect().name == 'postgres', 'This script can only be used with PostgreSQL.'
+ assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.'
self.conn = psycopg2.connect(**args)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 1 month
commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f3bb3c093851/
Changeset: f3bb3c093851
Branch: next-stable
User: Dave Bouvier
Date: 2013-05-29 21:24:52
Summary: Make the functional test results RSS feed output properly formatted data.
Affected #: 1 file
diff -r a6f688dade808b0e16903fbb50186ad9656c0d1c -r f3bb3c093851c7b07b8d24bfcfa30e986298fb89 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1468,25 +1468,39 @@
trans.model.Repository.table.c.user_id == user.id ) ):
if not metadata_row.tool_test_results:
continue
+ current_repository_errors = []
+ tool_dependency_errors = []
+ repository_dependency_errors = []
+ description_lines = []
# Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822
# section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT
time_tested = metadata_row.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' )
repository = metadata_row.repository
# Generate a citable URL for this repository with owner and changeset revision.
repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision )
- title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name )
passed_tests = len( metadata_row.tool_test_results.get( 'passed_tests', [] ) )
failed_tests = len( metadata_row.tool_test_results.get( 'failed_tests', [] ) )
missing_test_components = len( metadata_row.tool_test_results.get( 'missing_test_components', [] ) )
- description = '%d tests passed, %d tests failed, %d tests missing test components.' % \
- ( passed_tests, failed_tests, missing_test_components )
+ installation_errors = metadata_row.tool_test_results.get( 'installation_errors', [] )
+ if installation_errors:
+ tool_dependency_errors = installation_errors.get( 'tool_dependencies', [] )
+ repository_dependency_errors = installation_errors.get( 'repository_dependencies', [] )
+ current_repository_errors = installation_errors.get( 'current_repository', [] )
+ description_lines.append( '%d tests passed, %d tests failed, %d tests missing test components.' % \
+ ( passed_tests, failed_tests, missing_test_components ) )
+ if current_repository_errors:
+ description_lines.append( '\nThis repository did not install correctly. ' )
+ if tool_dependency_errors or repository_dependency_errors:
+ description_lines.append( '\n%d tool dependencies and %d repository dependencies failed to install. ' % \
+ len( tool_dependency_errors ), len( repository_dependency_errors ) )
+ title = 'Revision %s of %s' % ( metadata_row.changeset_revision, repository.name )
# The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated
# if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable
# that behavior.
functional_test_results.append( dict( title=title,
guid=repository_citable_url,
link=repository_citable_url,
- description=description,
+ description='\n'.join( description_lines ),
pubdate=time_tested ) )
trans.response.set_content_type( 'application/rss+xml' )
return trans.fill_template( '/rss.mako',
https://bitbucket.org/galaxy/galaxy-central/commits/07a135ce18a7/
Changeset: 07a135ce18a7
User: Dave Bouvier
Date: 2013-05-29 21:25:38
Summary: Merge with next-stable.
Affected #: 1 file
diff -r e3455a0928824b8ef0fb8f9337e3b0a1d194d2ed -r 07a135ce18a7e40009fe93654ce46030ff213799 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -1458,25 +1458,39 @@
trans.model.Repository.table.c.user_id == user.id ) ):
if not metadata_row.tool_test_results:
continue
+ current_repository_errors = []
+ tool_dependency_errors = []
+ repository_dependency_errors = []
+ description_lines = []
# Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822
# section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT
time_tested = metadata_row.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' )
repository = metadata_row.repository
# Generate a citable URL for this repository with owner and changeset revision.
repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision )
- title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name )
passed_tests = len( metadata_row.tool_test_results.get( 'passed_tests', [] ) )
failed_tests = len( metadata_row.tool_test_results.get( 'failed_tests', [] ) )
missing_test_components = len( metadata_row.tool_test_results.get( 'missing_test_components', [] ) )
- description = '%d tests passed, %d tests failed, %d tests missing test components.' % \
- ( passed_tests, failed_tests, missing_test_components )
+ installation_errors = metadata_row.tool_test_results.get( 'installation_errors', [] )
+ if installation_errors:
+ tool_dependency_errors = installation_errors.get( 'tool_dependencies', [] )
+ repository_dependency_errors = installation_errors.get( 'repository_dependencies', [] )
+ current_repository_errors = installation_errors.get( 'current_repository', [] )
+ description_lines.append( '%d tests passed, %d tests failed, %d tests missing test components.' % \
+ ( passed_tests, failed_tests, missing_test_components ) )
+ if current_repository_errors:
+ description_lines.append( '\nThis repository did not install correctly. ' )
+ if tool_dependency_errors or repository_dependency_errors:
+ description_lines.append( '\n%d tool dependencies and %d repository dependencies failed to install. ' % \
+ len( tool_dependency_errors ), len( repository_dependency_errors ) )
+ title = 'Revision %s of %s' % ( metadata_row.changeset_revision, repository.name )
# The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated
# if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable
# that behavior.
functional_test_results.append( dict( title=title,
guid=repository_citable_url,
link=repository_citable_url,
- description=description,
+ description='\n'.join( description_lines ),
pubdate=time_tested ) )
trans.response.set_content_type( 'application/rss+xml' )
return trans.fill_template( '/rss.mako',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 1 month