galaxy-commits January 2013

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commit/galaxy-central: jgoecks: Remove incorrect test parameter.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6538175fb3e6/ changeset: 6538175fb3e6 user: jgoecks date: 2013-01-17 21:57:21 summary: Remove incorrect test parameter. affected #: 1 file diff -r d4a61389668164e833eef418ab03c1467ba64d13 -r 6538175fb3e6483895aaadfdeddd09aac558fdf5 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -462,7 +462,6 @@ <param name="use_annotations" value="No" /><param name="use_juncs" value="No" /><param name="no_novel_juncs" value="No" /> - <param name="report_discordant_pairs" value="No" /><param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /> 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: 4 new changesets
by Bitbucket 17 Jan '13

17 Jan '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44d9d215b9c3/ changeset: 44d9d215b9c3 user: epaniagu date: 2011-11-22 21:42:18 summary: fix add/remove buttons in Repeat elements affected #: 1 file diff -r 9d6a9963b0da21fe3139fcefbd11c1ec6290a529 -r 44d9d215b9c337cf9b988976bf93f429dbd84ccb templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -139,13 +139,17 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %if input.min < len( repeat_state ): + <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif </div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor - <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %if input.max > len( repeat_state ): + <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif </div> %elif input.type == "conditional": <% https://bitbucket.org/galaxy/galaxy-central/commits/b6ff1a695e07/ changeset: b6ff1a695e07 user: epaniagu date: 2011-11-22 21:53:56 summary: replace len( repeat_state ) with a variable so there's only one call affected #: 1 file diff -r 44d9d215b9c337cf9b988976bf93f429dbd84ccb -r b6ff1a695e07e6a2443a3d6d0aa9a9066a155dbc templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -127,8 +127,11 @@ </div> %endif </div> - <% repeat_state = tool_state[input.name] %> - %for i in range( len( repeat_state ) ): + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): <div class="repeat-group-item"><% if input.name in errors: @@ -139,7 +142,7 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} - %if input.min < len( repeat_state ): + %if input.min < num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> %endif </div> @@ -147,7 +150,7 @@ <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor - %if input.max > len( repeat_state ): + %if input.max > num_repeats: <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> %endif </div> https://bitbucket.org/galaxy/galaxy-central/commits/8d068273cf5b/ changeset: 8d068273cf5b user: jgoecks date: 2013-01-17 21:32:34 summary: Merged in epaniagu/galaxy-central (pull request #24: Fix Add/Remove buttons for Repeat groups) affected #: 1 file diff -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 -r 8d068273cf5b1160a27977727a7ab6f2237d4bb7 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -135,8 +135,11 @@ </div> %endif </div> - <% repeat_state = tool_state[input.name] %> - %for i in range( len( repeat_state ) ): + <% + repeat_state = tool_state[input.name] + num_repeats = len( repeat_state ) + %> + %for i in range( num_repeats ): <div class="repeat-group-item"><% if input.name in errors: @@ -147,13 +150,25 @@ %><div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div> ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} +<<<<<<< local <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> +======= + %if input.min < num_repeats: + <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + %endif +>>>>>>> other </div> %if rep_errors.has_key( '__index__' ): <div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div> %endif %endfor +<<<<<<< local <div class="form-row"><input type="submit" class="btn" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> +======= + %if input.max > num_repeats: + <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + %endif +>>>>>>> other </div> %elif input.type == "conditional": <% https://bitbucket.org/galaxy/galaxy-central/commits/d4a613896681/ changeset: d4a613896681 user: jgoecks date: 2013-01-17 21:34:04 summary: Automated merge. affected #: 1 file diff -r 8d068273cf5b1160a27977727a7ab6f2237d4bb7 -r d4a61389668164e833eef418ab03c1467ba64d13 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -50,6 +50,41 @@ migrated_tool_panel_config = 'migrated_tools_conf.xml' installed_tool_panel_configs = [ 'shed_tool_conf.xml' ] +# should this serve static resources (scripts, images, styles, etc.) +STATIC_ENABLED = True + +def get_static_settings(): + """Returns dictionary of the settings necessary for a galaxy App + to be wrapped in the static middleware. + + This mainly consists of the filesystem locations of url-mapped + static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + return dict( + #TODO: static_enabled needed here? + static_enabled = True, + static_cache_time = 360, + static_dir = static_dir, + static_images_dir = os.path.join( static_dir, 'images', '' ), + static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), + static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), + static_robots_txt = os.path.join( static_dir, 'robots.txt' ), + ) + +def get_webapp_global_conf(): + """Get the global_conf dictionary sent as the first argument to app_factory. + """ + # (was originally sent 'dict()') - nothing here for now except static settings + global_conf = dict() + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + + def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. @@ -289,7 +324,8 @@ server = None if start_server: - webapp = buildapp.app_factory( dict(), use_translogger=False, static_enabled=False, app=app ) + webapp = buildapp.app_factory( get_webapp_global_conf(), app=app, + use_translogger=False, static_enabled=STATIC_ENABLED ) if galaxy_test_port is not None: server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Enable serving static files when running functional tests
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da89c3556c27/ changeset: da89c3556c27 user: carlfeberhard date: 2013-01-17 20:58:43 summary: Enable serving static files when running functional tests affected #: 1 file diff -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 -r da89c3556c27c8f1e5acf943c6983be5437efac6 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -50,6 +50,41 @@ migrated_tool_panel_config = 'migrated_tools_conf.xml' installed_tool_panel_configs = [ 'shed_tool_conf.xml' ] +# should this serve static resources (scripts, images, styles, etc.) +STATIC_ENABLED = True + +def get_static_settings(): + """Returns dictionary of the settings necessary for a galaxy App + to be wrapped in the static middleware. + + This mainly consists of the filesystem locations of url-mapped + static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + return dict( + #TODO: static_enabled needed here? + static_enabled = True, + static_cache_time = 360, + static_dir = static_dir, + static_images_dir = os.path.join( static_dir, 'images', '' ), + static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), + static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), + static_robots_txt = os.path.join( static_dir, 'robots.txt' ), + ) + +def get_webapp_global_conf(): + """Get the global_conf dictionary sent as the first argument to app_factory. + """ + # (was originally sent 'dict()') - nothing here for now except static settings + global_conf = dict() + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + + def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. @@ -289,7 +324,8 @@ server = None if start_server: - webapp = buildapp.app_factory( dict(), use_translogger=False, static_enabled=False, app=app ) + webapp = buildapp.app_factory( get_webapp_global_conf(), app=app, + use_translogger=False, static_enabled=STATIC_ENABLED ) if galaxy_test_port is not None: server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) else: 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: 4 new changesets
by Bitbucket 17 Jan '13

17 Jan '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2eb6dddb3866/ changeset: 2eb6dddb3866 user: fangly date: 2011-10-05 10:04:58 summary: Paired-end code that properly ignores description part of FASTQ headers affected #: 1 file diff -r 087a766b3eca312d49caffa6b821d304658825ae -r 2eb6dddb3866adef30b72e92e747d9ece4e11da9 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -514,9 +514,13 @@ self.apply_galaxy_conventions = apply_galaxy_conventions def close( self ): return self.file.close() - def get( self, sequence_id ): - if not isinstance( sequence_id, basestring ): - sequence_id = sequence_id.identifier + def get( self, sequence_identifier ): + # Input is either a sequence ID or a sequence object + if not isinstance( sequence_identifier, basestring ): + # Input was a sequence object (not a sequence ID). Get the sequence ID + sequence_identifier = sequence_identifier.identifier + # Get only the ID part of the sequence header + sequence_id, sequence_sep, sequence_desc = sequence_identifier.partition(' ') rval = None if sequence_id in self.offset_dict: initial_offset = self.file.tell() @@ -525,7 +529,7 @@ del self.offset_dict[ sequence_id ] self.file.seek( seq_offset ) rval = self.reader.next() - #assert rval.identifier == sequence_id, 'seq id mismatch' #should be able to remove this + #assert rval.id == sequence_id, 'seq id mismatch' #should be able to remove this self.file.seek( initial_offset ) else: while True: @@ -535,13 +539,14 @@ except StopIteration: self.eof = True break #eof, id not found, will return None - if fastq_read.identifier == sequence_id: + fastq_read_id, fastq_read_sep, fastq_read_desc = fastq_read.identifier.partition(' ') + if fastq_read_id == sequence_id: rval = fastq_read break else: - if fastq_read.identifier not in self.offset_dict: - self.offset_dict[ fastq_read.identifier ] = [] - self.offset_dict[ fastq_read.identifier ].append( offset ) + if fastq_read_id not in self.offset_dict: + self.offset_dict[ fastq_read_id ] = [] + self.offset_dict[ fastq_read_id ].append( offset ) if rval is not None and self.apply_galaxy_conventions: rval.apply_galaxy_conventions() return rval @@ -582,16 +587,18 @@ self.format = format self.force_quality_encoding = force_quality_encoding def join( self, read1, read2 ): - if read1.identifier.endswith( '/2' ) and read2.identifier.endswith( '/1' ): + read1_id, read1_sep, read1_desc = read1.identifier.partition(' ') + read2_id, read2_sep, read2_desc = read2.identifier.partition(' ') + if read1_id.endswith( '/2' ) and read2_id.endswith( '/1' ): #swap 1 and 2 tmp = read1 read1 = read2 read2 = tmp del tmp - if read1.identifier.endswith( '/1' ) and read2.identifier.endswith( '/2' ): - identifier = read1.identifier[:-2] - else: - identifier = read1.identifier + if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ): + read1_id = read1_id[:-2] + + identifier = read1_id + ' ' + read1_desc #use force quality encoding, if not present force to encoding of first read force_quality_encoding = self.force_quality_encoding @@ -621,17 +628,18 @@ rval.quality = "%s %s" % ( new_read1.quality.strip(), new_read2.quality.strip() ) return rval def get_paired_identifier( self, fastq_read ): - identifier = fastq_read.identifier - if identifier[-2] == '/': - if identifier[-1] == "1": - identifier = "%s2" % identifier[:-1] - elif identifier[-1] == "2": - identifier = "%s1" % identifier[:-1] - return identifier + read_id, read_sep, read_desc = fastq_read.identifier.partition(' ') + if read_id[-2] == '/': + if read_id[-1] == "1": + read_id = "%s2" % read_id[:-1] + elif read_id[-1] == "2": + read_id = "%s1" % read_id[:-1] + return read_id def is_first_mate( self, sequence_id ): is_first = None if not isinstance( sequence_id, basestring ): sequence_id = sequence_id.identifier + sequence_id, sequence_sep, sequence_desc = sequence_id.partition(' ') if sequence_id[-2] == '/': if sequence_id[-1] == "1": is_first = True https://bitbucket.org/galaxy/galaxy-central/commits/34e7cf3bcef0/ changeset: 34e7cf3bcef0 user: fangly date: 2011-11-30 02:38:52 summary: Avoid trailing whitespace affected #: 1 file diff -r 2eb6dddb3866adef30b72e92e747d9ece4e11da9 -r 34e7cf3bcef0eb7bf7d0684e8ac5d91e03750d8c lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -597,8 +597,10 @@ del tmp if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ): read1_id = read1_id[:-2] - - identifier = read1_id + ' ' + read1_desc + + identifier = read1_id + if read1_desc: + identifier = identifier + ' ' + read1_desc #use force quality encoding, if not present force to encoding of first read force_quality_encoding = self.force_quality_encoding https://bitbucket.org/galaxy/galaxy-central/commits/7d4a431f7188/ changeset: 7d4a431f7188 user: fangly date: 2011-11-30 03:01:07 summary: Updated tests for FASTQ interlacer/deinterlacer tool affected #: 2 files diff -r 34e7cf3bcef0eb7bf7d0684e8ac5d91e03750d8c -r 7d4a431f7188d71d5e0ba2655a10145ecbdb4468 test-data/paired_end_2.fastqsanger --- a/test-data/paired_end_2.fastqsanger +++ b/test-data/paired_end_2.fastqsanger @@ -1,6 +1,6 @@ -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/2 CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT diff -r 34e7cf3bcef0eb7bf7d0684e8ac5d91e03750d8c -r 7d4a431f7188d71d5e0ba2655a10145ecbdb4468 test-data/paired_end_merged.fastqsanger --- a/test-data/paired_end_merged.fastqsanger +++ b/test-data/paired_end_merged.fastqsanger @@ -2,9 +2,9 @@ NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG +1539:931/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/1 NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG https://bitbucket.org/galaxy/galaxy-central/commits/7848d6fd1b7a/ changeset: 7848d6fd1b7a user: jgoecks date: 2013-01-17 20:12:57 summary: Merged in fangly/galaxy-central (pull request #8: Paired-end code mishandles description of FASTQ headers) affected #: 3 files diff -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -514,9 +514,13 @@ self.apply_galaxy_conventions = apply_galaxy_conventions def close( self ): return self.file.close() - def get( self, sequence_id ): - if not isinstance( sequence_id, basestring ): - sequence_id = sequence_id.identifier + def get( self, sequence_identifier ): + # Input is either a sequence ID or a sequence object + if not isinstance( sequence_identifier, basestring ): + # Input was a sequence object (not a sequence ID). Get the sequence ID + sequence_identifier = sequence_identifier.identifier + # Get only the ID part of the sequence header + sequence_id, sequence_sep, sequence_desc = sequence_identifier.partition(' ') rval = None if sequence_id in self.offset_dict: initial_offset = self.file.tell() @@ -525,7 +529,7 @@ del self.offset_dict[ sequence_id ] self.file.seek( seq_offset ) rval = self.reader.next() - #assert rval.identifier == sequence_id, 'seq id mismatch' #should be able to remove this + #assert rval.id == sequence_id, 'seq id mismatch' #should be able to remove this self.file.seek( initial_offset ) else: while True: @@ -535,13 +539,14 @@ except StopIteration: self.eof = True break #eof, id not found, will return None - if fastq_read.identifier == sequence_id: + fastq_read_id, fastq_read_sep, fastq_read_desc = fastq_read.identifier.partition(' ') + if fastq_read_id == sequence_id: rval = fastq_read break else: - if fastq_read.identifier not in self.offset_dict: - self.offset_dict[ fastq_read.identifier ] = [] - self.offset_dict[ fastq_read.identifier ].append( offset ) + if fastq_read_id not in self.offset_dict: + self.offset_dict[ fastq_read_id ] = [] + self.offset_dict[ fastq_read_id ].append( offset ) if rval is not None and self.apply_galaxy_conventions: rval.apply_galaxy_conventions() return rval @@ -582,16 +587,20 @@ self.format = format self.force_quality_encoding = force_quality_encoding def join( self, read1, read2 ): - if read1.identifier.endswith( '/2' ) and read2.identifier.endswith( '/1' ): + read1_id, read1_sep, read1_desc = read1.identifier.partition(' ') + read2_id, read2_sep, read2_desc = read2.identifier.partition(' ') + if read1_id.endswith( '/2' ) and read2_id.endswith( '/1' ): #swap 1 and 2 tmp = read1 read1 = read2 read2 = tmp del tmp - if read1.identifier.endswith( '/1' ) and read2.identifier.endswith( '/2' ): - identifier = read1.identifier[:-2] - else: - identifier = read1.identifier + if read1_id.endswith( '/1' ) and read2_id.endswith( '/2' ): + read1_id = read1_id[:-2] + + identifier = read1_id + if read1_desc: + identifier = identifier + ' ' + read1_desc #use force quality encoding, if not present force to encoding of first read force_quality_encoding = self.force_quality_encoding @@ -621,17 +630,18 @@ rval.quality = "%s %s" % ( new_read1.quality.strip(), new_read2.quality.strip() ) return rval def get_paired_identifier( self, fastq_read ): - identifier = fastq_read.identifier - if identifier[-2] == '/': - if identifier[-1] == "1": - identifier = "%s2" % identifier[:-1] - elif identifier[-1] == "2": - identifier = "%s1" % identifier[:-1] - return identifier + read_id, read_sep, read_desc = fastq_read.identifier.partition(' ') + if read_id[-2] == '/': + if read_id[-1] == "1": + read_id = "%s2" % read_id[:-1] + elif read_id[-1] == "2": + read_id = "%s1" % read_id[:-1] + return read_id def is_first_mate( self, sequence_id ): is_first = None if not isinstance( sequence_id, basestring ): sequence_id = sequence_id.identifier + sequence_id, sequence_sep, sequence_desc = sequence_id.partition(' ') if sequence_id[-2] == '/': if sequence_id[-1] == "1": is_first = True diff -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 test-data/paired_end_2.fastqsanger --- a/test-data/paired_end_2.fastqsanger +++ b/test-data/paired_end_2.fastqsanger @@ -1,6 +1,6 @@ -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/2 CTCGCACGGCCGCCTCGACCACTTGGTCTGGCGTCATGCGCAATTTTTTCTCCATGTGGAACGGGCTGGTGGCGATGAACGTATGAATATGCCCCCGCGCT diff -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 -r 7848d6fd1b7a3ef8330ad1b31f5a3521094ad706 test-data/paired_end_merged.fastqsanger --- a/test-data/paired_end_merged.fastqsanger +++ b/test-data/paired_end_merged.fastqsanger @@ -2,9 +2,9 @@ NACATCAACACTCAGTAACGGCTGGCGCAAAATGGCATTGATTAACGAAGACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG +1539:931/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB -@1539:931/2 +@1539:931/2 this read has a description GCGCGTAACGTTTCACCTCGAGATCGTTGTCGGCCGCAATCTCCTGGGGGCGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT -+1539:931/2 ++1539:931/2 this read has a description aee_dcadeeWcaaadJbdaff[fffc]dcfe[dRc^\[^QVOZXXZSPFWNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @2971:937/1 NCGGAGACTTCGAGGCCATCCAGTCGATTGCCAAAGTCATCAAGGGGTCGACGATCTGCTCCCTTGCCCGTTCCAACGAGAATGAAATCCGCCGCGCGTGG Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Comment and naming fix for migration script 108.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1b95e5b076fe/ changeset: 1b95e5b076fe user: jgoecks date: 2013-01-17 19:56:26 summary: Comment and naming fix for migration script 108. affected #: 1 file diff -r 1314572f86e121aa734ea27a52601fbcdb450278 -r 1b95e5b076fee018402e5c94534a2e65ea6c5315 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -71,10 +71,10 @@ except Exception, e: log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) ) - # Drop the Job table's exit_code column. + # Drop the LDDA table's extended metadata ID column. try: - job_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) - extended_metadata_id = job_table.c.extended_metadata_id + ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) + extended_metadata_id = ldda_table.c.extended_metadata_id extended_metadata_id.drop() except Exception, e: log.debug( "Dropping 'extended_metadata_id' column from library_dataset_dataset_association table failed: %s" % ( str( e ) ) ) 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 Bitbucket 17 Jan '13

17 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ccc640f65971/ changeset: ccc640f65971 user: kellrott date: 2013-01-15 22:57:14 summary: Adding exception catches to database 108 downgrade step to fix failure issue with downgrading postgres database (foreign key rules violated...) affected #: 1 file diff -r 4bd419751ed3e8cc54913fa37389111a0e7faaa9 -r ccc640f65971632ea6de7a94bc01d24954102487 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -61,8 +61,15 @@ def downgrade(): metadata.reflect() - ExtendedMetadata_table.drop() - ExtendedMetadataIndex_table.drop() + try: + ExtendedMetadataIndex_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata_index' table failed: %s" % ( str( e ) ) ) + + try: + ExtendedMetadata_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) ) # Drop the Job table's exit_code column. try: https://bitbucket.org/galaxy/galaxy-central/commits/1314572f86e1/ changeset: 1314572f86e1 user: jgoecks date: 2013-01-17 19:52:01 summary: Merged in kellrott/galaxy-central (pull request #109: Fixing database v108 downgrade failure) affected #: 1 file diff -r b14f68fb3e853313d944f934cf279b3517d4a7e6 -r 1314572f86e121aa734ea27a52601fbcdb450278 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- a/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -61,8 +61,15 @@ def downgrade(): metadata.reflect() - ExtendedMetadata_table.drop() - ExtendedMetadataIndex_table.drop() + try: + ExtendedMetadataIndex_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata_index' table failed: %s" % ( str( e ) ) ) + + try: + ExtendedMetadata_table.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata' table failed: %s" % ( str( e ) ) ) # Drop the Job table's exit_code column. try: 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: jgoecks: Use correct index tables for setting dbkey of Tophat2 outputs.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b14f68fb3e85/ changeset: b14f68fb3e85 user: jgoecks date: 2013-01-17 18:56:03 summary: Use correct index tables for setting dbkey of Tophat2 outputs. affected #: 1 file diff -r f11abc888753d0b8efeb4cae653a21ca64a2ae5b -r b14f68fb3e853313d944f934cf279b3517d4a7e6 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -323,7 +323,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> @@ -342,7 +342,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> @@ -361,7 +361,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> @@ -380,7 +380,7 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option> 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: Readd a request param that is no longer needed to a request between Galaxy and the tool shed to ensure backward compatibility.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f11abc888753/ changeset: f11abc888753 user: greg date: 2013-01-17 16:40:01 summary: Readd a request param that is no longer needed to a request between Galaxy and the tool shed to ensure backward compatibility. affected #: 1 file diff -r 6e1e7bee1e6f1b10eed3ba023e6ed0badf16ed38 -r f11abc888753d0b8efeb4cae653a21ca64a2ae5b lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -711,7 +711,8 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s' % ( tool_shed_url, repository_name, changeset_revision ) + url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ + ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() response.close() 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: inithello: Test for reinstalling an uninstalled repository that now has a new changeset adding repository dependencies.
by Bitbucket 17 Jan '13

17 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6e1e7bee1e6f/ changeset: 6e1e7bee1e6f user: inithello date: 2013-01-17 16:18:36 summary: Test for reinstalling an uninstalled repository that now has a new changeset adding repository dependencies. affected #: 2 files diff -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 -r 6e1e7bee1e6f1b10eed3ba023e6ed0badf16ed38 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -711,6 +711,8 @@ url = '/admin_toolshed/reselect_tool_panel_section?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed=[] ) + # Build the url that will simulate a filled-out form being submitted. Due to a limitation in twill, the reselect_tool_panel_section + # form doesn't get parsed correctly. repo_dependencies = self.create_checkbox_query_string( field_name='install_repository_dependencies', value=install_repository_dependencies ) tool_dependencies = self.create_checkbox_query_string( field_name='install_tool_dependencies', value=install_tool_dependencies ) encoded_repository_id = self.security.encode_id( installed_repository.id ) diff -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 -r 6e1e7bee1e6f1b10eed3ba023e6ed0badf16ed38 test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -0,0 +1,105 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os, logging +import tool_shed.base.test_db_util as test_db_util + +column_repository_name = 'column_maker_1087' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_1087' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +category_name = 'Test 1087 Advanced Circular Dependencies' +category_description = 'Test circular dependency features' + +log = logging.getLogger( __name__ ) + +class TestRepositoryDependencies( ShedTwillTestCase ): + '''Test installing a repository, then updating it to include repository dependencies.''' + def test_0000_create_or_login_admin_user( self ): + """Create necessary user accounts and login as an admin user.""" + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email ) + assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_create_and_populate_column_repository( self ): + """Create a category for this test suite and add repositories to it.""" + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'column_maker/column_maker.tar', + strings_displayed=[], + commit_message='Uploaded column_maker.tar.' ) + def test_0010_create_and_populate_convert_repository( self ): + '''Create and populate the convert_chars repository.''' + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + 'convert_chars/convert_chars.tar', + strings_displayed=[], + commit_message='Uploaded convert_chars.tar.' ) + def test_0015_install_and_uninstall_column_repository( self ): + '''Install and uninstall the column_maker repository.''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( column_repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=True, + new_tool_panel_section='column_maker', + strings_not_displayed=[ 'install_repository_dependencies' ] ) + installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) + self.uninstall_repository( installed_column_repository, remove_from_disk=True ) + def test_0020_upload_dependency_xml( self ): + '''Upload a repository_dependencies.xml file to column_maker that specifies convert_chars.''' + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_1085', additional_paths=[ 'column' ] ) + self.create_repository_dependency( column_repository, depends_on=[ convert_repository ], filepath=repository_dependencies_path ) + def test_0025_verify_repository_dependency( self ): + '''Verify that the new revision of column_maker now depends on convert_chars.''' + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + self.check_repository_dependency( column_repository, convert_repository ) + log.debug( [ repository.id for repository in test_db_util.get_all_installed_repositories() ] ) + def test_0030_reinstall_column_repository( self ): + '''Reinstall column_maker and verify that it now shows repository dependencies.''' + installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + strings_displayed=[ 'Handle repository dependencies', convert_repository.name, self.get_repository_tip( convert_repository ) ] + # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall. + url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_column_repository.id ) + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed ) + uninstalled_repositories = [ ( column_repository_name, common.test_user_1_name ) ] + self.verify_installed_uninstalled_repositories( uninstalled_repositories=uninstalled_repositories, installed_repositories=[] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Properly handle updates which have become available for tool shed repositories while they were ninstalled when reinstalling them.
by Bitbucket 16 Jan '13

16 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e6302ee56ed0/ changeset: e6302ee56ed0 user: greg date: 2013-01-16 21:39:22 summary: Properly handle updates which have become available for tool shed repositories while they were ninstalled when reinstalling them. affected #: 8 files diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -596,8 +596,7 @@ # In this case, a record for the repository will exist in the database with the status of 'New'. repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) if repository and repository.metadata: - installed_rd, missing_rd = \ - get_installed_and_missing_repository_dependencies( trans, repository ) + installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository ) else: installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) # Discover all repository dependencies and retrieve information for installing them. diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -66,7 +66,7 @@ tool_dependencies[ dependency_key ] = requirements_dict return tool_dependencies def build_readme_files_dict( metadata, tool_path=None ): - """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received repository_metadata.""" + """Return a dictionary of valid readme file name <-> readme file content pairs for all readme files contained in the received metadata.""" readme_files_dict = {} if metadata: if 'readme_files' in metadata: @@ -128,10 +128,14 @@ containers_dict[ 'readme_files' ] = readme_files_root_folder # Installed repository dependencies container. if repository_dependencies: + if new_install: + label = 'Repository dependencies' + else: + label = 'Installed repository dependencies' folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( trans=trans, folder_id=folder_id, repository_dependencies=repository_dependencies, - label='Installed repository dependencies', + label=label, installed=True ) containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Missing repository dependencies container. @@ -777,17 +781,20 @@ sa_session.flush() return tool_shed_repository def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, repository=None, - repository_metadata=None, metadata=None, repository_dependencies=None ): + repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): """ Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. - This method is called from Galaxy in two places: - 1. During the tool shed repository installation process (via the tool shed's get_repository_information() method)- in this case both the received - repository and repository_metadata will be objects. - 2. When a tool shed repository that was uninstalled from a Galaxy instance is being re-installed - in this case, both repository and - repository_metadata will be None, but metadata will be the tool_shed_repository metadata on the Galaxy side, and the repository_dependencies will - be an object previously retrieved from the tool shed. + This method is called from Galaxy unser three scenarios: + 1. During the tool shed repository installation process via the tool shed's get_repository_information() method. In this case both the received + repository and repository_metadata will be objects., but tool_dependencies and repository_dependencies will be None + 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no updates available. In this case, both + repository and repository_metadata will be None, but tool_dependencies and repository_dependencies will be objects previously retrieved from the + tool shed if the repository includes definitions for them. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates available. In this case, this + method is reached via the tool shed's get_updated_repository_information() method, and both repository and repository_metadata will be objects + but tool_dependencies and repository_dependencies will be None. """ repo_info_dict = {} repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) @@ -806,27 +813,24 @@ all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ) - if metadata: - tool_dependencies = metadata.get( 'tool_dependencies', None ) - if tool_dependencies: - new_tool_dependencies = {} - for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key in [ 'set_environment' ]: - new_set_environment_dict_list = [] - for set_environment_dict in requirements_dict: - set_environment_dict[ 'repository_name' ] = repository_name - set_environment_dict[ 'repository_owner' ] = repository_owner - set_environment_dict[ 'changeset_revision' ] = changeset_revision - new_set_environment_dict_list.append( set_environment_dict ) - new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list - else: - requirements_dict[ 'repository_name' ] = repository_name - requirements_dict[ 'repository_owner' ] = repository_owner - requirements_dict[ 'changeset_revision' ] = changeset_revision - new_tool_dependencies[ dependency_key ] = requirements_dict - tool_dependencies = new_tool_dependencies - else: - tool_dependencies = None + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + new_tool_dependencies = {} + for dependency_key, requirements_dict in tool_dependencies.items(): + if dependency_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + set_environment_dict[ 'repository_name' ] = repository_name + set_environment_dict[ 'repository_owner' ] = repository_owner + set_environment_dict[ 'changeset_revision' ] = changeset_revision + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list + else: + requirements_dict[ 'repository_name' ] = repository_name + requirements_dict[ 'repository_owner' ] = repository_owner + requirements_dict[ 'changeset_revision' ] = changeset_revision + new_tool_dependencies[ dependency_key ] = requirements_dict + tool_dependencies = new_tool_dependencies # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), str( repository_clone_url ), diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1406,7 +1406,7 @@ a local Galaxy instance. """ includes_tools = False - includes_repository_dependencies = False + has_repository_dependencies = False includes_tool_dependencies = False repo_info_dicts = [] for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): @@ -1417,8 +1417,8 @@ metadata = repository_metadata.metadata if not includes_tools and 'tools' in metadata: includes_tools = True - if not includes_repository_dependencies and 'repository_dependencies' in metadata: - includes_repository_dependencies = True + if not has_repository_dependencies and 'repository_dependencies' in metadata: + has_repository_dependencies = True if not includes_tool_dependencies and 'tool_dependencies' in metadata: includes_tool_dependencies = True repo_dir = repository.repo_path( trans.app ) @@ -1431,11 +1431,12 @@ repository_owner=repository.user.username, repository_name=repository.name, repository=repository, - metadata=None, - repository_metadata=repository_metadata ) + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) @web.json @@ -1465,10 +1466,6 @@ def get_tool_dependencies( self, trans, **kwd ): """Handle a request from a Galaxy instance.""" params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) @@ -1478,10 +1475,8 @@ break metadata = downloadable_revision.metadata tool_dependencies = metadata.get( 'tool_dependencies', '' ) - from_install_manager = kwd.get( 'from_install_manager', False ) - if from_install_manager: - if tool_dependencies: - return encoding_util.tool_shed_encode( tool_dependencies ) + if tool_dependencies: + return encoding_util.tool_shed_encode( tool_dependencies ) return '' @web.expose def get_tool_versions( self, trans, **kwd ): @@ -1506,6 +1501,53 @@ if tool_version_dicts: return json.to_json_string( tool_version_dicts ) return '' + @web.json + def get_updated_repository_information( self, trans, name, owner, changeset_revision, **kwd ): + """Generate a disctionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance.""" + repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository_id = trans.security.encode_id( repository.id ) + repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) + repo_info_dict = suc.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) + metadata = repository_metadata.metadata + if metadata: + readme_files_dict = suc.build_readme_files_dict( metadata ) + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + else: + readme_files_dict = None + includes_tools = False + # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies. + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if repository_dependencies: + has_repository_dependencies = True + else: + has_repository_dependencies = False + if tool_dependencies: + includes_tool_dependencies = True + else: + includes_tool_dependencies = False + return dict( includes_tools=includes_tools, + has_repository_dependencies=has_repository_dependencies, + includes_tool_dependencies=includes_tool_dependencies, + readme_files_dict=readme_files_dict, + repo_info_dict=repo_info_dict ) def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions.""" encoded_id = trans.security.encode_id( repository.id ) diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -485,10 +485,14 @@ sub_folder.repository_dependencies.append( repository_dependency ) for repository_dependency in rd_value: if trans.webapp.name == 'galaxy': - # We have two extra items in the tuple, repository.id and repository.status. - tool_shed_repository_id = repository_dependency[ 4 ] - installation_status = repository_dependency[ 5 ] - repository_dependency = repository_dependency[ 0:4 ] + if len( repository_dependency ) == 6: + # We have two extra items in the tuple, repository.id and repository.status. + tool_shed_repository_id = repository_dependency[ 4 ] + installation_status = repository_dependency[ 5 ] + repository_dependency = repository_dependency[ 0:4 ] + else: + tool_shed_repository_id = None + installation_status = 'unknown' else: tool_shed_repository_id = None installation_status = None diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -711,8 +711,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s&from_install_manager=True' % \ - ( tool_shed_url, repository_name, changeset_revision ) + url = '%s/repository/get_tool_dependencies?name=%s&owner=devteam&changeset_revision=%s' % ( tool_shed_url, repository_name, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() response.close() diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -374,21 +374,41 @@ if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies - # will be current. + # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled. current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) if current_ctx_rev == repository.ctx_rev: - includes_tools = repository.includes_tools - has_repository_dependencies = repository.has_repository_dependencies - if includes_tools or has_repository_dependencies: - # Only allow selecting a different section in the tool panel if the repository was uninstalled. - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='reselect_tool_panel_section', - **kwd ) ) + # The uninstalled repository is current. + if repository.includes_tools or repository.has_repository_dependencies: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reselect_tool_panel_section', + **kwd ) ) + else: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reinstall_repository', + **kwd ) ) else: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='reinstall_repository', - **kwd ) ) + # The uninstalled repository has updates available in the tool shed. + updated_repo_info_dict = self.get_updated_repository_information( trans=trans, + repository_id=trans.security.encode_id( repository.id ), + repository_name=repository.name, + repository_owner=repository.owner, + changeset_revision=current_changeset_revision ) + has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) + includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) + if has_repository_dependencies or includes_tool_dependencies: + json_repo_info_dict = json.to_json_string( updated_repo_info_dict ) + encoded_repo_info_dict = encoding_util.tool_shed_encode( json_repo_info_dict ) + kwd[ 'latest_changeset_revision' ] = current_changeset_revision + kwd[ 'latest_ctx_rev' ] = current_ctx_rev + kwd[ 'updated_repo_info_dict' ] = encoded_repo_info_dict + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reselect_tool_panel_section', + **kwd ) ) + else: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='reinstall_repository', + **kwd ) ) else: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='activate_repository', @@ -581,6 +601,45 @@ else: text = '' return text + @web.expose + @web.require_admin + def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): + """ + Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, + owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need + it so that we can derive the tool shed from which it was installed. + """ + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + url = suc.url_join( tool_shed_url, + 'repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository_name, repository_owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + raw_text = response.read() + response.close() + if len( raw_text ) > 2: + encoded_text = json.from_json_string( raw_text ) + text = encoding_util.tool_shed_decode( encoded_text ) + else: + text = '' + return text + @web.expose + @web.require_admin + def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): + """ + Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an + uninstalled tool shed repository. + """ + repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + url = suc.url_join( tool_shed_url, + 'repository/get_updated_repository_information?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository_name, repository_owner, changeset_revision ) ) + response = urllib2.urlopen( url ) + raw_text = response.read() + response.close() + repo_information_dict = json.from_json_string( raw_text ) + return repo_information_dict def get_versions_of_tool( self, app, guid ): tool_version = shed_util.get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) @@ -1149,7 +1208,7 @@ status = kwd.get( 'status', 'done' ) tool_shed_url = kwd[ 'tool_shed_url' ] # Handle repository dependencies. - includes_repository_dependencies = util.string_as_bool( kwd.get( 'includes_repository_dependencies', False ) ) + has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) @@ -1173,12 +1232,12 @@ response.close() repo_information_dict = json.from_json_string( raw_text ) includes_tools = util.string_as_bool( repo_information_dict.get( 'includes_tools', False ) ) - includes_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_repository_dependencies', False ) ) + has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) ) includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] - if ( not includes_tools and not includes_repository_dependencies ) or \ - ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): + if ( not includes_tools and not has_repository_dependencies ) or \ + ( ( includes_tools or has_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tools: shed_tool_conf = kwd[ 'shed_tool_conf' ] @@ -1241,7 +1300,7 @@ for tsr in created_or_updated_tool_shed_repositories: tool_panel_section_keys.append( tool_panel_section_key ) new_kwd = dict( includes_tools=includes_tools, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, install_repository_dependencies=install_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies=install_tool_dependencies, @@ -1331,7 +1390,7 @@ includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies_check_box=install_tool_dependencies_check_box, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, new_tool_panel_section=new_tool_panel_section, containers_dict=containers_dict, @@ -1364,7 +1423,7 @@ tool_panel_section_key = None tool_panel_section_keys = [] metadata = tool_shed_repository.metadata - # Keep track of tool dependencies define dfor the current repository or those defined for any of it's repository dependencies. + # Keep track of tool dependencies defined for the current repository or those defined for any of it's repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools: # Handle the selected tool panel location for loading tools included in the tool shed repository. @@ -1381,7 +1440,7 @@ tool_shed_repository.installed_changeset_revision, tool_shed_repository.ctx_rev, repository_clone_url, - tool_shed_repository.metadata, + metadata, trans.model.ToolShedRepository.installation_status.NEW, tool_shed_repository.installed_changeset_revision, tool_shed_repository.owner, @@ -1402,6 +1461,10 @@ changeset_revision=tool_shed_repository.changeset_revision ) else: repository_dependencies = None + if metadata: + tool_dependencies = metadata.get( 'tool_dependencies', None ) + else: + tool_dependencies = None repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.changeset_revision, @@ -1410,15 +1473,15 @@ repository_name=tool_shed_repository.name, repository=None, repository_metadata=None, - metadata=metadata, + tool_dependencies=tool_dependencies, repository_dependencies=repository_dependencies ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ - shed_util.create_repository_dependency_objects( trans, - tool_path, - tool_shed_url, - repo_info_dicts, + shed_util.create_repository_dependency_objects( trans=trans, + tool_path=tool_path, + tool_shed_url=tool_shed_url, + repo_info_dicts=repo_info_dicts, reinstalling=True, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, @@ -1472,40 +1535,62 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): - """Select or change the tool panel section to contain the tools included in the tool shed repositories being reinstalled.""" + """ + Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates + available for the repository in the tool shed, the tool_dependencies and repository_dependencies associated with the updated changeset revision + will have been retrieved from the tool shed and passed in the received kwd. In this case, the stored tool shed repository metqdata from the + Galaxy database will not be used since it is outdated. + """ message = '' - repository_id = kwd[ 'id' ] + repository_id = kwd.get( 'id', None ) + latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) + latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - ctx_rev = suc.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app ) - repository_dependencies = self.get_repository_dependencies( trans=trans, - repository_id=repository_id, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.changeset_revision ) - if repository_dependencies: - includes_repository_dependencies = True + if latest_changeset_revision and latest_ctx_rev: + # There are updates available in the tool shed for the repository, so use the receieved dependency information which was retrieved from + # the tool shed. + encoded_updated_repo_info_dict = kwd.get( 'updated_repo_info_dict', None ) + updated_repo_info_dict = encoding_util.tool_shed_decode( encoded_updated_repo_info_dict ) + readme_files_dict = updated_repo_info_dict.get( 'readme_files_dict', None ) + includes_tools = updated_repo_info_dict.get( 'includes_tools', False ) + has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) + includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) + repo_info_dict = updated_repo_info_dict[ 'repo_info_dict' ] else: - includes_repository_dependencies = False - includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies - repo_info_dict = suc.create_repo_info_dict( trans=trans, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - repository=None, - repository_metadata=None, - metadata=metadata, - repository_dependencies=repository_dependencies ) - if includes_repository_dependencies: - # Discover all repository dependencies and retrieve information for installing them. - required_repo_info_dicts = shed_util.get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) + # There are no updates available from the tool shed for the repository, so use it's locally stored metadata. + if metadata: + readme_files_dict = suc.build_readme_files_dict( metadata ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + else: + readme_files_dict = None + tool_dependencies = None + includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies + repository_dependencies = self.get_repository_dependencies( trans=trans, + repository_id=repository_id, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + changeset_revision=tool_shed_repository.changeset_revision ) + repo_info_dict = suc.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=tool_shed_repository.ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) + repository_name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ + shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + if installed_repository_dependencies or missing_repository_dependencies: + has_repository_dependencies = True else: - required_repo_info_dicts = None + has_repository_dependencies = False # Get the location in the tool panel in which the tool was originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -1533,14 +1618,14 @@ message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' - # Populate the containers_dict from the metadata for the tool shed repository we're reinstalling, but make sure to include tool dependencies defined for - # all of the repository's repository dependencies. - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - repository=tool_shed_repository, - reinstalling=True, - required_repo_info_dicts=required_repo_info_dicts ) + containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) @@ -1561,7 +1646,7 @@ no_changes_check_box=no_changes_check_box, original_section_name=original_section_name, includes_tool_dependencies=includes_tool_dependencies, - includes_repository_dependencies=includes_repository_dependencies, + has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, install_tool_dependencies_check_box=install_tool_dependencies_check_box, containers_dict=containers_dict, diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -33,7 +33,7 @@ ${render_readme_section( containers_dict )} <div style="clear: both"></div> %endif - %if includes_repository_dependencies or includes_tool_dependencies: + %if has_repository_dependencies or includes_tool_dependencies: <div class="form-row"><table class="colored" width="100%"><th bgcolor="#EBD9B2">Confirm dependency installation</th> diff -r f199b236ceb08e9588351223b6277861e9f87325 -r e6302ee56ed03e4cc9f95ff1720b08721ced5600 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -17,10 +17,10 @@ <% # Handle the case where an uninstalled repository encountered errors during the process of being reinstalled. In - # this case, the repository metadata is an empty dictionary, but one or both of includes_repository_dependencies + # this case, the repository metadata is an empty dictionary, but one or both of has_repository_dependencies # and includes_tool_dependencies may be True. If either of these are True but we have no metadata, we cannot install # repository dependencies on this pass. - if includes_repository_dependencies: + if has_repository_dependencies: repository_dependencies = containers_dict[ 'repository_dependencies' ] missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ] if repository_dependencies or missing_repository_dependencies: 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 January 2013