galaxy-commits May 2013

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218 discussions

commit/galaxy-central: jgoecks: Trackster: fix syntax error.
by commits-noreply＠bitbucket.org 30 May '13

30 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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 30 May '13

30 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 May '13

30 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: clean up fastqc updates a tiny bit
by commits-noreply＠bitbucket.org 30 May '13

30 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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 30 May '13

30 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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 29 May '13

29 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 May '13

29 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 May '13

29 May '13

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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 May '13

29 May '13

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 29 May '13

29 May '13

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/ -- This is a commit notification from bitbucket.org. 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galaxy-commits May 2013