1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/fa97a5c307d2/
changeset: fa97a5c307d2
user: John Duddy
date: 2011-10-31 21:13:12
summary: Fix copy/paste errors in histry contents API
affected #: 2 files
diff -r 22d844537368bff2acb8eb50bce6561a673002ef -r fa97a5c307d228cd53673eca55fce0c9f12cfe4e lib/galaxy/web/api/history_contents.py
--- a/lib/galaxy/web/api/history_contents.py
+++ b/lib/galaxy/web/api/history_contents.py
@@ -50,7 +50,9 @@
"""
content_id = id
try:
- content = self.get_history_dataset_association( trans, content_id, check_ownership=True, check_accessible=True )
+ # get the history just for the access checks
+ history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=False )
+ content = self.get_history_dataset_association( trans, history, content_id, check_ownership=True, check_accessible=True )
except Exception, e:
return str( e )
try:
diff -r 22d844537368bff2acb8eb50bce6561a673002ef -r fa97a5c307d228cd53673eca55fce0c9f12cfe4e lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -233,16 +233,18 @@
else:
error( "You are not allowed to access this dataset" )
return data
- def get_history_dataset_association( self, trans, dataset_id, check_ownership=True, check_accessible=False ):
+ def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False ):
"""Get a HistoryDatasetAssociation from the database by id, verifying ownership."""
- hda = self.get_object( trans, id, 'HistoryDatasetAssociation', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted )
- self.security_check( trans, history, check_ownership=check_ownership, check_accessible=False ) # check accessibility here
+ self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible )
+ hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False )
+
if check_accessible:
if trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ):
if hda.state == trans.model.Dataset.states.UPLOAD:
error( "Please wait until this dataset finishes uploading before attempting to view it." )
else:
error( "You are not allowed to access this dataset" )
+ return hda
def get_data( self, dataset, preview=True ):
""" Gets a dataset's data. """
# Get data from file, truncating if necessary.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5f63ee75a786/
changeset: 5f63ee75a786
user: dan
date: 2011-11-09 15:41:12
summary: Remove "-targetNotSorted" argument from GATK indel realigner: vanished without warning or notice.
affected #: 1 file
diff -r a77cd7bbe375eb7884cfa5ff38d078033f89c1ab -r 5f63ee75a7862d1747a39c878849f9c04bd5a1d5 tools/gatk/indel_realigner.xml
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -1,4 +1,4 @@
-<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.3">
+<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.4"><description>- perform local realignment</description><requirements><requirement type="package" version="1.2">gatk</requirement>
@@ -90,7 +90,6 @@
##start analysis specific options
-d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
-p '
- -targetNotSorted ##always resort input intervals
--disable_bam_indexing
'
#if $analysis_param_type.analysis_param_type_selector == "advanced":
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/a77cd7bbe375/
changeset: a77cd7bbe375
user: dan
date: 2011-11-08 22:53:19
summary: Update FASTQ Groomer tool help to indicate that Illumina 1.8+ is Sanger encoded.
affected #: 1 file
diff -r bc399a95e31ea30ef80893b3bc318f45cda3241a -r a77cd7bbe375eb7884cfa5ff38d078033f89c1ab tools/fastq/fastq_groomer.xml
--- a/tools/fastq/fastq_groomer.xml
+++ b/tools/fastq/fastq_groomer.xml
@@ -16,7 +16,7 @@
<param name="input_file" type="data" format="fastq" label="File to groom" /><param name="input_type" type="select" label="Input FASTQ quality scores type"><option value="solexa">Solexa</option>
- <option value="illumina">Illumina 1.3+</option>
+ <option value="illumina">Illumina 1.3-1.7</option><option value="sanger" selected="True">Sanger</option><option value="cssanger">Color Space Sanger</option></param>
@@ -358,6 +358,10 @@
Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
+.. class:: infomark
+
+Output from Illumina 1.8+ pipelines are Sanger encoded.
+
------
**Citation**
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/fa29a49205a2/
changeset: fa29a49205a2
user: greg
date: 2011-11-08 21:18:24
summary: Fix for generating metadata in tool shed repositories for a tool that does not use a tool_data_table entry for a dynamic SelectField input parameter.
affected #: 2 files
diff -r 9ee23aa36ec3807092ce1b8f3031ba751f1368e6 -r fa29a49205a226fa872601b4aac577973468e486 lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -1147,21 +1147,20 @@
def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ):
# The sample_files list contains all files whose name ends in .sample
sample_files = []
+ # Find all special .sample files first.
+ for root, dirs, files in os.walk( repo_files_dir ):
+ if root.find( '.hg' ) < 0:
+ for name in files:
+ if name.endswith( '.sample' ):
+ sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
# The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs
repository_tools_tups = []
for root, dirs, files in os.walk( repo_files_dir ):
- if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0:
+ if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
if '.hg' in dirs:
- # Don't visit .hg directories - should be impossible since we don't
- # allow uploaded archives that contain .hg dirs, but just in case...
dirs.remove( '.hg' )
if 'hgrc' in files:
- # Don't include hgrc files in commit.
files.remove( 'hgrc' )
- # Find all special .sample files first.
- for name in files:
- if name.endswith( '.sample' ):
- sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
for name in files:
# Find all tool configs.
if name.endswith( '.xml' ):
diff -r 9ee23aa36ec3807092ce1b8f3031ba751f1368e6 -r fa29a49205a226fa872601b4aac577973468e486 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -214,7 +214,8 @@
copy_sample_loc_file( trans, sample_file )
options.index_file = index_tail
options.missing_index_file = None
- options.tool_data_table.missing_index_file = None
+ if options.tool_data_table:
+ options.tool_data_table.missing_index_file = None
sample_found = True
break
if not sample_found:
@@ -325,8 +326,14 @@
if ctx is not None:
metadata_dict = {}
if changeset_revision == repository.tip:
+ # Find all special .sample files first.
for root, dirs, files in os.walk( repo_dir ):
- if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0:
+ if root.find( '.hg' ) < 0:
+ for name in files:
+ if name.endswith( '.sample' ):
+ sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
+ for root, dirs, files in os.walk( repo_dir ):
+ if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
if '.hg' in dirs:
# Don't visit .hg directories - should be impossible since we don't
# allow uploaded archives that contain .hg dirs, but just in case...
@@ -334,10 +341,6 @@
if 'hgrc' in files:
# Don't include hgrc files in commit.
files.remove( 'hgrc' )
- # Find all special .sample files first.
- for name in files:
- if name.endswith( '.sample' ):
- sample_files.append( os.path.abspath( os.path.join( root, name ) ) )
for name in files:
# Find all tool configs.
if name.endswith( '.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/changeset/d161bb983743/
changeset: d161bb983743
user: dan
date: 2011-11-08 16:59:27
summary: Squash SAMTools stderr chatter when using FreeBayes which would cause error state. FreeBayes should be updated to e.g. have access to built-in reference genomes, etc.
affected #: 1 file
diff -r d09e2505fc105eaf9e04c4c973df613f873f6dca -r d161bb98374369c0cc3aa77eed4e162273e64bb3 tools/human_genome_variation/freebayes.xml
--- a/tools/human_genome_variation/freebayes.xml
+++ b/tools/human_genome_variation/freebayes.xml
@@ -5,11 +5,11 @@
</requirements><description>Bayesian genetic variant detector</description><command>
- ln -s $reference localref.fa;
- ln -s $bamfile localbam.bam;
- samtools faidx localref.fa;
- samtools sort localbam.bam localbam.bam;
- samtools index localbam.bam;
+ ln -s $reference localref.fa &&
+ ln -s $bamfile localbam.bam &&
+ samtools faidx localref.fa 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
+ samtools sort localbam.bam localbam.bam 2>&1 || echo "Error running samtools sort for FreeBayes" >&2 &&
+ samtools index localbam.bam 2>&1 || echo "Error running samtools index for FreeBayes" >&2 &&
freebayes --fasta-reference localref.fa localbam.bam --vcf $output
#if $params.source_select == "full":
$params.showRefRepeats
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d09e2505fc10/
changeset: d09e2505fc10
user: natefoo
date: 2011-11-08 16:23:52
summary: Invalidate other Galaxy sessions upon password change. Thanks Bob Harris!
affected #: 1 file
diff -r ba739e96c1a14d649c37655cecfc5b835ab343d2 -r d09e2505fc105eaf9e04c4c973df613f873f6dca lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -753,7 +753,7 @@
password = kwd.get( 'password', '' )
confirm = kwd.get( 'confirm', '' )
ok = True
- if not webapp == 'galaxy' and not is_admin:
+ if not is_admin:
# If the current user is changing their own password, validate their current password
current = kwd.get( 'current', '' )
if not trans.user.check_password( current ):
@@ -768,10 +768,17 @@
else:
# Save new password
user.set_password_cleartext( password )
+ # Invalidate all other sessions
+ for other_galaxy_session in trans.sa_session.query( trans.app.model.GalaxySession ) \
+ .filter( and_( trans.app.model.GalaxySession.table.c.user_id==trans.user.id,
+ trans.app.model.GalaxySession.table.c.is_valid==True,
+ trans.app.model.GalaxySession.table.c.id!=trans.galaxy_session.id ) ):
+ other_galaxy_session.is_valid = False
+ trans.sa_session.add( other_galaxy_session )
trans.sa_session.add( user )
trans.sa_session.flush()
trans.log_event( "User change password" )
- message = 'The password has been changed.'
+ message = 'The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted).'
elif user and params.get( 'edit_user_info_button', False ):
# Edit user information - webapp MUST BE 'galaxy'
user_type_fd_id = params.get( 'user_type_fd_id', 'none' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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