galaxy-commits December 2013

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commit/galaxy-central: jmchilton: Re-tweak config.py imports for legacy installs.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a2bad69f03f4/ Changeset: a2bad69f03f4 User: jmchilton Date: 2013-12-17 17:10:41 Summary: Re-tweak config.py imports for legacy installs. Affected #: 1 file diff -r 374783ca6a480fbb571bfe9eb46052667b9d0479 -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -1,6 +1,8 @@ """ Universe configuration builder. """ +# absolute_import needed for tool_shed package. +from __future__ import absolute_import import sys, os, tempfile, re import logging, logging.config 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: 9 new changesets
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0084ac72aa7b/ Changeset: 0084ac72aa7b User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: In convert_read_to_format, adjust when new_encoding logic is calculated. Doesn't change the behavior or optimize anything, this is just done to simplify subsequent commits. Baseline: I took the first 100 megabytes of a 26 gigabyte example of a FASTQ file filtered with the FASTQ filter tool that I found in an "Important Galaxy User"'s history on main. I ran with the same command-line on my dev box with the start of this file and using Python's -m to profile function times and total amount of time to serve as a baseline as I optimized the FASTQ filter code. Here is the start of the output: Kept 135848 of 250000 reads (54.34%). 200015991 function calls (199765991 primitive calls) in 136.934 seconds Extrapolating this out, that 26 gigabyte file would take roughly 10 hours to process on my laptop - this is slightly longer than what it took on main - indicating to me this is likely not disk bound since my SSD would probably outperform main? Affected #: 1 file diff -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 -r 0084ac72aa7bdd253454027edf1bcbb3cdeb496d lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -89,7 +89,6 @@ score_list = self.convert_score_solexa_to_phred( self.get_decimal_quality_scores() ) else: score_list = self.get_decimal_quality_scores() - new_read.quality = "%s " % " ".join( map( str, new_class.restrict_scores_to_valid_range( score_list ) ) ) #need trailing space to be valid decimal fastq if force_quality_encoding is None: if self.is_ascii_encoded(): new_encoding = 'ascii' @@ -97,6 +96,7 @@ new_encoding = 'decimal' else: new_encoding = force_quality_encoding + new_read.quality = "%s " % " ".join( map( str, new_class.restrict_scores_to_valid_range( score_list ) ) ) #need trailing space to be valid decimal fastq if new_encoding == 'ascii': new_read.quality = "".join( new_read.get_ascii_quality_scores() ) return new_read https://bitbucket.org/galaxy/galaxy-central/commits/046c608abfa3/ Changeset: 046c608abfa3 User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: Restructure fastq_filter to only call execfile once and reuse the same function. After this optimization: Kept 135848 of 250000 reads (54.34%). 200015991 function calls (199765991 primitive calls) in 85.375 seconds Down from 136.934 seconds on previous changeset. Main Difference: (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 250000 45.130 0.000 67.811 0.000 {execfile} - became - 1 0.000 0.000 0.000 0.000 {execfile} Affected #: 2 files diff -r 0084ac72aa7bdd253454027edf1bcbb3cdeb496d -r 046c608abfa31091f3e030db3979f848666fa602 tools/fastq/fastq_filter.py --- a/tools/fastq/fastq_filter.py +++ b/tools/fastq/fastq_filter.py @@ -18,10 +18,10 @@ i = None reads_kept = 0 + execfile(script_filename, globals()) for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): - local = {'fastq_read':fastq_read, 'ret_val':False} - execfile( script_filename, {}, local ) - if local['ret_val']: + ret_val = fastq_read_pass_filter( fastq_read ) ## fastq_read_pass_filter defined in script_filename + if ret_val: out.write( fastq_read ) reads_kept += 1 out.close() diff -r 0084ac72aa7bdd253454027edf1bcbb3cdeb496d -r 046c608abfa31091f3e030db3979f848666fa602 tools/fastq/fastq_filter.xml --- a/tools/fastq/fastq_filter.xml +++ b/tools/fastq/fastq_filter.xml @@ -96,7 +96,6 @@ return False #end for return True -ret_val = fastq_read_pass_filter( fastq_read ) </configfile></configfiles><outputs> https://bitbucket.org/galaxy/galaxy-central/commits/04c47872b79e/ Changeset: 04c47872b79e User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: Utilize optimized in place alternatives to restrict_scores_to_valid_range. Separate out ascii vs. decimal encoding branches of convert_read_to_format and use these new transform_ alternatives operate "in place" (don't produce new lists/allocate memory). The ascii version transforms to ascii in place instead of requiring another call and creating another array. Runtime Result: Kept 135848 of 250000 reads (54.34%). 117148711 function calls (116898711 primitive calls) in 48.272 seconds Down from 85.375 seconds on previous changeset. Main Difference: (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 135848 1.185 0.000 59.856 0.000 fastq.py:71(convert_read_to_format) -became- 135848 0.502 0.000 22.979 0.000 fastq.py:99(convert_read_to_format) About a third the time is spent convert reads to the correct format. This is a varaint of the core optimization I made when optimizing the FASTQ groomer for MSI - it has likewise a substantial impact on the performance of that tool. Affected #: 1 file diff -r 046c608abfa31091f3e030db3979f848666fa602 -r 04c47872b79eea8dd0b745aed3e7324513653d78 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -35,6 +35,34 @@ return max( min( score, cls.quality_max ), cls.quality_min ) return map( restrict_score, decimal_score_list ) @classmethod + def transform_scores_to_valid_range( cls, decimal_score_list): + cls_quality_max = cls.quality_max + cls_quality_min = cls.quality_min + for i in range( len( decimal_score_list ) ): + score = decimal_score_list[i] + if(score > cls_quality_max): + transformed_score = cls_quality_max + elif( score < cls_quality_min ): + transformed_score = cls_quality_min + else: + transformed_score = score + decimal_score_list[i] = str(transformed_score) + @classmethod + def transform_scores_to_valid_range_ascii( cls, decimal_score_list ): + cls_quality_max = cls.quality_max + cls_quality_min = cls.quality_min + to_quality = cls.ascii_min - cls.quality_min + for i in range( len( decimal_score_list ) ): + score = decimal_score_list[i] + if(score > cls_quality_max): + transformed_score = cls_quality_max + elif( score < cls_quality_min ): + transformed_score = cls_quality_min + else: + transformed_score = score + transformed_score = chr(transformed_score + to_quality) + decimal_score_list[i] = transformed_score + @classmethod def convert_base_to_color_space( cls, sequence ): return cls.color_space_converter.to_color_space( sequence ) @classmethod @@ -96,9 +124,14 @@ new_encoding = 'decimal' else: new_encoding = force_quality_encoding - new_read.quality = "%s " % " ".join( map( str, new_class.restrict_scores_to_valid_range( score_list ) ) ) #need trailing space to be valid decimal fastq if new_encoding == 'ascii': - new_read.quality = "".join( new_read.get_ascii_quality_scores() ) + new_class.transform_scores_to_valid_range_ascii( score_list ) + restricted_scores = map( str, score_list ) + new_read.quality = "".join( restricted_scores ) + else: # decimal + new_class.transform_scores_to_valid_range( score_list ) + restricted_scores = map( str, score_list ) + new_read.quality = "%s " % " ".join( restricted_scores ) #need trailing space to be valid decimal fastq return new_read def get_sequence( self ): return self.sequence https://bitbucket.org/galaxy/galaxy-central/commits/f54589589c1b/ Changeset: f54589589c1b User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: No need to map(str) over chr and join, can just join chr's. Prevent an extra array creation and chr-> str map per base. Shaves 10% off remaining run time of filter on SSD. Kept 135848 of 250000 reads (54.34%). 117012863 function calls (116762863 primitive calls) in 46.897 seconds Down from 48.272 seconds on previous changset. Main Difference: (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 135848 0.502 0.000 22.979 0.000 fastq.py:99(convert_read_to_format) -became- 135848 0.448 0.000 21.159 0.000 fastq.py:99(convert_read_to_format) Not huge, but a consistent improvement. Affected #: 1 file diff -r 04c47872b79eea8dd0b745aed3e7324513653d78 -r f54589589c1b3882127aa96cc1d62b7eba9bef61 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -1,4 +1,4 @@ -#Dan Blankenberg +##Dan Blankenberg import math import string import transform @@ -126,12 +126,10 @@ new_encoding = force_quality_encoding if new_encoding == 'ascii': new_class.transform_scores_to_valid_range_ascii( score_list ) - restricted_scores = map( str, score_list ) - new_read.quality = "".join( restricted_scores ) + new_read.quality = "".join( score_list ) else: # decimal new_class.transform_scores_to_valid_range( score_list ) - restricted_scores = map( str, score_list ) - new_read.quality = "%s " % " ".join( restricted_scores ) #need trailing space to be valid decimal fastq + new_read.quality = "%s " % " ".join( score_list ) #need trailing space to be valid decimal fastq return new_read def get_sequence( self ): return self.sequence https://bitbucket.org/galaxy/galaxy-central/commits/6d723e3bf2eb/ Changeset: 6d723e3bf2eb User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: Precompute difference ascii -> decimal difference. Kept 135848 of 250000 reads (54.34%). 117012863 function calls (116762863 primitive calls) in 39.416 seconds Down from 46.897 seconds on previous changeset. Main Difference WRT: (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 385848 18.215 0.000 22.866 0.000 fastq.py:90(get_decimal_quality_scores) -became- 385848 11.415 0.000 15.546 0.000 fastq.py:91(get_decimal_quality_scores) Looks like a math optimization but actual optimization is coming from reading local variable instead of dereferencing object variable twice per base per. Affected #: 1 file diff -r f54589589c1b3882127aa96cc1d62b7eba9bef61 -r 6d723e3bf2ebddf0730e7b38761ca2b511d129c3 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -82,14 +82,16 @@ quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: try: - return [ chr( int( val ) + self.ascii_min - self.quality_min ) for val in quality.split() ] + to_quality = self.ascii_min - self.quality_min + return [ chr( int( val ) + to_quality ) for val in quality.split() ] except ValueError, e: raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) else: return [] def get_decimal_quality_scores( self ): if self.is_ascii_encoded(): - return [ ord( val ) - self.ascii_min + self.quality_min for val in self.quality ] + to_quality = self.quality_min - self.ascii_min + return [ ord( val ) + to_quality for val in self.quality ] else: quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: https://bitbucket.org/galaxy/galaxy-central/commits/6265e769718e/ Changeset: 6265e769718e User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: Do not generate arrays just to check length. ... just compute what length would be. Kept 135848 of 250000 reads (54.34%). 117012863 function calls (116762863 primitive calls) in 38.412 seconds Down from 39.416 seconds on previous changeset. Main Difference: (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 500000 0.518 0.000 1.889 0.000 fastq.py:171(insufficient_quality_length) 250000 0.322 0.000 1.103 0.000 fastq.py:173(assert_sequence_quality_lengths) - became - 500000 0.306 0.000 0.932 0.000 fastq.py:187(insufficient_quality_length) 250000 0.164 0.000 0.478 0.000 fastq.py:189(assert_sequence_quality_lengths) Affected #: 1 file diff -r 6d723e3bf2ebddf0730e7b38761ca2b511d129c3 -r 6265e769718e2487b4089c181948769cf67869ce lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -88,6 +88,22 @@ raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) else: return [] + def get_ascii_quality_scores_len( self ): + """ + Compute ascii quality score length, without generating relatively + expensive qualty score array. + """ + if self.is_ascii_encoded(): + return len( self.quality ) + else: + quality = self.quality.rstrip() + if quality: + try: + return len( quality.split() ) + except ValueError, e: + raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) + else: + return 0 def get_decimal_quality_scores( self ): if self.is_ascii_encoded(): to_quality = self.quality_min - self.ascii_min @@ -168,9 +184,9 @@ return False return True def insufficient_quality_length( self ): - return len( self.get_ascii_quality_scores() ) < len( self.sequence ) + return self.get_ascii_quality_scores_len() < len( self.sequence ) def assert_sequence_quality_lengths( self ): - qual_len = len( self.get_ascii_quality_scores() ) + qual_len = self.get_ascii_quality_scores_len() seq_len = len( self.sequence ) assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) def reverse( self, clone = True ): @@ -235,11 +251,11 @@ return False def insufficient_quality_length( self ): if self.has_adapter_base(): - return len( self.get_ascii_quality_scores() ) + 1 < len( self.sequence ) + return self.get_ascii_quality_scores_len() + 1 < len( self.sequence ) return fastqSequencingRead.insufficient_quality_length( self ) def assert_sequence_quality_lengths( self ): if self.has_adapter_base(): - qual_len = len( self.get_ascii_quality_scores() ) + qual_len = self.get_ascii_quality_scores_len() seq_len = len( self.sequence ) assert ( qual_len + 1 == seq_len ) or ( qual_len == seq_len ), "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) #SRA adds FAKE/DUMMY quality scores to the adapter base, we'll allow the reading of the Improper score here, but remove it in the Reader when "apply_galaxy_conventions" is set to True else: https://bitbucket.org/galaxy/galaxy-central/commits/b5970d24670f/ Changeset: b5970d24670f User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: Eliminate a few extra calls to is_ascii_encoded. Kept 135848 of 250000 reads (54.34%). 117127015 function calls (116877015 primitive calls) in 38.632 seconds Down from 39.416 seconds on previous changeset. Main Difference (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 385848 11.289 0.000 15.499 0.000 fastq.py:91(get_decimal_quality_scores) 1271696 0.716 0.000 0.716 0.000 fastq.py:71(is_ascii_encoded) 250000 0.185 0.000 10.434 0.000 fastq.py:107(get_decimal_quality_scores) 385848 11.380 0.000 15.368 0.000 fastq.py:109(__get_decimal_quality_scores) 1135848 0.649 0.000 0.649 0.000 fastq.py:71(is_ascii_encoded) Affected #: 1 file diff -r 6265e769718e2487b4089c181948769cf67869ce -r b5970d24670fefc0bf028bcab681f81ef2dd62e9 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -105,7 +105,9 @@ else: return 0 def get_decimal_quality_scores( self ): - if self.is_ascii_encoded(): + return self.__get_decimal_quality_scores(self.is_ascii_encoded()) + def __get_decimal_quality_scores( self, ascii ): + if ascii: to_quality = self.quality_min - self.ascii_min return [ ord( val ) + to_quality for val in self.quality ] else: @@ -128,15 +130,16 @@ else: new_read.sequence = self.convert_color_to_base_space( self.sequence ) new_read.description = self.description + is_ascii = self.is_ascii_encoded() if self.score_system != new_read.score_system: if self.score_system == 'phred': - score_list = self.convert_score_phred_to_solexa( self.get_decimal_quality_scores() ) + score_list = self.convert_score_phred_to_solexa( self.__get_decimal_quality_scores(is_ascii) ) else: - score_list = self.convert_score_solexa_to_phred( self.get_decimal_quality_scores() ) + score_list = self.convert_score_solexa_to_phred( self.__get_decimal_quality_scores(is_ascii) ) else: - score_list = self.get_decimal_quality_scores() + score_list = self.__get_decimal_quality_scores(is_ascii) if force_quality_encoding is None: - if self.is_ascii_encoded(): + if is_ascii: new_encoding = 'ascii' else: new_encoding = 'decimal' https://bitbucket.org/galaxy/galaxy-central/commits/bb6c21a42274/ Changeset: bb6c21a42274 User: jmchilton Date: 2013-11-13 05:02:58 Summary: FASTQ Opt: Disable formatting output, reading is already enforcing it? This is would be huge optimization for filter at this point - it cuts the runtime of my filter test to half of what is remaining. This changeset if just leaving a comment because I am not certain the results are the same - though I strongly suspect they would be - I just want some confirmation before pulling the trigger. None of the test cases fail as a result of this or any of these changesets. Kept 135848 of 250000 reads (54.34%). 60407639 function calls in 18.837 seconds If change made, this would be down from 38.632 seconds on previous call. Main Difference: (ncalls|tottime|percall|cumtime|percall|filename:lineno(function)) 135848 0.357 0.000 19.710 0.000 fastq.py:631(write) - to - 135848 0.219 0.000 0.609 0.000 fastq.py:631(write) Affected #: 1 file diff -r b5970d24670fefc0bf028bcab681f81ef2dd62e9 -r bb6c21a422741b32ab78f7a4fe6dae571019d532 tools/fastq/fastq_filter.py --- a/tools/fastq/fastq_filter.py +++ b/tools/fastq/fastq_filter.py @@ -14,6 +14,8 @@ os.mkdir( additional_files_path ) shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) ) + ## Dan, Others: Can we simply drop the "format=input_type" here since it is specified in reader. + ## This optimization would cut runtime roughly in half (for my test case anyway). -John out = fastqWriter( open( output_filename, 'wb' ), format = input_type ) i = None https://bitbucket.org/galaxy/galaxy-central/commits/374783ca6a48/ Changeset: 374783ca6a48 User: dannon Date: 2013-12-17 16:42:49 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #259) FASTQ Optimizations (Round 1 - Filtering) Affected #: 3 files diff -r 31179a01a1ec4176884926907b212259e4148319 -r 374783ca6a480fbb571bfe9eb46052667b9d0479 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -1,4 +1,4 @@ -#Dan Blankenberg +##Dan Blankenberg import math import string import transform @@ -35,6 +35,34 @@ return max( min( score, cls.quality_max ), cls.quality_min ) return map( restrict_score, decimal_score_list ) @classmethod + def transform_scores_to_valid_range( cls, decimal_score_list): + cls_quality_max = cls.quality_max + cls_quality_min = cls.quality_min + for i in range( len( decimal_score_list ) ): + score = decimal_score_list[i] + if(score > cls_quality_max): + transformed_score = cls_quality_max + elif( score < cls_quality_min ): + transformed_score = cls_quality_min + else: + transformed_score = score + decimal_score_list[i] = str(transformed_score) + @classmethod + def transform_scores_to_valid_range_ascii( cls, decimal_score_list ): + cls_quality_max = cls.quality_max + cls_quality_min = cls.quality_min + to_quality = cls.ascii_min - cls.quality_min + for i in range( len( decimal_score_list ) ): + score = decimal_score_list[i] + if(score > cls_quality_max): + transformed_score = cls_quality_max + elif( score < cls_quality_min ): + transformed_score = cls_quality_min + else: + transformed_score = score + transformed_score = chr(transformed_score + to_quality) + decimal_score_list[i] = transformed_score + @classmethod def convert_base_to_color_space( cls, sequence ): return cls.color_space_converter.to_color_space( sequence ) @classmethod @@ -54,14 +82,34 @@ quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: try: - return [ chr( int( val ) + self.ascii_min - self.quality_min ) for val in quality.split() ] + to_quality = self.ascii_min - self.quality_min + return [ chr( int( val ) + to_quality ) for val in quality.split() ] except ValueError, e: raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) else: return [] + def get_ascii_quality_scores_len( self ): + """ + Compute ascii quality score length, without generating relatively + expensive qualty score array. + """ + if self.is_ascii_encoded(): + return len( self.quality ) + else: + quality = self.quality.rstrip() + if quality: + try: + return len( quality.split() ) + except ValueError, e: + raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) + else: + return 0 def get_decimal_quality_scores( self ): - if self.is_ascii_encoded(): - return [ ord( val ) - self.ascii_min + self.quality_min for val in self.quality ] + return self.__get_decimal_quality_scores(self.is_ascii_encoded()) + def __get_decimal_quality_scores( self, ascii ): + if ascii: + to_quality = self.quality_min - self.ascii_min + return [ ord( val ) + to_quality for val in self.quality ] else: quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: @@ -82,23 +130,27 @@ else: new_read.sequence = self.convert_color_to_base_space( self.sequence ) new_read.description = self.description + is_ascii = self.is_ascii_encoded() if self.score_system != new_read.score_system: if self.score_system == 'phred': - score_list = self.convert_score_phred_to_solexa( self.get_decimal_quality_scores() ) + score_list = self.convert_score_phred_to_solexa( self.__get_decimal_quality_scores(is_ascii) ) else: - score_list = self.convert_score_solexa_to_phred( self.get_decimal_quality_scores() ) + score_list = self.convert_score_solexa_to_phred( self.__get_decimal_quality_scores(is_ascii) ) else: - score_list = self.get_decimal_quality_scores() - new_read.quality = "%s " % " ".join( map( str, new_class.restrict_scores_to_valid_range( score_list ) ) ) #need trailing space to be valid decimal fastq + score_list = self.__get_decimal_quality_scores(is_ascii) if force_quality_encoding is None: - if self.is_ascii_encoded(): + if is_ascii: new_encoding = 'ascii' else: new_encoding = 'decimal' else: new_encoding = force_quality_encoding if new_encoding == 'ascii': - new_read.quality = "".join( new_read.get_ascii_quality_scores() ) + new_class.transform_scores_to_valid_range_ascii( score_list ) + new_read.quality = "".join( score_list ) + else: # decimal + new_class.transform_scores_to_valid_range( score_list ) + new_read.quality = "%s " % " ".join( score_list ) #need trailing space to be valid decimal fastq return new_read def get_sequence( self ): return self.sequence @@ -135,9 +187,9 @@ return False return True def insufficient_quality_length( self ): - return len( self.get_ascii_quality_scores() ) < len( self.sequence ) + return self.get_ascii_quality_scores_len() < len( self.sequence ) def assert_sequence_quality_lengths( self ): - qual_len = len( self.get_ascii_quality_scores() ) + qual_len = self.get_ascii_quality_scores_len() seq_len = len( self.sequence ) assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) def reverse( self, clone = True ): @@ -202,11 +254,11 @@ return False def insufficient_quality_length( self ): if self.has_adapter_base(): - return len( self.get_ascii_quality_scores() ) + 1 < len( self.sequence ) + return self.get_ascii_quality_scores_len() + 1 < len( self.sequence ) return fastqSequencingRead.insufficient_quality_length( self ) def assert_sequence_quality_lengths( self ): if self.has_adapter_base(): - qual_len = len( self.get_ascii_quality_scores() ) + qual_len = self.get_ascii_quality_scores_len() seq_len = len( self.sequence ) assert ( qual_len + 1 == seq_len ) or ( qual_len == seq_len ), "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i with adapter base)" % ( qual_len, seq_len ) #SRA adds FAKE/DUMMY quality scores to the adapter base, we'll allow the reading of the Improper score here, but remove it in the Reader when "apply_galaxy_conventions" is set to True else: diff -r 31179a01a1ec4176884926907b212259e4148319 -r 374783ca6a480fbb571bfe9eb46052667b9d0479 tools/fastq/fastq_filter.py --- a/tools/fastq/fastq_filter.py +++ b/tools/fastq/fastq_filter.py @@ -14,14 +14,16 @@ os.mkdir( additional_files_path ) shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) ) + ## Dan, Others: Can we simply drop the "format=input_type" here since it is specified in reader. + ## This optimization would cut runtime roughly in half (for my test case anyway). -John out = fastqWriter( open( output_filename, 'wb' ), format = input_type ) i = None reads_kept = 0 + execfile(script_filename, globals()) for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): - local = {'fastq_read':fastq_read, 'ret_val':False} - execfile( script_filename, {}, local ) - if local['ret_val']: + ret_val = fastq_read_pass_filter( fastq_read ) ## fastq_read_pass_filter defined in script_filename + if ret_val: out.write( fastq_read ) reads_kept += 1 out.close() diff -r 31179a01a1ec4176884926907b212259e4148319 -r 374783ca6a480fbb571bfe9eb46052667b9d0479 tools/fastq/fastq_filter.xml --- a/tools/fastq/fastq_filter.xml +++ b/tools/fastq/fastq_filter.xml @@ -96,7 +96,6 @@ return False #end for return True -ret_val = fastq_read_pass_filter( fastq_read ) </configfile></configfiles><outputs> 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 17 Dec '13

17 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f6723d1ddaf5/ Changeset: f6723d1ddaf5 Branch: yhoogstrate/some-minor-select-field-changes-includin-1387270048132 User: yhoogstrate Date: 2013-12-17 09:49:21 Summary: Some minor select field changes including Illumina 1.8+ Affected #: 1 file diff -r af87cdcf36084831fce7d99e621b1efc943d2aff -r f6723d1ddaf5c15e194aa5bde2fc78937b9c5423 tools/fastq/fastq_groomer.xml --- a/tools/fastq/fastq_groomer.xml +++ b/tools/fastq/fastq_groomer.xml @@ -17,7 +17,7 @@ <param name="input_type" type="select" label="Input FASTQ quality scores type"><option value="solexa">Solexa</option><option value="illumina">Illumina 1.3-1.7</option> - <option value="sanger" selected="True">Sanger</option> + <option value="sanger" selected="True">Sanger & Illumina 1.8+</option><option value="cssanger">Color Space Sanger</option></param><conditional name="options_type"> @@ -31,7 +31,7 @@ <when value="advanced"><param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format."><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 (recommended)</option><option value="cssanger">Color Space Sanger</option></param> https://bitbucket.org/galaxy/galaxy-central/commits/31179a01a1ec/ Changeset: 31179a01a1ec User: dannon Date: 2013-12-17 16:18:22 Summary: Merged in yhoogstrate/galaxy-central/yhoogstrate/some-minor-select-field-changes-includin-1387270048132 (pull request #276) Some minor select field changes including Illumina 1.8+ Affected #: 1 file diff -r 029cc5c14f1a8fb81e4bbdc3872757b297e1efa0 -r 31179a01a1ec4176884926907b212259e4148319 tools/fastq/fastq_groomer.xml --- a/tools/fastq/fastq_groomer.xml +++ b/tools/fastq/fastq_groomer.xml @@ -17,7 +17,7 @@ <param name="input_type" type="select" label="Input FASTQ quality scores type"><option value="solexa">Solexa</option><option value="illumina">Illumina 1.3-1.7</option> - <option value="sanger" selected="True">Sanger</option> + <option value="sanger" selected="True">Sanger & Illumina 1.8+</option><option value="cssanger">Color Space Sanger</option></param><conditional name="options_type"> @@ -31,7 +31,7 @@ <when value="advanced"><param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format."><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 (recommended)</option><option value="cssanger">Color Space Sanger</option></param> 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: greg: Handle strangely defined tool tests when setting metadata in tool shed repositories.
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/029cc5c14f1a/ Changeset: 029cc5c14f1a User: greg Date: 2013-12-17 16:08:03 Summary: Handle strangely defined tool tests when setting metadata in tool shed repositories. Affected #: 2 files diff -r 97c69fcfeaac1756a7ad5d92c8ade74b2d611561 -r 029cc5c14f1a8fb81e4bbdc3872757b297e1efa0 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -927,10 +927,13 @@ guid = suc.generate_tool_guid( repository_clone_url, tool ) # Handle tool.requirements. tool_requirements = [] - for tr in tool.requirements: - requirement_dict = dict( name=tr.name, - type=tr.type, - version=tr.version ) + for tool_requirement in tool.requirements: + name = str( tool_requirement.name ) + type = str( tool_requirement.type ) + version = str( tool_requirement.version ) if tool_requirement.version else None + requirement_dict = dict( name=name, + type=type, + version=version ) tool_requirements.append( requirement_dict ) # Handle tool.tests. tool_tests = [] @@ -941,18 +944,31 @@ value, extra = required_file required_files.append( ( value ) ) inputs = [] - for input_field, values in ttb.inputs.iteritems(): - if len( values ) == 1: - inputs.append( ( input_field, values[0] ) ) - else: - inputs.append( ( input_field, values ) ) + for param_name, values in ttb.inputs.iteritems(): + # Handle improperly defined or strange test parameters and values. + if param_name is not None: + if values is None: + # An example is the 3rd test in http://testtoolshed.g2.bx.psu.edu/view/devteam/samtools_rmdup + # which is defined as: + # <test> + # <param name="input1" value="1.bam" ftype="bam" /> + # <param name="bam_paired_end_type_selector" value="PE" /> + # <param name="force_se" /> + # <output name="output1" file="1.bam" ftype="bam" sort="True" /> + # </test> + inputs.append( ( param_name, values ) ) + else: + if len( values ) == 1: + inputs.append( ( param_name, values[ 0 ] ) ) + else: + inputs.append( ( param_name, values ) ) outputs = [] for output in ttb.outputs: name, file_name, extra = output outputs.append( ( name, suc.strip_path( file_name ) if file_name else None ) ) if file_name not in required_files and file_name is not None: required_files.append( file_name ) - test_dict = dict( name=ttb.name, + test_dict = dict( name=str( ttb.name ), required_files=required_files, inputs=inputs, outputs=outputs ) diff -r 97c69fcfeaac1756a7ad5d92c8ade74b2d611561 -r 029cc5c14f1a8fb81e4bbdc3872757b297e1efa0 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -254,11 +254,8 @@ else: deleted = False uninstalled = False - tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, - tool_shed, - name, - owner, - installed_changeset_revision ) + tool_shed_repository = \ + get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ) if tool_shed_repository: log.debug( "Updating an existing row for repository '%s' in the tool_shed_repository table, status set to '%s'." % ( str( name ), str( status ) ) ) tool_shed_repository.description = description @@ -271,19 +268,20 @@ tool_shed_repository.status = status else: log.debug( "Adding new row for repository '%s' in the tool_shed_repository table, status set to '%s'." % ( str( name ), str( status ) ) ) - tool_shed_repository = app.install_model.ToolShedRepository( tool_shed=tool_shed, - name=name, - description=description, - owner=owner, - installed_changeset_revision=installed_changeset_revision, - changeset_revision=current_changeset_revision, - ctx_rev=ctx_rev, - metadata=metadata_dict, - includes_datatypes=includes_datatypes, - dist_to_shed=dist_to_shed, - deleted=deleted, - uninstalled=uninstalled, - status=status ) + tool_shed_repository = \ + app.install_model.ToolShedRepository( tool_shed=tool_shed, + name=name, + description=description, + owner=owner, + installed_changeset_revision=installed_changeset_revision, + changeset_revision=current_changeset_revision, + ctx_rev=ctx_rev, + metadata=metadata_dict, + includes_datatypes=includes_datatypes, + dist_to_shed=dist_to_shed, + deleted=deleted, + uninstalled=uninstalled, + status=status ) context.add( tool_shed_repository ) context.flush() return tool_shed_repository 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: 3 new changesets
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/08320798463e/ Changeset: 08320798463e User: nsoranzo Date: 2013-12-06 11:17:25 Summary: Specify mosaik v. 1.1.0021 (last compatible with the wrapper). Add requirement for samtools. Affected #: 1 file diff -r a29d54619813d5da992b897557162a360b8d610c -r 08320798463e173f61f0b53fbd2db43419d373e2 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -1,7 +1,10 @@ <?xml version="1.0"?><tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"><description/> - <requirements><requirement type="package">mosaik</requirement></requirements> + <requirements> + <requirement type="package" version="1.1.0021">mosaik</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements><command> #set $processors = '-p ${GALAXY_SLOTS:-4}' #set $lm = '' https://bitbucket.org/galaxy/galaxy-central/commits/5fbc02eff708/ Changeset: 5fbc02eff708 User: nsoranzo Date: 2013-12-06 11:20:56 Summary: Fix for failure preparing job: "NotFound: cannot find 'mfl'" with paired-end library. Add mate FASTQ file to inputs. 'ls' param was not used. Add missing '-mfl ' to MosaikBuild command. Remove always empty $lm variable. Add <version_command>. Affected #: 1 file diff -r 08320798463e173f61f0b53fbd2db43419d373e2 -r 5fbc02eff708cc86afd60a4fa7588c9f72e877b5 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -1,28 +1,30 @@ <?xml version="1.0"?> -<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"> +<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.2"><description/><requirements><requirement type="package" version="1.1.0021">mosaik</requirement><requirement type="package" version="0.1.18">samtools</requirement></requirements> + <version_command>MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}$;[[:digit:]]\{1,2\}$\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}'</version_command><command> #set $processors = '-p ${GALAXY_SLOTS:-4}' - #set $lm = '' - #if $paired.kind == 'single': - #set $mfl = '' - #set $ls = '' - #else: - #set $ls = '-ls $mfl' - #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': ${genomeSource.indexReference.fields.path} #else: - $genomeSource.historyReference + ${genomeSource.historyReference} #end if - -oa mosaik_ref_file; - MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file; - MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15; + -oa mosaik_ref_file; + MosaikBuild -q $reads + #if $paired.kind == 'single' + #set $ls_string = '' + #else + -q2 ${paired.reads2} + -mfl ${paired.mfl} + #set $ls_string = '-ls %s' % $paired.ls + #end if + -st $st -out mosaik_reads_file; + MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15; MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; #if str($outFormat) == 'bam': samtools sort sam_bam_file sorted_bam; @@ -50,12 +52,12 @@ <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional> - <param format="fastq" name="reads" type="data" label="Fastq Reads File"/> - <param name="outFormat" type="select" label="Output Format"> - <option value="sam">Sam</option> - <option value="bam">Bam</option> + <param format="fastq" name="reads" type="data" label="FASTQ reads file" /> + <param name="outFormat" type="select" label="Output format"> + <option value="sam">SAM</option> + <option value="bam">BAM</option></param> - <param name="st" type="select" label="Sequencing Technology Used"> + <param name="st" type="select" label="Sequencing technology used"><option value="454">454</option><option value="illumina">Illumina</option><option value="solid">Solid</option> @@ -69,14 +71,15 @@ </param><when value="single"/><when value="paired"> - <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/> - <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/> + <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" /> + <param name="mfl" type="integer" value="200" label="Median fragment length" /> + <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /></when></conditional> - <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/> - <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/> - <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/> - <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/> + <param name="mm" type="integer" value="6" label="Number of mismatches allowed per sequence" /> + <param name="act" type="integer" value="35" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" /> + <param name="bw" type="integer" value="9" label="Smith-Waterman band width" /> + <param name="mhp" type="integer" value="100" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /></inputs><outputs><data format="sam" name="output"> https://bitbucket.org/galaxy/galaxy-central/commits/97c69fcfeaac/ Changeset: 97c69fcfeaac User: dannon Date: 2013-12-17 15:00:44 Summary: Merged in nsoranzo/galaxy-central (pull request #271) Fixes for MOSAIK tool Affected #: 1 file diff -r 3eb13c85bf4140448865328b9c6feaed96d8682f -r 97c69fcfeaac1756a7ad5d92c8ade74b2d611561 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -1,25 +1,30 @@ <?xml version="1.0"?> -<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"> +<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.2"><description/> - <requirements><requirement type="package">mosaik</requirement></requirements> + <requirements> + <requirement type="package" version="1.1.0021">mosaik</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <version_command>MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}$;[[:digit:]]\{1,2\}$\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}'</version_command><command> #set $processors = '-p ${GALAXY_SLOTS:-4}' - #set $lm = '' - #if $paired.kind == 'single': - #set $mfl = '' - #set $ls = '' - #else: - #set $ls = '-ls $mfl' - #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': ${genomeSource.indexReference.fields.path} #else: - $genomeSource.historyReference + ${genomeSource.historyReference} #end if - -oa mosaik_ref_file; - MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file; - MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15; + -oa mosaik_ref_file; + MosaikBuild -q $reads + #if $paired.kind == 'single' + #set $ls_string = '' + #else + -q2 ${paired.reads2} + -mfl ${paired.mfl} + #set $ls_string = '-ls %s' % $paired.ls + #end if + -st $st -out mosaik_reads_file; + MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15; MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; #if str($outFormat) == 'bam': samtools sort sam_bam_file sorted_bam; @@ -47,12 +52,12 @@ <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional> - <param format="fastq" name="reads" type="data" label="Fastq Reads File"/> - <param name="outFormat" type="select" label="Output Format"> - <option value="sam">Sam</option> - <option value="bam">Bam</option> + <param format="fastq" name="reads" type="data" label="FASTQ reads file" /> + <param name="outFormat" type="select" label="Output format"> + <option value="sam">SAM</option> + <option value="bam">BAM</option></param> - <param name="st" type="select" label="Sequencing Technology Used"> + <param name="st" type="select" label="Sequencing technology used"><option value="454">454</option><option value="illumina">Illumina</option><option value="solid">Solid</option> @@ -66,14 +71,15 @@ </param><when value="single"/><when value="paired"> - <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/> - <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/> + <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" /> + <param name="mfl" type="integer" value="200" label="Median fragment length" /> + <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /></when></conditional> - <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/> - <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/> - <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/> - <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/> + <param name="mm" type="integer" value="6" label="Number of mismatches allowed per sequence" /> + <param name="act" type="integer" value="35" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" /> + <param name="bw" type="integer" value="9" label="Smith-Waterman band width" /> + <param name="mhp" type="integer" value="100" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /></inputs><outputs><data format="sam" name="output"> 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 17 Dec '13

17 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b92f61b482d9/ Changeset: b92f61b482d9 User: BjoernGruening Date: 2013-11-11 10:09:54 Summary: add dependency of type package to the ccat wrapper Affected #: 1 file diff -r 8e448f2ac955e6d434476b18c59b2cffcfc55404 -r b92f61b482d9b5897cb78ac260ae1dcec3260045 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -10,6 +10,7 @@ '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements><requirement type="binary" version="3.0">CCAT</requirement> + <requirement type="package" version="3.0">CCAT</requirement></requirements><inputs><param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > https://bitbucket.org/galaxy/galaxy-central/commits/3eb13c85bf41/ Changeset: 3eb13c85bf41 User: BjoernGruening Date: 2013-11-11 15:35:45 Summary: remove binary dependency Affected #: 1 file diff -r b92f61b482d9b5897cb78ac260ae1dcec3260045 -r 3eb13c85bf4140448865328b9c6feaed96d8682f tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -9,7 +9,6 @@ 'CCAT in Galaxy' '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements> - <requirement type="binary" version="3.0">CCAT</requirement><requirement type="package" version="3.0">CCAT</requirement></requirements><inputs> 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 17 Dec '13

17 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/714f5b1ac790/ Changeset: 714f5b1ac790 User: jmchilton Date: 2013-12-15 23:16:34 Summary: Move history contents filtering logic into model. Filtering for deleted, visible, and ids with ORM should prevent loading unneeded objects into memory (a history with 1000 items and 5 visible will now only cause 5 items to be loaded instead of 1000 just to filter out 5). Simplifies history_contents API logic somewhat, allows easier 'unit' testing (included), and provides a clearer entry point for additional 'showing' additional contents types (read dataset collections). Affected #: 3 files diff -r 4fe46fd3181bfb63e8093200d71801cb507b586d -r 714f5b1ac7902cc5b79d5fdf6390ea70b7e17afb lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -19,6 +19,7 @@ import socket import time from string import Template +from itertools import ifilter import galaxy.datatypes import galaxy.datatypes.registry @@ -43,6 +44,11 @@ # Default Value Required for unit tests datatypes_registry.load_datatypes() +# When constructing filters with in for a fixed set of ids, maximum +# number of items to place in the IN statement. Different databases +# are going to have different limits so it is likely best to not let +# this be unlimited - filter in Python if over this limit. +MAX_IN_FILTER_LENGTH = 100 class NoConverterException(Exception): def __init__(self, value): @@ -893,6 +899,32 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + def contents_iter( self, **kwds ): + """ + Fetch filtered list of contents of history. + """ + python_filter = None + db_session = object_session( self ) + assert db_session != None + query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) ) + if deleted is not None: + query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) ) + visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) ) + if visible is not None: + query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) ) + if 'ids' in kwds: + ids = kwds['ids'] + max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH) + if len(ids) < max_in_filter_length: + query = query.filter( HistoryDatasetAssociation.id.in_(ids) ) + else: + python_filter = lambda hda: hda.id in ids + if python_filter: + return ifilter(python_filter, query) + else: + return query + def copy_tags_from(self,target_user,source_history): for src_shta in source_history.tags: new_shta = src_shta.copy() diff -r 4fe46fd3181bfb63e8093200d71801cb507b586d -r 714f5b1ac7902cc5b79d5fdf6390ea70b7e17afb lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -51,47 +51,28 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - # if ids, return _FULL_ data (as show) for each id passed + contents_kwds = {} if ids: - ids = ids.split( ',' ) - for index, hda in enumerate( history.datasets ): - encoded_hda_id = trans.security.encode_id( hda.id ) - if encoded_hda_id in ids: - #TODO: share code with show - rval.append( self._detailed_hda_dict( trans, hda ) ) - - # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history + ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) ) + contents_kwds[ 'ids' ] = ids + # If explicit ids given, always used detailed result. + details = 'all' else: + contents_kwds[ 'deleted' ] = kwd.get( 'deleted', None ) + contents_kwds[ 'visible' ] = kwd.get( 'visible', None ) # details param allows a mixed set of summary and detailed hdas #TODO: this is getting convoluted due to backwards compat details = kwd.get( 'details', None ) or [] if details and details != 'all': details = util.listify( details ) - # by default return all datasets - even if deleted or hidden (defaulting the next switches to None) - # if specified return those datasets that match the setting - # backwards compat - return_deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) - return_visible = util.string_as_bool_or_none( kwd.get( 'visible', None ) ) - - for hda in history.datasets: - # if either return_ setting has been requested (!= None), skip hdas that don't match the request - if return_deleted is not None: - if( ( return_deleted and not hda.deleted ) - or ( not return_deleted and hda.deleted ) ): - continue - if return_visible is not None: - if( ( return_visible and not hda.visible ) - or ( not return_visible and hda.visible ) ): - continue - - encoded_hda_id = trans.security.encode_id( hda.id ) - if( ( encoded_hda_id in details ) - or ( details == 'all' ) ): - rval.append( self._detailed_hda_dict( trans, hda ) ) - else: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) - + for hda in history.contents_iter( **contents_kwds ): + encoded_hda_id = trans.security.encode_id( hda.id ) + detailed = details == 'all' or ( encoded_hda_id in details ) + if detailed: + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) rval = "Error in history API at listing contents: " + str( e ) diff -r 4fe46fd3181bfb63e8093200d71801cb507b586d -r 714f5b1ac7902cc5b79d5fdf6390ea70b7e17afb test/unit/test_galaxy_mapping.py --- a/test/unit/test_galaxy_mapping.py +++ b/test/unit/test_galaxy_mapping.py @@ -180,6 +180,39 @@ assert hist1.name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. + def test_history_contents( self ): + model = self.model + u = model.User( email="contents(a)foo.bar.baz", password="password" ) + # gs = model.GalaxySession() + h1 = model.History( name="HistoryContentsHistory1", user=u) + + self.persist( u, h1, expunge=True ) + + d1 = self.new_hda( h1, name="1" ) + d2 = self.new_hda( h1, name="2", visible=False ) + d3 = self.new_hda( h1, name="3", deleted=True ) + d4 = self.new_hda( h1, name="4", visible=False, deleted=True ) + + def contents_iter_names(**kwds): + history = model.context.query( model.History ).filter( + model.History.name == "HistoryContentsHistory1" + ).first() + return set( map( lambda hda: hda.name, history.contents_iter( **kwds ) ) ) + + assert contents_iter_names() == set( [ "1", "2", "3", "4" ] ) + assert contents_iter_names( deleted=False ) == set( [ "1", "2" ] ) + assert contents_iter_names( visible=True ) == set( [ "1", "3" ] ) + assert contents_iter_names( visible=False ) == set( [ "2", "4" ] ) + assert contents_iter_names( deleted=True, visible=False ) == set( [ "4" ] ) + + assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ] ) == set( [ "1", "2", "3", "4" ] ) + assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ], max_in_filter_length=1 ) == set( [ "1", "2", "3", "4" ] ) + + assert contents_iter_names( ids=[ d1.id, d3.id ] ) == set( [ "1", "3" ] ) + + def new_hda( self, history, **kwds ): + return self.persist( self.model.HistoryDatasetAssociation( history=history, create_dataset=True, sa_session=self.model.session, **kwds ), flush=True ) + @classmethod def setUpClass(cls): # Start the database and connect the mapping @@ -191,10 +224,16 @@ return cls.model.session.query( type ) @classmethod - def persist(cls, *args): + def persist(cls, *args, **kwargs): + session = cls.model.session + flush = kwargs.get('flush', True) for arg in args: - cls.model.session.add( arg ) - cls.expunge() + session.add( arg ) + if flush: + session.flush() + if kwargs.get('expunge', not flush): + cls.expunge() + return arg # Return last or only arg. @classmethod def expunge(cls): https://bitbucket.org/galaxy/galaxy-central/commits/8e448f2ac955/ Changeset: 8e448f2ac955 User: jmchilton Date: 2013-12-17 14:31:52 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #275) Move history contents filtering logic into model. Affected #: 3 files diff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 -r 8e448f2ac955e6d434476b18c59b2cffcfc55404 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -19,6 +19,7 @@ import socket import time from string import Template +from itertools import ifilter import galaxy.datatypes import galaxy.datatypes.registry @@ -43,6 +44,11 @@ # Default Value Required for unit tests datatypes_registry.load_datatypes() +# When constructing filters with in for a fixed set of ids, maximum +# number of items to place in the IN statement. Different databases +# are going to have different limits so it is likely best to not let +# this be unlimited - filter in Python if over this limit. +MAX_IN_FILTER_LENGTH = 100 class NoConverterException(Exception): def __init__(self, value): @@ -893,6 +899,32 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + def contents_iter( self, **kwds ): + """ + Fetch filtered list of contents of history. + """ + python_filter = None + db_session = object_session( self ) + assert db_session != None + query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) ) + if deleted is not None: + query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) ) + visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) ) + if visible is not None: + query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) ) + if 'ids' in kwds: + ids = kwds['ids'] + max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH) + if len(ids) < max_in_filter_length: + query = query.filter( HistoryDatasetAssociation.id.in_(ids) ) + else: + python_filter = lambda hda: hda.id in ids + if python_filter: + return ifilter(python_filter, query) + else: + return query + def copy_tags_from(self,target_user,source_history): for src_shta in source_history.tags: new_shta = src_shta.copy() diff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 -r 8e448f2ac955e6d434476b18c59b2cffcfc55404 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -51,47 +51,28 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - # if ids, return _FULL_ data (as show) for each id passed + contents_kwds = {} if ids: - ids = ids.split( ',' ) - for index, hda in enumerate( history.datasets ): - encoded_hda_id = trans.security.encode_id( hda.id ) - if encoded_hda_id in ids: - #TODO: share code with show - rval.append( self._detailed_hda_dict( trans, hda ) ) - - # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history + ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) ) + contents_kwds[ 'ids' ] = ids + # If explicit ids given, always used detailed result. + details = 'all' else: + contents_kwds[ 'deleted' ] = kwd.get( 'deleted', None ) + contents_kwds[ 'visible' ] = kwd.get( 'visible', None ) # details param allows a mixed set of summary and detailed hdas #TODO: this is getting convoluted due to backwards compat details = kwd.get( 'details', None ) or [] if details and details != 'all': details = util.listify( details ) - # by default return all datasets - even if deleted or hidden (defaulting the next switches to None) - # if specified return those datasets that match the setting - # backwards compat - return_deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) - return_visible = util.string_as_bool_or_none( kwd.get( 'visible', None ) ) - - for hda in history.datasets: - # if either return_ setting has been requested (!= None), skip hdas that don't match the request - if return_deleted is not None: - if( ( return_deleted and not hda.deleted ) - or ( not return_deleted and hda.deleted ) ): - continue - if return_visible is not None: - if( ( return_visible and not hda.visible ) - or ( not return_visible and hda.visible ) ): - continue - - encoded_hda_id = trans.security.encode_id( hda.id ) - if( ( encoded_hda_id in details ) - or ( details == 'all' ) ): - rval.append( self._detailed_hda_dict( trans, hda ) ) - else: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) - + for hda in history.contents_iter( **contents_kwds ): + encoded_hda_id = trans.security.encode_id( hda.id ) + detailed = details == 'all' or ( encoded_hda_id in details ) + if detailed: + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) rval = "Error in history API at listing contents: " + str( e ) diff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 -r 8e448f2ac955e6d434476b18c59b2cffcfc55404 test/unit/test_galaxy_mapping.py --- a/test/unit/test_galaxy_mapping.py +++ b/test/unit/test_galaxy_mapping.py @@ -180,6 +180,39 @@ assert hist1.name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. + def test_history_contents( self ): + model = self.model + u = model.User( email="contents(a)foo.bar.baz", password="password" ) + # gs = model.GalaxySession() + h1 = model.History( name="HistoryContentsHistory1", user=u) + + self.persist( u, h1, expunge=True ) + + d1 = self.new_hda( h1, name="1" ) + d2 = self.new_hda( h1, name="2", visible=False ) + d3 = self.new_hda( h1, name="3", deleted=True ) + d4 = self.new_hda( h1, name="4", visible=False, deleted=True ) + + def contents_iter_names(**kwds): + history = model.context.query( model.History ).filter( + model.History.name == "HistoryContentsHistory1" + ).first() + return set( map( lambda hda: hda.name, history.contents_iter( **kwds ) ) ) + + assert contents_iter_names() == set( [ "1", "2", "3", "4" ] ) + assert contents_iter_names( deleted=False ) == set( [ "1", "2" ] ) + assert contents_iter_names( visible=True ) == set( [ "1", "3" ] ) + assert contents_iter_names( visible=False ) == set( [ "2", "4" ] ) + assert contents_iter_names( deleted=True, visible=False ) == set( [ "4" ] ) + + assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ] ) == set( [ "1", "2", "3", "4" ] ) + assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ], max_in_filter_length=1 ) == set( [ "1", "2", "3", "4" ] ) + + assert contents_iter_names( ids=[ d1.id, d3.id ] ) == set( [ "1", "3" ] ) + + def new_hda( self, history, **kwds ): + return self.persist( self.model.HistoryDatasetAssociation( history=history, create_dataset=True, sa_session=self.model.session, **kwds ), flush=True ) + @classmethod def setUpClass(cls): # Start the database and connect the mapping @@ -191,10 +224,16 @@ return cls.model.session.query( type ) @classmethod - def persist(cls, *args): + def persist(cls, *args, **kwargs): + session = cls.model.session + flush = kwargs.get('flush', True) for arg in args: - cls.model.session.add( arg ) - cls.expunge() + session.add( arg ) + if flush: + session.flush() + if kwargs.get('expunge', not flush): + cls.expunge() + return arg # Return last or only arg. @classmethod def expunge(cls): 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 17 Dec '13

17 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee365d4406e6/ Changeset: ee365d4406e6 User: jmchilton Date: 2013-12-13 06:25:25 Summary: casperjs: Fix user login, registration, logout for recent masthead changes... They are generated in javascript instead of HTML now so I don't think they are available when page loads. My fix is to wait for the User menu to appear before attempting these operations. Affected #: 4 files diff -r b3eeedb81a1e0db8d643af0cbba68f55eb49cdb0 -r ee365d4406e604b573c3011e5b642dd7075f561d test/casperjs/api-configuration-tests.js --- a/test/casperjs/api-configuration-tests.js +++ b/test/casperjs/api-configuration-tests.js @@ -102,18 +102,19 @@ //}, function failedLoginRegister(){ // this.info( 'Admin level configuration API tests not run: no admin account available' ); spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + spaceghost.waitForMasthead( function() { + if( spaceghost.user.userIsAdmin() ){ + this.test.comment( 'index should get a (full) list of configuration settings ' + + 'when requested by an admin user' ); + configIndex = this.api.configuration.index(); + this.debug( this.jsonStr( configIndex ) ); + this.test.assert( utils.isObject( configIndex ), "index returned an object" ); + this.test.assert( hasKeys( configIndex, adminKeys ), 'Has the proper keys' ); - if( spaceghost.user.userIsAdmin() ){ - this.test.comment( 'index should get a (full) list of configuration settings ' - + 'when requested by an admin user' ); - configIndex = this.api.configuration.index(); - this.debug( this.jsonStr( configIndex ) ); - this.test.assert( utils.isObject( configIndex ), "index returned an object" ); - this.test.assert( hasKeys( configIndex, adminKeys ), 'Has the proper keys' ); - - } else { - this.info( 'Admin level configuration API tests not run: no admin account available' ); - } + } else { + this.info( 'Admin level configuration API tests not run: no admin account available' ); + } + }); }); // =================================================================== diff -r b3eeedb81a1e0db8d643af0cbba68f55eb49cdb0 -r ee365d4406e604b573c3011e5b642dd7075f561d test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -44,17 +44,18 @@ }; spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.clickLabel( spaceghost.data.labels.masthead.menus.user ); - this.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); + this.waitForMasthead( function() { + this.clickLabel( spaceghost.data.labels.masthead.menus.user ); + this.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); - this.withMainPanel( function mainBeforeRegister(){ - spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') registering user:\n' - + spaceghost.jsonStr( userInfo ) ); - this.fill( spaceghost.data.selectors.registrationPage.form, userInfo, false ); - // need manual submit (not a normal html form) - this.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); + this.withMainPanel( function mainBeforeRegister(){ + spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') registering user:\n' + + spaceghost.jsonStr( userInfo ) ); + this.fill( spaceghost.data.selectors.registrationPage.form, userInfo, false ); + // need manual submit (not a normal html form) + this.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); + }); }); - //// debugging //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterRegister(){ // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); @@ -79,24 +80,26 @@ }; spaceghost.thenOpen( spaceghost.baseUrl, function(){ - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); + spaceghost.waitForMasthead( function() { + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); - spaceghost.withMainPanel( function mainBeforeLogin(){ - spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' - + spaceghost.jsonStr( loginInfo ) ); - spaceghost.fill( spaceghost.data.selectors.loginPage.form, loginInfo, false ); - spaceghost.click( xpath( spaceghost.data.selectors.loginPage.submit_xpath ) ); + spaceghost.withMainPanel( function mainBeforeLogin(){ + spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' + + spaceghost.jsonStr( loginInfo ) ); + spaceghost.fill( spaceghost.data.selectors.loginPage.form, loginInfo, false ); + spaceghost.click( xpath( spaceghost.data.selectors.loginPage.submit_xpath ) ); + }); + + //// debugging + //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ + // //TODO: prob. could use a more generalized form of this for url breakdown/checking + // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); + // } + //}); }); - - //// debugging - //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ - // //TODO: prob. could use a more generalized form of this for url breakdown/checking - // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); - // } - //}); }); }; @@ -133,17 +136,19 @@ var spaceghost = this.spaceghost; this._submitLogin( email, password ); - spaceghost.withMainPanel( function mainAfterLogin(){ - if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ - var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ - this.warning( 'Login failed: ' + messageInfo.text ); - throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.text ); + spaceghost.waitForMasthead( function() { + spaceghost.withMainPanel( function mainAfterLogin(){ + if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ + var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ + this.warning( 'Login failed: ' + messageInfo.text ); + throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.text ); + } } - } - if( spaceghost.user.loggedInAs() === email ){ - spaceghost.info( 'logged in as ' + email ); - } + if( spaceghost.user.loggedInAs() === email ){ + spaceghost.info( 'logged in as ' + email ); + } + }); }); return spaceghost; }; @@ -173,8 +178,10 @@ spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.info( 'user logging out' ); //TODO: handle already logged out - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); + spaceghost.waitForMasthead( function _logout() { + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); + }); }); return spaceghost; }; diff -r b3eeedb81a1e0db8d643af0cbba68f55eb49cdb0 -r ee365d4406e604b573c3011e5b642dd7075f561d test/casperjs/registration-tests.js --- a/test/casperjs/registration-tests.js +++ b/test/casperjs/registration-tests.js @@ -62,18 +62,24 @@ this.user._submitRegistration( email, password, username, confirm ); }); spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.clickLabel( 'User' ); - this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); + this.waitForMasthead( function() { + this.clickLabel( 'User' ); + this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); + }); }); // ------------------------------------------------------------------- log out that user spaceghost.then( function(){ - this.test.comment( 'logging out user: ' + email ); - this.user.logout(); + this.waitForMasthead( function() { + this.test.comment( 'logging out user: ' + email ); + this.user.logout(); + }); }); spaceghost.then( function(){ - this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); - this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); + this.waitForMasthead( function() { + this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); + this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); + }); }); // ------------------------------------------------------------------- bad user registrations diff -r b3eeedb81a1e0db8d643af0cbba68f55eb49cdb0 -r ee365d4406e604b573c3011e5b642dd7075f561d test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -1103,6 +1103,10 @@ return match[2]; }; +SpaceGhost.prototype.waitForMasthead = function wait( then ) { + return this.waitForText( this.data.labels.masthead.menus.user, then ); +} + // =================================================================== TEST DATA /** General use selectors, labels, and text. Kept here to allow a centralized location. https://bitbucket.org/galaxy/galaxy-central/commits/90a639389de4/ Changeset: 90a639389de4 User: jmchilton Date: 2013-12-17 14:30:24 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #274) casperjs: Fix user login, registration, logout for recent masthead changes... Affected #: 4 files diff -r af87cdcf36084831fce7d99e621b1efc943d2aff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 test/casperjs/api-configuration-tests.js --- a/test/casperjs/api-configuration-tests.js +++ b/test/casperjs/api-configuration-tests.js @@ -102,18 +102,19 @@ //}, function failedLoginRegister(){ // this.info( 'Admin level configuration API tests not run: no admin account available' ); spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + spaceghost.waitForMasthead( function() { + if( spaceghost.user.userIsAdmin() ){ + this.test.comment( 'index should get a (full) list of configuration settings ' + + 'when requested by an admin user' ); + configIndex = this.api.configuration.index(); + this.debug( this.jsonStr( configIndex ) ); + this.test.assert( utils.isObject( configIndex ), "index returned an object" ); + this.test.assert( hasKeys( configIndex, adminKeys ), 'Has the proper keys' ); - if( spaceghost.user.userIsAdmin() ){ - this.test.comment( 'index should get a (full) list of configuration settings ' - + 'when requested by an admin user' ); - configIndex = this.api.configuration.index(); - this.debug( this.jsonStr( configIndex ) ); - this.test.assert( utils.isObject( configIndex ), "index returned an object" ); - this.test.assert( hasKeys( configIndex, adminKeys ), 'Has the proper keys' ); - - } else { - this.info( 'Admin level configuration API tests not run: no admin account available' ); - } + } else { + this.info( 'Admin level configuration API tests not run: no admin account available' ); + } + }); }); // =================================================================== diff -r af87cdcf36084831fce7d99e621b1efc943d2aff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -44,17 +44,18 @@ }; spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.clickLabel( spaceghost.data.labels.masthead.menus.user ); - this.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); + this.waitForMasthead( function() { + this.clickLabel( spaceghost.data.labels.masthead.menus.user ); + this.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); - this.withMainPanel( function mainBeforeRegister(){ - spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') registering user:\n' - + spaceghost.jsonStr( userInfo ) ); - this.fill( spaceghost.data.selectors.registrationPage.form, userInfo, false ); - // need manual submit (not a normal html form) - this.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); + this.withMainPanel( function mainBeforeRegister(){ + spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') registering user:\n' + + spaceghost.jsonStr( userInfo ) ); + this.fill( spaceghost.data.selectors.registrationPage.form, userInfo, false ); + // need manual submit (not a normal html form) + this.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); + }); }); - //// debugging //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterRegister(){ // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); @@ -79,24 +80,26 @@ }; spaceghost.thenOpen( spaceghost.baseUrl, function(){ - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); + spaceghost.waitForMasthead( function() { + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); - spaceghost.withMainPanel( function mainBeforeLogin(){ - spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' - + spaceghost.jsonStr( loginInfo ) ); - spaceghost.fill( spaceghost.data.selectors.loginPage.form, loginInfo, false ); - spaceghost.click( xpath( spaceghost.data.selectors.loginPage.submit_xpath ) ); + spaceghost.withMainPanel( function mainBeforeLogin(){ + spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' + + spaceghost.jsonStr( loginInfo ) ); + spaceghost.fill( spaceghost.data.selectors.loginPage.form, loginInfo, false ); + spaceghost.click( xpath( spaceghost.data.selectors.loginPage.submit_xpath ) ); + }); + + //// debugging + //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ + // //TODO: prob. could use a more generalized form of this for url breakdown/checking + // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); + // } + //}); }); - - //// debugging - //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ - // //TODO: prob. could use a more generalized form of this for url breakdown/checking - // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); - // } - //}); }); }; @@ -133,17 +136,19 @@ var spaceghost = this.spaceghost; this._submitLogin( email, password ); - spaceghost.withMainPanel( function mainAfterLogin(){ - if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ - var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ - this.warning( 'Login failed: ' + messageInfo.text ); - throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.text ); + spaceghost.waitForMasthead( function() { + spaceghost.withMainPanel( function mainAfterLogin(){ + if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ + var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ + this.warning( 'Login failed: ' + messageInfo.text ); + throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.text ); + } } - } - if( spaceghost.user.loggedInAs() === email ){ - spaceghost.info( 'logged in as ' + email ); - } + if( spaceghost.user.loggedInAs() === email ){ + spaceghost.info( 'logged in as ' + email ); + } + }); }); return spaceghost; }; @@ -173,8 +178,10 @@ spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.info( 'user logging out' ); //TODO: handle already logged out - spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); + spaceghost.waitForMasthead( function _logout() { + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); + }); }); return spaceghost; }; diff -r af87cdcf36084831fce7d99e621b1efc943d2aff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 test/casperjs/registration-tests.js --- a/test/casperjs/registration-tests.js +++ b/test/casperjs/registration-tests.js @@ -62,18 +62,24 @@ this.user._submitRegistration( email, password, username, confirm ); }); spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.clickLabel( 'User' ); - this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); + this.waitForMasthead( function() { + this.clickLabel( 'User' ); + this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); + }); }); // ------------------------------------------------------------------- log out that user spaceghost.then( function(){ - this.test.comment( 'logging out user: ' + email ); - this.user.logout(); + this.waitForMasthead( function() { + this.test.comment( 'logging out user: ' + email ); + this.user.logout(); + }); }); spaceghost.then( function(){ - this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); - this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); + this.waitForMasthead( function() { + this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); + this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); + }); }); // ------------------------------------------------------------------- bad user registrations diff -r af87cdcf36084831fce7d99e621b1efc943d2aff -r 90a639389de4a4348a32e21d87a13de4b1a72f56 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -1103,6 +1103,10 @@ return match[2]; }; +SpaceGhost.prototype.waitForMasthead = function wait( then ) { + return this.waitForText( this.data.labels.masthead.menus.user, then ); +} + // =================================================================== TEST DATA /** General use selectors, labels, and text. Kept here to allow a centralized location. 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: greg: Eliminate deprecated repositories from the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af87cdcf3608/ Changeset: af87cdcf3608 User: greg Date: 2013-12-17 04:06:16 Summary: Eliminate deprecated repositories from the tool shed's install and test framework. Affected #: 1 file diff -r 422f9675cb5025e20b402ad92aa591a87ca3a883 -r af87cdcf36084831fce7d99e621b1efc943d2aff test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -176,14 +176,14 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] -testing_single_repository = {} +testing_single_repository_dict = {} if 'repository_name' in os.environ and 'repository_owner' in os.environ: - testing_single_repository[ 'name' ] = os.environ[ 'repository_name' ] - testing_single_repository[ 'owner' ] = os.environ[ 'repository_owner' ] + testing_single_repository_dict[ 'name' ] = str( os.environ[ 'repository_name' ] ) + testing_single_repository_dict[ 'owner' ] = str( os.environ[ 'repository_owner' ] ) if 'repository_revision' in os.environ: - testing_single_repository[ 'changeset_revision' ] = os.environ[ 'repository_revision' ] + testing_single_repository_dict[ 'changeset_revision' ] = str( os.environ[ 'repository_revision' ] ) else: - testing_single_repository[ 'changeset_revision' ] = None + testing_single_repository_dict[ 'changeset_revision' ] = None class ReportResults( Plugin ): @@ -364,6 +364,8 @@ log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) repository_dicts = [] parts = [ 'repository_revisions' ] + # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility + # is guaranteed and we currently do not guarantee reproducibility. params = dict( do_not_test='false', downloadable='true', includes_tools='true', @@ -381,21 +383,25 @@ if error_message: log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) else: - # Don't test empty repositories. - changeset_revision = baseline_repository_dict[ 'changeset_revision' ] - if changeset_revision != suc.INITIAL_CHANGELOG_HASH: - # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and - # append it to the list of repository_dicts to install and test. - if latest_revision_only: - latest_revision = repository_dict[ 'latest_revision' ] - if changeset_revision == latest_revision: + # Don't test deprecated repositories since testing them is necessary only if reproducibility is guaranteed + # and we are not currently guaranteeing reproducibility. + deprecated = asbool( repository_dict.get( 'deprecated', False ) ) + if not deprecated: + # Don't test empty repositories. + changeset_revision = baseline_repository_dict[ 'changeset_revision' ] + if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and + # append it to the list of repository_dicts to install and test. + if latest_revision_only: + latest_revision = repository_dict[ 'latest_revision' ] + if changeset_revision == latest_revision: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + else: repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - else: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if testing_single_repository: - tsr_name = testing_single_repository[ 'name' ] - tsr_owner = testing_single_repository[ 'owner' ] - tsr_changeset_revision = testing_single_repository[ 'changeset_revision' ] + if testing_single_repository_dict: + tsr_name = testing_single_repository_dict[ 'name' ] + tsr_owner = testing_single_repository_dict[ 'owner' ] + tsr_changeset_revision = testing_single_repository_dict[ 'changeset_revision' ] log.debug( 'Testing single repository with name %s and owner %s.' % ( str( tsr_name ), str( tsr_owner ) ) ) for repository_to_install in repository_dicts: rti_name = repository_to_install[ 'name' ] 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: greg: Handle exceptions when uninstalling repositories in the tool shed's install nad test framework.
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/422f9675cb50/ Changeset: 422f9675cb50 User: greg Date: 2013-12-17 01:27:28 Summary: Handle exceptions when uninstalling repositories in the tool shed's install nad test framework. Affected #: 1 file diff -r 46521f5722c621a8b84d2a8101af87d82cc5eba8 -r 422f9675cb5025e20b402ad92aa591a87ca3a883 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -1220,9 +1220,9 @@ for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): print "# " for repository_dict in grouped_repository_dicts: - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] - changeset_revision = repository_dict[ 'changeset_revision' ] + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, results_dict ): @@ -1328,15 +1328,20 @@ owner=owner, changeset_revision=changeset_revision ) log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and all of its repository dependencies, deleting each of them from disk. - result, _ = run_tests( test_config ) - success = result.wasSuccessful() - if success: + try: + test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed + # repository and all of its repository dependencies, deleting each of them from disk. + result, _ = run_tests( test_config ) + repository_uninstall_successful = result.wasSuccessful() + except Exception, e: + repository_uninstall_successful = False + log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ + ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) + if repository_uninstall_successful: # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. # We have to do this through Twill in order to maintain app.toolbox and shed_tool_conf.xml in a state that # is valid for future tests. Since some of the repository's repository dependencies may require other of @@ -1356,15 +1361,19 @@ ( rd_changeset_revision, rd_name, rd_owner ) ) # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's # web interface. - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. - result, _ = run_tests( test_config ) - success = result.wasSuccessful() - if not success: - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed: %s' % \ + try: + test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. + result, _ = run_tests( test_config ) + if not result.wasSuccessful(): + # We won't set ok here because we'll continue to uninstall whatever we can. + log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) ) + except Exception, e: + log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) else: log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) 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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galaxy-commits December 2013