From 1d17a29c7947993ae7cca998eff25c1ff998ebdb Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 14 Nov 2016 21:12:14 +0000 Subject: [PATCH] Fixes for pycodestyle 2.2.0 --- .ci/flake8_lint_include_list.txt | 1 + client/galaxy/style/source_material/circle.py | 1 + contrib/galaxy_config_merger.py | 1 + contrib/nagios/check_galaxy.py | 3 ++- cron/add_manual_builds.py | 1 + cron/build_chrom_db.py | 1 + cron/parse_builds.py | 1 + cron/parse_builds_3_sites.py | 1 + doc/parse_gx_xsd.py | 1 + doc/patch.py | 1 + lib/galaxy/auth/__init__.py | 1 + lib/galaxy/auth/providers/ldap_ad.py | 1 + lib/galaxy/auth/providers/pam_auth.py | 1 + lib/galaxy/datatypes/assembly.py | 1 + lib/galaxy/datatypes/binary.py | 26 +++++++++++++++++++ .../datatypes/constructive_solid_geometry.py | 2 ++ .../converters/bed_to_gff_converter.py | 1 + .../bedgraph_to_array_tree_converter.py | 2 +- lib/galaxy/datatypes/converters/bgzip.py | 1 + .../datatypes/converters/fasta_to_len.py | 3 ++- .../fastqsolexa_to_fasta_converter.py | 3 ++- .../fastqsolexa_to_qual_converter.py | 1 + .../converters/gff_to_bed_converter.py | 1 + .../gff_to_interval_index_converter.py | 1 + .../converters/interval_to_bed_converter.py | 1 + .../interval_to_bedstrict_converter.py | 1 + .../converters/interval_to_coverage.py | 1 + .../datatypes/converters/interval_to_fli.py | 1 + .../interval_to_interval_index_converter.py | 3 ++- .../converters/interval_to_tabix_converter.py | 1 + .../picard_interval_list_to_bed6_converter.py | 1 + .../pileup_to_interval_index_converter.py | 3 ++- .../ref_to_seq_taxonomy_converter.py | 1 + lib/galaxy/datatypes/converters/sam_to_bam.py | 1 + .../datatypes/converters/tabular_to_dbnsfp.py | 1 + .../vcf_to_interval_index_converter.py | 1 + .../datatypes/converters/vcf_to_vcf_bgzip.py | 1 + .../wiggle_to_array_tree_converter.py | 1 + .../converters/wiggle_to_simple_converter.py | 1 + .../display_applications/parameters.py | 1 + lib/galaxy/datatypes/images.py | 1 + lib/galaxy/datatypes/msa.py | 1 + lib/galaxy/datatypes/neo4j.py | 1 + lib/galaxy/datatypes/proteomics.py | 2 ++ lib/galaxy/datatypes/sniff.py | 2 ++ lib/galaxy/datatypes/triples.py | 1 + lib/galaxy/external_services/actions.py | 1 + lib/galaxy/external_services/parameters.py | 1 + .../result_handlers/basic.py | 1 + lib/galaxy/external_services/service.py | 1 + lib/galaxy/forms/forms.py | 1 + lib/galaxy/jobs/command_factory.py | 1 + lib/galaxy/jobs/dynamic_tool_destination.py | 1 + lib/galaxy/managers/collections_util.py | 1 + lib/galaxy/model/mapping.py | 5 ++++ lib/galaxy/model/metadata.py | 2 ++ .../versions/0007_sharing_histories.py | 1 + .../migrate/versions/0008_galaxy_forms.py | 1 + .../0010_hda_display_at_authz_table.py | 1 + .../versions/0011_v0010_mysql_index_fix.py | 1 + .../migrate/versions/0012_user_address.py | 1 + ...0013_change_lib_item_templates_to_forms.py | 1 + .../versions/0016_v0015_mysql_index_fix.py | 1 + .../0018_ordered_tags_and_page_tags.py | 1 + .../versions/0020_library_upload_job.py | 1 + .../migrate/versions/0026_cloud_tables.py | 1 + .../versions/0050_drop_cloud_tables.py | 1 + .../versions/0052_sample_dataset_table.py | 1 + .../versions/0091_add_tool_version_tables.py | 1 + lib/galaxy/queue_worker.py | 1 + lib/galaxy/sample_tracking/data_transfer.py | 1 + lib/galaxy/sample_tracking/request_types.py | 1 + lib/galaxy/sample_tracking/sample.py | 1 + lib/galaxy/security/passwords.py | 2 +- lib/galaxy/tools/execute.py | 1 + lib/galaxy/tools/imp_exp/export_history.py | 1 + lib/galaxy/tools/parameters/basic.py | 1 + .../tools/parameters/dataset_matcher.py | 1 + lib/galaxy/tools/parameters/output_collect.py | 1 + lib/galaxy/tools/parameters/validation.py | 1 + lib/galaxy/tools/util/galaxyops/__init__.py | 1 + lib/galaxy/util/pastescript/loadwsgi.py | 12 ++++++++- lib/galaxy/util/pastescript/serve.py | 2 +- lib/galaxy/web/framework/base.py | 16 +++++++----- lib/galaxy/web/framework/middleware/error.py | 3 +++ .../web/framework/middleware/translogger.py | 3 ++- lib/galaxy/web/framework/openid_manager.py | 2 ++ .../versions/0013_add_review_tables.py | 1 + lib/galaxy/workflow/extract.py | 1 + lib/galaxy/workflow/run.py | 2 ++ lib/galaxy/workflow/schedulers/core.py | 1 + lib/galaxy_utils/sequence/fastq.py | 1 + lib/galaxy_utils/sequence/vcf.py | 1 + lib/mimeparse.py | 1 + lib/tool_shed/util/workflow_util.py | 1 + scripts/api/data_manager_example_execute.py | 1 + scripts/api/example_watch_folder.py | 1 + ...ows_from_installed_tool_shed_repository.py | 1 + scripts/api/install_tool_shed_repositories.py | 1 + scripts/api/load_data_with_metadata.py | 1 + scripts/api/repair_tool_shed_repository.py | 1 + ...eset_metadata_on_installed_repositories.py | 1 + scripts/api/search.py | 1 + scripts/api/sequencer_configuration_create.py | 1 + scripts/api/workflow_execute.py | 1 + scripts/api/workflow_execute_parameters.py | 1 + scripts/api/workflow_import.py | 1 + scripts/auth/pam_auth_helper.py | 1 + scripts/build_toolbox.py | 1 + scripts/build_universe_config.py | 1 + scripts/check_galaxy.py | 4 +-- scripts/check_python.py | 1 + scripts/cleanup_datasets/cleanup_datasets.py | 1 + scripts/cleanup_datasets/pgcleanup.py | 1 + .../rename_purged_datasets.py | 1 + .../cleanup_datasets/update_dataset_size.py | 1 + scripts/cleanup_datasets/update_metadata.py | 1 + scripts/communication/communication_server.py | 2 +- scripts/create_db.py | 1 + scripts/data_libraries/build_lucene_index.py | 1 + scripts/data_libraries/build_whoosh_index.py | 1 + scripts/drmaa_external_killer.py | 1 + scripts/drmaa_external_runner.py | 1 + scripts/external_chown_script.py | 1 + scripts/extract_dataset_part.py | 1 + scripts/extract_toolbox_sections.py | 1 + scripts/functional_tests.py | 1 + scripts/grt.py | 1 + scripts/loc_files/create_all_fasta_loc.py | 1 + scripts/manage_db.py | 1 + scripts/microbes/BeautifulSoup.py | 1 + scripts/microbes/create_bacteria_loc_file.py | 1 + scripts/microbes/create_bacteria_table.py | 1 + scripts/microbes/get_builds_lengths.py | 1 + scripts/microbes/harvest_bacteria.py | 1 + scripts/others/incorrect_gops_jobs.py | 1 + scripts/others/incorrect_gops_join_jobs.py | 1 + scripts/set_dataset_sizes.py | 1 + scripts/set_user_disk_usage.py | 1 + scripts/slideshow/build_slideshow.py | 1 + scripts/summarize_timings.py | 1 + scripts/sync_reports_config.py | 1 + .../api/add_repository_registry_entry.py | 1 + scripts/tool_shed/api/create_categories.py | 1 + scripts/tool_shed/api/create_users.py | 1 + scripts/tool_shed/api/export.py | 1 + .../api/get_filtered_repository_revisions.py | 1 + scripts/tool_shed/api/import_capsule.py | 1 + .../api/remove_repository_registry_entry.py | 1 + .../api/reset_metadata_on_repositories.py | 1 + .../bootstrap_tool_shed/bootstrap_util.py | 1 + .../create_user_with_api_key.py | 1 + scripts/tool_shed/build_ts_whoosh_index.py | 1 + scripts/tool_shed/check_download_urls.py | 1 + ...mpty_tool_dependency_installation_paths.py | 1 + ...mpty_tool_dependency_installation_paths.py | 1 + .../clean_up_tool_dependency_directory.py | 1 + ...deprecate_repositories_without_metadata.py | 1 + .../migrate_tools_to_repositories.py | 1 + ...ol_dependency_installation_dir_contents.py | 1 + scripts/tools/maf/check_loc_file.py | 1 + scripts/tools/re_escape_output.py | 1 + scripts/transfer.py | 1 + scripts/update_shed_config_path.py | 1 + test/api/test_workflows.py | 1 + test/api/workflows_format_2/main.py | 1 + test/base/api_asserts.py | 1 + test/base/driver_util.py | 2 ++ .../dataproviders/test_line_dataproviders.py | 1 + .../test_dynamic_tool_destination.py | 1 + test/unit/managers/test_DatasetManager.py | 1 + test/unit/managers/test_HDAManager.py | 1 + test/unit/managers/test_HDCAManager.py | 1 + .../managers/test_HistoryContentsManager.py | 2 +- test/unit/managers/test_HistoryManager.py | 1 + .../plugins/test_VisualizationsRegistry.py | 10 +++---- test/unit/workflows/test_modules.py | 1 + tools/data_source/data_source.py | 1 + tools/data_source/genbank.py | 1 + tools/data_source/upload.py | 1 + tools/evolution/add_scores.py | 1 + tools/extract/extract_genomic_dna.py | 1 + tools/extract/liftOver_wrapper.py | 1 + tools/filters/axt_to_fasta.py | 1 + tools/filters/bed_to_gff_converter.py | 1 + tools/filters/catWrapper.py | 1 + tools/filters/convert_characters.py | 1 + tools/filters/gff/extract_GFF_Features.py | 1 + tools/filters/gff/gff_filter_by_attribute.py | 3 ++- .../gff/gff_filter_by_feature_count.py | 1 + .../gtf_filter_by_attribute_values_list.py | 1 + tools/filters/gff_to_bed_converter.py | 1 + tools/filters/grep.py | 1 + tools/filters/gtf_to_bedgraph_converter.py | 1 + tools/filters/join.py | 1 + tools/filters/joinWrapper.py | 1 + tools/filters/lav_to_bed.py | 1 + tools/filters/mergeCols.py | 1 + tools/filters/random_lines_two_pass.py | 1 + tools/filters/randomlines.py | 1 + tools/filters/secure_hash_message_digest.py | 1 + tools/filters/sorter.py | 1 + tools/filters/trimmer.py | 1 + tools/filters/ucsc_gene_bed_to_exon_bed.py | 1 + tools/filters/ucsc_gene_bed_to_intron_bed.py | 1 + tools/filters/ucsc_gene_table_to_intervals.py | 1 + tools/filters/uniq.py | 1 + tools/filters/wiggle_to_simple.py | 1 + tools/genomespace/genomespace_exporter.py | 1 + tools/genomespace/genomespace_file_browser.py | 1 + tools/genomespace/genomespace_importer.py | 1 + tools/maf/interval2maf.py | 1 + tools/maf/interval_maf_to_merged_fasta.py | 1 + tools/maf/maf_by_block_number.py | 1 + tools/maf/maf_filter.py | 1 + tools/maf/maf_limit_size.py | 1 + tools/maf/maf_limit_to_species.py | 1 + tools/maf/maf_reverse_complement.py | 1 + tools/maf/maf_split_by_species.py | 1 + tools/maf/maf_stats.py | 1 + tools/maf/maf_thread_for_species.py | 1 + tools/maf/maf_to_bed.py | 1 + tools/maf/maf_to_fasta_multiple_sets.py | 1 + tools/maf/maf_to_interval.py | 1 + tools/maf/vcf_to_maf_customtrack.py | 1 + tools/meme/fimo_wrapper.py | 1 + tools/metag_tools/blat_wrapper.py | 1 + .../next_gen_conversion/fastq_conversions.py | 1 + tools/next_gen_conversion/fastq_gen_conv.py | 1 + tools/next_gen_conversion/solid2fastq.py | 1 + tools/next_gen_conversion/solid_to_fastq.py | 1 + tools/ngs_simulation/ngs_simulation.py | 1 + tools/phenotype_association/pagetag.py | 1 + tools/phenotype_association/senatag.py | 1 + tools/solid_tools/maq_cs_wrapper.py | 1 + tools/solid_tools/solid_qual_stats.py | 1 + tools/sr_assembly/velveth_wrapper.py | 1 + tools/sr_mapping/bfast_wrapper.py | 1 + tools/sr_mapping/srma_wrapper.py | 1 + tools/stats/aggregate_scores_in_intervals.py | 1 + tools/stats/filtering.py | 1 + tools/stats/grouping.py | 1 + tools/stats/gsummary.py | 1 + 243 files changed, 312 insertions(+), 26 deletions(-) diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt index e10870983a9..42434fd2045 100644 --- a/.ci/flake8_lint_include_list.txt +++ b/.ci/flake8_lint_include_list.txt @@ -320,6 +320,7 @@ lib/galaxy/web/base/controllers/__init__.py lib/galaxy/web/base/__init__.py lib/galaxy/web/buildapp.py lib/galaxy/web/formatting.py +lib/galaxy/web/framework/base.py lib/galaxy/web/framework/decorators.py lib/galaxy/web/framework/helpers/grids.py lib/galaxy/web/framework/__init__.py diff --git a/client/galaxy/style/source_material/circle.py b/client/galaxy/style/source_material/circle.py index f1f014b9565..6f6e977e200 100755 --- a/client/galaxy/style/source_material/circle.py +++ b/client/galaxy/style/source_material/circle.py @@ -27,6 +27,7 @@ def parse_css_color( color ): raise Exception( "Color should be 3 hex numbers" ) return r / 256, g / 256, b / 256 + size = int( sys.argv[1] ) surface = cairo.ImageSurface( cairo.FORMAT_ARGB32, size, size ) diff --git a/contrib/galaxy_config_merger.py b/contrib/galaxy_config_merger.py index 5e2c14938ee..38b5d3cc6aa 100644 --- a/contrib/galaxy_config_merger.py +++ b/contrib/galaxy_config_merger.py @@ -87,5 +87,6 @@ def main(): logging.info("read Galaxy galaxy.ini.sample for detailed information.") + if __name__ == '__main__': main() diff --git a/contrib/nagios/check_galaxy.py b/contrib/nagios/check_galaxy.py index 75abb60fcd0..dd45f986171 100755 --- a/contrib/nagios/check_galaxy.py +++ b/contrib/nagios/check_galaxy.py @@ -61,6 +61,7 @@ tools = { def usage(): sys.exit("usage: check_galaxy.py ") + try: opts, args = getopt.getopt( sys.argv[1:], 'n' ) except getopt.GetoptError as e: @@ -347,7 +348,7 @@ def dprint(str): if debug: print(str) -# do stuff here + if __name__ == "__main__": dprint("checking %s" % server) diff --git a/cron/add_manual_builds.py b/cron/add_manual_builds.py index 4b8a311855a..263a2fc284d 100644 --- a/cron/add_manual_builds.py +++ b/cron/add_manual_builds.py @@ -43,6 +43,7 @@ def add_manual_builds(input_file, build_file, chr_dir): continue build_file_out.close() + if __name__ == "__main__": if len(sys.argv) < 4: sys.exit("USAGE: python add_manual_builds.py input_file builds.txt chrom_length_dir") diff --git a/cron/build_chrom_db.py b/cron/build_chrom_db.py index 4cb7f34c895..ce472d257ee 100644 --- a/cron/build_chrom_db.py +++ b/cron/build_chrom_db.py @@ -47,6 +47,7 @@ def getchrominfo(url, db): else: raise Exception("Problem parsing line '%s'" % line) + if __name__ == "__main__": if len(sys.argv) == 1: sys.exit("Path to place chromInfo tables must be specified.") diff --git a/cron/parse_builds.py b/cron/parse_builds.py index 06566e55cb0..c30197184f8 100644 --- a/cron/parse_builds.py +++ b/cron/parse_builds.py @@ -44,6 +44,7 @@ def getbuilds(url): description = " ".join(fields) yield [build, description] + if __name__ == "__main__": if len(sys.argv) > 1: URL = sys.argv[1] diff --git a/cron/parse_builds_3_sites.py b/cron/parse_builds_3_sites.py index 2a9e41533c3..b22cd449bf9 100644 --- a/cron/parse_builds_3_sites.py +++ b/cron/parse_builds_3_sites.py @@ -41,6 +41,7 @@ def main(): builds = list(build_dict.keys()) yield [names[i], trackurl, builds] + if __name__ == "__main__": for site in main(): print(site[0] + "\t" + site[1] + "\t" + ",".join(site[2])) diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py index 0ff1b034cbe..cf72dfdaf98 100644 --- a/doc/parse_gx_xsd.py +++ b/doc/parse_gx_xsd.py @@ -166,5 +166,6 @@ def _doc_or_none(tag): else: return doc_el.text + if __name__ == '__main__': main() diff --git a/doc/patch.py b/doc/patch.py index 60a030c3f6a..efcfaf2c343 100755 --- a/doc/patch.py +++ b/doc/patch.py @@ -58,6 +58,7 @@ class NullHandler(logging.Handler): def createLock(self): self.lock = None + logger.addHandler(NullHandler()) # ----------------------------------------------- diff --git a/lib/galaxy/auth/__init__.py b/lib/galaxy/auth/__init__.py index 67a1db2a810..387a952e5ff 100644 --- a/lib/galaxy/auth/__init__.py +++ b/lib/galaxy/auth/__init__.py @@ -156,6 +156,7 @@ class AuthManager(object): log.exception( "Active Authenticators Failure" ) raise + Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options']) diff --git a/lib/galaxy/auth/providers/ldap_ad.py b/lib/galaxy/auth/providers/ldap_ad.py index 2e253a65af1..69ffa9cab79 100644 --- a/lib/galaxy/auth/providers/ldap_ad.py +++ b/lib/galaxy/auth/providers/ldap_ad.py @@ -198,4 +198,5 @@ class ActiveDirectory(LDAP): logic in the future. """ plugin_type = 'activedirectory' + __all__ = ('LDAP', 'ActiveDirectory') diff --git a/lib/galaxy/auth/providers/pam_auth.py b/lib/galaxy/auth/providers/pam_auth.py index 40bc3bcf192..8763a181933 100644 --- a/lib/galaxy/auth/providers/pam_auth.py +++ b/lib/galaxy/auth/providers/pam_auth.py @@ -148,4 +148,5 @@ class PAM(AuthProvider): def authenticate_user(self, user, password, options): return self.authenticate(user.email, user.username, password, options)[0] + __all__ = ('PAM', ) diff --git a/lib/galaxy/datatypes/assembly.py b/lib/galaxy/datatypes/assembly.py index 1b9256dfefa..015d5f8ba1c 100644 --- a/lib/galaxy/datatypes/assembly.py +++ b/lib/galaxy/datatypes/assembly.py @@ -229,6 +229,7 @@ class Velvet( Html ): Html.set_meta( self, dataset, **kwd ) self.regenerate_primary_file(dataset) + if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__]) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 187d6192bdb..87882101b50 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -103,6 +103,7 @@ class Ab1( Binary ): except: return "Binary ab1 sequence file (%s)" % ( nice_size( dataset.get_size() ) ) + Binary.register_unsniffable_binary_ext("ab1") @@ -121,6 +122,7 @@ class Idat( Binary ): except: return False + Binary.register_sniffable_binary_format("idat", "idat", Idat) @@ -152,6 +154,7 @@ class Cel( Binary ): except: return False + Binary.register_sniffable_binary_format("cel", "cel", Cel) @@ -177,6 +180,7 @@ class CompressedArchive( Binary ): except: return "Compressed binary file (%s)" % ( nice_size( dataset.get_size() ) ) + Binary.register_unsniffable_binary_ext("compressed_archive") @@ -211,6 +215,7 @@ class GenericAsn1Binary( Binary ): edam_format = "format_1966" edam_data = "data_0849" + Binary.register_unsniffable_binary_ext("asn1-binary") @@ -530,6 +535,7 @@ class Bam( Binary ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.SamtoolsDataProvider( dataset_source, **settings ) + Binary.register_sniffable_binary_format("bam", "bam", Bam) @@ -601,6 +607,7 @@ class CRAM( Binary ): except: return False + Binary.register_sniffable_binary_format('cram', 'cram', CRAM) @@ -651,6 +658,7 @@ class Bcf( Binary): os.remove( dataset_symlink ) dataset.metadata.bcf_index = index_file + Binary.register_sniffable_binary_format("bcf", "bcf", Bcf) @@ -697,6 +705,7 @@ class H5( Binary ): except: return "Binary HDF5 file (%s)" % ( nice_size( dataset.get_size() ) ) + Binary.register_sniffable_binary_format("h5", "h5", H5) @@ -720,6 +729,7 @@ class Scf( Binary ): except: return "Binary scf sequence file (%s)" % ( nice_size( dataset.get_size() ) ) + Binary.register_unsniffable_binary_ext("scf") @@ -754,6 +764,7 @@ class Sff( Binary ): except: return "Binary sff file (%s)" % ( nice_size( dataset.get_size() ) ) + Binary.register_sniffable_binary_format("sff", "sff", Sff) @@ -797,6 +808,7 @@ class BigWig(Binary): except: return "Binary UCSC %s file (%s)" % ( self._name, nice_size( dataset.get_size() ) ) + Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig) @@ -811,6 +823,7 @@ class BigBed(BigWig): self._magic = 0x8789F2EB self._name = "BigBed" + Binary.register_sniffable_binary_format("bigbed", "bigbed", BigBed) @@ -845,6 +858,7 @@ class TwoBit (Binary): except: return "Binary TwoBit format nucleotide file (%s)" % (nice_size(dataset.get_size())) + Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit) @@ -1069,6 +1083,7 @@ class IdpDB( SQlite ): except: return "IDPickerDB SQLite file (%s)" % ( nice_size( dataset.get_size() ) ) + Binary.register_sniffable_binary_format( "gemini.sqlite", "gemini.sqlite", GeminiSQLite ) Binary.register_sniffable_binary_format( "idpdb", "idpdb", IdpDB ) Binary.register_sniffable_binary_format( "mz.sqlite", "mz.sqlite", MzSQlite ) @@ -1092,6 +1107,7 @@ class Xlsx(Binary): except: return False + Binary.register_sniffable_binary_format("xlsx", "xlsx", Xlsx) @@ -1126,6 +1142,7 @@ class Sra( Binary ): except: return 'Binary sra file (%s)' % (nice_size(dataset.get_size())) + Binary.register_sniffable_binary_format('sra', 'sra', Sra) @@ -1146,6 +1163,7 @@ class RData( Binary ): except: return False + Binary.register_sniffable_binary_format('RData', 'RData', RData) @@ -1189,6 +1207,7 @@ class OxliCountGraph(OxliBinary): def sniff(self, filename): return OxliBinary._sniff(filename, b"01") + Binary.register_sniffable_binary_format("oxli.countgraph", "oxlicg", OxliCountGraph) @@ -1216,6 +1235,7 @@ class OxliNodeGraph(OxliBinary): def sniff(self, filename): return OxliBinary._sniff(filename, b"02") + Binary.register_sniffable_binary_format("oxli.nodegraph", "oxling", OxliNodeGraph) @@ -1244,6 +1264,7 @@ class OxliTagSet(OxliBinary): def sniff(self, filename): return OxliBinary._sniff(filename, b"03") + Binary.register_sniffable_binary_format("oxli.tagset", "oxlits", OxliTagSet) @@ -1266,6 +1287,7 @@ class OxliStopTags(OxliBinary): def sniff(self, filename): return OxliBinary._sniff(filename, b"04") + Binary.register_sniffable_binary_format("oxli.stoptags", "oxlist", OxliStopTags) @@ -1294,6 +1316,7 @@ class OxliSubset(OxliBinary): def sniff(self, filename): return OxliBinary._sniff(filename, b"05") + Binary.register_sniffable_binary_format("oxli.subset", "oxliss", OxliSubset) @@ -1322,6 +1345,7 @@ class OxliGraphLabels(OxliBinary): def sniff(self, filename): return OxliBinary._sniff(filename, b"06") + Binary.register_sniffable_binary_format("oxli.graphlabels", "oxligl", OxliGraphLabels) @@ -1376,6 +1400,7 @@ class SearchGuiArchive ( CompressedArchive ): except: return "SearchGUI Archive, version %s" % ( dataset.metadata.searchgui_version or 'unknown' ) + Binary.register_sniffable_binary_format("searchgui_archive", "searchgui_archive", SearchGuiArchive) @@ -1409,4 +1434,5 @@ class NetCDF( Binary ): except: return False + Binary.register_sniffable_binary_format("netcdf", "netcdf", NetCDF) diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py index 43f1747d2e7..83b540399e2 100644 --- a/lib/galaxy/datatypes/constructive_solid_geometry.py +++ b/lib/galaxy/datatypes/constructive_solid_geometry.py @@ -130,6 +130,7 @@ class PlyBinary(Ply, Binary): def __init__(self, **kwd): Binary.__init__(self, **kwd) + Binary.register_sniffable_binary_format("plybinary", "plybinary", PlyBinary) @@ -456,6 +457,7 @@ class VtkBinary(Vtk, Binary): def __init__(self, **kwd): Binary.__init__(self, **kwd) + Binary.register_sniffable_binary_format("vtkbinary", "vtkbinary", VtkBinary) diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.py b/lib/galaxy/datatypes/converters/bed_to_gff_converter.py index b1d7df54732..82171549f04 100644 --- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.py +++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.py @@ -73,5 +73,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py index 5180863f127..3fedd8572e8 100644 --- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py +++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py @@ -38,7 +38,6 @@ class BedGraphReader: def main(): - input_fname = sys.argv[1] out_fname = sys.argv[2] @@ -52,5 +51,6 @@ def main(): FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) ) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/bgzip.py b/lib/galaxy/datatypes/converters/bgzip.py index 5d2547019f8..3cd6062c990 100644 --- a/lib/galaxy/datatypes/converters/bgzip.py +++ b/lib/galaxy/datatypes/converters/bgzip.py @@ -46,5 +46,6 @@ def main(): ctabix.tabix_compress(tmpfile.name, output_fname, force=True) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.py b/lib/galaxy/datatypes/converters/fasta_to_len.py index bc814d4f91b..9d8fbf4869f 100644 --- a/lib/galaxy/datatypes/converters/fasta_to_len.py +++ b/lib/galaxy/datatypes/converters/fasta_to_len.py @@ -4,8 +4,8 @@ Input: fasta, int Output: tabular Return titles with lengths of corresponding seq """ - import sys + assert sys.version_info[:2] >= ( 2, 4 ) @@ -48,5 +48,6 @@ def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) out.close() + if __name__ == "__main__" : compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True ) diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py index 067993fb985..988fcb57cfa 100644 --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py @@ -13,8 +13,8 @@ the order should be: Usage: %python fastqsolexa_to_fasta_converter.py """ - import sys + assert sys.version_info[:2] >= ( 2, 4 ) @@ -50,5 +50,6 @@ def __main__(): outfile.close() + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py index 53ff8cc05a6..2ac16725685 100644 --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py @@ -93,5 +93,6 @@ def __main__(): outfile_score.close() + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/gff_to_bed_converter.py b/lib/galaxy/datatypes/converters/gff_to_bed_converter.py index ee82cde9601..788931866a3 100644 --- a/lib/galaxy/datatypes/converters/gff_to_bed_converter.py +++ b/lib/galaxy/datatypes/converters/gff_to_bed_converter.py @@ -42,5 +42,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py index eaca2e6240d..c6b081b5de6 100644 --- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py @@ -36,5 +36,6 @@ def main(): index.write( open(out_fname, "w") ) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py index 67b57fcde9e..36fec42571b 100644 --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py @@ -61,5 +61,6 @@ def __main__(): if skipped_lines > 0: print("Skipped %d blank or invalid lines starting with line # %d." % ( skipped_lines, first_skipped_line )) + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py index d4bf8ca3b47..8c34e384b43 100644 --- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py @@ -153,5 +153,6 @@ def __main__(): if skipped_lines > 0: print("Skipped %d blank or invalid lines starting with line # %d." % ( skipped_lines, first_skipped_line )) + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.py b/lib/galaxy/datatypes/converters/interval_to_coverage.py index 47882f7be6a..e58b3ec764b 100644 --- a/lib/galaxy/datatypes/converters/interval_to_coverage.py +++ b/lib/galaxy/datatypes/converters/interval_to_coverage.py @@ -120,6 +120,7 @@ class CoverageWriter( object ): self.out_stream.flush() self.out_stream.close() + if __name__ == "__main__": options, args = doc_optparse.parse( __doc__ ) try: diff --git a/lib/galaxy/datatypes/converters/interval_to_fli.py b/lib/galaxy/datatypes/converters/interval_to_fli.py index 94d94601583..467fb90228a 100644 --- a/lib/galaxy/datatypes/converters/interval_to_fli.py +++ b/lib/galaxy/datatypes/converters/interval_to_fli.py @@ -102,5 +102,6 @@ def main(): out.write( entry.ljust( max_len ) + '\n' ) out.close() + if __name__ == '__main__': main() diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py index 901816d912c..acdd493d030 100644 --- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py @@ -8,10 +8,10 @@ usage: %prog in_file out_file -s, --start-col: start column, default=2 -e, --end-col: end column, default=3 """ - from __future__ import division import optparse + from bx.interval_index_file import Indexes @@ -46,5 +46,6 @@ def main(): index.write( open(output_fname, "w") ) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py index febca96c711..487e3e9c7aa 100644 --- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py @@ -36,5 +36,6 @@ def main(): if os.path.getsize(index_fname) == 0: sys.stderr.write("The converted tabix index file is empty, meaning the input data is invalid.") + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py index 36357cbc042..e9ebd89e8b1 100644 --- a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py +++ b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py @@ -40,5 +40,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py index 9c879dc05bb..a8f6271a1ee 100644 --- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py @@ -5,10 +5,10 @@ Convert from pileup file to interval index file. usage: %prog in_file out_file """ - from __future__ import division import optparse + from bx.interval_index_file import Indexes @@ -31,5 +31,6 @@ def main(): index.write( open(output_fname, "w") ) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py index 2f2cf67730a..55266c6e7b3 100644 --- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py +++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py @@ -23,5 +23,6 @@ def __main__(): outfile.close() + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.py b/lib/galaxy/datatypes/converters/sam_to_bam.py index ca3fecf5949..97b97c6efbb 100644 --- a/lib/galaxy/datatypes/converters/sam_to_bam.py +++ b/lib/galaxy/datatypes/converters/sam_to_bam.py @@ -71,5 +71,6 @@ def __main__(): cleanup_before_exit( tmp_dir ) + if __name__ == "__main__": __main__() diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py index 407bc6e6e5d..4e1f909bc13 100644 --- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py +++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py @@ -30,5 +30,6 @@ def main(): # Column indices are 0-based. ctabix.tabix_index(output_fname, seq_col=options.chrom_col, start_col=options.start_col, end_col=options.end_col) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py index 076cd6e2f0b..e8d76b428fb 100644 --- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py @@ -30,5 +30,6 @@ def main(): index.write( open( out_file, "w" ) ) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py index eebf5cc5278..6966ac93b2b 100644 --- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py @@ -20,5 +20,6 @@ def main(): ctabix.tabix_compress(input_fname, output_fname, force=True) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py index f5201f6c290..820ba7a1efa 100644 --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py @@ -25,5 +25,6 @@ def main(): FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) ) + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py index bd40e9c1482..b615b97c27c 100644 --- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py +++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py @@ -44,5 +44,6 @@ def main(): in_file.close() out_file.close() + if __name__ == "__main__": main() diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py index 715dc4ba79c..b771aed0278 100644 --- a/lib/galaxy/datatypes/display_applications/parameters.py +++ b/lib/galaxy/datatypes/display_applications/parameters.py @@ -152,6 +152,7 @@ class DisplayApplicationTemplateParameter( DisplayApplicationParameter ): value = value.strip() return DisplayParameterValueWrapper( value, self, other_values, dataset_hash, user_hash, trans ) + parameter_type_to_class = { DisplayApplicationDataParameter.type: DisplayApplicationDataParameter, DisplayApplicationTemplateParameter.type: DisplayApplicationTemplateParameter } diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index f3858ccc68e..eca69056962 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -152,6 +152,7 @@ class Pdf( Image ): except IndexError: return False + Binary.register_sniffable_binary_format("pdf", "pdf", Pdf) diff --git a/lib/galaxy/datatypes/msa.py b/lib/galaxy/datatypes/msa.py index 6dabf6ae125..7b31ac86adf 100644 --- a/lib/galaxy/datatypes/msa.py +++ b/lib/galaxy/datatypes/msa.py @@ -91,6 +91,7 @@ class HmmerPress( Binary ): # Profiles (remained) self.add_composite_file('model.hmm.h3p', is_binary=True) + Binary.register_unsniffable_binary_ext("hmmpress") diff --git a/lib/galaxy/datatypes/neo4j.py b/lib/galaxy/datatypes/neo4j.py index 91f8be3a9a7..f3b97b9e85a 100644 --- a/lib/galaxy/datatypes/neo4j.py +++ b/lib/galaxy/datatypes/neo4j.py @@ -128,6 +128,7 @@ class Neo4jDB(Neo4j, Data): self.add_composite_file('neostore.schemastore.db.id', is_binary=True) self.add_composite_file('neostore.transaction.db.0', is_binary=True) + if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__]) diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py index f1dd1285b8f..eb22d3be33d 100644 --- a/lib/galaxy/datatypes/proteomics.py +++ b/lib/galaxy/datatypes/proteomics.py @@ -51,6 +51,7 @@ class Wiff(Binary): rval.append('') return "\n".join(rval) + Binary.register_sniffable_binary_format("wiff", "wiff", Wiff ) @@ -293,6 +294,7 @@ class ThermoRAW(Binary): except: return "Thermo Finnigan RAW file (%s)" % (nice_size(dataset.get_size())) + Binary.register_sniffable_binary_format("thermo.raw", "raw", ThermoRAW ) diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py index bacae3210df..2c797417854 100644 --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -465,6 +465,7 @@ def handle_uploaded_dataset_file( filename, datatypes_registry, ext='auto', is_m raise InappropriateDatasetContentError( 'The uploaded file contains inappropriate HTML content.' ) return ext + AUTO_DETECT_EXTENSIONS = [ 'auto' ] # should 'data' also cause auto detect? DECOMPRESSION_FUNCTIONS = dict( gzip=gzip.GzipFile ) COMPRESSION_CHECK_FUNCTIONS = [ ( 'gzip', is_gzip ) ] @@ -477,6 +478,7 @@ for exts in COMPRESSION_DATATYPES.values(): class InappropriateDatasetContentError( Exception ): pass + if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__]) diff --git a/lib/galaxy/datatypes/triples.py b/lib/galaxy/datatypes/triples.py index b5e7775573b..af82f3a6465 100644 --- a/lib/galaxy/datatypes/triples.py +++ b/lib/galaxy/datatypes/triples.py @@ -184,4 +184,5 @@ class HDT( binary.Binary, Triples ): dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + binary.Binary.register_sniffable_binary_format('HDT', 'HDT', HDT) diff --git a/lib/galaxy/external_services/actions.py b/lib/galaxy/external_services/actions.py index c62dadf3e34..9e4ed1a14e3 100644 --- a/lib/galaxy/external_services/actions.py +++ b/lib/galaxy/external_services/actions.py @@ -175,6 +175,7 @@ class ExternalServiceTemplateAction( ExternalServiceAction ): def perform_action( self, param_dict ): return ExternalServiceValueResult( self.name, param_dict, self.template.build_template( param_dict ) ) + action_type_to_class = { ExternalServiceWebAction.type: ExternalServiceWebAction, ExternalServiceWebAPIAction.type: ExternalServiceWebAPIAction, diff --git a/lib/galaxy/external_services/parameters.py b/lib/galaxy/external_services/parameters.py index 4bb9356f1cf..78122aed2c5 100644 --- a/lib/galaxy/external_services/parameters.py +++ b/lib/galaxy/external_services/parameters.py @@ -40,4 +40,5 @@ class ExternalServiceTemplateParameter( ExternalServiceParameter ): value = value.strip() return value + parameter_type_to_class = { ExternalServiceTemplateParameter.type: ExternalServiceTemplateParameter } diff --git a/lib/galaxy/external_services/result_handlers/basic.py b/lib/galaxy/external_services/result_handlers/basic.py index 2b1669e77df..5785f2c93a5 100644 --- a/lib/galaxy/external_services/result_handlers/basic.py +++ b/lib/galaxy/external_services/result_handlers/basic.py @@ -62,6 +62,7 @@ class ExternalServiceActionJQueryGridResultHandler( ExternalServiceActionResultH rval = loads( result.content ) return trans.fill_template( '/external_services/generic_jquery_grid.mako', result=rval, param_dict=param_dict, action=self.parent ) + result_type_to_class = {} for handler_class in [ ExternalServiceActionResultHandler, ExternalServiceActionURLRedirectResultHandler, ExternalServiceActionJQueryGridResultHandler, ExternalServiceActionJSONResultHandler ]: result_type_to_class[handler_class.type] = handler_class diff --git a/lib/galaxy/external_services/service.py b/lib/galaxy/external_services/service.py index c05de42480b..05f8bc3abad 100644 --- a/lib/galaxy/external_services/service.py +++ b/lib/galaxy/external_services/service.py @@ -148,6 +148,7 @@ class ItemIsInstanceExternalServiceActionsGroupWhen( ExternalServiceActionsGroup ref = self.get_ref( param_dict ) return ref.__class__.__name__.lower() in map( lambda x: x.lower(), self.value.split( '.' ) ) # HACK! + when_type_to_class = {} for class_type in [ ValueExternalServiceActionsGroupWhen, BooleanExternalServiceActionsGroupWhen, ItemIsInstanceExternalServiceActionsGroupWhen]: when_type_to_class[ class_type.type ] = class_type diff --git a/lib/galaxy/forms/forms.py b/lib/galaxy/forms/forms.py index 2907405e5f9..2686864bf72 100644 --- a/lib/galaxy/forms/forms.py +++ b/lib/galaxy/forms/forms.py @@ -311,6 +311,7 @@ class FormDefinitionSelectFieldFactory( FormDefinitionFieldFactory ): rval['selectlist'].append( value ) return rval + field_type_factories = dict( [ ( field.type, field() ) for field in ( FormDefinitionTextFieldFactory, FormDefinitionPasswordFieldFactory, FormDefinitionAddressFieldFactory, diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py index e1fe506f410..b8cc0791637 100644 --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -242,4 +242,5 @@ class CommandsBuilder(object): self.append_command(YIELD_CAPTURED_CODE) return self.commands + __all__ = ( "build_command", ) diff --git a/lib/galaxy/jobs/dynamic_tool_destination.py b/lib/galaxy/jobs/dynamic_tool_destination.py index 87aa3128c9d..bec27cb7ef7 100755 --- a/lib/galaxy/jobs/dynamic_tool_destination.py +++ b/lib/galaxy/jobs/dynamic_tool_destination.py @@ -1371,6 +1371,7 @@ def map_tool_to_destination( return destination + if __name__ == '__main__': """ This function is responsible for running the app if directly run through the diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py index 21725877075..16bfaee8199 100644 --- a/lib/galaxy/managers/collections_util.py +++ b/lib/galaxy/managers/collections_util.py @@ -94,4 +94,5 @@ def dictify_element( element ): dictified[ "object" ] = object_detials return dictified + __all__ = ( 'api_payload_to_create_params', 'dictify_dataset_collection_instance' ) diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index 293d8d32c54..28dba680878 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -2445,6 +2445,7 @@ simple_mapping( model.Tag, def tag_mapping( tag_association_class, backref_name ): simple_mapping( tag_association_class, tag=relation( model.Tag, backref=backref_name), user=relation( model.User ) ) + tag_mapping( model.HistoryTagAssociation, "tagged_histories" ) tag_mapping( model.DatasetTagAssociation, "tagged_datasets" ) tag_mapping( model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations" ) @@ -2462,6 +2463,7 @@ def annotation_mapping( annotation_class, **kwds ): kwds = dict( (key, relation( value ) ) for key, value in kwds.items() ) simple_mapping( annotation_class, **dict(user=relation( model.User ), **kwds ) ) + annotation_mapping( model.HistoryAnnotationAssociation, history=model.History ) annotation_mapping( model.HistoryDatasetAssociationAnnotationAssociation, hda=model.HistoryDatasetAssociation ) annotation_mapping( model.StoredWorkflowAnnotationAssociation, stored_workflow=model.StoredWorkflow ) @@ -2479,6 +2481,7 @@ def rating_mapping( rating_class, **kwds ): kwds = dict( (key, relation( value ) ) for key, value in kwds.items() ) simple_mapping( rating_class, **dict(user=relation( model.User ), **kwds ) ) + rating_mapping( model.HistoryRatingAssociation, history=model.History ) rating_mapping( model.HistoryDatasetAssociationRatingAssociation, hda=model.HistoryDatasetAssociation ) rating_mapping( model.StoredWorkflowRatingAssociation, stored_workflow=model.StoredWorkflow ) @@ -2546,6 +2549,7 @@ def db_next_hid( self, n=1 ): trans.rollback() raise + model.History._next_hid = db_next_hid @@ -2556,6 +2560,7 @@ def _workflow_invocation_update( self ): stmt = table.update().values(update_time=now_val).where(and_(table.c.id == self.id, table.c.update_time < now_val)) conn.execute(stmt) + model.WorkflowInvocation.update = _workflow_invocation_update diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py index 52c459d2503..932020ba3aa 100644 --- a/lib/galaxy/model/metadata.py +++ b/lib/galaxy/model/metadata.py @@ -340,6 +340,7 @@ class MetadataElementSpec( object ): spec_dict.update( self.__dict__ ) return ( "{name} ({param_class}): {desc}, defaults to '{default}'".format( **spec_dict ) ) + # create a statement class that, when called, # will add a new MetadataElementSpec to a class's metadata_spec MetadataElement = Statement( MetadataElementSpec ) @@ -872,6 +873,7 @@ class JobExternalOutputMetadataWrapper( object ): sa_session.add( metadata_files ) sa_session.flush() + __all__ = ( "Statement", "MetadataElement", diff --git a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py index e2b81763b2e..c40f076fe95 100644 --- a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py +++ b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py @@ -29,6 +29,7 @@ def display_migration_details(): print("histories in the same way that workflows are shared.") print("========================================") + HistoryUserShareAssociation_table = Table( "history_user_share_association", metadata, Column( "id", Integer, primary_key=True ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), diff --git a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py index 778d923c019..5499381ec24 100644 --- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py @@ -45,6 +45,7 @@ def display_migration_details(): print("8) sample_event") print("========================================") + FormDefinitionCurrent_table = Table('form_definition_current', metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py index 3ac6258f99c..ccd78551545 100644 --- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py @@ -41,6 +41,7 @@ def display_migration_details(): print("is too long.") print("========================================") + HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py index b0473ce4722..680ac57e102 100644 --- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py @@ -32,6 +32,7 @@ def display_migration_details(): print("to be manually created.") print("========================================") + HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0012_user_address.py b/lib/galaxy/model/migrate/versions/0012_user_address.py index b3df2e4dc9e..5091e28fc54 100644 --- a/lib/galaxy/model/migrate/versions/0012_user_address.py +++ b/lib/galaxy/model/migrate/versions/0012_user_address.py @@ -35,6 +35,7 @@ def display_migration_details(): print("which is a string, allowing for more flexibility with request states.") print("========================================") + UserAddress_table = Table( "user_address", metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py index daa5096a449..dabafd76f03 100644 --- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py +++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py @@ -51,6 +51,7 @@ def display_migration_details(): print("an index with a shortened name.") print("========================================") + LibraryInfoAssociation_table = Table( 'library_info_association', metadata, Column( "id", Integer, primary_key=True), Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), diff --git a/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py b/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py index 1fbb2343825..24ecd090b39 100644 --- a/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py +++ b/lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py @@ -24,6 +24,7 @@ def display_migration_details(): print("name length limit and thus the index 'ix_hda_ta_history_dataset_association_id'") print("has to be manually created.") + HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), diff --git a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py index 4788160261f..3fd2853f5c9 100644 --- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py @@ -23,6 +23,7 @@ def display_migration_details(): print("This migration script provides support for (a) ordering tags by recency and") print("(b) tagging pages. This script deletes all existing tags.") + HistoryTagAssociation_table = Table( "history_tag_association", metadata, Column( "id", Integer, primary_key=True ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), diff --git a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py index 8e83b40aa04..3608553c0f5 100644 --- a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py +++ b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py @@ -30,6 +30,7 @@ are added to the Job object. An index is also added to the dataset.state column.""") print("========================================") + JobToOutputLibraryDatasetAssociation_table = Table( "job_to_output_library_dataset", metadata, Column( "id", Integer, primary_key=True ), Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), diff --git a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py index 474a59468d0..3f298903ff2 100644 --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py @@ -16,6 +16,7 @@ def display_migration_details(): print("This script adds tables needed for Galaxy cloud functionality.") print("========================================") + CloudImage_table = Table( "cloud_image", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py b/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py index 5508bc0b48e..4de62c8df5e 100644 --- a/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py +++ b/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py @@ -16,6 +16,7 @@ def display_migration_details(): print("This script drops tables that were associated with the old Galaxy Cloud functionality.") print("========================================") + CloudImage_table = Table( "cloud_image", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py index 26e7ca09c23..d34c6f09027 100644 --- a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py +++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py @@ -35,6 +35,7 @@ def localtimestamp(migrate_engine): else: raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + SampleDataset_table = Table('sample_dataset', metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py index 8737d6ac615..7b33cdd22eb 100644 --- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py +++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py @@ -42,6 +42,7 @@ def localtimestamp(migrate_engine): else: raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + ToolVersion_table = Table( "tool_version", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py index 4ef670ef733..be16dceb165 100644 --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -126,6 +126,7 @@ def admin_job_lock(app, **kwargs): log.info("Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")) + control_message_to_task = { 'create_panel_section': create_panel_section, 'reload_tool': reload_tool, 'reload_toolbox': reload_toolbox, diff --git a/lib/galaxy/sample_tracking/data_transfer.py b/lib/galaxy/sample_tracking/data_transfer.py index c91f38941ab..13b3a662c57 100644 --- a/lib/galaxy/sample_tracking/data_transfer.py +++ b/lib/galaxy/sample_tracking/data_transfer.py @@ -54,4 +54,5 @@ class FtpDataTransferFactory( DataTransferFactory ): def parse( self, elem ): pass + data_transfer_factories = dict( [ ( data_transfer.type, data_transfer() ) for data_transfer in [ ScpDataTransferFactory, HttpDataTransferFactory, FtpDataTransferFactory ] ] ) diff --git a/lib/galaxy/sample_tracking/request_types.py b/lib/galaxy/sample_tracking/request_types.py index cfb09fd9c22..632b19047e9 100644 --- a/lib/galaxy/sample_tracking/request_types.py +++ b/lib/galaxy/sample_tracking/request_types.py @@ -29,4 +29,5 @@ class RequestTypeFactory( object ): self.sample_state_factory.from_elem( rval, sample_state_elem ) # should this be the return value?? return rval + request_type_factory = RequestTypeFactory( sample_state_factory, RENAME_DATASET_OPTIONS ) diff --git a/lib/galaxy/sample_tracking/sample.py b/lib/galaxy/sample_tracking/sample.py index a4627849718..64b406232b9 100644 --- a/lib/galaxy/sample_tracking/sample.py +++ b/lib/galaxy/sample_tracking/sample.py @@ -22,4 +22,5 @@ class SampleStateFactory( object ): description = elem.get( 'description', None ) return self.new( request_type, name, description=description ) + sample_state_factory = SampleStateFactory() diff --git a/lib/galaxy/security/passwords.py b/lib/galaxy/security/passwords.py index 299f6d6bd96..79dc573e120 100644 --- a/lib/galaxy/security/passwords.py +++ b/lib/galaxy/security/passwords.py @@ -53,9 +53,9 @@ def check_password_PBKDF2( guess, hashed ): encoded_guess = b64encode( hashed_guess ) return safe_str_cmp( encoded_original, encoded_guess ) + # Taken from https://github.com/mitsuhiko/python-pbkdf2/blob/master/pbkdf2.py # (c) Copyright 2011 by Armin Ronacher, BSD LICENSE - _pack_int = Struct('>I').pack diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py index 0a15dc80079..45fd192162c 100644 --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -203,4 +203,5 @@ class ToolExecutionTracker( object ): trans.sa_session.flush() self.implicit_collections = collections + __all__ = ( 'execute', ) diff --git a/lib/galaxy/tools/imp_exp/export_history.py b/lib/galaxy/tools/imp_exp/export_history.py index 39520925d59..618c63e1267 100644 --- a/lib/galaxy/tools/imp_exp/export_history.py +++ b/lib/galaxy/tools/imp_exp/export_history.py @@ -107,5 +107,6 @@ def main(): status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip ) print status + if __name__ == "__main__": main() diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 5076dd8bd56..e96d55cd077 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2061,6 +2061,7 @@ class LibraryDatasetToolParameter( ToolParameter ): d['multiple'] = self.multiple return d + parameter_types = dict( text=TextToolParameter, integer=IntegerToolParameter, diff --git a/lib/galaxy/tools/parameters/dataset_matcher.py b/lib/galaxy/tools/parameters/dataset_matcher.py index 6ff696e6880..9d3a0171b63 100644 --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -180,4 +180,5 @@ class DatasetCollectionMatcher( object ): break return valid + __all__ = ( 'DatasetMatcher', 'DatasetCollectionMatcher' ) diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/tools/parameters/output_collect.py index 6dff4027022..a34fa5c57a1 100644 --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -494,6 +494,7 @@ class CollectedDatasetMatch( object ): except IndexError: return self.collector.default_visible + UNSET = object() diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py index e450db7ca91..eb8961b3296 100644 --- a/lib/galaxy/tools/parameters/validation.py +++ b/lib/galaxy/tools/parameters/validation.py @@ -426,6 +426,7 @@ class MetadataInDataTableColumnValidator( Validator ): return raise ValueError( self.message ) + validator_types = dict( expression=ExpressionValidator, regex=RegexValidator, in_range=InRangeValidator, diff --git a/lib/galaxy/tools/util/galaxyops/__init__.py b/lib/galaxy/tools/util/galaxyops/__init__.py index d2316b2e893..b7a4a5f2dd8 100644 --- a/lib/galaxy/tools/util/galaxyops/__init__.py +++ b/lib/galaxy/tools/util/galaxyops/__init__.py @@ -13,6 +13,7 @@ def fail( msg ): print >> sys.stderr, msg sys.exit( 1 ) + # Default chrom, start, end, strand cols for a bed file BED_DEFAULT_COLS = 0, 1, 2, 5 diff --git a/lib/galaxy/util/pastescript/loadwsgi.py b/lib/galaxy/util/pastescript/loadwsgi.py index 8eb6e9a2dd0..ab31383bebc 100644 --- a/lib/galaxy/util/pastescript/loadwsgi.py +++ b/lib/galaxy/util/pastescript/loadwsgi.py @@ -31,6 +31,7 @@ def print_(template, *args, **kwargs): template = template % kwargs sys.stdout.writelines(template) + if sys.version_info < (3, 0): def reraise(t, e, tb): exec('raise t, e, tb', dict(t=t, e=e, tb=tb)) @@ -188,6 +189,7 @@ class _App(_ObjectType): else: assert 0, "Protocol %r unknown" % context.protocol + APP = _App() @@ -210,6 +212,7 @@ class _Filter(_ObjectType): else: assert 0, "Protocol %r unknown" % context.protocol + FILTER = _Filter() @@ -232,6 +235,7 @@ class _Server(_ObjectType): else: assert 0, "Protocol %r unknown" % context.protocol + SERVER = _Server() @@ -248,6 +252,7 @@ class _PipeLine(_ObjectType): app = filter_(app) return app + PIPELINE = _PipeLine() @@ -259,6 +264,7 @@ class _FilterApp(_ObjectType): filter_ = context.filter_context.create() return filter_(next_app) + FILTER_APP = _FilterApp() @@ -276,8 +282,8 @@ class _FilterWith(_App): return filter_(filtered(app)) return composed -FILTER_WITH = _FilterWith() +FILTER_WITH = _FilterWith() ############################################################ # Loaders @@ -302,6 +308,7 @@ def appconfig(uri, name=None, relative_to=None, global_conf=None): global_conf=global_conf) return context.config() + _loaders = {} @@ -360,6 +367,7 @@ def _loadconfig(object_type, uri, path, name, relative_to, loader.update_defaults(global_conf, overwrite=False) return loader.get_context(object_type, name, global_conf) + _loaders['config'] = _loadconfig @@ -368,6 +376,7 @@ def _loadegg(object_type, uri, spec, name, relative_to, loader = EggLoader(spec) return loader.get_context(object_type, name, global_conf) + _loaders['egg'] = _loadegg @@ -377,6 +386,7 @@ def _loadfunc(object_type, uri, spec, name, relative_to, loader = FuncLoader(spec) return loader.get_context(object_type, name, global_conf) + _loaders['call'] = _loadfunc ############################################################ diff --git a/lib/galaxy/util/pastescript/serve.py b/lib/galaxy/util/pastescript/serve.py index 6e3e4180161..49fca8c6eab 100644 --- a/lib/galaxy/util/pastescript/serve.py +++ b/lib/galaxy/util/pastescript/serve.py @@ -1015,8 +1015,8 @@ def _turn_sigterm_into_systemexit(): raise SystemExit signal.signal(signal.SIGTERM, handle_term) -# ---- from paste.script.command -------------------------------------- +# ---- from paste.script.command -------------------------------------- python_version = sys.version.splitlines()[0].strip() parser = optparse.OptionParser(add_help_option=False, diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py index 5c80c0f9039..e227a8080eb 100644 --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -1,24 +1,21 @@ """ A simple WSGI application/framework. """ - import cgi # For FieldStorage import logging import os.path import socket import tarfile import tempfile -import types import time +import types +from Cookie import SimpleCookie import routes import webob - -from Cookie import SimpleCookie - # We will use some very basic HTTP/wsgi utilities from the paste library -from paste.request import get_cookies from paste import httpexceptions +from paste.request import get_cookies from paste.response import HeaderDict from galaxy.util import smart_str @@ -42,6 +39,8 @@ def __resource_with_deleted( self, member_name, collection_name, **kwargs ): self.connect( 'undelete_deleted_' + member_name, member_path + '/undelete', controller=collection_name, action='undelete', conditions=dict( method=['POST'] ) ) self.resource( member_name, collection_name, **kwargs ) + + routes.Mapper.resource_with_deleted = __resource_with_deleted @@ -267,6 +266,8 @@ class LazyProperty( object ): value = self.func( obj ) setattr( obj, self.func.func_name, value ) return value + + lazy_property = LazyProperty @@ -312,6 +313,8 @@ class FieldStorage( cgi.FieldStorage ): self.read_lines_to_outerboundary() else: self.read_lines_to_eof() + + cgi.FieldStorage = FieldStorage @@ -427,6 +430,7 @@ class Response( object ): else: return self.status + # ---- Utilities ------------------------------------------------------------ CHUNK_SIZE = 2 ** 16 diff --git a/lib/galaxy/web/framework/middleware/error.py b/lib/galaxy/web/framework/middleware/error.py index 18a409b0b47..581d9896f78 100644 --- a/lib/galaxy/web/framework/middleware/error.py +++ b/lib/galaxy/web/framework/middleware/error.py @@ -27,6 +27,8 @@ __all__ = ('ErrorMiddleware', 'handle_exception') class _NoDefault(object): def __repr__(self): return '' + + NoDefault = _NoDefault() @@ -487,6 +489,7 @@ def error_template(head_html, exception, extra): def make_error_middleware(app, global_conf, **kw): return ErrorMiddleware(app, global_conf=global_conf, **kw) + doc_lines = ErrorMiddleware.__doc__.splitlines(True) for i in range(len(doc_lines)): if doc_lines[i].strip().startswith('Settings'): diff --git a/lib/galaxy/web/framework/middleware/translogger.py b/lib/galaxy/web/framework/middleware/translogger.py index a112685472b..286f39ba51c 100644 --- a/lib/galaxy/web/framework/middleware/translogger.py +++ b/lib/galaxy/web/framework/middleware/translogger.py @@ -3,10 +3,10 @@ """ Middleware for logging requests, using Apache combined log format """ - import logging import time import urllib + from six import string_types @@ -117,4 +117,5 @@ def make_filter( setup_console_handler=asbool(setup_console_handler), set_logger_level=set_logger_level) + make_filter.__doc__ = TransLogger.__doc__ diff --git a/lib/galaxy/web/framework/openid_manager.py b/lib/galaxy/web/framework/openid_manager.py index 23c6851fb90..3856b222ff3 100644 --- a/lib/galaxy/web/framework/openid_manager.py +++ b/lib/galaxy/web/framework/openid_manager.py @@ -28,6 +28,8 @@ log = logging.getLogger( __name__ ) def oidlog( message, level=0 ): log.debug( message ) + + if oidutil is not None: oidutil.log = oidlog diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py index 6422468d048..d153ff60218 100644 --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py @@ -52,6 +52,7 @@ def boolean_false(migrate_engine): else: raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + RepositoryReview_table = Table( "repository_review", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=NOW ), diff --git a/lib/galaxy/workflow/extract.py b/lib/galaxy/workflow/extract.py index 4f47835fd76..8bf16245826 100644 --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -371,4 +371,5 @@ def __cleanup_param_values( inputs, values ): cleanup( "", inputs, values ) return associations + __all__ = ( 'summarize', 'extract_workflow' ) diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py index 6061254f58c..3afb3ed6414 100644 --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -228,6 +228,7 @@ class WorkflowInvoker( object ): jobs = step.module.execute( self.trans, self.progress, self.workflow_invocation, step ) return jobs + STEP_OUTPUT_DELAYED = object() @@ -397,4 +398,5 @@ class WorkflowProgress( object ): except modules.DelayedWorkflowEvaluation: self.mark_step_outputs_delayed( step ) + __all__ = ( 'invoke', 'WorkflowRunConfig' ) diff --git a/lib/galaxy/workflow/schedulers/core.py b/lib/galaxy/workflow/schedulers/core.py index e513a258ed9..ec59029e0b9 100644 --- a/lib/galaxy/workflow/schedulers/core.py +++ b/lib/galaxy/workflow/schedulers/core.py @@ -42,4 +42,5 @@ class CoreWorkflowSchedulingPlugin( ActiveWorkflowSchedulingPlugin ): workflow_invocation=workflow_invocation, ) + __all__ = ( 'CoreWorkflowSchedulingPlugin', ) diff --git a/lib/galaxy_utils/sequence/fastq.py b/lib/galaxy_utils/sequence/fastq.py index 5a7cc3cc340..da47279898f 100644 --- a/lib/galaxy_utils/sequence/fastq.py +++ b/lib/galaxy_utils/sequence/fastq.py @@ -364,6 +364,7 @@ class fastqCSSangerRead( fastqSequencingRead ): else: self.quality = " ".join( map( str, self.get_decimal_quality_scores()[1:] ) ) + FASTQ_FORMATS = {} for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqCSSangerRead ]: FASTQ_FORMATS[ format.format ] = format diff --git a/lib/galaxy_utils/sequence/vcf.py b/lib/galaxy_utils/sequence/vcf.py index 4e70cd3e3ea..e4d93e585d3 100644 --- a/lib/galaxy_utils/sequence/vcf.py +++ b/lib/galaxy_utils/sequence/vcf.py @@ -63,6 +63,7 @@ class VariantCall40( VariantCall33 ): class VariantCall41( VariantCall40 ): version = 'VCFv4.1' + # VCF Format version lookup dict VCF_FORMATS = {} for format in [ VariantCall33, VariantCall40, VariantCall41 ]: diff --git a/lib/mimeparse.py b/lib/mimeparse.py index 8cbfc550f6b..39040af2e33 100755 --- a/lib/mimeparse.py +++ b/lib/mimeparse.py @@ -131,6 +131,7 @@ def best_match(supported, header): weighted_matches.sort() return weighted_matches[-1][0][1] and weighted_matches[-1][1] or '' + if __name__ == "__main__": import unittest diff --git a/lib/tool_shed/util/workflow_util.py b/lib/tool_shed/util/workflow_util.py index d21c671fbdd..d25f563920d 100644 --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -146,6 +146,7 @@ class RepoWorkflowModuleFactory( WorkflowModuleFactory ): module_method_kwds[ 'tools_metadata' ] = tools_metadata return self.module_types[ type ].from_workflow_step( trans, step, **module_method_kwds ) + tool_shed_module_types = module_types.copy() tool_shed_module_types[ 'tool' ] = RepoToolModule module_factory = RepoWorkflowModuleFactory( tool_shed_module_types ) diff --git a/scripts/api/data_manager_example_execute.py b/scripts/api/data_manager_example_execute.py index 5e1c84bdf43..cfdc85b20d1 100644 --- a/scripts/api/data_manager_example_execute.py +++ b/scripts/api/data_manager_example_execute.py @@ -51,6 +51,7 @@ def dataset_is_terminal( hda_id, api_key, galaxy_url ): dataset_state = get_dataset_state( hda_id, api_key, galaxy_url ) return dataset_state in [ 'ok', 'error' ] + if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option( '-k', '--key', dest='api_key', action='store', type="string", default=None, help='API Key.' ) diff --git a/scripts/api/example_watch_folder.py b/scripts/api/example_watch_folder.py index 86eaa486f2f..50dfd17ea24 100755 --- a/scripts/api/example_watch_folder.py +++ b/scripts/api/example_watch_folder.py @@ -75,6 +75,7 @@ def main(api_key, api_url, in_folder, out_folder, data_library, workflow): shutil.move(fullpath, os.path.join(out_folder, fname)) time.sleep(10) + if __name__ == '__main__': try: api_key = sys.argv[1] diff --git a/scripts/api/import_workflows_from_installed_tool_shed_repository.py b/scripts/api/import_workflows_from_installed_tool_shed_repository.py index 52b6fec2191..a3d59fc4a29 100644 --- a/scripts/api/import_workflows_from_installed_tool_shed_repository.py +++ b/scripts/api/import_workflows_from_installed_tool_shed_repository.py @@ -51,6 +51,7 @@ def main( options ): else: print("Invalid tool_shed / name / owner / changeset_revision.") + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Import workflows contained in an installed tool shed repository via the Galaxy API.' ) parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" ) diff --git a/scripts/api/install_tool_shed_repositories.py b/scripts/api/install_tool_shed_repositories.py index 1589c0f507d..133381f87b3 100644 --- a/scripts/api/install_tool_shed_repositories.py +++ b/scripts/api/install_tool_shed_repositories.py @@ -51,6 +51,7 @@ def main( options ): data[ 'install_tool_dependencies' ] = options.install_tool_dependencies submit( options.api, '%s%s' % ( options.local_url.rstrip( '/' ), '/api/tool_shed_repositories/new/install_repository_revision' ), data ) + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) diff --git a/scripts/api/load_data_with_metadata.py b/scripts/api/load_data_with_metadata.py index 1c7d2e6bb5d..036eb78a61d 100755 --- a/scripts/api/load_data_with_metadata.py +++ b/scripts/api/load_data_with_metadata.py @@ -71,6 +71,7 @@ def main(api_key, api_url, in_folder, data_library, uuid_field=None): print("Loading", fullpath) load_file(fullpath, api_key, api_url, library_id, library_folder_id, uuid_field) + if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument("api_key", help="API KEY") diff --git a/scripts/api/repair_tool_shed_repository.py b/scripts/api/repair_tool_shed_repository.py index 18c8a3e61e5..4926c501587 100644 --- a/scripts/api/repair_tool_shed_repository.py +++ b/scripts/api/repair_tool_shed_repository.py @@ -47,6 +47,7 @@ def main( options ): else: print("Invalid tool_shed / name / owner / changeset_revision.") + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) diff --git a/scripts/api/reset_metadata_on_installed_repositories.py b/scripts/api/reset_metadata_on_installed_repositories.py index 50f7399e5be..e7c5b96f7d0 100644 --- a/scripts/api/reset_metadata_on_installed_repositories.py +++ b/scripts/api/reset_metadata_on_installed_repositories.py @@ -18,6 +18,7 @@ def main( options ): url = '%s/api/tool_shed_repositories/reset_metadata_on_installed_repositories' % base_galaxy_url submit( options.api, url, {} ) + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Reset metadata on all Tool Shed repositories installed into Galaxy via the Galaxy API.' ) parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" ) diff --git a/scripts/api/search.py b/scripts/api/search.py index 3fff1bf3863..e503db4634e 100644 --- a/scripts/api/search.py +++ b/scripts/api/search.py @@ -27,6 +27,7 @@ class RemoteGalaxy(object): req = requests.post(c_url, data=json.dumps(payload), params=params, headers={'Content-Type': 'application/json'} ) return req.json() + if __name__ == "__main__": server = sys.argv[1] api_key = sys.argv[2] diff --git a/scripts/api/sequencer_configuration_create.py b/scripts/api/sequencer_configuration_create.py index c21abf4d262..7fbf6ed9cd9 100755 --- a/scripts/api/sequencer_configuration_create.py +++ b/scripts/api/sequencer_configuration_create.py @@ -45,5 +45,6 @@ def main(): sys.exit( 1 ) return create_sequencer_configuration( key, base_url, request_form_filename, sample_form_filename, request_type_filename, email_addresses, return_formatted=True ) + if __name__ == "__main__": main() diff --git a/scripts/api/workflow_execute.py b/scripts/api/workflow_execute.py index cd37368fccf..d56b88fc1ce 100755 --- a/scripts/api/workflow_execute.py +++ b/scripts/api/workflow_execute.py @@ -28,5 +28,6 @@ def main(): sys.exit(1) submit( sys.argv[1], sys.argv[2], data ) + if __name__ == '__main__': main() diff --git a/scripts/api/workflow_execute_parameters.py b/scripts/api/workflow_execute_parameters.py index e14c3277d4a..f54ebb46cb3 100644 --- a/scripts/api/workflow_execute_parameters.py +++ b/scripts/api/workflow_execute_parameters.py @@ -50,5 +50,6 @@ def main(): sys.exit(1) submit( sys.argv[1], sys.argv[2], data ) + if __name__ == '__main__': main() diff --git a/scripts/api/workflow_import.py b/scripts/api/workflow_import.py index d1464668d6f..bf83ed90393 100755 --- a/scripts/api/workflow_import.py +++ b/scripts/api/workflow_import.py @@ -26,5 +26,6 @@ def main(): # print display( api_key, api_base_url + "/api/workflows" ) submit( api_key, api_url, data, return_formatted=False ) + if __name__ == '__main__': main() diff --git a/scripts/auth/pam_auth_helper.py b/scripts/auth/pam_auth_helper.py index 7bb9b3ad149..14d5e50fae7 100755 --- a/scripts/auth/pam_auth_helper.py +++ b/scripts/auth/pam_auth_helper.py @@ -18,6 +18,7 @@ except ImportError: def handle_timeout(signum, stack): raise IOError("Timed out reading input") + # set timeout so we don't block on reading stdin signal.alarm(TIMEOUT) diff --git a/scripts/build_toolbox.py b/scripts/build_toolbox.py index 3e2a69c8c9d..7de2176607b 100644 --- a/scripts/build_toolbox.py +++ b/scripts/build_toolbox.py @@ -167,5 +167,6 @@ def assemble(): print(prettify(toolboxelement)) + if __name__ == "__main__": assemble() diff --git a/scripts/build_universe_config.py b/scripts/build_universe_config.py index 08ce733a350..da54f11b10d 100644 --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -29,5 +29,6 @@ def merge(): parser.write(open(destination, 'w')) + if __name__ == '__main__': merge() diff --git a/scripts/check_galaxy.py b/scripts/check_galaxy.py index e0eebc0f99d..5e3a4a93dfd 100755 --- a/scripts/check_galaxy.py +++ b/scripts/check_galaxy.py @@ -53,6 +53,7 @@ tools = { def usage(): sys.exit("usage: check_galaxy.py ") + try: opts, args = getopt.getopt( sys.argv[1:], 'n' ) except getopt.GetoptError as e: @@ -366,9 +367,8 @@ def dprint(str): if debug: print(str) -# do stuff here -if __name__ == "__main__": +if __name__ == "__main__": dprint("checking %s" % server) b = Browser() diff --git a/scripts/check_python.py b/scripts/check_python.py index c5d245198a0..f23a12f75ba 100644 --- a/scripts/check_python.py +++ b/scripts/check_python.py @@ -19,6 +19,7 @@ def check_python(): print(msg, file=sys.stderr) raise + if __name__ == '__main__': rval = 0 try: diff --git a/scripts/cleanup_datasets/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py index 7653db51a10..c4ce1680bc4 100755 --- a/scripts/cleanup_datasets/cleanup_datasets.py +++ b/scripts/cleanup_datasets/cleanup_datasets.py @@ -543,5 +543,6 @@ class CleanupDatasetsApplication( object ): def shutdown( self ): self.object_store.shutdown() + if __name__ == "__main__": main() diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py index 4d3fc3b66dd..ee16591f9fb 100755 --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -769,6 +769,7 @@ class Cleanup(object): self._close_logfile() + if __name__ == '__main__': cleanup = Cleanup() try: diff --git a/scripts/cleanup_datasets/rename_purged_datasets.py b/scripts/cleanup_datasets/rename_purged_datasets.py index b8fa75b4b90..f9d888d0d93 100755 --- a/scripts/cleanup_datasets/rename_purged_datasets.py +++ b/scripts/cleanup_datasets/rename_purged_datasets.py @@ -46,5 +46,6 @@ def main(): print("# Error, exception " + str( exc ) + " caught attempting to rename " + purged_filename, file=out) print("# Renamed " + str( renamed_files ) + " files", file=out) + if __name__ == "__main__": main() diff --git a/scripts/cleanup_datasets/update_dataset_size.py b/scripts/cleanup_datasets/update_dataset_size.py index 9f71deafd6b..15e4b5dd051 100755 --- a/scripts/cleanup_datasets/update_dataset_size.py +++ b/scripts/cleanup_datasets/update_dataset_size.py @@ -45,5 +45,6 @@ def main(): app.shutdown() sys.exit(0) + if __name__ == "__main__": main() diff --git a/scripts/cleanup_datasets/update_metadata.py b/scripts/cleanup_datasets/update_metadata.py index 73b1bd58174..c27580721a7 100755 --- a/scripts/cleanup_datasets/update_metadata.py +++ b/scripts/cleanup_datasets/update_metadata.py @@ -57,5 +57,6 @@ def main(): app.shutdown() sys.exit(0) + if __name__ == "__main__": main() diff --git a/scripts/communication/communication_server.py b/scripts/communication/communication_server.py index d113b544023..53b394e7dbe 100755 --- a/scripts/communication/communication_server.py +++ b/scripts/communication/communication_server.py @@ -128,6 +128,7 @@ def crossdomain(origin=None, methods=None, headers=None, return update_wrapper(wrapped_function, f) return decorator + script_dir = os.path.dirname(os.path.realpath( __file__)) communication_directory = os.path.join( script_dir, 'template' ) @@ -203,7 +204,6 @@ def leave(message): if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Real-time communication server for Galaxy.') parser.add_argument('--port', type=int, default="7070", help='Port number on which the server should run.') parser.add_argument('--host', default='localhost', help='Hostname of the communication server.') diff --git a/scripts/create_db.py b/scripts/create_db.py index 0f0e919be15..0d73b2986eb 100755 --- a/scripts/create_db.py +++ b/scripts/create_db.py @@ -35,5 +35,6 @@ def invoke_create(): elif config['database'] == 'install': create_install_db(config['db_url']) + if __name__ == "__main__": invoke_create() diff --git a/scripts/data_libraries/build_lucene_index.py b/scripts/data_libraries/build_lucene_index.py index 1029c0d356e..5ffec9c9d75 100644 --- a/scripts/data_libraries/build_lucene_index.py +++ b/scripts/data_libraries/build_lucene_index.py @@ -105,5 +105,6 @@ def get_sa_session( ini_file ): create_tables=False ) return model.context.current, ini_config + if __name__ == "__main__": main( *sys.argv[1:] ) diff --git a/scripts/data_libraries/build_whoosh_index.py b/scripts/data_libraries/build_whoosh_index.py index 2f8a5958237..811ccdbb095 100644 --- a/scripts/data_libraries/build_whoosh_index.py +++ b/scripts/data_libraries/build_whoosh_index.py @@ -83,6 +83,7 @@ def get_sa_session_and_needed_config_settings( ini_file ): model = galaxy.model.mapping.init( config_settings.file_path, db_con, engine_options={}, create_tables=False ) return model.context.current, config_settings + if __name__ == "__main__": if whoosh_search_enabled: ini_file = sys.argv[1] diff --git a/scripts/drmaa_external_killer.py b/scripts/drmaa_external_killer.py index 9aff1d60d70..bdac6618fa9 100755 --- a/scripts/drmaa_external_killer.py +++ b/scripts/drmaa_external_killer.py @@ -49,5 +49,6 @@ def main(): s.control(jobID, drmaa.JobControlAction.TERMINATE) s.exit() + if __name__ == "__main__": main() diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py index 408ad021034..1231af99574 100755 --- a/scripts/drmaa_external_runner.py +++ b/scripts/drmaa_external_runner.py @@ -131,5 +131,6 @@ def main(): # Print the Job-ID and exit. Galaxy will pick it up from there. print(jobId) + if __name__ == "__main__": main() diff --git a/scripts/external_chown_script.py b/scripts/external_chown_script.py index b986e93fb6b..cf47e555919 100755 --- a/scripts/external_chown_script.py +++ b/scripts/external_chown_script.py @@ -20,5 +20,6 @@ def main(): os.system('chown -Rh %s %s' % (galaxy_user_name, path)) os.system('chgrp -Rh %s %s' % (gid, path)) + if __name__ == "__main__": main() diff --git a/scripts/extract_dataset_part.py b/scripts/extract_dataset_part.py index 470205b60aa..26bcc4e250f 100644 --- a/scripts/extract_dataset_part.py +++ b/scripts/extract_dataset_part.py @@ -44,4 +44,5 @@ def __main__(): sys.stderr.write(str(e)) sys.exit(1) + __main__() diff --git a/scripts/extract_toolbox_sections.py b/scripts/extract_toolbox_sections.py index c1ef29a698a..89a898a2c42 100644 --- a/scripts/extract_toolbox_sections.py +++ b/scripts/extract_toolbox_sections.py @@ -132,5 +132,6 @@ def getfnl(startdir): filenamelist.append(fullfn) return filenamelist + if __name__ == "__main__": main() diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py index 463b8428e26..b7b056c6ad6 100644 --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -116,5 +116,6 @@ def _check_arg( name ): ret_val = False return ret_val + if __name__ == "__main__": driver_util.drive_test(find_test_driver()) diff --git a/scripts/grt.py b/scripts/grt.py index 1c7918c22ed..a87ea5eb1de 100644 --- a/scripts/grt.py +++ b/scripts/grt.py @@ -222,5 +222,6 @@ def main(argv): with open(args.config, 'w') as f: yaml.dump(config_dict, f, default_flow_style=False) + if __name__ == '__main__': main(sys.argv) diff --git a/scripts/loc_files/create_all_fasta_loc.py b/scripts/loc_files/create_all_fasta_loc.py index 8dc56048f20..946499c799d 100644 --- a/scripts/loc_files/create_all_fasta_loc.py +++ b/scripts/loc_files/create_all_fasta_loc.py @@ -298,5 +298,6 @@ def __main__(): # close up output loc file all_fasta_loc.close() + if __name__ == '__main__': __main__() diff --git a/scripts/manage_db.py b/scripts/manage_db.py index 57da9490929..7d1bfb120ab 100644 --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -18,5 +18,6 @@ def invoke_migrate_main(): main( repository=repo, url=db_url ) + if __name__ == "__main__": invoke_migrate_main() diff --git a/scripts/microbes/BeautifulSoup.py b/scripts/microbes/BeautifulSoup.py index 4c684cc0fe9..5ff92040207 100644 --- a/scripts/microbes/BeautifulSoup.py +++ b/scripts/microbes/BeautifulSoup.py @@ -1531,6 +1531,7 @@ class RobustInsanelyWackAssHTMLParser(MinimalSoup): class SimplifyingSOAPParser(BeautifulSOAP): pass + ###################################################### # # Bonus library: Unicode, Dammit diff --git a/scripts/microbes/create_bacteria_loc_file.py b/scripts/microbes/create_bacteria_loc_file.py index c8c5e24a1b9..812317068a1 100644 --- a/scripts/microbes/create_bacteria_loc_file.py +++ b/scripts/microbes/create_bacteria_loc_file.py @@ -68,5 +68,6 @@ def __main__(): if os.path.exists( os.path.join( org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'] ) ): print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join( org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'] ) ) + if __name__ == "__main__": __main__() diff --git a/scripts/microbes/create_bacteria_table.py b/scripts/microbes/create_bacteria_table.py index 42c8435d197..a8a237e0652 100644 --- a/scripts/microbes/create_bacteria_table.py +++ b/scripts/microbes/create_bacteria_table.py @@ -74,5 +74,6 @@ def __main__(): out_str = out_str + "||" print out_str + if __name__ == "__main__": __main__() diff --git a/scripts/microbes/get_builds_lengths.py b/scripts/microbes/get_builds_lengths.py index 398abcebaa8..a32a6fcd4e3 100644 --- a/scripts/microbes/get_builds_lengths.py +++ b/scripts/microbes/get_builds_lengths.py @@ -55,5 +55,6 @@ def __main__(): chrs.append( "%s=%s" % ( chrom['chromosome'], chrom['length'] ) ) print "%s\t%s\t%s" % ( build, org['name'], ",".join( chrs ) ) + if __name__ == "__main__": __main__() diff --git a/scripts/microbes/harvest_bacteria.py b/scripts/microbes/harvest_bacteria.py index 3b427906969..9b0bfb8eb0f 100644 --- a/scripts/microbes/harvest_bacteria.py +++ b/scripts/microbes/harvest_bacteria.py @@ -250,5 +250,6 @@ def __main__(): print "[", ( time.time() - start_time ) / 60, "minutes. ]" print "[", ( time.time() - start_time ) / 60 / 60, "hours. ]" + if __name__ == "__main__": __main__() diff --git a/scripts/others/incorrect_gops_jobs.py b/scripts/others/incorrect_gops_jobs.py index fc22ac5e71a..962ba88fb02 100755 --- a/scripts/others/incorrect_gops_jobs.py +++ b/scripts/others/incorrect_gops_jobs.py @@ -104,5 +104,6 @@ def main(): jobs[ jid ][ 'user_email' ] ) sys.exit(0) + if __name__ == "__main__": main() diff --git a/scripts/others/incorrect_gops_join_jobs.py b/scripts/others/incorrect_gops_join_jobs.py index e8de640614d..d612f4f9243 100644 --- a/scripts/others/incorrect_gops_join_jobs.py +++ b/scripts/others/incorrect_gops_join_jobs.py @@ -94,5 +94,6 @@ def main(): jobs[ jid ][ 'user_email' ] ) sys.exit(0) + if __name__ == "__main__": main() diff --git a/scripts/set_dataset_sizes.py b/scripts/set_dataset_sizes.py index 4889a62ed6e..7b37210bb40 100644 --- a/scripts/set_dataset_sizes.py +++ b/scripts/set_dataset_sizes.py @@ -34,6 +34,7 @@ def init(): return (mapping.init( config.file_path, config.database_connection, create_tables=False, object_store=object_store ), object_store) + if __name__ == '__main__': print 'Loading Galaxy model...' model, object_store = init() diff --git a/scripts/set_user_disk_usage.py b/scripts/set_user_disk_usage.py index 57dc3ceb749..06c1b457775 100755 --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -74,6 +74,7 @@ def quotacheck( sa_session, users, engine ): sa_session.add( user ) sa_session.flush() + if __name__ == '__main__': print 'Loading Galaxy model...' model, object_store, engine = init() diff --git a/scripts/slideshow/build_slideshow.py b/scripts/slideshow/build_slideshow.py index 6331f3af0e5..fac0da49568 100644 --- a/scripts/slideshow/build_slideshow.py +++ b/scripts/slideshow/build_slideshow.py @@ -23,5 +23,6 @@ def main(argv=None): print html open(output, "w").write(html) + if __name__ == "__main__": main() diff --git a/scripts/summarize_timings.py b/scripts/summarize_timings.py index 1740563358a..5cf4295bc79 100644 --- a/scripts/summarize_timings.py +++ b/scripts/summarize_timings.py @@ -46,5 +46,6 @@ def main(argv=None): ) print(message) + if __name__ == "__main__": main() diff --git a/scripts/sync_reports_config.py b/scripts/sync_reports_config.py index 812c3f30e6e..f1d2c190316 100644 --- a/scripts/sync_reports_config.py +++ b/scripts/sync_reports_config.py @@ -57,5 +57,6 @@ def get_synced_line(reports_line, universe_config): def get_universe_line(property_name, universe_config): return "%s=%s\n" % (property_name, universe_config.get(MAIN_SECTION, property_name)) + if __name__ == '__main__': sync() diff --git a/scripts/tool_shed/api/add_repository_registry_entry.py b/scripts/tool_shed/api/add_repository_registry_entry.py index afd71498ec7..d6b30e2ea2c 100644 --- a/scripts/tool_shed/api/add_repository_registry_entry.py +++ b/scripts/tool_shed/api/add_repository_registry_entry.py @@ -28,6 +28,7 @@ def main( options ): else: print "An API key for an admin user in the Tool Shed is required to add entries into the Tool Shed's repository registry." + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Add entries into the Tool Shed repository registry for a specified repository.' ) parser.add_argument( "-a", "--api_key", dest="api_key", required=True, help="API Key for user adding entries into the Tool Shed's repository registry." ) diff --git a/scripts/tool_shed/api/create_categories.py b/scripts/tool_shed/api/create_categories.py index f2cf778b8b5..35d82f59944 100644 --- a/scripts/tool_shed/api/create_categories.py +++ b/scripts/tool_shed/api/create_categories.py @@ -46,6 +46,7 @@ def main( options ): create_response_dict = dict( response=response ) create_response_dicts.append( create_response_dict ) + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Retrieve a list of categories from a Tool Shed and create them in another Tool Shed.' ) parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which categories will be created" ) diff --git a/scripts/tool_shed/api/create_users.py b/scripts/tool_shed/api/create_users.py index f2d45317751..6661b37e44f 100644 --- a/scripts/tool_shed/api/create_users.py +++ b/scripts/tool_shed/api/create_users.py @@ -49,6 +49,7 @@ def main( options ): create_response_dict = dict( response=response ) create_response_dicts.append( create_response_dict ) + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Retrieve a list of users from a Tool Shed and create them in another Tool Shed.' ) parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which users will be created" ) diff --git a/scripts/tool_shed/api/export.py b/scripts/tool_shed/api/export.py index 5773354558d..0d18e2b6abc 100644 --- a/scripts/tool_shed/api/export.py +++ b/scripts/tool_shed/api/export.py @@ -121,6 +121,7 @@ def main( options ): else: print "Invalid tool_shed / name / owner ." + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Installation of tool shed repositories via the Galaxy API.' ) parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) diff --git a/scripts/tool_shed/api/get_filtered_repository_revisions.py b/scripts/tool_shed/api/get_filtered_repository_revisions.py index 83c3ffcf4ca..546b03c2438 100644 --- a/scripts/tool_shed/api/get_filtered_repository_revisions.py +++ b/scripts/tool_shed/api/get_filtered_repository_revisions.py @@ -79,6 +79,7 @@ def main( options ): print '\n\n', repository_dicts print '\nThe url:\n\n', api_url, '\n\nreturned ', len( repository_dicts ), ' repository dictionaries...' + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Get a filtered list of repository dictionaries.' ) parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) diff --git a/scripts/tool_shed/api/import_capsule.py b/scripts/tool_shed/api/import_capsule.py index 97fef3fa617..6eb9d00c635 100644 --- a/scripts/tool_shed/api/import_capsule.py +++ b/scripts/tool_shed/api/import_capsule.py @@ -36,6 +36,7 @@ def main( options ): log.exception( str( e ) ) sys.exit( 1 ) + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Import the contents of a repository capsule via the Tool Shed API.' ) parser.add_argument( "-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL" ) diff --git a/scripts/tool_shed/api/remove_repository_registry_entry.py b/scripts/tool_shed/api/remove_repository_registry_entry.py index a3e4581263d..adaac6486b4 100644 --- a/scripts/tool_shed/api/remove_repository_registry_entry.py +++ b/scripts/tool_shed/api/remove_repository_registry_entry.py @@ -28,6 +28,7 @@ def main( options ): else: print "An API key for an admin user in the Tool Shed is required to remove entries from the Tool Shed's repository registry." + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Remove entries from the Tool Shed repository registry for a specified repository.' ) parser.add_argument( "-a", "--api_key", dest="api_key", required=True, help="API Key for user removing entries from the Tool Shed's repository registry." ) diff --git a/scripts/tool_shed/api/reset_metadata_on_repositories.py b/scripts/tool_shed/api/reset_metadata_on_repositories.py index 2098977ed3d..ef7607a6c98 100644 --- a/scripts/tool_shed/api/reset_metadata_on_repositories.py +++ b/scripts/tool_shed/api/reset_metadata_on_repositories.py @@ -79,6 +79,7 @@ def main( options ): # An nginx timeout undoubtedly occurred. sys.exit( 1 ) + if __name__ == '__main__': parser = argparse.ArgumentParser( description='Reset metadata on certain repositories in the Tool Shed via the Tool Shed API.' ) parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key" ) diff --git a/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py b/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py index 980873e2df8..fb2e9c8e2c3 100755 --- a/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py +++ b/scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py @@ -120,6 +120,7 @@ def main( args ): else: return 1 + parser = optparse.OptionParser() parser.add_option( '-c', '--config_file', dest='config', action='store', default='config/tool_shed.ini.sample' ) parser.add_option( '-e', '--execute', dest='method', action='store', default='check_db' ) diff --git a/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py b/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py index d431307ba67..0cc4fe90e88 100644 --- a/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py +++ b/scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py @@ -116,6 +116,7 @@ def validate_publicname( username ): return "Public name must contain only lower-case letters, numbers and '-'" return '' + if __name__ == "__main__": parser = optparse.OptionParser( description='Create a user with API key.' ) parser.add_option( '-c', dest='config', action='store', help='.ini file to retried toolshed configuration from' ) diff --git a/scripts/tool_shed/build_ts_whoosh_index.py b/scripts/tool_shed/build_ts_whoosh_index.py index d5f5ddaf57e..8f40c215edd 100644 --- a/scripts/tool_shed/build_ts_whoosh_index.py +++ b/scripts/tool_shed/build_ts_whoosh_index.py @@ -210,6 +210,7 @@ def get_sa_session_and_needed_config_settings( path_to_tool_shed_config ): model = galaxy.webapps.tool_shed.model.mapping.init( config_settings.file_path, db_con, engine_options={}, create_tables=False ) return model.context.current, config_settings + if __name__ == "__main__": parser = OptionParser() parser.add_option("-c", "--config", dest="path_to_tool_shed_config", default="config/tool_shed.ini", help="specify tool_shed.ini location") diff --git a/scripts/tool_shed/check_download_urls.py b/scripts/tool_shed/check_download_urls.py index de8409aeee5..c67667558b7 100644 --- a/scripts/tool_shed/check_download_urls.py +++ b/scripts/tool_shed/check_download_urls.py @@ -34,5 +34,6 @@ def main(): except Exception as e: print "Unable to check XML file '%s': %s" % ( path, e ) + if __name__ == "__main__": main() diff --git a/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py b/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py index 27b4b3d4b00..dbba90a88e0 100644 --- a/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py +++ b/scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py @@ -49,6 +49,7 @@ def main( args ): print 'No empty tool dependency installation directories found.' return 0 + if __name__ == '__main__': description = 'Determine if there are any tool dependency installation paths that should be removed. Remove them if ' description += 'the --delete command line argument is provided.' diff --git a/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py b/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py index 4b0721f7ed8..f48136d775a 100644 --- a/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py +++ b/scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py @@ -110,6 +110,7 @@ def main( args ): print empty_installation_path return 0 + if __name__ == '__main__': description = 'Determine if there are any tool dependency installation paths that should be removed. Remove them if ' description += 'the --delete command line argument is provided with a true value.' diff --git a/scripts/tool_shed/clean_up_tool_dependency_directory.py b/scripts/tool_shed/clean_up_tool_dependency_directory.py index 9be61276f8d..86a6d37e7f1 100644 --- a/scripts/tool_shed/clean_up_tool_dependency_directory.py +++ b/scripts/tool_shed/clean_up_tool_dependency_directory.py @@ -18,6 +18,7 @@ def main( args ): else: os.remove( full_path ) + if __name__ == '__main__': description = 'Clean out the configured tool dependency path, creating it if it does not exist.' parser = argparse.ArgumentParser( description=description ) diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py index e0caea75238..5832e31065a 100644 --- a/scripts/tool_shed/deprecate_repositories_without_metadata.py +++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py @@ -170,5 +170,6 @@ class DeprecateRepositoriesApplication( object ): def shutdown( self ): pass + if __name__ == "__main__": main() diff --git a/scripts/tool_shed/migrate_tools_to_repositories.py b/scripts/tool_shed/migrate_tools_to_repositories.py index f5025b8e03b..f724f29c529 100644 --- a/scripts/tool_shed/migrate_tools_to_repositories.py +++ b/scripts/tool_shed/migrate_tools_to_repositories.py @@ -332,5 +332,6 @@ def main(): print "##########################################" sys.exit(0) + if __name__ == "__main__": main() diff --git a/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py b/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py index 31e374e7ff1..794738ea585 100644 --- a/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py +++ b/scripts/tool_shed/show_tool_dependency_installation_dir_contents.py @@ -47,6 +47,7 @@ def get_tool_dependency_dirs( app ): dependency_paths.append( tool_dependency.installation_directory( app ) ) return dependency_paths + if __name__ == '__main__': description = 'Clean out or list the contents any tool dependency directory under the provided' description += 'tool dependency path. Remove any non-empty directories found if the ' diff --git a/scripts/tools/maf/check_loc_file.py b/scripts/tools/maf/check_loc_file.py index 3e61dc713e9..175f4fb206d 100644 --- a/scripts/tools/maf/check_loc_file.py +++ b/scripts/tools/maf/check_loc_file.py @@ -51,5 +51,6 @@ def __main__(): except Exception as e: print "Line %i is invalid: %s" % ( i, e ) + if __name__ == "__main__": __main__() diff --git a/scripts/tools/re_escape_output.py b/scripts/tools/re_escape_output.py index 9fd74d68d11..69508c2d640 100644 --- a/scripts/tools/re_escape_output.py +++ b/scripts/tools/re_escape_output.py @@ -29,5 +29,6 @@ def __main__(): output.writelines( lines ) output.close() + if __name__ == "__main__": __main__() diff --git a/scripts/transfer.py b/scripts/transfer.py index 84f0c446fed..3ac085b982a 100644 --- a/scripts/transfer.py +++ b/scripts/transfer.py @@ -285,6 +285,7 @@ def scp_transfer( transfer_job ): except Exception as e: return dict( state=transfer_job.states.ERROR, info='Error during file transfer: %s' % str( e ) ) + if __name__ == '__main__': arg_handler = ArgHandler() arg_handler.parse() diff --git a/scripts/update_shed_config_path.py b/scripts/update_shed_config_path.py index c7222aa3725..5b34f773451 100644 --- a/scripts/update_shed_config_path.py +++ b/scripts/update_shed_config_path.py @@ -45,6 +45,7 @@ def create_database( config_file ): model = mapping.init( database_connection ) return install_session, model + if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument( '--config_file', dest='config_file', required=True, help="The path to your Galaxy configuration .ini file." ) diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py index a98f87cc1f8..a8d3476c1c6 100644 --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -1701,4 +1701,5 @@ steps: 'input_steps', ) + RunJobsSummary = namedtuple('RunJobsSummary', ['history_id', 'workflow_id', 'invocation_id', 'inputs', 'jobs']) diff --git a/test/api/workflows_format_2/main.py b/test/api/workflows_format_2/main.py index 0a79382ea5e..77458568494 100644 --- a/test/api/workflows_format_2/main.py +++ b/test/api/workflows_format_2/main.py @@ -36,6 +36,7 @@ def convert_and_import_workflow(has_workflow, **kwds): import_kwds["publish"] = True return galaxy_interface.import_workflow(workflow, **import_kwds) + __all__ = ( 'convert_and_import_workflow', ) diff --git a/test/base/api_asserts.py b/test/base/api_asserts.py index 12f7b554eb9..19878851663 100644 --- a/test/base/api_asserts.py +++ b/test/base/api_asserts.py @@ -32,4 +32,5 @@ def assert_error_code_is( response, error_code ): err_code = response[ "err_code" ] assert err_code == int( error_code ), ASSERT_FAIL_ERROR_CODE % ( err_code, int( error_code ) ) + assert_has_key = assert_has_keys diff --git a/test/base/driver_util.py b/test/base/driver_util.py index 974abc691a8..12191216c18 100644 --- a/test/base/driver_util.py +++ b/test/base/driver_util.py @@ -478,6 +478,7 @@ def build_shed_app(simple_kwargs): log.info( "Embedded Toolshed application started" ) return app + ServerWrapper = collections.namedtuple('ServerWrapper', ['app', 'server', 'name', 'host', 'port']) @@ -492,6 +493,7 @@ def _stop(self): self.app.shutdown() log.info("Application %s stopped." % self.name) + ServerWrapper.stop = _stop diff --git a/test/unit/datatypes/dataproviders/test_line_dataproviders.py b/test/unit/datatypes/dataproviders/test_line_dataproviders.py index 56767e787ca..6742e069c20 100644 --- a/test/unit/datatypes/dataproviders/test_line_dataproviders.py +++ b/test/unit/datatypes/dataproviders/test_line_dataproviders.py @@ -299,5 +299,6 @@ class Test_BlockDataProvider( test_base_dataproviders.Test_FilteredDataProvider self.assertEqual( data, [{ 'id': 'One', 'seq': 'ABCD' }, { 'id': 'Two', 'seq': 'ABCDEFGH' }] ) self.assertCounters( provider, 2, 2, 2 ) + if __name__ == '__main__': unittest.main() diff --git a/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py b/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py index 8cbbefce773..c012220b849 100644 --- a/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py +++ b/test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py @@ -770,5 +770,6 @@ class TestDynamicToolDestination(unittest.TestCase): self.assertEqual(dt.bytes_to_str( "1000000000\n" ), "953.67 MB") self.assertEqual(dt.bytes_to_str( 1024, "fda" ), "1.00 KB") + if __name__ == '__main__': unittest.main() diff --git a/test/unit/managers/test_DatasetManager.py b/test/unit/managers/test_DatasetManager.py index f600dbc498d..cdcb5f3612a 100644 --- a/test/unit/managers/test_DatasetManager.py +++ b/test/unit/managers/test_DatasetManager.py @@ -214,6 +214,7 @@ class DatasetRBACPermissionsTestCase( BaseTestCase ): def testable_url_for(*a, **k): return '(fake url): %s, %s' % ( a, k ) + DatasetSerializer.url_for = staticmethod( testable_url_for ) diff --git a/test/unit/managers/test_HDAManager.py b/test/unit/managers/test_HDAManager.py index cd7aa448d6a..6bac97fa36b 100644 --- a/test/unit/managers/test_HDAManager.py +++ b/test/unit/managers/test_HDAManager.py @@ -351,6 +351,7 @@ class HDAManagerTestCase( HDATestCase ): def testable_url_for(*a, **k): return '(fake url): %s, %s' % ( a, k ) + hdas.HDASerializer.url_for = staticmethod( testable_url_for ) diff --git a/test/unit/managers/test_HDCAManager.py b/test/unit/managers/test_HDCAManager.py index cefd918b472..140bbd80708 100644 --- a/test/unit/managers/test_HDCAManager.py +++ b/test/unit/managers/test_HDCAManager.py @@ -60,6 +60,7 @@ class HDCATestCase( BaseTestCase, CreatesCollectionsMixin ): def testable_url_for(*a, **k): return '(fake url): %s, %s' % ( a, k ) + hdcas.HDCASerializer.url_for = staticmethod( testable_url_for ) diff --git a/test/unit/managers/test_HistoryContentsManager.py b/test/unit/managers/test_HistoryContentsManager.py index 57bbf646df2..2b9706bce41 100644 --- a/test/unit/managers/test_HistoryContentsManager.py +++ b/test/unit/managers/test_HistoryContentsManager.py @@ -346,7 +346,7 @@ class HistoryContentsFilterParserTestCase( HistoryAsContainerBaseTestCase ): self.assertRaises( ValueError, self.filter_parser.parse_date, '2009-02-13 18:13:00.' ) self.assertRaises( ValueError, self.filter_parser.parse_date, '2009-02-13 18:13:00.1234567' ) -# ============================================================================= + if __name__ == '__main__': # or more generally, nosetests test_resourcemanagers.py -s -v unittest.main() diff --git a/test/unit/managers/test_HistoryManager.py b/test/unit/managers/test_HistoryManager.py index 5d48a94de27..955aa1af6d8 100644 --- a/test/unit/managers/test_HistoryManager.py +++ b/test/unit/managers/test_HistoryManager.py @@ -385,6 +385,7 @@ class HistoryManagerTestCase( BaseTestCase ): def testable_url_for(*a, **k): return '(fake url): %s, %s' % ( a, k ) + HistorySerializer.url_for = staticmethod( testable_url_for ) hdas.HDASerializer.url_for = staticmethod( testable_url_for ) diff --git a/test/unit/visualizations/plugins/test_VisualizationsRegistry.py b/test/unit/visualizations/plugins/test_VisualizationsRegistry.py index 3e1b9bb12e3..f86f9100974 100644 --- a/test/unit/visualizations/plugins/test_VisualizationsRegistry.py +++ b/test/unit/visualizations/plugins/test_VisualizationsRegistry.py @@ -93,11 +93,6 @@ class VisualizationsRegistry_TestCase( test_utils.unittest.TestCase ): 'vis1.xml': 'blerbler' }, }, - 'not_a_vis1': { - # no config - 'static': {}, - 'templates': {}, - }, # empty 'not_a_vis2': {}, 'not_a_vis3': 'blerbler', @@ -107,6 +102,11 @@ class VisualizationsRegistry_TestCase( test_utils.unittest.TestCase ): 'not_a_vis4.xml': 'blerbler' } }, + 'not_a_vis5': { + # no config + 'static': {}, + 'templates': {}, + }, } }) mock_app = galaxy_mock.MockApp( root=mock_app_dir.root_path ) diff --git a/test/unit/workflows/test_modules.py b/test/unit/workflows/test_modules.py index a8ef67ef0fd..04a0c878390 100644 --- a/test/unit/workflows/test_modules.py +++ b/test/unit/workflows/test_modules.py @@ -230,6 +230,7 @@ def test_tool_version_same(): ) assert not module.version_changes + TEST_WORKFLOW_YAML = """ steps: - type: "data_input" diff --git a/tools/data_source/data_source.py b/tools/data_source/data_source.py index 80756c23d7f..53121f1376c 100644 --- a/tools/data_source/data_source.py +++ b/tools/data_source/data_source.py @@ -114,5 +114,6 @@ def __main__(): json_file.write( "%s\n" % dumps( info ) ) + if __name__ == "__main__": __main__() diff --git a/tools/data_source/genbank.py b/tools/data_source/genbank.py index 1276814e22b..91f59d3c64b 100644 --- a/tools/data_source/genbank.py +++ b/tools/data_source/genbank.py @@ -18,6 +18,7 @@ def make_fasta(rec): body = '\n'.join(textwrap.wrap(rec.seq.data, width=80)) return head, body + if __name__ == '__main__': mode = sys.argv[1] text = sys.argv[2] diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py index 85355c3eb3b..972d62c5686 100644 --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -420,5 +420,6 @@ def __main__(): except: pass + if __name__ == '__main__': __main__() diff --git a/tools/evolution/add_scores.py b/tools/evolution/add_scores.py index db4edef05c9..f9a4493b060 100755 --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -108,5 +108,6 @@ def main(): ifh.close() ofh.close() + if __name__ == "__main__": main() diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py index 4df31361d03..38707ee4084 100755 --- a/tools/extract/extract_genomic_dna.py +++ b/tools/extract/extract_genomic_dna.py @@ -311,5 +311,6 @@ def __main__(): os.remove( seq_path ) os.remove( tmp_name ) + if __name__ == "__main__": __main__() diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver_wrapper.py index 83fe6ea9110..0ba1af81e08 100644 --- a/tools/extract/liftOver_wrapper.py +++ b/tools/extract/liftOver_wrapper.py @@ -36,6 +36,7 @@ def safe_bed_file(infile): out_handle.close() return fname + if len( sys.argv ) < 9: stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey infile_type minMatch multiple " ) diff --git a/tools/filters/axt_to_fasta.py b/tools/filters/axt_to_fasta.py index da442c9282f..d0b08594c4f 100644 --- a/tools/filters/axt_to_fasta.py +++ b/tools/filters/axt_to_fasta.py @@ -47,5 +47,6 @@ def print_component_as_fasta(c, id=None): print(header) print(c.text) + if __name__ == "__main__": main() diff --git a/tools/filters/bed_to_gff_converter.py b/tools/filters/bed_to_gff_converter.py index b1d7df54732..82171549f04 100644 --- a/tools/filters/bed_to_gff_converter.py +++ b/tools/filters/bed_to_gff_converter.py @@ -73,5 +73,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/tools/filters/catWrapper.py b/tools/filters/catWrapper.py index af59240d0ea..e45553f7a75 100644 --- a/tools/filters/catWrapper.py +++ b/tools/filters/catWrapper.py @@ -27,5 +27,6 @@ def main(): except: stop_err("Error encountered with cat.") + if __name__ == "__main__": main() diff --git a/tools/filters/convert_characters.py b/tools/filters/convert_characters.py index 8d977bb1a09..efbb1543b5b 100644 --- a/tools/filters/convert_characters.py +++ b/tools/filters/convert_characters.py @@ -49,5 +49,6 @@ def __main__(): if skipped: print("Skipped %d lines as invalid." % skipped) + if __name__ == "__main__": __main__() diff --git a/tools/filters/gff/extract_GFF_Features.py b/tools/filters/gff/extract_GFF_Features.py index 0b0a5bbe67d..0396d12a5e0 100644 --- a/tools/filters/gff/extract_GFF_Features.py +++ b/tools/filters/gff/extract_GFF_Features.py @@ -49,5 +49,6 @@ def main(): print('Column %d features: %s' % ( column + 1, features )) + if __name__ == "__main__": main() diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py index a731df826b5..68c4a7b5a8d 100644 --- a/tools/filters/gff/gff_filter_by_attribute.py +++ b/tools/filters/gff/gff_filter_by_attribute.py @@ -38,10 +38,10 @@ def check_for_executable( text, description='' ): if operand in secured: stop_err( "Illegal value '%s' in %s '%s'" % ( operand, description, text ) ) + # # Process inputs. # - in_fname = sys.argv[1] out_fname = sys.argv[2] cond_text = sys.argv[3] @@ -97,6 +97,7 @@ def get_value(name, a_type, values_dict): else: return None + # Read and filter input file, skipping invalid lines code = ''' for i, line in enumerate( open( in_fname ) ): diff --git a/tools/filters/gff/gff_filter_by_feature_count.py b/tools/filters/gff/gff_filter_by_feature_count.py index ea03f992548..7c5a9454027 100644 --- a/tools/filters/gff/gff_filter_by_feature_count.py +++ b/tools/filters/gff/gff_filter_by_feature_count.py @@ -88,5 +88,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/tools/filters/gff/gtf_filter_by_attribute_values_list.py b/tools/filters/gff/gtf_filter_by_attribute_values_list.py index 8ddf043d457..9ff4c5379db 100644 --- a/tools/filters/gff/gtf_filter_by_attribute_values_list.py +++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.py @@ -61,6 +61,7 @@ def gff_filter( gff_file, attribute_name, ids_file, output_file ): output.write( line ) output.close() + if __name__ == "__main__": # Handle args. if len( sys.argv ) != 5: diff --git a/tools/filters/gff_to_bed_converter.py b/tools/filters/gff_to_bed_converter.py index 898bbc6cf30..b0ccd89fbaa 100644 --- a/tools/filters/gff_to_bed_converter.py +++ b/tools/filters/gff_to_bed_converter.py @@ -131,5 +131,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/tools/filters/grep.py b/tools/filters/grep.py index 5aa9c4e68da..81486ec843d 100644 --- a/tools/filters/grep.py +++ b/tools/filters/grep.py @@ -132,5 +132,6 @@ def main(): # return error code return errorcode + if __name__ == "__main__": main() diff --git a/tools/filters/gtf_to_bedgraph_converter.py b/tools/filters/gtf_to_bedgraph_converter.py index 1988161aa83..eb6304887e6 100644 --- a/tools/filters/gtf_to_bedgraph_converter.py +++ b/tools/filters/gtf_to_bedgraph_converter.py @@ -82,5 +82,6 @@ def __main__(): info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line ) print(info_msg) + if __name__ == "__main__": __main__() diff --git a/tools/filters/join.py b/tools/filters/join.py index 43caa87c4be..6b610f244e2 100644 --- a/tools/filters/join.py +++ b/tools/filters/join.py @@ -385,5 +385,6 @@ def main(): return join_files( filename1, column1, filename2, column2, out_filename, split, options.buffer, options.keep_unmatched, options.keep_partial, options.index_depth, fill_options=fill_options ) + if __name__ == "__main__": main() diff --git a/tools/filters/joinWrapper.py b/tools/filters/joinWrapper.py index e2a9820d418..7e931bf23b1 100644 --- a/tools/filters/joinWrapper.py +++ b/tools/filters/joinWrapper.py @@ -72,5 +72,6 @@ def main(): except Exception as exj: stop_err('Error joining the two datasets -> %s' % str(exj)) + if __name__ == "__main__": main() diff --git a/tools/filters/lav_to_bed.py b/tools/filters/lav_to_bed.py index 04b52fec3ad..264a6b0c5e4 100644 --- a/tools/filters/lav_to_bed.py +++ b/tools/filters/lav_to_bed.py @@ -48,5 +48,6 @@ def main(): print("%d lav blocks read, %d regions written\n" % (lavsRead, bedsWritten)) + if __name__ == "__main__": main() diff --git a/tools/filters/mergeCols.py b/tools/filters/mergeCols.py index 97b0187d489..9e27a20ae71 100644 --- a/tools/filters/mergeCols.py +++ b/tools/filters/mergeCols.py @@ -38,5 +38,6 @@ def __main__(): if skipped_lines > 0: print('Skipped %d invalid lines' % skipped_lines) + if __name__ == "__main__": __main__() diff --git a/tools/filters/random_lines_two_pass.py b/tools/filters/random_lines_two_pass.py index e02086f9394..44847a1388b 100644 --- a/tools/filters/random_lines_two_pass.py +++ b/tools/filters/random_lines_two_pass.py @@ -73,5 +73,6 @@ def __main__(): if options.seed is not None: print('Used random seed of "%s".' % options.seed) + if __name__ == "__main__": __main__() diff --git a/tools/filters/randomlines.py b/tools/filters/randomlines.py index b44dcafb4c6..eae7cf97e34 100644 --- a/tools/filters/randomlines.py +++ b/tools/filters/randomlines.py @@ -31,5 +31,6 @@ def main(): open(sys.argv[3], 'w').write( "\n".join(kept) ) + if __name__ == "__main__": main() diff --git a/tools/filters/secure_hash_message_digest.py b/tools/filters/secure_hash_message_digest.py index cbf4d8ac5f8..27872d90d42 100644 --- a/tools/filters/secure_hash_message_digest.py +++ b/tools/filters/secure_hash_message_digest.py @@ -43,5 +43,6 @@ def __main__(): output.write( '%s\n' % ( '\t'.join( x.hexdigest() for x in algorithms.values() ) ) ) output.close() + if __name__ == "__main__": __main__() diff --git a/tools/filters/sorter.py b/tools/filters/sorter.py index d9619bce5e2..dda21f166c9 100644 --- a/tools/filters/sorter.py +++ b/tools/filters/sorter.py @@ -53,5 +53,6 @@ def main(): # exit sys.exit(0) + if __name__ == "__main__": main() diff --git a/tools/filters/trimmer.py b/tools/filters/trimmer.py index 366b3516524..9c71ff2f8bb 100644 --- a/tools/filters/trimmer.py +++ b/tools/filters/trimmer.py @@ -108,5 +108,6 @@ options (listed below) default to 'None' if omitted line = '\t'.join(fields) print(line) + if __name__ == "__main__": main() diff --git a/tools/filters/ucsc_gene_bed_to_exon_bed.py b/tools/filters/ucsc_gene_bed_to_exon_bed.py index 38aea650cfc..301a6704e76 100755 --- a/tools/filters/ucsc_gene_bed_to_exon_bed.py +++ b/tools/filters/ucsc_gene_bed_to_exon_bed.py @@ -134,5 +134,6 @@ def print_tab_sep(out_file, *args ): """Print items in `l` to stdout separated by tabs""" print('\t'.join(str( f ) for f in args), file=out_file) + if __name__ == "__main__": main() diff --git a/tools/filters/ucsc_gene_bed_to_intron_bed.py b/tools/filters/ucsc_gene_bed_to_intron_bed.py index 73e0c427a2b..9be6f91313d 100755 --- a/tools/filters/ucsc_gene_bed_to_intron_bed.py +++ b/tools/filters/ucsc_gene_bed_to_intron_bed.py @@ -80,5 +80,6 @@ def print_tab_sep(out_file, *args ): """Print items in `l` to stdout separated by tabs""" print('\t'.join(str( f ) for f in args), file=out_file) + if __name__ == "__main__": main() diff --git a/tools/filters/ucsc_gene_table_to_intervals.py b/tools/filters/ucsc_gene_table_to_intervals.py index 31dd80fd766..744610a2606 100755 --- a/tools/filters/ucsc_gene_table_to_intervals.py +++ b/tools/filters/ucsc_gene_table_to_intervals.py @@ -112,5 +112,6 @@ def print_tab_sep(out_file, *args ): """Print items in `l` to stdout separated by tabs""" print('\t'.join(str( f ) for f in args), file=out_file) + if __name__ == "__main__": main() diff --git a/tools/filters/uniq.py b/tools/filters/uniq.py index f7513dd1c1c..07bbefacb9b 100644 --- a/tools/filters/uniq.py +++ b/tools/filters/uniq.py @@ -136,5 +136,6 @@ def main(): print("Count of unique values in " + columns_for_display) return errorcode + if __name__ == "__main__": main() diff --git a/tools/filters/wiggle_to_simple.py b/tools/filters/wiggle_to_simple.py index 2dacdf58544..855523b1b62 100755 --- a/tools/filters/wiggle_to_simple.py +++ b/tools/filters/wiggle_to_simple.py @@ -43,5 +43,6 @@ def main(): in_file.close() out_file.close() + if __name__ == "__main__": main() diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py index ee903f9c483..7e3f40908b7 100644 --- a/tools/genomespace/genomespace_exporter.py +++ b/tools/genomespace/genomespace_exporter.py @@ -314,6 +314,7 @@ def send_file_to_genomespace( genomespace_site, username, token, source_filename log_file.write( "\n" ) return upload_result + if __name__ == '__main__': # Parse Command Line parser = optparse.OptionParser() diff --git a/tools/genomespace/genomespace_file_browser.py b/tools/genomespace/genomespace_file_browser.py index dee609d21d6..07559fe80af 100644 --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -206,6 +206,7 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit metadata_parameter_file.close() return True + if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option( '-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file' ) diff --git a/tools/genomespace/genomespace_importer.py b/tools/genomespace/genomespace_importer.py index 127cda206ca..c06f00aff80 100644 --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -207,6 +207,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge metadata_parameter_file.close() return True + if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option( '-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file' ) diff --git a/tools/maf/interval2maf.py b/tools/maf/interval2maf.py index 94622807df7..73cf6c81310 100755 --- a/tools/maf/interval2maf.py +++ b/tools/maf/interval2maf.py @@ -140,5 +140,6 @@ def __main__(): else: print("No valid regions have been provided.") + if __name__ == "__main__": __main__() diff --git a/tools/maf/interval_maf_to_merged_fasta.py b/tools/maf/interval_maf_to_merged_fasta.py index cf7d81f058c..a2375ec769b 100644 --- a/tools/maf/interval_maf_to_merged_fasta.py +++ b/tools/maf/interval_maf_to_merged_fasta.py @@ -199,5 +199,6 @@ def __main__(): if line_count > 0 and options.geneBED: print("This tool requires your input file to conform to the 12 column BED standard.") + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_by_block_number.py b/tools/maf/maf_by_block_number.py index b31f0706124..060df3aa07d 100644 --- a/tools/maf/maf_by_block_number.py +++ b/tools/maf/maf_by_block_number.py @@ -45,5 +45,6 @@ def __main__(): if len( failed_lines ) > 0: print("Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )) + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_filter.py b/tools/maf/maf_filter.py index 4ece84307bc..eae705359d7 100644 --- a/tools/maf/maf_filter.py +++ b/tools/maf/maf_filter.py @@ -69,5 +69,6 @@ def main(): else: print('Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )) + if __name__ == "__main__": main() diff --git a/tools/maf/maf_limit_size.py b/tools/maf/maf_limit_size.py index eaeb434164e..0c0324ed92e 100644 --- a/tools/maf/maf_limit_size.py +++ b/tools/maf/maf_limit_size.py @@ -32,5 +32,6 @@ def __main__(): blocks_kept += 1 print('Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )) + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_limit_to_species.py b/tools/maf/maf_limit_to_species.py index 397daa7d5fe..ac4abde8ab2 100644 --- a/tools/maf/maf_limit_to_species.py +++ b/tools/maf/maf_limit_to_species.py @@ -49,5 +49,6 @@ def main(): print("Restricted to species: %s." % ", ".join( species )) print("%i MAF blocks have been kept." % maf_blocks_kept) + if __name__ == "__main__": main() diff --git a/tools/maf/maf_reverse_complement.py b/tools/maf/maf_reverse_complement.py index 9b2d11a6f9d..681a944223e 100644 --- a/tools/maf/maf_reverse_complement.py +++ b/tools/maf/maf_reverse_complement.py @@ -39,5 +39,6 @@ def __main__(): print("%i regions were reverse complemented." % count) maf_writer.close() + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_split_by_species.py b/tools/maf/maf_split_by_species.py index f48dfc3cec9..07a876fd60e 100644 --- a/tools/maf/maf_split_by_species.py +++ b/tools/maf/maf_split_by_species.py @@ -41,5 +41,6 @@ def __main__(): else: print("No alignment blocks were created.") + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_stats.py b/tools/maf/maf_stats.py index 9976d12ac68..261244ea12d 100644 --- a/tools/maf/maf_stats.py +++ b/tools/maf/maf_stats.py @@ -110,5 +110,6 @@ def __main__(): print("%i regions were invalid." % ( num_bad_region )) maf_utilities.remove_temp_index_file( index_filename ) + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_thread_for_species.py b/tools/maf/maf_thread_for_species.py index a355174531d..581a936852a 100644 --- a/tools/maf/maf_thread_for_species.py +++ b/tools/maf/maf_thread_for_species.py @@ -50,5 +50,6 @@ def main(): print("Restricted to species: %s." % ", ".join( species )) + if __name__ == "__main__": main() diff --git a/tools/maf/maf_to_bed.py b/tools/maf/maf_to_bed.py index fa0de931c44..803bf97c810 100644 --- a/tools/maf/maf_to_bed.py +++ b/tools/maf/maf_to_bed.py @@ -79,5 +79,6 @@ def __main__(): print("#FILE1_DBKEY\t%s" % ( primary_spec )) + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_to_fasta_multiple_sets.py b/tools/maf/maf_to_fasta_multiple_sets.py index 0c8da4c99c5..54c30e51b33 100755 --- a/tools/maf/maf_to_fasta_multiple_sets.py +++ b/tools/maf/maf_to_fasta_multiple_sets.py @@ -56,5 +56,6 @@ def __main__(): file_out.write( "\n" ) file_out.close() + if __name__ == "__main__": __main__() diff --git a/tools/maf/maf_to_interval.py b/tools/maf/maf_to_interval.py index a19e39600fb..8cbddaca900 100644 --- a/tools/maf/maf_to_interval.py +++ b/tools/maf/maf_to_interval.py @@ -66,5 +66,6 @@ def __main__(): for file_out in out_files.values(): file_out.close() + if __name__ == "__main__": __main__() diff --git a/tools/maf/vcf_to_maf_customtrack.py b/tools/maf/vcf_to_maf_customtrack.py index a5a828dfbee..2c49819d25d 100644 --- a/tools/maf/vcf_to_maf_customtrack.py +++ b/tools/maf/vcf_to_maf_customtrack.py @@ -158,5 +158,6 @@ def main(): if non_spec_skipped: print('Skipped %i non-specification compliant indels.' % non_spec_skipped) + if __name__ == "__main__": main() diff --git a/tools/meme/fimo_wrapper.py b/tools/meme/fimo_wrapper.py index 34c66a49a41..86e5c63130c 100644 --- a/tools/meme/fimo_wrapper.py +++ b/tools/meme/fimo_wrapper.py @@ -73,5 +73,6 @@ def main(): out_file.write( "%s\n" % "\t".join( [ fields[1], str( start ), str( end ), fields[0], fields[4], strand, sequence, fields[5], fields[6] ] ) ) out_file.close() + if __name__ == "__main__": main() diff --git a/tools/metag_tools/blat_wrapper.py b/tools/metag_tools/blat_wrapper.py index f73420d6dbe..54d460693d5 100644 --- a/tools/metag_tools/blat_wrapper.py +++ b/tools/metag_tools/blat_wrapper.py @@ -107,5 +107,6 @@ def __main__(): os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) ) os.remove( output_tempfile ) + if __name__ == '__main__': __main__() diff --git a/tools/next_gen_conversion/fastq_conversions.py b/tools/next_gen_conversion/fastq_conversions.py index 7b7a84af775..57373467e12 100644 --- a/tools/next_gen_conversion/fastq_conversions.py +++ b/tools/next_gen_conversion/fastq_conversions.py @@ -40,5 +40,6 @@ def __main__(): except Exception as eq: stop_err("Error converting data format.\n" + str(eq)) + if __name__ == "__main__": __main__() diff --git a/tools/next_gen_conversion/fastq_gen_conv.py b/tools/next_gen_conversion/fastq_gen_conv.py index b5fc87ce69d..2e2e2be55fd 100644 --- a/tools/next_gen_conversion/fastq_gen_conv.py +++ b/tools/next_gen_conversion/fastq_gen_conv.py @@ -172,5 +172,6 @@ def __main__(): outmsg += '\nThere were %s bad blocks skipped' % (bad_blocks) sys.stdout.write(outmsg) + if __name__ == "__main__": __main__() diff --git a/tools/next_gen_conversion/solid2fastq.py b/tools/next_gen_conversion/solid2fastq.py index db5d3c4885a..ec41bd6a3ec 100644 --- a/tools/next_gen_conversion/solid2fastq.py +++ b/tools/next_gen_conversion/solid2fastq.py @@ -196,5 +196,6 @@ def main(): f_out.close() + if __name__ == "__main__": main() diff --git a/tools/next_gen_conversion/solid_to_fastq.py b/tools/next_gen_conversion/solid_to_fastq.py index 8030da2985b..dc748adbef3 100644 --- a/tools/next_gen_conversion/solid_to_fastq.py +++ b/tools/next_gen_conversion/solid_to_fastq.py @@ -69,5 +69,6 @@ def __main__(): tmpf.close() sys.stdout.write('converted SOLiD data') + if __name__ == "__main__": __main__() diff --git a/tools/ngs_simulation/ngs_simulation.py b/tools/ngs_simulation/ngs_simulation.py index a4eb4d8b3de..c30ed448567 100644 --- a/tools/ngs_simulation/ngs_simulation.py +++ b/tools/ngs_simulation/ngs_simulation.py @@ -275,5 +275,6 @@ def __main__(): dev.off() ''' ) + if __name__ == "__main__": __main__() diff --git a/tools/phenotype_association/pagetag.py b/tools/phenotype_association/pagetag.py index f005a99951d..fd521798698 100755 --- a/tools/phenotype_association/pagetag.py +++ b/tools/phenotype_association/pagetag.py @@ -269,6 +269,7 @@ def usage(): print("-f,--freq : the minimum MAF required (default: 0.0)", file=f) print("-s,--sample : a list of samples to be clustered", file=f) + if __name__ == "__main__": try: opts, args = getopt(argv[1:], "hds:r:f:", diff --git a/tools/phenotype_association/senatag.py b/tools/phenotype_association/senatag.py index 02e74a793cb..61e4e39df8c 100755 --- a/tools/phenotype_association/senatag.py +++ b/tools/phenotype_association/senatag.py @@ -222,6 +222,7 @@ def usage(): print("-e,--excluded : file with names of SNPs that cannot be TagSNPs", file=f) print("-r,--required : file with names of SNPs that should be TagSNPs", file=f) + if __name__ == "__main__": try: opts, args = getopt(argv[1:], "hdr:e:", diff --git a/tools/solid_tools/maq_cs_wrapper.py b/tools/solid_tools/maq_cs_wrapper.py index 3dcb1897479..1a8917e1d14 100644 --- a/tools/solid_tools/maq_cs_wrapper.py +++ b/tools/solid_tools/maq_cs_wrapper.py @@ -268,5 +268,6 @@ def __main__(): fout_c.seek(0) os.system("cat %s %s %s %s %s | cat > %s" % (fcov.name, fout_a.name, fout_t.name, fout_g.name, fout_c.name, out_f3name)) + if __name__ == "__main__": __main__() diff --git a/tools/solid_tools/solid_qual_stats.py b/tools/solid_tools/solid_qual_stats.py index 742ea062387..d8299e606ec 100644 --- a/tools/solid_tools/solid_qual_stats.py +++ b/tools/solid_tools/solid_qual_stats.py @@ -135,5 +135,6 @@ def __main__(): if invalid_positions: print("Skipped stats computation for %d read positions." % invalid_positions) + if __name__ == "__main__": __main__() diff --git a/tools/sr_assembly/velveth_wrapper.py b/tools/sr_assembly/velveth_wrapper.py index 8e0ea0a5b6f..cbdbec672ce 100644 --- a/tools/sr_assembly/velveth_wrapper.py +++ b/tools/sr_assembly/velveth_wrapper.py @@ -56,5 +56,6 @@ def __main__(): f.write("\n".join( rval )) f.write('\n') + if __name__ == "__main__": __main__() diff --git a/tools/sr_mapping/bfast_wrapper.py b/tools/sr_mapping/bfast_wrapper.py index f72cc9142cb..f240a6401b9 100644 --- a/tools/sr_mapping/bfast_wrapper.py +++ b/tools/sr_mapping/bfast_wrapper.py @@ -346,5 +346,6 @@ def __main__(): if os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) + if __name__ == "__main__": __main__() diff --git a/tools/sr_mapping/srma_wrapper.py b/tools/sr_mapping/srma_wrapper.py index 31cd3e73be1..7c73fc68601 100644 --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -196,5 +196,6 @@ def __main__(): if os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) + if __name__ == "__main__": __main__() diff --git a/tools/stats/aggregate_scores_in_intervals.py b/tools/stats/aggregate_scores_in_intervals.py index 9e18d8776b2..2fb7d410dc3 100755 --- a/tools/stats/aggregate_scores_in_intervals.py +++ b/tools/stats/aggregate_scores_in_intervals.py @@ -247,5 +247,6 @@ def main(): if skipped_lines == i: print('Consider changing the metadata for the input dataset by clicking on the pencil icon in the history item.') + if __name__ == "__main__": main() diff --git a/tools/stats/filtering.py b/tools/stats/filtering.py index c6781e3b598..068b89c3c9a 100644 --- a/tools/stats/filtering.py +++ b/tools/stats/filtering.py @@ -139,6 +139,7 @@ def stop_err( msg ): sys.stderr.write( msg ) sys.exit() + in_fname = sys.argv[1] out_fname = sys.argv[2] cond_text = sys.argv[3] diff --git a/tools/stats/grouping.py b/tools/stats/grouping.py index 9aef12f9cff..cbad9d4826e 100644 --- a/tools/stats/grouping.py +++ b/tools/stats/grouping.py @@ -174,5 +174,6 @@ def main(): fout.close() tmpfile.close() + if __name__ == "__main__": main() diff --git a/tools/stats/gsummary.py b/tools/stats/gsummary.py index 9181c8caf5e..0ede475517b 100755 --- a/tools/stats/gsummary.py +++ b/tools/stats/gsummary.py @@ -119,5 +119,6 @@ def main(): if skipped_lines: print("Skipped %d invalid lines beginning with line #%d. See tool tips for data requirements." % ( skipped_lines, first_invalid_line )) + if __name__ == "__main__": main()