mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merging with dev
This commit is contained in:
anuprulez
@@ -9,72 +9,15 @@ lib/galaxy/actions/
|
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lib/galaxy/auth/
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lib/galaxy/config.py
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lib/galaxy/containers/
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lib/galaxy/dataset_collections/builder.py
|
||||
lib/galaxy/dataset_collections/__init__.py
|
||||
lib/galaxy/dataset_collections/structure.py
|
||||
lib/galaxy/dataset_collections/subcollections.py
|
||||
lib/galaxy/dataset_collections/type_description.py
|
||||
lib/galaxy/dataset_collections/types/__init__.py
|
||||
lib/galaxy/datatypes/assembly.py
|
||||
lib/galaxy/datatypes/binary.py
|
||||
lib/galaxy/datatypes/checkers.py
|
||||
lib/galaxy/datatypes/constructive_solid_geometry.py
|
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lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
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lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
|
||||
lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
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lib/galaxy/datatypes/converters/bed_to_gff_converter.py
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lib/galaxy/datatypes/converters/bgzip.py
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lib/galaxy/datatypes/converters/fasta_to_len.py
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lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
|
||||
lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
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lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
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lib/galaxy/datatypes/converters/gff_to_bed_converter.py
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lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
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lib/galaxy/datatypes/converters/__init__.py
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lib/galaxy/datatypes/converters/interval_to_bed_converter.py
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lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
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lib/galaxy/datatypes/converters/interval_to_coverage.py
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lib/galaxy/datatypes/converters/interval_to_fli.py
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lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
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lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
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lib/galaxy/datatypes/converters/lped_to_fped_converter.py
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lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
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lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
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lib/galaxy/datatypes/converters/maf_to_interval_converter.py
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lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
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lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
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lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
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lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
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lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
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lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
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lib/galaxy/datatypes/coverage.py
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lib/galaxy/datatypes/dataproviders/base.py
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lib/galaxy/datatypes/dataproviders/exceptions.py
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lib/galaxy/datatypes/dataproviders/__init__.py
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lib/galaxy/datatypes/data.py
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lib/galaxy/datatypes/display_applications/__init__.py
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lib/galaxy/datatypes/display_applications/util.py
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lib/galaxy/datatypes/genetics.py
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lib/galaxy/datatypes/images.py
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lib/galaxy/datatypes/__init__.py
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lib/galaxy/datatypes/interval.py
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lib/galaxy/datatypes/metadata.py
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lib/galaxy/datatypes/msa.py
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lib/galaxy/datatypes/ngsindex.py
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lib/galaxy/datatypes/proteomics.py
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lib/galaxy/datatypes/registry.py
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lib/galaxy/datatypes/sequence.py
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lib/galaxy/datatypes/tabular.py
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lib/galaxy/datatypes/text.py
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lib/galaxy/datatypes/tracks.py
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lib/galaxy/datatypes/util/
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lib/galaxy/dataset_collections/
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lib/galaxy/datatypes/
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lib/galaxy/dependencies/
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lib/galaxy/eggs/
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lib/galaxy/exceptions/__init__.py
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lib/galaxy/exceptions/
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lib/galaxy/external_services/__init__.py
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lib/galaxy/external_services/parameters.py
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lib/galaxy/external_services/result_handlers/basic.py
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lib/galaxy/external_services/result_handlers/__init__.py
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lib/galaxy_ext/
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lib/galaxy/forms/__init__.py
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lib/galaxy/jobs/actions/
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lib/galaxy/jobs/command_factory.py
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@@ -113,15 +56,7 @@ lib/galaxy/managers/lddas.py
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lib/galaxy/managers/libraries.py
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lib/galaxy/managers/secured.py
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lib/galaxy/managers/taggable.py
|
||||
lib/galaxy/model/__init__.py
|
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lib/galaxy/model/item_attrs.py
|
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lib/galaxy/model/mapping.py
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lib/galaxy/model/metadata.py
|
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lib/galaxy/model/migrate/
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lib/galaxy/model/orm/
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lib/galaxy/model/tool_shed_install/migrate/__init__.py
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lib/galaxy/model/tool_shed_install/migrate/versions/
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lib/galaxy/model/util.py
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lib/galaxy/model/
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lib/galaxy/objectstore/pulsar.py
|
||||
lib/galaxy/objectstore/s3_multipart_upload.py
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lib/galaxy/openid/__init__.py
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@@ -129,7 +64,7 @@ lib/galaxy/quota/
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lib/galaxy/sample_tracking/data_transfer.py
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lib/galaxy/sample_tracking/__init__.py
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lib/galaxy/sample_tracking/sample.py
|
||||
lib/galaxy/security/validate_user_input.py
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lib/galaxy/security/
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lib/galaxy/tags/
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lib/galaxy/tools/
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lib/galaxy/util/
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@@ -174,6 +109,7 @@ lib/galaxy/webapps/galaxy/api/samples.py
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lib/galaxy/webapps/galaxy/api/tools.py
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lib/galaxy/webapps/galaxy/api/tours.py
|
||||
lib/galaxy/webapps/galaxy/api/workflows.py
|
||||
lib/galaxy/webapps/galaxy/config_watchers.py
|
||||
lib/galaxy/webapps/galaxy/controllers/async.py
|
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lib/galaxy/webapps/galaxy/controllers/data_manager.py
|
||||
lib/galaxy/webapps/galaxy/controllers/error.py
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@@ -186,7 +122,6 @@ lib/galaxy/webapps/galaxy/controllers/requests.py
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lib/galaxy/webapps/galaxy/controllers/search.py
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||||
lib/galaxy/webapps/galaxy/controllers/tool_runner.py
|
||||
lib/galaxy/webapps/galaxy/controllers/userskeys.py
|
||||
lib/galaxy/webapps/galaxy/config_watchers.py
|
||||
lib/galaxy/webapps/galaxy/__init__.py
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||||
lib/galaxy/webapps/__init__.py
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lib/galaxy/webapps/reports/config.py
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@@ -209,13 +144,11 @@ lib/galaxy/webapps/tool_shed/util/__init__.py
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lib/galaxy/webapps/tool_shed/util/ratings_util.py
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lib/galaxy/webapps/tool_shed/util/shed_statistics.py
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lib/galaxy/webapps/util.py
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||||
lib/galaxy/workflow/extract.py
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||||
lib/galaxy/workflow/__init__.py
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||||
lib/galaxy/workflow/render.py
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||||
lib/galaxy/workflow/run.py
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||||
lib/galaxy/workflow/schedulers/
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||||
lib/galaxy/workflow/steps.py
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||||
lib/galaxy/work/__init__.py
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||||
lib/galaxy/webhooks/
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||||
lib/galaxy/work/
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||||
lib/galaxy/workflow/
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||||
lib/galaxy_ext/
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||||
lib/log_tempfile.py
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||||
lib/mimeparse.py
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||||
lib/psyco_full.py
|
||||
lib/tool_shed/
|
||||
@@ -366,6 +299,7 @@ test/unit/shed_unit/test_fabric_util.py
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||||
test/unit/shed_unit/test_td_common_util.py
|
||||
test/unit/test_galaxy_transactions.py
|
||||
test/unit/test_lazy_process.py
|
||||
test/unit/test_objectstore.py
|
||||
test/unit/test_routes.py
|
||||
test/unit/test_security_helper.py
|
||||
test/unit/test_sockets.py
|
||||
@@ -393,6 +327,5 @@ test/unit/web/base/__init__.py
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||||
test/unit/web/framework/__init__.py
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test/unit/web/__init__.py
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||||
test/unit/workflows/
|
||||
test/unit/test_objectstore.py
|
||||
tool_list.py
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||||
tools/
|
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|
||||
+4
-27
@@ -8,23 +8,7 @@ lib/galaxy/auth/
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lib/galaxy/config.py
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lib/galaxy/containers/
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lib/galaxy/dataset_collections/
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lib/galaxy/datatypes/assembly.py
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lib/galaxy/datatypes/binary.py
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lib/galaxy/datatypes/constructive_solid_geometry.py
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lib/galaxy/datatypes/converters/
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lib/galaxy/datatypes/dataproviders/
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lib/galaxy/datatypes/data.py
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||||
lib/galaxy/datatypes/genetics.py
|
||||
lib/galaxy/datatypes/images.py
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||||
lib/galaxy/datatypes/interval.py
|
||||
lib/galaxy/datatypes/msa.py
|
||||
lib/galaxy/datatypes/ngsindex.py
|
||||
lib/galaxy/datatypes/proteomics.py
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||||
lib/galaxy/datatypes/registry.py
|
||||
lib/galaxy/datatypes/sequence.py
|
||||
lib/galaxy/datatypes/sniff.py
|
||||
lib/galaxy/datatypes/tabular.py
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||||
lib/galaxy/datatypes/tracks.py
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||||
lib/galaxy/datatypes/
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lib/galaxy/dependencies/
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lib/galaxy/eggs/
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lib/galaxy/exceptions/
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@@ -32,12 +16,7 @@ lib/galaxy/external_services/
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lib/galaxy/forms/
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lib/galaxy/jobs/
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lib/galaxy/managers/
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||||
lib/galaxy/model/__init__.py
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lib/galaxy/model/item_attrs.py
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||||
lib/galaxy/model/mapping.py
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||||
lib/galaxy/model/metadata.py
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||||
lib/galaxy/model/migrate/
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||||
lib/galaxy/model/orm/now.py
|
||||
lib/galaxy/model/
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lib/galaxy/objectstore/
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lib/galaxy/openid/
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lib/galaxy/quota/
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@@ -69,11 +48,9 @@ lib/galaxy/webapps/tool_shed/controllers/user.py
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lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
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||||
lib/galaxy/webapps/tool_shed/__init__.py
|
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lib/galaxy/webapps/tool_shed/util/ratings_util.py
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||||
lib/galaxy/webhooks/
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||||
lib/galaxy/work/
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lib/galaxy/workflow/extract.py
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||||
lib/galaxy/workflow/run.py
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||||
lib/galaxy/workflow/schedulers/
|
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lib/galaxy/workflow/steps.py
|
||||
lib/galaxy/workflow/
|
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lib/galaxy_ext/
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||||
lib/log_tempfile.py
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lib/psyco_full.py
|
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|
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@@ -17,6 +17,7 @@ database/files
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database/jobs_directory
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database/job_working_directory
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database/pbs
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database/test_errors
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database/tmp
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database/*.sqlite
|
||||
database/openid_consumer_cache
|
||||
|
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@@ -90,7 +90,7 @@ window.app = function app( options, bootstrapped ){
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'(/)pages(/)(:action_id)' : 'show_pages',
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'(/)visualizations/list_published(/)' : 'show_visualizations',
|
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'(/)workflows/list_published(/)' : 'show_workflows_published',
|
||||
'(/)histories(/)list(/)' : 'show_histories',
|
||||
'(/)histories(/)(:action_id)' : 'show_histories',
|
||||
'(/)datasets(/)list(/)' : 'show_datasets',
|
||||
'(/)workflow/configure_menu(/)' : 'show_configure_menu',
|
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'(/)workflow/import_workflow' : 'show_import_workflow',
|
||||
@@ -136,8 +136,8 @@ window.app = function app( options, bootstrapped ){
|
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this.page.display( new GridView( { url_base: Galaxy.root + 'workflow/list_published', dict_format: true } ) );
|
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},
|
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|
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show_histories : function() {
|
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this.page.display( new HistoryList.View() );
|
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show_histories : function( action_id ) {
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this.page.display( new HistoryList.View( { action_id: action_id } ) );
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},
|
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|
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show_datasets : function() {
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|
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@@ -221,28 +221,40 @@ var Collection = Backbone.Collection.extend({
|
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//
|
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// User tab.
|
||||
//
|
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var userTab = {};
|
||||
if ( !Galaxy.user.id ){
|
||||
var userTab = {
|
||||
id : 'user',
|
||||
title : _l('Login or Register'),
|
||||
cls : 'loggedout-only',
|
||||
tooltip : _l('Account registration or login'),
|
||||
menu : [{
|
||||
title : _l('Login'),
|
||||
url : 'user/login',
|
||||
target : 'galaxy_main',
|
||||
noscratchbook : true
|
||||
}]
|
||||
};
|
||||
options.allow_user_creation && userTab.menu.push({
|
||||
title : _l('Register'),
|
||||
url : 'user/create',
|
||||
target : 'galaxy_main',
|
||||
noscratchbook : true
|
||||
});
|
||||
this.add( userTab );
|
||||
if ( options.allow_user_creation ) {
|
||||
userTab = {
|
||||
id : 'user',
|
||||
title : _l('Login or Register'),
|
||||
cls : 'loggedout-only',
|
||||
tooltip : _l('Account registration or login'),
|
||||
menu : [{
|
||||
title : _l('Login'),
|
||||
url : 'user/login',
|
||||
target : 'galaxy_main',
|
||||
noscratchbook : true
|
||||
}, {
|
||||
title: _l('Register'),
|
||||
url: 'user/create',
|
||||
target: 'galaxy_main',
|
||||
noscratchbook: true
|
||||
}
|
||||
]
|
||||
};
|
||||
} else {
|
||||
userTab = {
|
||||
id: 'user',
|
||||
title: _l('Login'),
|
||||
cls: 'loggedout-only',
|
||||
tooltip: _l('Login'),
|
||||
url: 'user/login',
|
||||
target: 'galaxy_main',
|
||||
noscratchbook: true
|
||||
};
|
||||
}
|
||||
} else {
|
||||
var userTab = {
|
||||
userTab = {
|
||||
id : 'user',
|
||||
title : _l('User'),
|
||||
cls : 'loggedin-only',
|
||||
@@ -290,8 +302,8 @@ var Collection = Backbone.Collection.extend({
|
||||
target : '_top'
|
||||
}]
|
||||
};
|
||||
this.add( userTab );
|
||||
}
|
||||
this.add( userTab );
|
||||
var activeView = this.get( options.active_view );
|
||||
activeView && activeView.set( 'active', true );
|
||||
return new jQuery.Deferred().resolve().promise();
|
||||
|
||||
@@ -285,7 +285,7 @@ var DatasetCollection = Backbone.Model
|
||||
// ........................................................................ searchable
|
||||
/** searchable attributes for collections */
|
||||
searchAttributes : [
|
||||
'name'
|
||||
'name', 'tags'
|
||||
],
|
||||
|
||||
// ........................................................................ misc
|
||||
|
||||
@@ -7,7 +7,7 @@ define( [ 'utils/utils', 'mvc/grid/grid-view', 'mvc/history/history-model', 'mvc
|
||||
this.setElement( $( '<div/>' ) );
|
||||
this.model = new Backbone.Model();
|
||||
Utils.get({
|
||||
url : Galaxy.root + 'history/list',
|
||||
url : Galaxy.root + 'history/' + options.action_id,
|
||||
success : function( response ) {
|
||||
response[ 'dict_format' ] = true;
|
||||
_.each( response[ 'operations' ], function( operation ) {
|
||||
|
||||
@@ -22,9 +22,9 @@ var menu = [
|
||||
},
|
||||
{
|
||||
html : _l( 'Histories Shared with Me' ),
|
||||
href : 'history/list_shared'
|
||||
href : 'histories/list_shared',
|
||||
target : '_top'
|
||||
},
|
||||
|
||||
{
|
||||
html : _l( 'Current History' ),
|
||||
header : true,
|
||||
|
||||
@@ -66,14 +66,23 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
|
||||
// build request url
|
||||
var build_url = '';
|
||||
var build_data = {};
|
||||
var job_id = '';
|
||||
// When re-running a job the job_id is found in the new_options object.
|
||||
// When re-running a job and requesting a new tool_version,
|
||||
// the job_id is in the options object.
|
||||
if ( new_options.job_id ) {
|
||||
build_url = Galaxy.root + 'api/jobs/' + new_options.job_id + '/build_for_rerun';
|
||||
job_id = new_options.job_id;
|
||||
} else if (options.job_id) {
|
||||
job_id = options.job_id;
|
||||
}
|
||||
if ( job_id ) {
|
||||
build_url = Galaxy.root + 'api/jobs/' + job_id + '/build_for_rerun';
|
||||
} else {
|
||||
build_url = Galaxy.root + 'api/tools/' + options.id + '/build';
|
||||
build_data = $.extend( {}, Galaxy.params );
|
||||
build_data[ 'tool_id' ] && ( delete build_data[ 'tool_id' ] );
|
||||
options.version && ( build_data[ 'tool_version' ] = options.version );
|
||||
}
|
||||
options.version && ( build_data[ 'tool_version' ] = options.version );
|
||||
|
||||
// get initial model
|
||||
Utils.get({
|
||||
|
||||
@@ -796,7 +796,6 @@
|
||||
margin-right: 5px;
|
||||
}
|
||||
.ui-color-picker-label {
|
||||
float: left;
|
||||
line-height: 1.2em;
|
||||
margin-bottom: 5px;
|
||||
}
|
||||
|
||||
@@ -608,6 +608,7 @@
|
||||
<datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
|
||||
<datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
|
||||
<datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
|
||||
<datatype extension="ptkscmp" type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents" display_in_upload="true"/>
|
||||
<datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
|
||||
<datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
|
||||
<datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
|
||||
@@ -623,6 +624,7 @@
|
||||
defined format first, followed by next-most rigidly defined,
|
||||
and so on.
|
||||
-->
|
||||
<sniffer type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents"/>
|
||||
<sniffer type="galaxy.datatypes.plant_tribes:Smat"/>
|
||||
<sniffer type="galaxy.datatypes.mothur:Sabund"/>
|
||||
<sniffer type="galaxy.datatypes.mothur:Otu"/>
|
||||
|
||||
@@ -926,11 +926,9 @@ class ConfiguresGalaxyMixin:
|
||||
from galaxy import tools
|
||||
from galaxy.managers.citations import CitationsManager
|
||||
from galaxy.tools.deps import containers
|
||||
from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
|
||||
import galaxy.tools.search
|
||||
|
||||
self.citations_manager = CitationsManager( self )
|
||||
self.tool_version_cache = ToolVersionCache(self)
|
||||
|
||||
self._toolbox_lock = threading.RLock()
|
||||
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
|
||||
|
||||
@@ -1,6 +1,10 @@
|
||||
from galaxy.util import bunch
|
||||
from galaxy import exceptions
|
||||
from .structure import get_structure, leaf
|
||||
from galaxy.util import bunch
|
||||
|
||||
from .structure import (
|
||||
get_structure,
|
||||
leaf
|
||||
)
|
||||
|
||||
CANNOT_MATCH_ERROR_MESSAGE = "Cannot match collection types."
|
||||
|
||||
@@ -23,8 +27,8 @@ class CollectionsToMatch( object ):
|
||||
def has_collections( self ):
|
||||
return len( self.collections ) > 0
|
||||
|
||||
def iteritems( self ):
|
||||
return self.collections.iteritems()
|
||||
def items( self ):
|
||||
return self.collections.items()
|
||||
|
||||
|
||||
class MatchingCollections( object ):
|
||||
@@ -71,7 +75,7 @@ class MatchingCollections( object ):
|
||||
return None
|
||||
|
||||
matching_collections = MatchingCollections()
|
||||
for input_key, to_match in collections_to_match.iteritems():
|
||||
for input_key, to_match in collections_to_match.items():
|
||||
hdca = to_match.hdca
|
||||
collection_type_description = collection_type_descriptions.for_collection_type( hdca.collection.collection_type )
|
||||
subcollection_type = to_match.subcollection_type
|
||||
|
||||
@@ -1,7 +1,10 @@
|
||||
from .types import list
|
||||
from .types import paired
|
||||
from galaxy import model
|
||||
|
||||
from .types import (
|
||||
list,
|
||||
paired
|
||||
)
|
||||
|
||||
PLUGIN_CLASSES = [list.ListDatasetCollectionType, paired.PairedDatasetCollectionType]
|
||||
|
||||
|
||||
|
||||
@@ -124,7 +124,7 @@ class Tree( object ):
|
||||
|
||||
|
||||
def dict_map( func, input_dict ):
|
||||
return dict( [ ( k, func(v) ) for k, v in input_dict.items() ] )
|
||||
return dict( ( k, func(v) ) for k, v in input_dict.items() )
|
||||
|
||||
|
||||
def get_structure( dataset_collection_instance, collection_type_description, leaf_subcollection_type=None ):
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
from ..types import BaseDatasetCollectionType
|
||||
|
||||
from galaxy.model import DatasetCollectionElement
|
||||
|
||||
from ..types import BaseDatasetCollectionType
|
||||
|
||||
|
||||
class ListDatasetCollectionType( BaseDatasetCollectionType ):
|
||||
""" A flat list of named elements.
|
||||
@@ -12,7 +12,7 @@ class ListDatasetCollectionType( BaseDatasetCollectionType ):
|
||||
pass
|
||||
|
||||
def generate_elements( self, elements ):
|
||||
for identifier, element in elements.iteritems():
|
||||
for identifier, element in elements.items():
|
||||
association = DatasetCollectionElement(
|
||||
element=element,
|
||||
element_identifier=identifier,
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
from ..types import BaseDatasetCollectionType
|
||||
|
||||
from galaxy.model import DatasetCollectionElement, HistoryDatasetAssociation
|
||||
|
||||
from ..types import BaseDatasetCollectionType
|
||||
|
||||
FORWARD_IDENTIFIER = "forward"
|
||||
REVERSE_IDENTIFIER = "reverse"
|
||||
|
||||
|
||||
@@ -30,14 +30,16 @@
|
||||
|
||||
Covers the ``blastxml`` format and the BLAST databases.
|
||||
"""
|
||||
|
||||
import logging
|
||||
import os
|
||||
from time import sleep
|
||||
|
||||
from galaxy.datatypes.data import get_file_peek
|
||||
from galaxy.datatypes.data import Data, Text
|
||||
from galaxy.datatypes.xml import GenericXml
|
||||
from .data import (
|
||||
Data,
|
||||
get_file_peek,
|
||||
Text
|
||||
)
|
||||
from .xml import GenericXml
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
from __future__ import absolute_import
|
||||
|
||||
import galaxy.datatypes.tabular
|
||||
import galaxy.datatypes.metadata
|
||||
import galaxy.datatypes.tabular
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
|
||||
|
||||
|
||||
@@ -5,18 +5,19 @@ from __future__ import division
|
||||
import sys
|
||||
|
||||
from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
|
||||
from six import Iterator
|
||||
|
||||
BLOCK_SIZE = 100
|
||||
|
||||
|
||||
class BedGraphReader:
|
||||
class BedGraphReader(Iterator):
|
||||
def __init__( self, f ):
|
||||
self.f = f
|
||||
|
||||
def __iter__( self ):
|
||||
return self
|
||||
|
||||
def next( self ):
|
||||
def __next__( self ):
|
||||
while True:
|
||||
line = self.f.readline()
|
||||
if not line:
|
||||
@@ -46,7 +47,7 @@ def main():
|
||||
# Fill array from reader
|
||||
d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )
|
||||
|
||||
for array_tree in d.itervalues():
|
||||
for array_tree in d.values():
|
||||
array_tree.root.build_summary()
|
||||
|
||||
FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
|
||||
|
||||
@@ -10,9 +10,8 @@
|
||||
Input: fasta
|
||||
Output: tabular
|
||||
"""
|
||||
|
||||
import sys
|
||||
import os
|
||||
import sys
|
||||
|
||||
seq_hash = {}
|
||||
|
||||
|
||||
@@ -89,7 +89,7 @@ def main():
|
||||
out = open( out_fname, 'w' )
|
||||
max_len = 0
|
||||
entries = []
|
||||
for name in sorted( name_loc_dict.iterkeys() ):
|
||||
for name in sorted( name_loc_dict.keys() ):
|
||||
loc = name_loc_dict[ name ]
|
||||
entry = '%s\t%s\t%s' % ( name.lower(), name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
|
||||
if len( entry ) > max_len:
|
||||
|
||||
@@ -3,9 +3,9 @@
|
||||
from __future__ import print_function
|
||||
|
||||
import os
|
||||
import subprocess
|
||||
import sys
|
||||
import tempfile
|
||||
import subprocess
|
||||
import time
|
||||
|
||||
prog = "pbed_ldreduced_converter.py"
|
||||
|
||||
@@ -4,9 +4,8 @@ convert a ref.taxonomy file to a seq.taxonomy file
|
||||
Usage:
|
||||
%python ref_to_seq_taxonomy_converter.py <ref.taxonom> <seq.taxonomy>
|
||||
"""
|
||||
|
||||
import sys
|
||||
import re
|
||||
import sys
|
||||
|
||||
assert sys.version_info[:2] >= (2, 4)
|
||||
|
||||
|
||||
@@ -5,12 +5,12 @@
|
||||
A wrapper script for converting SAM to BAM, with sorting.
|
||||
%prog input_filename.sam output_filename.bam
|
||||
"""
|
||||
import os
|
||||
import sys
|
||||
import optparse
|
||||
import tempfile
|
||||
import subprocess
|
||||
import os
|
||||
import shutil
|
||||
import subprocess
|
||||
import sys
|
||||
import tempfile
|
||||
from distutils.version import LooseVersion
|
||||
|
||||
CHUNK_SIZE = 2 ** 20 # 1mb
|
||||
|
||||
@@ -1,5 +1,4 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Convert from VCF file to interval index file.
|
||||
"""
|
||||
@@ -7,9 +6,8 @@ from __future__ import division
|
||||
|
||||
import optparse
|
||||
|
||||
from bx.interval_index_file import Indexes
|
||||
|
||||
import galaxy_utils.sequence.vcf
|
||||
from bx.interval_index_file import Indexes
|
||||
|
||||
|
||||
def main():
|
||||
|
||||
@@ -20,7 +20,7 @@ def main():
|
||||
# Fill array from reader
|
||||
d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )
|
||||
|
||||
for array_tree in d.itervalues():
|
||||
for array_tree in d.values():
|
||||
array_tree.root.build_summary()
|
||||
|
||||
FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
|
||||
|
||||
@@ -11,7 +11,10 @@ import sys
|
||||
|
||||
import bx.wiggle
|
||||
|
||||
from galaxy.util.ucsc import UCSCOutWrapper, UCSCLimitException
|
||||
from galaxy.util.ucsc import (
|
||||
UCSCLimitException,
|
||||
UCSCOutWrapper
|
||||
)
|
||||
|
||||
|
||||
def stop_err( msg ):
|
||||
|
||||
@@ -22,29 +22,6 @@ class LastzCoverage( Tabular ):
|
||||
MetadataElement( name="reverseCol", desc="Optional reverse read column", param=metadata.ColumnParameter, optional=True, no_value=0 )
|
||||
MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )
|
||||
|
||||
def get_track_window(self, dataset, data, start, end):
|
||||
"""
|
||||
Assumes we have a numpy file.
|
||||
"""
|
||||
# Maybe if we import here people will still be able to use Galaxy when numpy kills it
|
||||
import numpy
|
||||
|
||||
range = end - start
|
||||
# Determine appropriate resolution to plot ~1000 points
|
||||
resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
|
||||
# Restrict to valid range
|
||||
resolution = min( resolution, 10000 )
|
||||
resolution = max( resolution, 1 )
|
||||
# Memory map the array (don't load all the data)
|
||||
data = numpy.load( data )
|
||||
# Grab just what we need
|
||||
t_start = math.floor( start / resolution )
|
||||
t_end = math.ceil( end / resolution )
|
||||
x = numpy.arange( t_start, t_end ) * resolution
|
||||
y = data[ t_start : t_end ]
|
||||
|
||||
return zip(x.tolist(), y.tolist())
|
||||
|
||||
def get_track_resolution( self, dataset, start, end):
|
||||
range = end - start
|
||||
# Determine appropriate resolution to plot ~1000 points
|
||||
|
||||
@@ -1054,8 +1054,7 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skip
|
||||
count = 0
|
||||
file_type = None
|
||||
data_checked = False
|
||||
temp = compression_utils.get_fileobj( file_name, "U" )
|
||||
try:
|
||||
with compression_utils.get_fileobj( file_name, "U" ) as temp:
|
||||
while count < LINE_COUNT:
|
||||
line = temp.readline( WIDTH )
|
||||
if line and not is_multi_byte and not data_checked:
|
||||
@@ -1083,8 +1082,6 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skip
|
||||
if not skip_line:
|
||||
lines.append( line )
|
||||
count += 1
|
||||
finally:
|
||||
temp.close()
|
||||
if file_type == 'binary':
|
||||
text = "%s file" % file_type
|
||||
else:
|
||||
|
||||
@@ -4,16 +4,18 @@ Chunk (N number of bytes at M offset to a source's beginning) provider.
|
||||
Primarily for file sources but usable by any iterator that has both
|
||||
seek and read( N ).
|
||||
"""
|
||||
import os
|
||||
import base64
|
||||
import base
|
||||
import exceptions
|
||||
|
||||
import logging
|
||||
import os
|
||||
|
||||
from . import (
|
||||
base,
|
||||
exceptions
|
||||
)
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
class ChunkDataProvider( base.DataProvider ):
|
||||
"""
|
||||
Data provider that yields chunks of data from its file.
|
||||
|
||||
@@ -2,9 +2,10 @@
|
||||
Providers that provide lists of lists generally where each line of a source
|
||||
is further subdivided into multiple data (e.g. columns from a line).
|
||||
"""
|
||||
import logging
|
||||
import re
|
||||
|
||||
from six.moves.urllib.parse import unquote_plus
|
||||
import re
|
||||
|
||||
from . import line
|
||||
|
||||
@@ -15,7 +16,6 @@ TransposedColumnarDataProvider: provides each column as a single array
|
||||
- see existing visualizations/dataprovider/basic.ColumnDataProvider
|
||||
"""
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
|
||||
@@ -5,18 +5,23 @@ Dataproviders that use either:
|
||||
- or provide data in some way relevant to bioinformatic data
|
||||
(e.g. parsing genomic regions from their source)
|
||||
"""
|
||||
|
||||
|
||||
import base
|
||||
import line
|
||||
import column
|
||||
import external
|
||||
from galaxy.util import sqlite
|
||||
import logging
|
||||
import sys
|
||||
|
||||
from bx import seq as bx_seq
|
||||
from bx import wiggle as bx_wig
|
||||
from bx import bbi as bx_bbi
|
||||
from bx import (
|
||||
bbi as bx_bbi,
|
||||
seq as bx_seq,
|
||||
wiggle as bx_wig
|
||||
)
|
||||
|
||||
from galaxy.util import sqlite
|
||||
|
||||
from . import (
|
||||
base,
|
||||
column,
|
||||
external,
|
||||
line
|
||||
)
|
||||
|
||||
_TODO = """
|
||||
use bx as much as possible
|
||||
@@ -25,7 +30,6 @@ gff3 hierarchies
|
||||
change SamtoolsDataProvider to use pysam
|
||||
"""
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
@@ -150,7 +154,7 @@ class DatasetDataProvider( base.DataProvider ):
|
||||
"""
|
||||
region_column_names = ( 'chromCol', 'startCol', 'endCol' )
|
||||
region_indices = [ self.get_metadata_column_index_by_name( name ) for name in region_column_names ]
|
||||
if check and not all( map( lambda i: i is not None, region_indices) ):
|
||||
if check and not all( _ is not None for _ in region_indices ):
|
||||
raise ValueError( "Could not determine proper column indices for chrom, start, end: %s" % ( str( region_indices ) ) )
|
||||
return region_indices
|
||||
|
||||
@@ -296,7 +300,7 @@ class GenomicRegionDataProvider( column.ColumnarDataProvider ):
|
||||
if end_column is None:
|
||||
end_column = dataset_source.get_metadata_column_index_by_name( 'endCol' )
|
||||
indeces = [ chrom_column, start_column, end_column ]
|
||||
if not all( map( lambda i: i is not None, indeces ) ):
|
||||
if not all( _ is not None for _ in indeces ):
|
||||
raise ValueError( "Could not determine proper column indeces for" +
|
||||
" chrom, start, end: %s" % ( str( indeces ) ) )
|
||||
kwargs.update({ 'indeces' : indeces })
|
||||
|
||||
@@ -14,11 +14,12 @@ DataProvider related decorators.
|
||||
# adapted from: http://stackoverflow.com
|
||||
# /questions/14095616/python-can-i-programmatically-decorate-class-methods-from-a-class-instance
|
||||
|
||||
from functools import wraps
|
||||
import urllib2
|
||||
import copy
|
||||
|
||||
import logging
|
||||
from functools import wraps
|
||||
|
||||
from six.moves.urllib.parse import unquote
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
_DATAPROVIDER_CLASS_MAP_KEY = 'dataproviders'
|
||||
@@ -65,7 +66,7 @@ def has_dataproviders( cls ):
|
||||
# scan for methods with dataprovider names and add them to the map
|
||||
# note: this has a 'cascading' effect
|
||||
# where it's possible to override a super's provider with a sub's
|
||||
for attr_key, attr_value in cls.__dict__.iteritems():
|
||||
for attr_key, attr_value in cls.__dict__.items():
|
||||
# can't use isinstance( attr_value, MethodType ) bc of wrapping
|
||||
if( ( callable( attr_value ) ) and
|
||||
( not attr_key.startswith( "__" ) ) and
|
||||
@@ -129,7 +130,7 @@ def _parse_query_string_settings( query_kwargs, settings=None ):
|
||||
'float' : float,
|
||||
'bool' : bool,
|
||||
'list:str' : lambda s: list_from_query_string( s ),
|
||||
'list:escaped' : lambda s: [ urllib2.unquote( e ) for e in list_from_query_string( s ) ],
|
||||
'list:escaped' : lambda s: [ unquote( e ) for e in list_from_query_string( s ) ],
|
||||
'list:int' : lambda s: [ int( i ) for i in list_from_query_string( s ) ],
|
||||
}
|
||||
settings = settings or {}
|
||||
|
||||
@@ -2,14 +2,18 @@
|
||||
Data providers that iterate over a source that is not in memory
|
||||
or not in a file.
|
||||
"""
|
||||
|
||||
import base
|
||||
import gzip
|
||||
import line
|
||||
import logging
|
||||
import subprocess
|
||||
import tempfile
|
||||
import urllib
|
||||
import urllib2
|
||||
|
||||
from six.moves.urllib.parse import urlencode
|
||||
from six.moves.urllib.request import urlopen
|
||||
|
||||
from . import (
|
||||
base,
|
||||
line
|
||||
)
|
||||
|
||||
_TODO = """
|
||||
YAGNI: ftp, image, cryptos, sockets
|
||||
@@ -17,7 +21,6 @@ job queue
|
||||
admin: admin server log rgx/stats, ps aux
|
||||
"""
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
@@ -105,13 +108,13 @@ class URLDataProvider( base.DataProvider ):
|
||||
self.method = method
|
||||
|
||||
self.data = data or {}
|
||||
encoded_data = urllib.urlencode( self.data )
|
||||
encoded_data = urlencode( self.data )
|
||||
|
||||
if method == 'GET':
|
||||
self.url += '?%s' % ( encoded_data )
|
||||
opened = urllib2.urlopen( url )
|
||||
opened = urlopen( url )
|
||||
elif method == 'POST':
|
||||
opened = urllib2.urlopen( url, encoded_data )
|
||||
opened = urlopen( url, encoded_data )
|
||||
else:
|
||||
raise ValueError( 'Not a valid method: %s' % ( method ) )
|
||||
|
||||
|
||||
@@ -1,14 +1,17 @@
|
||||
"""
|
||||
Dataproviders that iterate over lines from their sources.
|
||||
"""
|
||||
import logging
|
||||
from xml.etree.ElementTree import (
|
||||
Element,
|
||||
iterparse
|
||||
)
|
||||
|
||||
import line
|
||||
from xml.etree.ElementTree import Element, iterparse
|
||||
from . import line
|
||||
|
||||
_TODO = """
|
||||
"""
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
|
||||
@@ -1,12 +1,12 @@
|
||||
"""
|
||||
Dataproviders that iterate over lines from their sources.
|
||||
"""
|
||||
|
||||
import collections
|
||||
import logging
|
||||
import re
|
||||
|
||||
from . import base
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
_TODO = """
|
||||
|
||||
@@ -1,16 +1,24 @@
|
||||
# Contains objects for using external display applications
|
||||
import logging
|
||||
import urllib
|
||||
from six import string_types
|
||||
from urllib import quote_plus
|
||||
from copy import deepcopy
|
||||
|
||||
from galaxy.util import parse_xml, string_as_bool
|
||||
from six import string_types
|
||||
from six.moves.urllib.parse import quote_plus
|
||||
|
||||
from galaxy.util import (
|
||||
parse_xml,
|
||||
string_as_bool
|
||||
)
|
||||
from galaxy.util.odict import odict
|
||||
from galaxy.util.template import fill_template
|
||||
from galaxy.web import url_for
|
||||
from parameters import DisplayApplicationParameter, DisplayApplicationDataParameter, DEFAULT_DATASET_NAME
|
||||
from util import encode_dataset_user
|
||||
|
||||
from .parameters import (
|
||||
DEFAULT_DATASET_NAME,
|
||||
DisplayApplicationDataParameter,
|
||||
DisplayApplicationParameter
|
||||
)
|
||||
from .util import encode_dataset_user
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
@@ -50,8 +58,8 @@ class DisplayApplicationLink( object ):
|
||||
action="display_application",
|
||||
dataset_id=dataset_hash,
|
||||
user_id=user_hash,
|
||||
app_name=urllib.quote_plus( self.display_application.id ),
|
||||
link_name=urllib.quote_plus( self.id ),
|
||||
app_name=quote_plus( self.display_application.id ),
|
||||
link_name=quote_plus( self.id ),
|
||||
app_action=None )
|
||||
|
||||
def get_inital_values( self, data, trans ):
|
||||
@@ -60,7 +68,7 @@ class DisplayApplicationLink( object ):
|
||||
else:
|
||||
rval = odict()
|
||||
rval.update( { 'BASE_URL': trans.request.base, 'APP': trans.app } ) # trans automatically appears as a response, need to add properties of trans that we want here
|
||||
for key, value in BASE_PARAMS.iteritems(): # add helper functions/variables
|
||||
for key, value in BASE_PARAMS.items(): # add helper functions/variables
|
||||
rval[ key ] = value
|
||||
rval[ DEFAULT_DATASET_NAME ] = data # always have the display dataset name available
|
||||
return rval
|
||||
@@ -70,7 +78,7 @@ class DisplayApplicationLink( object ):
|
||||
other_values[ 'DATASET_HASH' ] = dataset_hash
|
||||
other_values[ 'USER_HASH' ] = user_hash
|
||||
ready = True
|
||||
for name, param in self.parameters.iteritems():
|
||||
for name, param in self.parameters.items():
|
||||
assert name not in other_values, "The display parameter '%s' has been defined more than once." % name
|
||||
if param.ready( other_values ):
|
||||
if name in app_kwds and param.allow_override:
|
||||
@@ -142,7 +150,7 @@ class DynamicDisplayApplicationBuilder( object ):
|
||||
max_col = max( id_col, name_col )
|
||||
dynamic_params = {}
|
||||
if data_table is not None:
|
||||
max_col = max( [ max_col ] + data_table.columns.values() )
|
||||
max_col = max( [ max_col ] + list(data_table.columns.values()) )
|
||||
for key, value in data_table.columns.items():
|
||||
dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
|
||||
for dynamic_param in elem.findall( 'dynamic_param' ):
|
||||
@@ -174,7 +182,7 @@ class DynamicDisplayApplicationBuilder( object ):
|
||||
new_elem.set( 'id', fields[id_col] )
|
||||
new_elem.set( 'name', fields[name_col] )
|
||||
dynamic_values = {}
|
||||
for key, attributes in dynamic_params.iteritems():
|
||||
for key, attributes in dynamic_params.items():
|
||||
value = fields[ attributes[ 'column' ] ]
|
||||
if attributes['split']:
|
||||
value = value.split( attributes['separator'] )
|
||||
@@ -210,7 +218,7 @@ class PopulatedDisplayApplicationLink( object ):
|
||||
|
||||
def preparing_display( self ):
|
||||
if not self.ready:
|
||||
return self.link.parameters[ self.parameters.keys()[ -1 ] ].is_preparing( self.parameters )
|
||||
return self.link.parameters[ list(self.parameters.keys())[-1] ].is_preparing( self.parameters )
|
||||
return False
|
||||
|
||||
def prepare_display( self ):
|
||||
@@ -218,8 +226,8 @@ class PopulatedDisplayApplicationLink( object ):
|
||||
found_last = False
|
||||
if not self.ready and not self.preparing_display():
|
||||
other_values = self.parameters
|
||||
for name, param in self.link.parameters.iteritems():
|
||||
if found_last or other_values.keys()[ -1 ] == name: # found last parameter to be populated
|
||||
for name, param in self.link.parameters.items():
|
||||
if found_last or list(other_values.keys())[-1] == name: # found last parameter to be populated
|
||||
found_last = True
|
||||
value = param.prepare( other_values, self.dataset_hash, self.user_hash, self.trans )
|
||||
rval.append( { 'name': name, 'value': value, 'param': param } )
|
||||
@@ -231,7 +239,7 @@ class PopulatedDisplayApplicationLink( object ):
|
||||
|
||||
def get_prepare_steps( self, datasets_only=True ):
|
||||
rval = []
|
||||
for name, param in self.link.parameters.iteritems():
|
||||
for name, param in self.link.parameters.items():
|
||||
if datasets_only and not isinstance( param, DisplayApplicationDataParameter ):
|
||||
continue
|
||||
value = self.parameters.get( name, None )
|
||||
@@ -243,7 +251,7 @@ class PopulatedDisplayApplicationLink( object ):
|
||||
return fill_template( self.link.url.text, context=self.parameters )
|
||||
|
||||
def get_param_name_by_url( self, url ):
|
||||
for name, parameter in self.link.parameters.iteritems():
|
||||
for name, parameter in self.link.parameters.items():
|
||||
if parameter.build_url( self.parameters ) == url:
|
||||
return name
|
||||
raise ValueError( "Unknown URL parameter name provided: %s" % url )
|
||||
@@ -301,7 +309,7 @@ class DisplayApplication( object ):
|
||||
def filter_by_dataset( self, data, trans ):
|
||||
self._check_and_reload()
|
||||
filtered = DisplayApplication( self.id, self.name, self.app, version=self.version )
|
||||
for link_name, link_value in self.links.iteritems():
|
||||
for link_name, link_value in self.links.items():
|
||||
if link_value.filter_by_dataset( data, trans ):
|
||||
filtered.links[link_name] = link_value
|
||||
return filtered
|
||||
@@ -318,13 +326,11 @@ class DisplayApplication( object ):
|
||||
# We will not allow changing the id at this time (we'll need to fix several mappings upstream to handle this case)
|
||||
assert attr_dict.get( 'id' ) == self.id, ValueError( "You cannot reload a Display application where the ID has changed. You will need to restart the server instead." )
|
||||
# clear old links
|
||||
for key in self.links.keys():
|
||||
del self.links[key]
|
||||
self.links = {}
|
||||
# clear data table versions:
|
||||
for key in self._data_table_versions.keys():
|
||||
del self._data_table_versions[ key ]
|
||||
self._data_table_versions = {}
|
||||
# Set new attributes
|
||||
for key, value in attr_dict.iteritems():
|
||||
for key, value in attr_dict.items():
|
||||
setattr( self, key, value )
|
||||
# Load new links
|
||||
self._load_links_from_elem( elem )
|
||||
@@ -334,7 +340,7 @@ class DisplayApplication( object ):
|
||||
self._data_table_versions[ table_name ] = version
|
||||
|
||||
def _requires_reload( self ):
|
||||
for key, value in self._data_table_versions.iteritems():
|
||||
for key, value in self._data_table_versions.items():
|
||||
table = self.app.tool_data_tables.get( key, None )
|
||||
if table and not table.is_current_version( value ):
|
||||
return True
|
||||
|
||||
@@ -1,10 +1,12 @@
|
||||
# Contains parameters that are used in Display Applications
|
||||
import urllib
|
||||
import mimetypes
|
||||
|
||||
from six.moves.urllib.parse import quote_plus
|
||||
|
||||
from galaxy.util import string_as_bool
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.template import fill_template
|
||||
from galaxy.web import url_for
|
||||
import mimetypes
|
||||
|
||||
DEFAULT_DATASET_NAME = 'dataset'
|
||||
|
||||
@@ -110,7 +112,7 @@ class DisplayApplicationDataParameter( DisplayApplicationParameter ):
|
||||
if target_ext and not converted_dataset:
|
||||
if isinstance( data, DisplayDataValueWrapper ):
|
||||
data = data.value
|
||||
new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()[0]
|
||||
new_data = next(iter(data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()))
|
||||
new_data.hid = data.hid
|
||||
new_data.name = data.name
|
||||
trans.sa_session.add( new_data )
|
||||
@@ -193,8 +195,8 @@ class DisplayParameterValueWrapper( object ):
|
||||
action="display_application",
|
||||
dataset_id=self._dataset_hash,
|
||||
user_id=self._user_hash,
|
||||
app_name=urllib.quote_plus( self.parameter.link.display_application.id ),
|
||||
link_name=urllib.quote_plus( self.parameter.link.id ),
|
||||
app_name=quote_plus( self.parameter.link.display_application.id ),
|
||||
link_name=quote_plus( self.parameter.link.id ),
|
||||
app_action=self.action_name,
|
||||
action_param=self._url ) )
|
||||
|
||||
|
||||
@@ -1,15 +1,17 @@
|
||||
"""
|
||||
Graph content classes.
|
||||
"""
|
||||
import logging
|
||||
|
||||
import data
|
||||
import tabular
|
||||
import xml
|
||||
|
||||
import dataproviders
|
||||
from galaxy.util import simplegraph
|
||||
|
||||
import logging
|
||||
from . import (
|
||||
data,
|
||||
dataproviders,
|
||||
tabular,
|
||||
xml
|
||||
)
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
|
||||
@@ -7,7 +7,6 @@ import os
|
||||
import sys
|
||||
import tempfile
|
||||
|
||||
import numpy
|
||||
from bx.intervals.io import GenomicIntervalReader, ParseError
|
||||
from six.moves.urllib.parse import quote_plus
|
||||
|
||||
@@ -335,20 +334,6 @@ class Interval( Tabular ):
|
||||
except:
|
||||
return False
|
||||
|
||||
def get_track_window(self, dataset, data, start, end):
|
||||
"""
|
||||
Assumes the incoming track data is sorted already.
|
||||
"""
|
||||
window = list()
|
||||
for record in data:
|
||||
fields = record.rstrip("\n\r").split("\t")
|
||||
record_chrom = fields[dataset.metadata.chromCol - 1]
|
||||
record_start = int(fields[dataset.metadata.startCol - 1])
|
||||
record_end = int(fields[dataset.metadata.endCol - 1])
|
||||
if record_start < end and record_end > start:
|
||||
window.append( (record_chrom, record_start, record_end) ) # Yes I did want to use a generator here, but it doesn't work downstream
|
||||
return window
|
||||
|
||||
def get_track_resolution( self, dataset, start, end):
|
||||
return None
|
||||
|
||||
@@ -1259,26 +1244,6 @@ class Wiggle( Tabular, _RemoteCallMixin ):
|
||||
except:
|
||||
return False
|
||||
|
||||
def get_track_window(self, dataset, data, start, end):
|
||||
"""
|
||||
Assumes we have a numpy file.
|
||||
"""
|
||||
range = end - start
|
||||
# Determine appropriate resolution to plot ~1000 points
|
||||
resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
|
||||
# Restrict to valid range
|
||||
resolution = min( resolution, 100000 )
|
||||
resolution = max( resolution, 1 )
|
||||
# Memory map the array (don't load all the data)
|
||||
data = numpy.load( data )
|
||||
# Grab just what we need
|
||||
t_start = math.floor( start / resolution )
|
||||
t_end = math.ceil( end / resolution )
|
||||
x = numpy.arange( t_start, t_end ) * resolution
|
||||
y = data[ t_start : t_end ]
|
||||
|
||||
return list(zip(x.tolist(), y.tolist()))
|
||||
|
||||
def get_track_resolution( self, dataset, start, end):
|
||||
range = end - start
|
||||
# Determine appropriate resolution to plot ~1000 points
|
||||
|
||||
@@ -1,17 +1,18 @@
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
from galaxy.datatypes import data
|
||||
import logging
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.data import get_file_peek
|
||||
from galaxy.datatypes.tabular import Tabular
|
||||
from galaxy.datatypes.binary import Binary
|
||||
from galaxy.datatypes.xml import GenericXml
|
||||
import subprocess
|
||||
import os
|
||||
import subprocess
|
||||
|
||||
from galaxy.datatypes import (
|
||||
data,
|
||||
metadata
|
||||
)
|
||||
from galaxy.datatypes.binary import Binary
|
||||
from galaxy.datatypes.data import get_file_peek
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
from galaxy.datatypes import metadata
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.tabular import Tabular
|
||||
from galaxy.datatypes.xml import GenericXml
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -2,11 +2,12 @@
|
||||
Mothur Metagenomics Datatypes
|
||||
"""
|
||||
import logging
|
||||
import sys
|
||||
import re
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
import sys
|
||||
|
||||
from galaxy.datatypes.data import Text
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.tabular import Tabular
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -2,9 +2,9 @@
|
||||
Neo4j Composite Dataset
|
||||
"""
|
||||
import logging
|
||||
import sys
|
||||
import shutil
|
||||
import os
|
||||
import shutil
|
||||
import sys
|
||||
|
||||
from galaxy.datatypes.data import Data
|
||||
from galaxy.datatypes.images import Html
|
||||
@@ -29,7 +29,7 @@ class Neo4j(Html):
|
||||
'<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
|
||||
This composite dataset is composed of the following files:<p/><ul>' % (
|
||||
self.file_ext)]
|
||||
for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
|
||||
for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
|
||||
opt_text = ''
|
||||
if composite_file.optional:
|
||||
opt_text = ' (optional)'
|
||||
|
||||
@@ -4,6 +4,8 @@ import re
|
||||
|
||||
from galaxy.datatypes.data import get_file_peek, Text
|
||||
from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.tabular import Tabular
|
||||
from galaxy.datatypes.text import Html
|
||||
from galaxy.util import nice_size
|
||||
|
||||
@@ -89,6 +91,66 @@ class PlantTribes(Html):
|
||||
log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
|
||||
|
||||
|
||||
class PlantTribesKsComponents(Tabular):
|
||||
file_ext = "ptkscmp"
|
||||
MetadataElement(name="number_comp", default=0, desc="Number of significant components in the Ks distribution", readonly=True, visible=True, no_value=0)
|
||||
|
||||
def display_peek(self, dataset):
|
||||
try:
|
||||
return dataset.peek
|
||||
except:
|
||||
return "Significant components in the Ks distribution (%s)" % (nice_size(dataset.get_size()))
|
||||
|
||||
def set_meta(self, dataset, **kwd):
|
||||
"""
|
||||
Set the number of significant components in the Ks distribution.
|
||||
The dataset will always be on the order of less than 10 lines.
|
||||
"""
|
||||
super(PlantTribesKsComponents, self).set_meta(dataset, **kwd)
|
||||
significant_components = []
|
||||
with open(dataset.file_name) as fh:
|
||||
for i, line in enumerate(fh):
|
||||
if i == 0:
|
||||
# Skip the first line.
|
||||
continue
|
||||
line = line.strip()
|
||||
items = line.split()
|
||||
try:
|
||||
# Could be \t.
|
||||
significant_components.append(int(items[2]))
|
||||
except Exception:
|
||||
continue
|
||||
if len(significant_components) > 0:
|
||||
dataset.metadata.number_comp = max(significant_components)
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
|
||||
if (dataset.metadata.number_comp == 1):
|
||||
dataset.blurb = "1 significant component"
|
||||
else:
|
||||
dataset.blurb = "%s significant components" % dataset.metadata.number_comp
|
||||
else:
|
||||
dataset.peek = 'file does not exist'
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('test_tab.bed')
|
||||
>>> PlantTribesKsComponents().sniff(fname)
|
||||
False
|
||||
>>> fname = get_test_fname('1.ptkscmp')
|
||||
>>> PlantTribesKsComponents().sniff(fname)
|
||||
True
|
||||
"""
|
||||
try:
|
||||
line_item_str = get_headers(filename, '\\t', 1)[0][0]
|
||||
return line_item_str == 'species\tn\tnumber_comp\tlnL\tAIC\tBIC\tmean\tvariance\tporportion'
|
||||
except Exception:
|
||||
return False
|
||||
|
||||
|
||||
class PlantTribesOrtho(PlantTribes):
|
||||
"""
|
||||
PlantTribes sequences classified into precomputed, orthologous gene family
|
||||
|
||||
@@ -1,9 +1,10 @@
|
||||
"""
|
||||
Qualityscore class
|
||||
"""
|
||||
|
||||
import data
|
||||
import logging
|
||||
|
||||
from . import data
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
|
||||
@@ -143,13 +143,10 @@ class Sequence( data.Text ):
|
||||
if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences is not None:
|
||||
total_sequences = input_datasets[0].metadata.sequences
|
||||
else:
|
||||
in_file = compression_utils.get_fileobj(input_datasets[0].file_name)
|
||||
try:
|
||||
with compression_utils.get_fileobj(input_datasets[0].file_name) as in_file:
|
||||
total_sequences = long(0)
|
||||
for i, line in enumerate(in_file):
|
||||
total_sequences += 1
|
||||
finally:
|
||||
in_file.close()
|
||||
total_sequences /= 4
|
||||
|
||||
sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
|
||||
@@ -570,8 +567,7 @@ class BaseFastq ( Sequence ):
|
||||
data_lines = 0
|
||||
sequences = 0
|
||||
seq_counter = 0 # blocks should be 4 lines long
|
||||
in_file = compression_utils.get_fileobj(dataset.file_name)
|
||||
try:
|
||||
with compression_utils.get_fileobj(dataset.file_name) as in_file:
|
||||
for line in in_file:
|
||||
line = line.strip()
|
||||
if line and line.startswith( '#' ) and not data_lines:
|
||||
@@ -590,8 +586,6 @@ class BaseFastq ( Sequence ):
|
||||
sequences += 1
|
||||
dataset.metadata.data_lines = data_lines
|
||||
dataset.metadata.sequences = sequences
|
||||
finally:
|
||||
in_file.close()
|
||||
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
@@ -638,15 +632,15 @@ class BaseFastq ( Sequence ):
|
||||
|
||||
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
|
||||
if preview:
|
||||
fh = compression_utils.get_fileobj(dataset.file_name)
|
||||
max_peek_size = 1000000 # 1 MB
|
||||
if os.stat( dataset.file_name ).st_size < max_peek_size:
|
||||
mime = "text/plain"
|
||||
self._clean_and_set_mime_type( trans, mime )
|
||||
return fh.read()
|
||||
return trans.stream_template_mako( "/dataset/large_file.mako",
|
||||
truncated_data=fh.read(max_peek_size),
|
||||
data=dataset)
|
||||
with compression_utils.get_fileobj(dataset.file_name) as fh:
|
||||
max_peek_size = 1000000 # 1 MB
|
||||
if os.stat( dataset.file_name ).st_size < max_peek_size:
|
||||
mime = "text/plain"
|
||||
self._clean_and_set_mime_type( trans, mime )
|
||||
return fh.read()
|
||||
return trans.stream_template_mako( "/dataset/large_file.mako",
|
||||
truncated_data=fh.read(max_peek_size),
|
||||
data=dataset)
|
||||
else:
|
||||
return Sequence.display_data(self, trans, dataset, preview, filename, to_ext, **kwd)
|
||||
|
||||
|
||||
@@ -3,8 +3,9 @@ File format detector
|
||||
"""
|
||||
from __future__ import absolute_import
|
||||
|
||||
import gzip
|
||||
import bz2
|
||||
import codecs
|
||||
import gzip
|
||||
import logging
|
||||
import os
|
||||
import re
|
||||
@@ -13,13 +14,13 @@ import sys
|
||||
import tempfile
|
||||
import zipfile
|
||||
|
||||
from encodings import search_function as encodings_search_function
|
||||
from six import text_type
|
||||
|
||||
from galaxy import util
|
||||
from galaxy.util import multi_byte
|
||||
from galaxy.datatypes.binary import Binary
|
||||
from galaxy.util import (
|
||||
compression_utils,
|
||||
multi_byte,
|
||||
unicodify
|
||||
)
|
||||
from galaxy.util.checkers import (
|
||||
@@ -28,7 +29,6 @@ from galaxy.util.checkers import (
|
||||
is_bz2,
|
||||
is_gzip
|
||||
)
|
||||
from galaxy.datatypes.binary import Binary
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -48,7 +48,9 @@ def stream_to_open_named_file( stream, fd, filename, source_encoding=None, sourc
|
||||
is_compressed = False
|
||||
is_binary = False
|
||||
is_multi_byte = False
|
||||
if not target_encoding or not encodings_search_function( target_encoding ):
|
||||
try:
|
||||
codecs.lookup(target_encoding)
|
||||
except:
|
||||
target_encoding = util.DEFAULT_ENCODING # utf-8
|
||||
if not source_encoding:
|
||||
source_encoding = util.DEFAULT_ENCODING # sys.getdefaultencoding() would mimic old behavior (defaults to ascii)
|
||||
@@ -211,8 +213,7 @@ def get_headers( fname, sep, count=60, is_multi_byte=False, comment_designator=N
|
||||
[[''], ['chr7', 'bed2gff', 'AR', '26731313', '26731437', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731491', '26731536', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731541', '26731649', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731659', '26731841', '.', '+', '.', 'score']]
|
||||
"""
|
||||
headers = []
|
||||
in_file = compression_utils.get_fileobj(fname)
|
||||
try:
|
||||
with compression_utils.get_fileobj(fname) as in_file:
|
||||
idx = 0
|
||||
for line in in_file:
|
||||
line = line.rstrip('\n\r')
|
||||
@@ -228,8 +229,6 @@ def get_headers( fname, sep, count=60, is_multi_byte=False, comment_designator=N
|
||||
idx += 1
|
||||
if idx == count:
|
||||
break
|
||||
finally:
|
||||
in_file.close()
|
||||
return headers
|
||||
|
||||
|
||||
|
||||
@@ -787,8 +787,7 @@ class Eland( Tabular ):
|
||||
- LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct
|
||||
- We will only check that up to the first 5 alignments are correctly formatted.
|
||||
"""
|
||||
try:
|
||||
fh = compression_utils.get_fileobj(filename, gzip_only=True)
|
||||
with compression_utils.get_fileobj(filename, gzip_only=True) as fh:
|
||||
count = 0
|
||||
while True:
|
||||
line = fh.readline()
|
||||
@@ -799,34 +798,25 @@ class Eland( Tabular ):
|
||||
line_pieces = line.split('\t')
|
||||
if len(line_pieces) != 22:
|
||||
return False
|
||||
try:
|
||||
if long(line_pieces[1]) < 0:
|
||||
raise Exception('Out of range')
|
||||
if long(line_pieces[2]) < 0:
|
||||
raise Exception('Out of range')
|
||||
if long(line_pieces[3]) < 0:
|
||||
raise Exception('Out of range')
|
||||
int(line_pieces[4])
|
||||
int(line_pieces[5])
|
||||
# can get a lot more specific
|
||||
except ValueError:
|
||||
fh.close()
|
||||
return False
|
||||
if long(line_pieces[1]) < 0:
|
||||
raise Exception('Out of range')
|
||||
if long(line_pieces[2]) < 0:
|
||||
raise Exception('Out of range')
|
||||
if long(line_pieces[3]) < 0:
|
||||
raise Exception('Out of range')
|
||||
int(line_pieces[4])
|
||||
int(line_pieces[5])
|
||||
# can get a lot more specific
|
||||
count += 1
|
||||
if count == 5:
|
||||
break
|
||||
if count > 0:
|
||||
fh.close()
|
||||
return True
|
||||
except:
|
||||
pass
|
||||
fh.close()
|
||||
return False
|
||||
|
||||
def set_meta( self, dataset, overwrite=True, skip=None, max_data_lines=5, **kwd ):
|
||||
if dataset.has_data():
|
||||
dataset_fh = compression_utils.get_fileobj(dataset.file_name, gzip_only=True)
|
||||
try:
|
||||
with compression_utils.get_fileobj(dataset.file_name, gzip_only=True) as dataset_fh:
|
||||
lanes = {}
|
||||
tiles = {}
|
||||
barcodes = {}
|
||||
@@ -848,8 +838,6 @@ class Eland( Tabular ):
|
||||
reads[line_pieces[7]] = 1
|
||||
pass
|
||||
dataset.metadata.data_lines = i + 1
|
||||
finally:
|
||||
dataset_fh.close()
|
||||
dataset.metadata.comment_lines = 0
|
||||
dataset.metadata.columns = 21
|
||||
dataset.metadata.column_types = ['str', 'int', 'int', 'int', 'int', 'int', 'str', 'int', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str', 'str']
|
||||
|
||||
@@ -0,0 +1,11 @@
|
||||
species n number_comp lnL AIC BIC mean variance porportion
|
||||
species1 1184 1 -1527.4110 3058.82 3068.98 0.4656 0.1675 1.00
|
||||
species1 1184 2 -1490.7280 2991.46 3016.84 0.1718 0.0035 0.22
|
||||
0.6173 0.2275 0.78
|
||||
species1 1184 3 -1471.6980 2959.40 3000.01 0.6921 0.1806 0.65
|
||||
5.9251 3.0703 0.02
|
||||
0.1887 0.0054 0.33
|
||||
species1 1184 4 -1443.1050 2908.21 2964.05 0.1219 0.0002 0.10
|
||||
0.2589 0.0093 0.38
|
||||
0.7900 0.1030 0.42
|
||||
1.5944 1.7482 0.10
|
||||
@@ -1,12 +1,15 @@
|
||||
"""
|
||||
Triple format classes
|
||||
"""
|
||||
import re
|
||||
import data
|
||||
import logging
|
||||
import xml
|
||||
import text
|
||||
import binary
|
||||
import re
|
||||
|
||||
from . import (
|
||||
binary,
|
||||
data,
|
||||
text,
|
||||
xml
|
||||
)
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -6,6 +6,8 @@ import copy
|
||||
from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError
|
||||
from bx.tabular.io import Comment, Header
|
||||
|
||||
from six import Iterator
|
||||
|
||||
from galaxy.util.odict import odict
|
||||
|
||||
|
||||
@@ -117,7 +119,7 @@ class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ):
|
||||
return interval
|
||||
|
||||
|
||||
class GFFReaderWrapper( NiceReaderWrapper ):
|
||||
class GFFReaderWrapper( Iterator, NiceReaderWrapper ): # Iterator can be removed after bx-python library is ported to Python3
|
||||
"""
|
||||
Reader wrapper for GFF files.
|
||||
|
||||
@@ -149,15 +151,14 @@ class GFFReaderWrapper( NiceReaderWrapper ):
|
||||
self.default_strand, fix_strand=self.fix_strand )
|
||||
return interval
|
||||
|
||||
# For Python3 this needs to be changed to __next__() after bx-python library is ported too
|
||||
def next( self ):
|
||||
def __next__( self ):
|
||||
""" Returns next GFFFeature. """
|
||||
|
||||
#
|
||||
# Helper function.
|
||||
#
|
||||
|
||||
def handle_parse_error( parse_error ):
|
||||
def handle_parse_error( e ):
|
||||
""" Actions to take when ParseError found. """
|
||||
if self.outstream:
|
||||
if self.print_delegate and hasattr(self.print_delegate, "__call__"):
|
||||
@@ -434,19 +435,16 @@ def read_unordered_gtf( iterator, strict=False ):
|
||||
chroms_features = {}
|
||||
for count, intervals in enumerate( feature_intervals.values() ):
|
||||
# Sort intervals by start position.
|
||||
intervals.sort( lambda a, b: cmp( a.start, b.start ) )
|
||||
intervals.sort(key=lambda _: _.start)
|
||||
feature = GFFFeature( None, intervals=intervals )
|
||||
if feature.chrom not in chroms_features:
|
||||
chroms_features[ feature.chrom ] = []
|
||||
chroms_features[ feature.chrom ].append( feature )
|
||||
|
||||
# Sort features by chrom, start position.
|
||||
chroms_features_sorted = []
|
||||
for chrom_features in chroms_features.values():
|
||||
chroms_features_sorted.append( chrom_features )
|
||||
chroms_features_sorted.sort( lambda a, b: cmp( a[0].chrom, b[0].chrom ) )
|
||||
chroms_features_sorted = sorted(chroms_features.values(), key=lambda _: _[0].chrom)
|
||||
for features in chroms_features_sorted:
|
||||
features.sort( lambda a, b: cmp( a.start, b.start ) )
|
||||
features.sort(key=lambda _: _.start)
|
||||
|
||||
# Yield comments first, then features.
|
||||
# FIXME: comments can appear anywhere in file, not just the beginning.
|
||||
|
||||
@@ -1,10 +1,13 @@
|
||||
"""
|
||||
XML format classes
|
||||
"""
|
||||
import re
|
||||
import data
|
||||
import logging
|
||||
import dataproviders
|
||||
import re
|
||||
|
||||
from . import (
|
||||
data,
|
||||
dataproviders
|
||||
)
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@@ -1,11 +1,11 @@
|
||||
"""
|
||||
Determine what optional dependencies are needed.
|
||||
"""
|
||||
import pkg_resources
|
||||
|
||||
from os.path import dirname, join
|
||||
from xml.etree import ElementTree
|
||||
|
||||
import pkg_resources
|
||||
|
||||
from galaxy.util import asbool
|
||||
from galaxy.util.properties import load_app_properties
|
||||
|
||||
|
||||
@@ -23,7 +23,7 @@ bx-python
|
||||
MarkupSafe
|
||||
PyYAML
|
||||
SQLAlchemy
|
||||
mercurial
|
||||
mercurial!=4.1.1 #conda's mercurial 4.1.1. is broken
|
||||
pycrypto
|
||||
|
||||
# Install python_lzo if you want to support indexed access to lzo-compressed
|
||||
|
||||
@@ -1216,7 +1216,7 @@ class JobWrapper( object, HasResourceParameters ):
|
||||
# need to update all associated output hdas, i.e. history was shared with job running
|
||||
for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
|
||||
purged = dataset.dataset.purged
|
||||
if not purged:
|
||||
if not purged and dataset.dataset.external_filename is None:
|
||||
trynum = 0
|
||||
while trynum < self.app.config.retry_job_output_collection:
|
||||
try:
|
||||
|
||||
@@ -152,9 +152,9 @@ class User( object, Dictifiable ):
|
||||
histories, credentials, and roles.
|
||||
"""
|
||||
# attributes that will be accessed and returned when calling to_dict( view='collection' )
|
||||
dict_collection_visible_keys = ( 'id', 'email', 'username' )
|
||||
dict_collection_visible_keys = ( 'id', 'email', 'username', 'deleted', 'active', 'last_password_change' )
|
||||
# attributes that will be accessed and returned when calling to_dict( view='element' )
|
||||
dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' )
|
||||
dict_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change' )
|
||||
|
||||
def __init__( self, email=None, password=None ):
|
||||
self.email = email
|
||||
|
||||
@@ -2,10 +2,17 @@
|
||||
Shared model and mapping code between Galaxy and Tool Shed, trying to
|
||||
generalize to generic database connections.
|
||||
"""
|
||||
from inspect import (
|
||||
getmembers,
|
||||
isclass
|
||||
)
|
||||
|
||||
from sqlalchemy.orm import (
|
||||
scoped_session,
|
||||
sessionmaker
|
||||
)
|
||||
|
||||
from sqlalchemy.orm import scoped_session, sessionmaker
|
||||
from galaxy.util.bunch import Bunch
|
||||
from inspect import getmembers, isclass
|
||||
|
||||
|
||||
# TODO: Refactor this to be a proper class, not a bunch.
|
||||
|
||||
@@ -3,17 +3,21 @@ import copy
|
||||
import json
|
||||
import logging
|
||||
import uuid
|
||||
|
||||
from sys import getsizeof
|
||||
from itertools import chain
|
||||
from collections import deque
|
||||
from itertools import chain
|
||||
from sys import getsizeof
|
||||
|
||||
import sqlalchemy
|
||||
from sqlalchemy.ext.mutable import Mutable
|
||||
from sqlalchemy.types import (
|
||||
CHAR,
|
||||
LargeBinary,
|
||||
String,
|
||||
TypeDecorator
|
||||
)
|
||||
|
||||
from galaxy import app
|
||||
from galaxy.util.aliaspickler import AliasPickleModule
|
||||
from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator
|
||||
from sqlalchemy.ext.mutable import Mutable
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
@@ -234,6 +238,7 @@ def total_size(o, handlers={}, verbose=False):
|
||||
"""
|
||||
def dict_handler(d):
|
||||
return chain.from_iterable(d.items())
|
||||
|
||||
all_handlers = { tuple: iter,
|
||||
list: iter,
|
||||
deque: iter,
|
||||
@@ -268,7 +273,7 @@ class MetadataType( JSONType ):
|
||||
def process_bind_param(self, value, dialect):
|
||||
if value is not None:
|
||||
if app.app and app.app.config.max_metadata_value_size:
|
||||
for k, v in value.items():
|
||||
for k, v in list(value.items()):
|
||||
sz = total_size(v)
|
||||
if sz > app.app.config.max_metadata_value_size:
|
||||
del value[k]
|
||||
|
||||
@@ -32,12 +32,28 @@ import parsley
|
||||
from sqlalchemy import and_
|
||||
from sqlalchemy.orm import aliased
|
||||
|
||||
from galaxy.model import (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation,
|
||||
History, Library, LibraryFolder, LibraryDataset, StoredWorkflowTagAssociation,
|
||||
StoredWorkflow, HistoryTagAssociation, HistoryDatasetAssociationTagAssociation,
|
||||
ExtendedMetadata, ExtendedMetadataIndex, HistoryAnnotationAssociation, Job, JobParameter,
|
||||
JobToInputLibraryDatasetAssociation, JobToInputDatasetAssociation, JobToOutputDatasetAssociation,
|
||||
Page, PageRevision)
|
||||
from galaxy.model import (
|
||||
ExtendedMetadata,
|
||||
ExtendedMetadataIndex,
|
||||
History,
|
||||
HistoryAnnotationAssociation,
|
||||
HistoryDatasetAssociation,
|
||||
HistoryDatasetAssociationTagAssociation,
|
||||
HistoryTagAssociation,
|
||||
Job,
|
||||
JobParameter,
|
||||
JobToInputDatasetAssociation,
|
||||
JobToInputLibraryDatasetAssociation,
|
||||
JobToOutputDatasetAssociation,
|
||||
Library,
|
||||
LibraryDataset,
|
||||
LibraryDatasetDatasetAssociation,
|
||||
LibraryFolder,
|
||||
Page,
|
||||
PageRevision,
|
||||
StoredWorkflow,
|
||||
StoredWorkflowTagAssociation
|
||||
)
|
||||
from galaxy.model.tool_shed_install import ToolVersion
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
@@ -1,10 +1,12 @@
|
||||
import logging
|
||||
import os
|
||||
from galaxy.util.dictifiable import Dictifiable
|
||||
from galaxy.util.bunch import Bunch
|
||||
|
||||
from six.moves.urllib.parse import urljoin
|
||||
|
||||
from galaxy.util import asbool
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.dictifiable import Dictifiable
|
||||
from tool_shed.util import common_util
|
||||
from urlparse import urljoin
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
@@ -589,53 +591,6 @@ class ToolVersion( object, Dictifiable ):
|
||||
self.tool_id = tool_id
|
||||
self.tool_shed_repository = tool_shed_repository
|
||||
|
||||
def get_previous_version( self, app ):
|
||||
parent_id = app.tool_version_cache.tool_id_to_parent_id.get(self.id, None)
|
||||
if parent_id:
|
||||
return app.tool_version_cache.tool_version_by_id[parent_id]
|
||||
else:
|
||||
return None
|
||||
|
||||
def get_next_version( self, app ):
|
||||
child_id = app.tool_version_cache.parent_id_to_tool_id.get(self.id, None)
|
||||
if child_id:
|
||||
return app.tool_version_cache.tool_version_by_id[child_id]
|
||||
else:
|
||||
return None
|
||||
|
||||
def get_versions( self, app ):
|
||||
tool_versions = []
|
||||
|
||||
# Prepend ancestors.
|
||||
def __ancestors( app, tool_version ):
|
||||
# Should we handle multiple parents at each level?
|
||||
previous_version = tool_version.get_previous_version( app )
|
||||
if previous_version:
|
||||
if previous_version not in tool_versions:
|
||||
tool_versions.insert( 0, previous_version )
|
||||
__ancestors( app, previous_version )
|
||||
|
||||
# Append descendants.
|
||||
def __descendants( app, tool_version ):
|
||||
# Should we handle multiple child siblings at each level?
|
||||
next_version = tool_version.get_next_version( app )
|
||||
if next_version:
|
||||
if next_version not in tool_versions:
|
||||
tool_versions.append( next_version )
|
||||
__descendants( app, next_version )
|
||||
|
||||
__ancestors( app, self )
|
||||
if self not in tool_versions:
|
||||
tool_versions.append( self )
|
||||
__descendants( app, self )
|
||||
return tool_versions
|
||||
|
||||
def get_version_ids( self, app, reverse=False ):
|
||||
version_ids = [ tool_version.tool_id for tool_version in self.get_versions( app ) ]
|
||||
if reverse:
|
||||
version_ids.reverse()
|
||||
return version_ids
|
||||
|
||||
def to_dict( self, view='element' ):
|
||||
rval = super( ToolVersion, self ).to_dict( view=view )
|
||||
rval[ 'tool_name' ] = self.tool_id
|
||||
|
||||
@@ -1,11 +1,27 @@
|
||||
from sqlalchemy import (
|
||||
Boolean,
|
||||
Column,
|
||||
DateTime,
|
||||
ForeignKey,
|
||||
Integer,
|
||||
MetaData,
|
||||
String,
|
||||
Table,
|
||||
TEXT
|
||||
)
|
||||
from sqlalchemy.orm import (
|
||||
mapper,
|
||||
relation
|
||||
)
|
||||
|
||||
from galaxy.model import tool_shed_install as install_model
|
||||
from sqlalchemy import MetaData
|
||||
from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, String, Table, TEXT
|
||||
from sqlalchemy.orm import relation, mapper
|
||||
from galaxy.model.custom_types import JSONType, TrimmedString
|
||||
from galaxy.model.orm.now import now
|
||||
from galaxy.model.base import ModelMapping
|
||||
from galaxy.model.custom_types import (
|
||||
JSONType,
|
||||
TrimmedString
|
||||
)
|
||||
from galaxy.model.orm.engine_factory import build_engine
|
||||
from galaxy.model.orm.now import now
|
||||
|
||||
metadata = MetaData()
|
||||
|
||||
|
||||
@@ -1,14 +1,17 @@
|
||||
import sys
|
||||
import os.path
|
||||
import logging
|
||||
import os.path
|
||||
import sys
|
||||
|
||||
# from sqlalchemy import *
|
||||
from sqlalchemy import create_engine
|
||||
from sqlalchemy import MetaData
|
||||
from sqlalchemy import Table
|
||||
|
||||
from migrate.versioning import (
|
||||
repository,
|
||||
schema
|
||||
)
|
||||
from sqlalchemy import (
|
||||
create_engine,
|
||||
MetaData,
|
||||
Table
|
||||
)
|
||||
from sqlalchemy.exc import NoSuchTableError
|
||||
from migrate.versioning import repository, schema
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
@@ -102,10 +102,8 @@ def _get_new_toolbox(app):
|
||||
"""
|
||||
from galaxy import tools
|
||||
from galaxy.tools.special_tools import load_lib_tools
|
||||
from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
|
||||
if hasattr(app, 'tool_shed_repository_cache'):
|
||||
app.tool_shed_repository_cache.rebuild()
|
||||
app.tool_version_cache = ToolVersionCache(app) # Load new tools into version cache
|
||||
tool_configs = app.config.tool_configs
|
||||
if app.config.migrated_tools_config not in tool_configs:
|
||||
tool_configs.append(app.config.migrated_tools_config)
|
||||
@@ -122,7 +120,6 @@ def _get_new_toolbox(app):
|
||||
def reload_data_managers(app, **kwargs):
|
||||
reload_timer = util.ExecutionTimer()
|
||||
from galaxy.tools.data_manager.manager import DataManagers
|
||||
from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
|
||||
log.debug("Executing data managers reload on '%s'", app.config.server_name)
|
||||
if hasattr(app, 'tool_shed_repository_cache'):
|
||||
app.tool_shed_repository_cache.rebuild()
|
||||
@@ -131,7 +128,6 @@ def reload_data_managers(app, **kwargs):
|
||||
reload_count = app.data_managers._reload_count
|
||||
app.data_managers = DataManagers(app)
|
||||
app.data_managers._reload_count = reload_count + 1
|
||||
app.tool_version_cache = ToolVersionCache(app)
|
||||
if hasattr(app, 'tool_cache'):
|
||||
app.tool_cache.reset_status()
|
||||
log.debug("Data managers reloaded %s", reload_timer)
|
||||
|
||||
@@ -6,7 +6,7 @@ import logging
|
||||
import socket
|
||||
from datetime import datetime, timedelta
|
||||
|
||||
from sqlalchemy import and_, false, or_, not_
|
||||
from sqlalchemy import and_, false, not_, or_
|
||||
from sqlalchemy.orm import eagerload_all
|
||||
|
||||
from galaxy.util import listify
|
||||
@@ -1008,7 +1008,7 @@ class GalaxyRBACAgent( RBACAgent ):
|
||||
# Add the new permissions on library_item
|
||||
for item_class, permission_class in self.library_item_assocs:
|
||||
if isinstance( library_item, item_class ):
|
||||
for action, roles in permissions.items():
|
||||
for action, roles in list(permissions.items()):
|
||||
if isinstance( action, Action ):
|
||||
action = action.action
|
||||
for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]:
|
||||
|
||||
@@ -1,10 +1,11 @@
|
||||
import hmac
|
||||
import hashlib
|
||||
from struct import Struct
|
||||
from operator import xor
|
||||
from itertools import starmap
|
||||
from os import urandom
|
||||
import hmac
|
||||
from base64 import b64encode
|
||||
from itertools import starmap
|
||||
from operator import xor
|
||||
from os import urandom
|
||||
from struct import Struct
|
||||
|
||||
from galaxy.util import safe_str_cmp
|
||||
|
||||
SALT_LENGTH = 12
|
||||
@@ -77,6 +78,6 @@ def pbkdf2_bin( data, salt, iterations=1000, keylen=24, hashfunc=None ):
|
||||
rv = u = _pseudorandom(salt + _pack_int(block))
|
||||
for i in range(iterations - 1):
|
||||
u = _pseudorandom(''.join(map(chr, u)))
|
||||
rv = starmap( xor, zip( rv, u ) ) # Python < 2.6.8: starmap requires function inputs to be tuples, so we need to use zip instead of izip
|
||||
rv = starmap( xor, zip( rv, u ) )
|
||||
buf.extend(rv)
|
||||
return ''.join(map(chr, buf))[:keylen]
|
||||
|
||||
@@ -414,9 +414,8 @@ class Tool( object, Dictifiable ):
|
||||
self.guid = guid
|
||||
self.old_id = None
|
||||
self.version = None
|
||||
self._lineage = None
|
||||
self.dependencies = []
|
||||
# Enable easy access to this tool's version lineage.
|
||||
self.lineage_ids = []
|
||||
# populate toolshed repository info, if available
|
||||
self.populate_tool_shed_info()
|
||||
# add tool resource parameters
|
||||
@@ -440,17 +439,17 @@ class Tool( object, Dictifiable ):
|
||||
return self.app.model.context
|
||||
|
||||
@property
|
||||
def tool_version( self ):
|
||||
"""Return a ToolVersion if one exists for our id"""
|
||||
return self.app.tool_version_cache.tool_version_by_tool_id.get(self.id)
|
||||
def lineage(self):
|
||||
"""Return ToolLineage for this tool."""
|
||||
return self._lineage
|
||||
|
||||
@property
|
||||
def tool_versions( self ):
|
||||
# If we have versions, return them.
|
||||
tool_version = self.tool_version
|
||||
if tool_version:
|
||||
return tool_version.get_versions( self.app )
|
||||
return []
|
||||
if self.lineage:
|
||||
return self.lineage.get_versions()
|
||||
else:
|
||||
return []
|
||||
|
||||
@property
|
||||
def tool_shed_repository( self ):
|
||||
@@ -1795,7 +1794,7 @@ class Tool( object, Dictifiable ):
|
||||
if job:
|
||||
try:
|
||||
job_params = job.get_param_values( self.app, ignore_errors=True )
|
||||
tool_warnings = self.check_and_update_param_values( job_params, request_context, update_values=False )
|
||||
tool_warnings = self.check_and_update_param_values( job_params, request_context, update_values=True )
|
||||
self._map_source_to_history( request_context, self.inputs, job_params )
|
||||
tool_message = self._compare_tool_version( job )
|
||||
params_to_incoming( kwd, self.inputs, job_params, self.app )
|
||||
@@ -1832,11 +1831,7 @@ class Tool( object, Dictifiable ):
|
||||
tool_help = unicodify( tool_help, 'utf-8' )
|
||||
|
||||
# create tool versions
|
||||
tool_versions = []
|
||||
tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id )
|
||||
for t in tools:
|
||||
if t.version not in tool_versions:
|
||||
tool_versions.append( t.version )
|
||||
tool_versions = self.lineage.tool_versions
|
||||
|
||||
# update tool model
|
||||
tool_model.update({
|
||||
|
||||
@@ -289,9 +289,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
|
||||
inserted = True
|
||||
if not inserted:
|
||||
# Check the tool's installed versions.
|
||||
versions = []
|
||||
if hasattr(tool, 'lineage'):
|
||||
versions = tool.lineage.get_versions()
|
||||
versions = tool.lineage.get_versions()
|
||||
for tool_lineage_version in versions:
|
||||
lineage_id = tool_lineage_version.id
|
||||
index = self._integrated_tool_panel.index_of_tool_id(lineage_id)
|
||||
@@ -415,10 +413,11 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
|
||||
tool_ids = [tool_id]
|
||||
for tool_id in tool_ids:
|
||||
if tool_id in self._tools_by_id and not get_all_versions:
|
||||
if tool_version and tool_version in self._tool_versions_by_id[ tool_id ]:
|
||||
return self._tool_versions_by_id[ tool_id ][ tool_version ]
|
||||
# tool_id exactly matches an available tool by id (which is 'old' tool_id or guid)
|
||||
return self._tools_by_id[ tool_id ]
|
||||
if not tool_version:
|
||||
return self._tools_by_id[ tool_id ]
|
||||
elif tool_version in self._tool_versions_by_id[ tool_id ]:
|
||||
return self._tool_versions_by_id[ tool_id ][ tool_version ]
|
||||
elif exact:
|
||||
# We're looking for an exact match, so we skip lineage and
|
||||
# versionless mapping, though we may want to check duplicate
|
||||
@@ -427,8 +426,6 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
|
||||
# exact tool id match not found, or all versions requested, search for other options, e.g. migrated tools or different versions
|
||||
rval = []
|
||||
tool_lineage = self._lineage_map.get( tool_id )
|
||||
if not tool_lineage:
|
||||
tool_lineage = self._lineage_map.get_versionless( tool_id )
|
||||
if tool_lineage:
|
||||
lineage_tool_versions = tool_lineage.get_versions( )
|
||||
for lineage_tool_version in lineage_tool_versions:
|
||||
@@ -567,9 +564,8 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
|
||||
tool.installed_changeset_revision = tool_shed_repository.installed_changeset_revision
|
||||
tool.guid = guid
|
||||
tool.version = item.elem.find( "version" ).text
|
||||
# Make sure tools have a tool_version object.
|
||||
tool_lineage = self._lineage_map.register( tool, from_toolshed=guid )
|
||||
tool.lineage = tool_lineage
|
||||
# Make sure tools are registered in self._lineage_map.
|
||||
tool._lineage = self._lineage_map.register( tool )
|
||||
if item.has_elem:
|
||||
self._tool_tag_manager.handle_tags( tool.id, item.elem )
|
||||
self.__add_tool( tool, load_panel_dict, panel_dict )
|
||||
@@ -949,10 +945,8 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
|
||||
"""
|
||||
if tool_lineage is None:
|
||||
assert tool is not None
|
||||
if not hasattr( tool, "lineage" ):
|
||||
return None
|
||||
tool_lineage = tool.lineage
|
||||
lineage_tool_versions = tool_lineage.get_versions( reverse=True )
|
||||
lineage_tool_versions = reversed(tool_lineage.get_versions())
|
||||
for lineage_tool_version in lineage_tool_versions:
|
||||
lineage_tool = self._tool_from_lineage_version( lineage_tool_version )
|
||||
if lineage_tool:
|
||||
@@ -965,16 +959,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
|
||||
""" Return True if tool1 is considered "newer" given its own lineage
|
||||
description.
|
||||
"""
|
||||
if not hasattr( tool1, "lineage" ):
|
||||
return True
|
||||
lineage_tool_versions = tool1.lineage.get_versions()
|
||||
for lineage_tool_version in lineage_tool_versions:
|
||||
lineage_tool = self._tool_from_lineage_version( lineage_tool_version )
|
||||
if lineage_tool is tool1:
|
||||
return False
|
||||
if lineage_tool is tool2:
|
||||
return True
|
||||
return True
|
||||
return tool1.version_object > tool2.version_object
|
||||
|
||||
def _tool_from_lineage_version( self, lineage_tool_version ):
|
||||
if lineage_tool_version.id_based:
|
||||
|
||||
@@ -1,6 +1,5 @@
|
||||
from .factory import LineageMap
|
||||
from .interface import ToolLineage
|
||||
from .tool_shed import ToolVersionCache
|
||||
|
||||
|
||||
__all__ = ("LineageMap", "ToolLineage", "ToolVersionCache")
|
||||
__all__ = ("LineageMap", "ToolLineage")
|
||||
|
||||
@@ -1,15 +1,6 @@
|
||||
from .stock import StockLineage
|
||||
from .tool_shed import ToolShedLineage
|
||||
from galaxy.util.tool_version import remove_version_from_guid
|
||||
|
||||
|
||||
def remove_version_from_guid( guid ):
|
||||
"""
|
||||
Removes version from toolshed-derived tool_id(=guid).
|
||||
"""
|
||||
if "/repos/" not in guid:
|
||||
return None
|
||||
last_slash = guid.rfind('/')
|
||||
return guid[:last_slash]
|
||||
from .interface import ToolLineage
|
||||
|
||||
|
||||
class LineageMap(object):
|
||||
@@ -20,13 +11,17 @@ class LineageMap(object):
|
||||
self.lineage_map = {}
|
||||
self.app = app
|
||||
|
||||
def register(self, tool, from_toolshed=False):
|
||||
def register(self, tool):
|
||||
tool_id = tool.id
|
||||
versionless_tool_id = remove_version_from_guid( tool_id )
|
||||
if from_toolshed:
|
||||
lineage = ToolShedLineage.from_tool(self.app, tool)
|
||||
versionless_tool_id = remove_version_from_guid(tool_id)
|
||||
lineage = self.lineage_map.get(versionless_tool_id)
|
||||
if not lineage:
|
||||
lineage = ToolLineage.from_tool( tool )
|
||||
else:
|
||||
lineage = StockLineage.from_tool( tool )
|
||||
# A lineage for a tool with the same versionless_tool_id exists,
|
||||
# but this lineage may not have the current tools' version,
|
||||
# so we add tool.version to the lineage
|
||||
lineage.register_version(tool.version)
|
||||
if versionless_tool_id and versionless_tool_id not in self.lineage_map:
|
||||
self.lineage_map[versionless_tool_id] = lineage
|
||||
if tool_id not in self.lineage_map:
|
||||
@@ -34,14 +29,25 @@ class LineageMap(object):
|
||||
return self.lineage_map[tool_id]
|
||||
|
||||
def get(self, tool_id):
|
||||
"""
|
||||
Get lineage for `tool_id`.
|
||||
|
||||
By preference the lineage for a version-agnostic tool_id is returned.
|
||||
Falls back to fetching the lineage only when this fails.
|
||||
This happens when the tool_id does not contain a version.
|
||||
"""
|
||||
lineage = self._get_versionless(tool_id)
|
||||
if lineage:
|
||||
return lineage
|
||||
if tool_id not in self.lineage_map:
|
||||
lineage = ToolShedLineage.from_tool_id( self.app, tool_id )
|
||||
tool = self.app.toolbox._tools_by_id.get(tool_id)
|
||||
if tool:
|
||||
lineage = ToolLineage.from_tool( tool )
|
||||
if lineage:
|
||||
self.lineage_map[tool_id] = lineage
|
||||
return self.lineage_map.get(tool_id)
|
||||
|
||||
return self.lineage_map.get(tool_id, None)
|
||||
|
||||
def get_versionless(self, tool_id):
|
||||
def _get_versionless(self, tool_id):
|
||||
versionless_tool_id = remove_version_from_guid(tool_id)
|
||||
return self.lineage_map.get(versionless_tool_id, None)
|
||||
|
||||
|
||||
@@ -1,21 +1,8 @@
|
||||
from abc import (
|
||||
ABCMeta,
|
||||
abstractmethod
|
||||
)
|
||||
import threading
|
||||
|
||||
import six
|
||||
from distutils.version import LooseVersion
|
||||
|
||||
|
||||
@six.add_metaclass(ABCMeta)
|
||||
class ToolLineage(object):
|
||||
"""
|
||||
"""
|
||||
|
||||
@abstractmethod
|
||||
def get_versions( self, reverse=False ):
|
||||
""" Return an ordered list of lineages (ToolLineageVersion) in this
|
||||
chain, from oldest to newest.
|
||||
"""
|
||||
from galaxy.util.tool_version import remove_version_from_guid
|
||||
|
||||
|
||||
class ToolLineageVersion(object):
|
||||
@@ -27,15 +14,6 @@ class ToolLineageVersion(object):
|
||||
self.id = id
|
||||
self.version = version
|
||||
|
||||
@staticmethod
|
||||
def from_id_and_verion( id, version ):
|
||||
assert version is not None
|
||||
return ToolLineageVersion( id, version )
|
||||
|
||||
@staticmethod
|
||||
def from_guid( guid ):
|
||||
return ToolLineageVersion( guid, None )
|
||||
|
||||
@property
|
||||
def id_based( self ):
|
||||
""" Return True if the lineage is defined by GUIDs (in this
|
||||
@@ -50,3 +28,59 @@ class ToolLineageVersion(object):
|
||||
id=self.id,
|
||||
version=self.version,
|
||||
)
|
||||
|
||||
|
||||
class ToolLineage:
|
||||
""" Simple tool's loaded directly from file system with lineage
|
||||
determined solely by distutil's LooseVersion naming scheme.
|
||||
"""
|
||||
lineages_by_id = {}
|
||||
lock = threading.Lock()
|
||||
|
||||
def __init__(self, tool_id, **kwds):
|
||||
self.tool_id = tool_id
|
||||
self._tool_versions = set()
|
||||
|
||||
@property
|
||||
def tool_versions(self):
|
||||
return sorted(self._tool_versions, key=LooseVersion)
|
||||
|
||||
@property
|
||||
def tool_ids(self):
|
||||
versionless_tool_id = remove_version_from_guid(self.tool_id)
|
||||
tool_id = versionless_tool_id or self.tool_id
|
||||
return ["%s/%s" % (tool_id, version) for version in self.tool_versions]
|
||||
|
||||
@staticmethod
|
||||
def from_tool( tool ):
|
||||
tool_id = tool.id
|
||||
lineages_by_id = ToolLineage.lineages_by_id
|
||||
with ToolLineage.lock:
|
||||
if tool_id not in lineages_by_id:
|
||||
lineages_by_id[ tool_id ] = ToolLineage( tool_id )
|
||||
lineage = lineages_by_id[ tool_id ]
|
||||
lineage.register_version( tool.version )
|
||||
return lineage
|
||||
|
||||
def register_version( self, tool_version ):
|
||||
assert tool_version is not None
|
||||
self._tool_versions.add( str(tool_version) )
|
||||
|
||||
def get_versions( self ):
|
||||
"""
|
||||
Return an ordered list of lineages (ToolLineageVersion) in this
|
||||
chain, from oldest to newest.
|
||||
"""
|
||||
return [ ToolLineageVersion( tool_id, tool_version ) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions) ]
|
||||
|
||||
def get_version_ids(self, reverse=False):
|
||||
if reverse:
|
||||
return list(reversed(self.tool_ids))
|
||||
return self.tool_ids
|
||||
|
||||
def to_dict(self):
|
||||
return dict(
|
||||
tool_id=self.tool_id,
|
||||
tool_versions=list(self.tool_versions),
|
||||
lineage_type='stock',
|
||||
)
|
||||
|
||||
@@ -1,51 +0,0 @@
|
||||
import threading
|
||||
|
||||
from distutils.version import LooseVersion
|
||||
|
||||
from .interface import ToolLineage
|
||||
from .interface import ToolLineageVersion
|
||||
|
||||
|
||||
class StockLineage(ToolLineage):
|
||||
""" Simple tool's loaded directly from file system with lineage
|
||||
determined solely by distutil's LooseVersion naming scheme.
|
||||
"""
|
||||
lineages_by_id = {}
|
||||
lock = threading.Lock()
|
||||
|
||||
def __init__(self, tool_id, **kwds):
|
||||
self.tool_id = tool_id
|
||||
self.tool_versions = set()
|
||||
|
||||
@staticmethod
|
||||
def from_tool( tool ):
|
||||
tool_id = tool.id
|
||||
lineages_by_id = StockLineage.lineages_by_id
|
||||
with StockLineage.lock:
|
||||
if tool_id not in lineages_by_id:
|
||||
lineages_by_id[ tool_id ] = StockLineage( tool_id )
|
||||
lineage = lineages_by_id[ tool_id ]
|
||||
lineage.register_version( tool.version )
|
||||
return lineage
|
||||
|
||||
def register_version( self, tool_version ):
|
||||
assert tool_version is not None
|
||||
self.tool_versions.add( tool_version )
|
||||
|
||||
def get_versions( self, reverse=False ):
|
||||
versions = [ ToolLineageVersion( self.tool_id, v ) for v in self.tool_versions ]
|
||||
# Sort using LooseVersion which defines an appropriate __cmp__
|
||||
# method for comparing tool versions.
|
||||
return sorted( versions, key=_to_loose_version, reverse=reverse )
|
||||
|
||||
def to_dict(self):
|
||||
return dict(
|
||||
tool_id=self.tool_id,
|
||||
tool_versions=list(self.tool_versions),
|
||||
lineage_type='stock',
|
||||
)
|
||||
|
||||
|
||||
def _to_loose_version( tool_lineage_version ):
|
||||
version = str( tool_lineage_version.version )
|
||||
return LooseVersion( version )
|
||||
@@ -1,98 +0,0 @@
|
||||
from .interface import ToolLineage, ToolLineageVersion
|
||||
|
||||
try:
|
||||
from galaxy.model.tool_shed_install import ToolVersion
|
||||
except ImportError:
|
||||
ToolVersion = None
|
||||
|
||||
|
||||
class ToolVersionCache(object):
|
||||
"""
|
||||
Instances of this class allow looking up tool_version objects from memory
|
||||
(instead of querying the database) using the tool_version id or the tool_id.
|
||||
This is used to lookup parent tool_version ids using child tool_id, or the
|
||||
inverse, and getting all previous/next tool versions without numerous
|
||||
database requests.
|
||||
"""
|
||||
def __init__(self, app):
|
||||
self.app = app
|
||||
self.tool_version_by_id, self.tool_version_by_tool_id = self.get_tool_versions()
|
||||
self.tool_id_to_parent_id, self.parent_id_to_tool_id = self.get_tva_map()
|
||||
|
||||
def get_tva_map(self):
|
||||
"""
|
||||
Retrieves all ToolVersionAssociation objects from the database, and builds
|
||||
dictionaries that can be used to either get a tools' parent tool_version id
|
||||
(which can be used to get the parent's tool_version object), or to get the
|
||||
child's tool id using the parent's tool_version id.
|
||||
"""
|
||||
tvas = self.app.install_model.context.query(self.app.install_model.ToolVersionAssociation).all()
|
||||
tool_id_to_parent_id = {tva.tool_id: tva.parent_id for tva in tvas}
|
||||
parent_id_to_tool_id = {tva.parent_id: tva.tool_id for tva in tvas}
|
||||
return tool_id_to_parent_id, parent_id_to_tool_id
|
||||
|
||||
def get_tool_versions(self):
|
||||
"""
|
||||
Get all tool_version objects from the database and build 2 dictionaries,
|
||||
with tool_version id or tool_id as key and the tool_version object as value.
|
||||
"""
|
||||
tool_versions = self.app.install_model.context.query(self.app.install_model.ToolVersion).all()
|
||||
tool_version_by_id = {tv.id: tv for tv in tool_versions}
|
||||
tool_version_by_tool_id = {tv.tool_id: tv for tv in tool_versions}
|
||||
return tool_version_by_id, tool_version_by_tool_id
|
||||
|
||||
|
||||
class ToolShedLineage(ToolLineage):
|
||||
""" Representation of tool lineage derived from tool shed repository
|
||||
installations. """
|
||||
|
||||
def __init__(self, app, tool_version, tool_shed_repository=None):
|
||||
if ToolVersion is None:
|
||||
raise Exception("Tool shed models not present, can't create tool shed lineages.")
|
||||
self.app = app
|
||||
self.tool_version_id = tool_version.id
|
||||
# Only used for logging
|
||||
self._tool_shed_repository = tool_shed_repository
|
||||
|
||||
@staticmethod
|
||||
def from_tool( app, tool ):
|
||||
# Make sure the tool has a tool_version.
|
||||
if not get_installed_tool_version( app, tool.id ):
|
||||
tool_version = ToolVersion( tool_id=tool.id, tool_shed_repository=tool.tool_shed_repository )
|
||||
app.install_model.context.add( tool_version )
|
||||
app.install_model.context.flush()
|
||||
app.tool_version_cache = ToolVersionCache(app)
|
||||
return ToolShedLineage( app, tool.tool_version )
|
||||
|
||||
@staticmethod
|
||||
def from_tool_id( app, tool_id ):
|
||||
tool_version = get_installed_tool_version( app, tool_id )
|
||||
if tool_version:
|
||||
return ToolShedLineage( app, tool_version )
|
||||
else:
|
||||
return None
|
||||
|
||||
def get_version_ids( self, reverse=False ):
|
||||
tool_version = self.app.install_model.context.query( ToolVersion ).get( self.tool_version_id )
|
||||
result = tool_version.get_version_ids( self.app, reverse=reverse )
|
||||
return result
|
||||
|
||||
def get_versions( self, reverse=False ):
|
||||
return [ ToolLineageVersion.from_guid(_) for _ in self.get_version_ids( reverse=reverse ) ]
|
||||
|
||||
def to_dict(self):
|
||||
tool_shed_repository = self._tool_shed_repository
|
||||
rval = dict(
|
||||
tool_version_id=self.tool_version_id,
|
||||
tool_versions=[v.to_dict() for v in self.get_versions()],
|
||||
tool_shed_repository=tool_shed_repository if tool_shed_repository is not None else None,
|
||||
lineage_type='tool_shed',
|
||||
)
|
||||
return rval
|
||||
|
||||
|
||||
def get_installed_tool_version( app, tool_id ):
|
||||
return app.tool_version_cache.tool_version_by_tool_id.get(tool_id, None)
|
||||
|
||||
|
||||
__all__ = ( "ToolShedLineage", )
|
||||
@@ -0,0 +1,8 @@
|
||||
def remove_version_from_guid(guid):
|
||||
"""
|
||||
Removes version from toolshed-derived tool_id(=guid).
|
||||
"""
|
||||
if "/" not in guid:
|
||||
return None
|
||||
last_slash = guid.rfind('/')
|
||||
return guid[:last_slash]
|
||||
@@ -204,7 +204,7 @@ class JobController( BaseAPIController, UsesLibraryMixinItems ):
|
||||
job = self.__get_job(trans, id)
|
||||
if not job:
|
||||
raise exceptions.ObjectNotFound("Could not access job with id '%s'" % id)
|
||||
tool = self.app.toolbox.get_tool( job.tool_id, job.tool_version )
|
||||
tool = self.app.toolbox.get_tool( job.tool_id, kwd.get('tool_version') or job.tool_version )
|
||||
if tool is None:
|
||||
raise exceptions.ObjectNotFound( "Requested tool not found" )
|
||||
if not tool.is_workflow_compatible:
|
||||
|
||||
@@ -404,19 +404,19 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
|
||||
"""
|
||||
if payload:
|
||||
kwd.update(payload)
|
||||
kwd['space_to_tab'] = False
|
||||
kwd['to_posix_lines'] = True
|
||||
kwd[ 'space_to_tab' ] = False
|
||||
kwd[ 'to_posix_lines' ] = True
|
||||
kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
|
||||
kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' )
|
||||
kwd['link_data_only'] = 'link_to_files' if util.string_as_bool( kwd.get( 'link_data', False ) ) else 'copy_files'
|
||||
kwd[ 'link_data_only' ] = 'link_to_files' if util.asbool( kwd.get( 'link_data', False ) ) else 'copy_files'
|
||||
encoded_folder_id = kwd.get( 'encoded_folder_id', None )
|
||||
if encoded_folder_id is not None:
|
||||
folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id )
|
||||
else:
|
||||
raise exceptions.RequestParameterMissingException( 'The required atribute encoded_folder_id is missing.' )
|
||||
raise exceptions.RequestParameterMissingException( 'The required attribute encoded_folder_id is missing.' )
|
||||
path = kwd.get( 'path', None)
|
||||
if path is None:
|
||||
raise exceptions.RequestParameterMissingException( 'The required atribute path is missing.' )
|
||||
raise exceptions.RequestParameterMissingException( 'The required attribute path is missing.' )
|
||||
folder = self.folder_manager.get( trans, folder_id )
|
||||
|
||||
source = kwd.get( 'source', None )
|
||||
|
||||
@@ -15,6 +15,7 @@ from galaxy.web import _future_expose_api as expose_api
|
||||
from galaxy.web.base.controller import BaseAPIController
|
||||
|
||||
from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
|
||||
from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
|
||||
from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
|
||||
from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
|
||||
from tool_shed.util import common_util
|
||||
@@ -616,6 +617,46 @@ class ToolShedRepositoriesController( BaseAPIController ):
|
||||
all_installed_tool_shed_repositories.extend( installed_tool_shed_repositories )
|
||||
return all_installed_tool_shed_repositories
|
||||
|
||||
@expose_api
|
||||
def uninstall_repository(self, trans, id=None, **kwd):
|
||||
"""
|
||||
DELETE /api/tool_shed_repositories/id
|
||||
DELETE /api/tool_shed_repositories/
|
||||
|
||||
:param id: encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied
|
||||
:param kwd: 'remove_from_disk' : Remove repository from disk or deactivate repository.
|
||||
Defaults to `True` (= remove repository from disk).
|
||||
'name' : Repository name
|
||||
'owner' : Repository owner
|
||||
'changeset_revision': Changeset revision to uninstall
|
||||
'tool_shed_url' : Tool Shed URL
|
||||
"""
|
||||
if id:
|
||||
try:
|
||||
repository = repository_util.get_tool_shed_repository_by_id(self.app, id)
|
||||
except ValueError:
|
||||
raise HTTPBadRequest(detail="No repository with id '%s' found" % id)
|
||||
else:
|
||||
tsr_arguments = ['name', 'owner', 'changeset_revision', 'tool_shed_url']
|
||||
try:
|
||||
tsr_arguments = {key: kwd[key] for key in tsr_arguments}
|
||||
except KeyError as e:
|
||||
raise HTTPBadRequest(detail="Missing required parameter '%s'" % e.args[0])
|
||||
repository = repository_util.get_installed_repository(app=self.app,
|
||||
tool_shed=tsr_arguments['tool_shed_url'],
|
||||
name=tsr_arguments['name'],
|
||||
owner=tsr_arguments['owner'],
|
||||
changeset_revision=tsr_arguments['changeset_revision'])
|
||||
if not repository:
|
||||
raise HTTPBadRequest(detail="Repository not found")
|
||||
irm = InstalledRepositoryManager(app=self.app)
|
||||
errors = irm.uninstall_repository(repository=repository, remove_from_disk=kwd.get('remove_from_disk', True))
|
||||
if not errors:
|
||||
action = 'removed' if kwd.get('remove_from_disk', True) else 'deactivated'
|
||||
return {'message': 'The repository named %s has been %s.' % (repository.name, action)}
|
||||
else:
|
||||
raise Exception('Attempting to uninstall tool dependencies for repository named %s resulted in errors: %s' % (repository.name, errors))
|
||||
|
||||
@expose_api
|
||||
def repair_repository_revision( self, trans, payload, **kwd ):
|
||||
"""
|
||||
|
||||
@@ -113,10 +113,18 @@ class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, Cr
|
||||
item = user.to_dict( value_mapper={ 'id': trans.security.encode_id } )
|
||||
# If NOT configured to expose_email, do not expose email UNLESS the user is self, or
|
||||
# the user is an admin
|
||||
if not trans.app.config.expose_user_name and user is not trans.user and not trans.user_is_admin():
|
||||
del item['username']
|
||||
if not trans.app.config.expose_user_email and user is not trans.user and not trans.user_is_admin():
|
||||
del item['email']
|
||||
if user is not trans.user and not trans.user_is_admin():
|
||||
expose_keys = ["id"]
|
||||
if trans.app.config.expose_user_name:
|
||||
expose_keys.append("username")
|
||||
if trans.app.config.expose_user_email:
|
||||
expose_keys.append("email")
|
||||
new_item = {}
|
||||
for key, value in item.items():
|
||||
if key in expose_keys:
|
||||
new_item[key] = value
|
||||
item = new_item
|
||||
|
||||
# TODO: move into api_values
|
||||
rval.append( item )
|
||||
return rval
|
||||
|
||||
@@ -113,6 +113,7 @@ def paste_app_factory( global_conf, **kwargs ):
|
||||
webapp.add_client_route( '/pages/list' )
|
||||
webapp.add_client_route( '/pages/list_published' )
|
||||
webapp.add_client_route( '/histories/list' )
|
||||
webapp.add_client_route( '/histories/list_shared' )
|
||||
webapp.add_client_route( '/datasets/list' )
|
||||
webapp.add_client_route( '/workflow/run' )
|
||||
webapp.add_client_route( '/workflow/import_workflow' )
|
||||
@@ -826,12 +827,30 @@ def populate_api_routes( webapp, app ):
|
||||
action='status',
|
||||
conditions=dict( method=[ "GET" ] ) )
|
||||
|
||||
webapp.mapper.connect( 'install_repository',
|
||||
'/api/tool_shed_repositories',
|
||||
controller='tool_shed_repositories',
|
||||
action='install_repository_revision',
|
||||
conditions=dict( method=[ 'POST' ] ) )
|
||||
|
||||
webapp.mapper.connect( 'install_repository',
|
||||
'/api/tool_shed_repositories/install',
|
||||
controller='tool_shed_repositories',
|
||||
action='install',
|
||||
conditions=dict( method=[ 'POST' ] ) )
|
||||
|
||||
webapp.mapper.connect( 'tool_shed_repository',
|
||||
'/api/tool_shed_repositories',
|
||||
controller='tool_shed_repositories',
|
||||
action='uninstall_repository',
|
||||
conditions=dict( method=[ "DELETE" ]))
|
||||
|
||||
webapp.mapper.connect( 'tool_shed_repository',
|
||||
'/api/tool_shed_repositories/{id}',
|
||||
controller='tool_shed_repositories',
|
||||
action='uninstall_repository',
|
||||
conditions=dict( method=[ "DELETE" ]))
|
||||
|
||||
# Galaxy API for tool shed features.
|
||||
webapp.mapper.resource( 'tool_shed_repository',
|
||||
'tool_shed_repositories',
|
||||
|
||||
@@ -455,13 +455,17 @@ class ToolVersionListGrid( grids.Grid ):
|
||||
def get_value( self, trans, grid, tool_version ):
|
||||
tool_ids_str = ''
|
||||
toolbox = trans.app.toolbox
|
||||
for tool_id in tool_version.get_version_ids( trans.app ):
|
||||
if toolbox.has_tool( tool_id, exact=True ):
|
||||
link = url_for( controller='tool_runner', tool_id=tool_id )
|
||||
link_str = '<a target="_blank" href="%s">' % link
|
||||
tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % ( link_str, tool_id )
|
||||
else:
|
||||
tool_ids_str += '%s<br/>' % tool_id
|
||||
tool = toolbox._tools_by_id.get(tool_version.tool_id)
|
||||
if tool:
|
||||
for tool_id in tool.lineage.tool_ids:
|
||||
if toolbox.has_tool( tool_id, exact=True ):
|
||||
link = url_for( controller='tool_runner', tool_id=tool_id )
|
||||
link_str = '<a target="_blank" href="%s">' % link
|
||||
tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % ( link_str, tool_id )
|
||||
else:
|
||||
tool_ids_str += '%s<br/>' % tool_version.tool_id
|
||||
else:
|
||||
tool_ids_str += '%s<br/>' % tool_version.tool_id
|
||||
return tool_ids_str
|
||||
|
||||
# Grid definition
|
||||
|
||||
@@ -1,7 +1,6 @@
|
||||
import json
|
||||
import logging
|
||||
import os
|
||||
import shutil
|
||||
|
||||
from admin import AdminGalaxy
|
||||
from six import string_types
|
||||
@@ -13,8 +12,8 @@ from galaxy.tools.deps import views
|
||||
from galaxy.web.form_builder import CheckboxField
|
||||
from tool_shed.galaxy_install import dependency_display
|
||||
from tool_shed.galaxy_install import install_manager
|
||||
from tool_shed.galaxy_install.datatypes import custom_datatype_manager
|
||||
from tool_shed.galaxy_install.grids import admin_toolshed_grids
|
||||
from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
|
||||
from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
|
||||
from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
|
||||
from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
|
||||
@@ -249,84 +248,17 @@ class AdminToolshed( AdminGalaxy ):
|
||||
tool_shed_repositories = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] )
|
||||
if not isinstance( tool_shed_repositories, list ):
|
||||
tool_shed_repositories = [tool_shed_repositories]
|
||||
irm = InstalledRepositoryManager(app=trans.app)
|
||||
for tool_shed_repository in tool_shed_repositories:
|
||||
shed_tool_conf, tool_path, relative_install_dir = \
|
||||
suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
|
||||
if relative_install_dir:
|
||||
if tool_path:
|
||||
relative_install_dir = os.path.join( tool_path, relative_install_dir )
|
||||
repository_install_dir = os.path.abspath( relative_install_dir )
|
||||
else:
|
||||
repository_install_dir = None
|
||||
errors = ''
|
||||
if kwd.get( 'deactivate_or_uninstall_repository_button', False ):
|
||||
if tool_shed_repository.includes_tools_for_display_in_tool_panel:
|
||||
# Handle tool panel alterations.
|
||||
tpm = tool_panel_manager.ToolPanelManager( trans.app )
|
||||
tpm.remove_repository_contents( tool_shed_repository,
|
||||
shed_tool_conf,
|
||||
uninstall=remove_from_disk_checked )
|
||||
if tool_shed_repository.includes_data_managers:
|
||||
dmh = data_manager.DataManagerHandler( trans.app )
|
||||
dmh.remove_from_data_manager( tool_shed_repository )
|
||||
if tool_shed_repository.includes_datatypes:
|
||||
# Deactivate proprietary datatypes.
|
||||
cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app )
|
||||
installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository,
|
||||
repository_install_dir,
|
||||
deactivate=True )
|
||||
if installed_repository_dict:
|
||||
converter_path = installed_repository_dict.get( 'converter_path' )
|
||||
if converter_path is not None:
|
||||
cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True )
|
||||
display_path = installed_repository_dict.get( 'display_path' )
|
||||
if display_path is not None:
|
||||
cdl.load_installed_display_applications( installed_repository_dict, deactivate=True )
|
||||
errors = irm.uninstall_repository(repository=tool_shed_repository, remove_from_disk=remove_from_disk_checked)
|
||||
action = 'uninstalled' if remove_from_disk_checked else 'deactivated'
|
||||
status = max( status, statuses.index( 'done' ) )
|
||||
message += 'The repository named <b>%s</b> has been %s. ' % (escape( tool_shed_repository.name ), action)
|
||||
if remove_from_disk_checked:
|
||||
try:
|
||||
# Remove the repository from disk.
|
||||
shutil.rmtree( repository_install_dir )
|
||||
log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) )
|
||||
removed = True
|
||||
except Exception as e:
|
||||
log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) )
|
||||
if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ):
|
||||
removed = True
|
||||
log.debug( "Repository directory does not exist on disk, marking as uninstalled." )
|
||||
else:
|
||||
removed = False
|
||||
if removed:
|
||||
tool_shed_repository.uninstalled = True
|
||||
# Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any
|
||||
# repository dependencies.
|
||||
tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error
|
||||
tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed )
|
||||
for tool_dependency in tool_dependencies_to_uninstall:
|
||||
uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency )
|
||||
if error_message:
|
||||
errors = '%s %s' % ( errors, error_message )
|
||||
tool_shed_repository.deleted = True
|
||||
if remove_from_disk_checked:
|
||||
tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED
|
||||
tool_shed_repository.error_message = None
|
||||
if trans.app.config.manage_dependency_relationships:
|
||||
# Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
|
||||
# installed_repository_manager.
|
||||
trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
|
||||
else:
|
||||
tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED
|
||||
trans.install_model.context.current.add( tool_shed_repository )
|
||||
trans.install_model.context.current.flush()
|
||||
if remove_from_disk_checked:
|
||||
message += 'The repository named <b>%s</b> has been uninstalled. ' % escape( tool_shed_repository.name )
|
||||
if errors:
|
||||
message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors
|
||||
status = max( status, statuses.index( 'error' ) )
|
||||
else:
|
||||
status = max( status, statuses.index( 'done' ) )
|
||||
else:
|
||||
message = 'The repository named <b>%s</b> has been deactivated. ' % escape( tool_shed_repository.name )
|
||||
status = max( status, statuses.index( 'done' ) )
|
||||
status = statuses[ status ]
|
||||
if kwd.get( 'deactivate_or_uninstall_repository_button', False ):
|
||||
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
|
||||
@@ -2059,11 +1991,13 @@ class AdminToolshed( AdminGalaxy ):
|
||||
tool_config = tool_metadata[ 'tool_config' ]
|
||||
if shed_config_dict and shed_config_dict.get( 'tool_path' ):
|
||||
tool_config = os.path.join( shed_config_dict.get( 'tool_path' ), tool_config )
|
||||
tool = trans.app.toolbox.load_tool( os.path.abspath( tool_config ), guid=tool_metadata[ 'guid' ] )
|
||||
tool = trans.app.toolbox.get_tool(tool_id=tool_metadata[ 'guid' ], exact=True)
|
||||
if not tool:
|
||||
tool = trans.app.toolbox.load_tool( os.path.abspath( tool_config ), guid=tool_metadata[ 'guid' ] )
|
||||
if tool:
|
||||
tool._lineage = trans.app.toolbox._lineage_map.register( tool )
|
||||
if tool:
|
||||
tvm = tool_version_manager.ToolVersionManager( trans.app )
|
||||
tool_version = tvm.get_tool_version( str( tool.id ) )
|
||||
tool_lineage = tool_version.get_version_ids( trans.app, reverse=True )
|
||||
tool_lineage = tool.lineage.get_version_ids(reverse=True)
|
||||
break
|
||||
return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako",
|
||||
repository=repository,
|
||||
|
||||
@@ -153,7 +153,6 @@ class SharedHistoryListGrid( grids.Grid ):
|
||||
# Grid definition
|
||||
title = "Histories shared with you by others"
|
||||
model_class = model.History
|
||||
template = '/history/shared_grid.mako'
|
||||
default_sort_key = "-update_time"
|
||||
default_filter = {}
|
||||
columns = [
|
||||
@@ -164,9 +163,9 @@ class SharedHistoryListGrid( grids.Grid ):
|
||||
SharedByColumn( "Shared by", key="user_id" )
|
||||
]
|
||||
operations = [
|
||||
grids.GridOperation( "View", allow_multiple=False, target="_top" ),
|
||||
grids.GridOperation( "Copy" ),
|
||||
grids.GridOperation( "Unshare" )
|
||||
grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='view' ) ),
|
||||
grids.GridOperation( "Copy", allow_multiple=False ),
|
||||
grids.GridOperation( "Unshare", allow_multiple=False )
|
||||
]
|
||||
standard_filters = []
|
||||
|
||||
@@ -424,6 +423,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
return None, None
|
||||
|
||||
@web.expose
|
||||
@web.json
|
||||
@web.require_login( "work with shared histories" )
|
||||
def list_shared( self, trans, **kwargs ):
|
||||
"""List histories shared with current user by others"""
|
||||
@@ -431,14 +431,10 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
if 'operation' in kwargs:
|
||||
ids = galaxy.util.listify( kwargs.get( 'id', [] ) )
|
||||
operation = kwargs['operation'].lower()
|
||||
if operation == "view":
|
||||
# Display history.
|
||||
history = self.history_manager.get_accessible( self.decode_id( ids[0] ), trans.user, current_history=trans.history )
|
||||
return self.display_by_username_and_slug( trans, history.user.username, history.slug )
|
||||
elif operation == 'unshare':
|
||||
if operation == 'unshare':
|
||||
if not ids:
|
||||
message = "Select a history to unshare"
|
||||
return self.shared_list_grid( trans, status='error', message=message, **kwargs )
|
||||
status = 'error'
|
||||
for id in ids:
|
||||
# No need to check security, association below won't yield a
|
||||
# hit if this user isn't having the history shared with her.
|
||||
@@ -451,6 +447,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
message = "Unshared %d shared histories" % len( ids )
|
||||
status = 'done'
|
||||
# Render the list view
|
||||
kwargs[ 'dict_format' ] = True
|
||||
return self.shared_list_grid( trans, status=status, message=message, **kwargs )
|
||||
|
||||
# ......................................................................... html
|
||||
|
||||
@@ -87,7 +87,7 @@ class Library( BaseUIController ):
|
||||
}
|
||||
return trans.fill_template( 'galaxy.panels.mako',
|
||||
config={
|
||||
'title': 'Galaxy Data Libraries',
|
||||
'title': 'Data Libraries',
|
||||
'app': app } )
|
||||
|
||||
@web.expose
|
||||
|
||||
@@ -1,10 +1,10 @@
|
||||
"""
|
||||
This module manages loading of Galaxy webhooks.
|
||||
"""
|
||||
|
||||
import os
|
||||
import yaml
|
||||
import logging
|
||||
import os
|
||||
|
||||
import yaml
|
||||
|
||||
from galaxy.util import config_directories_from_setting
|
||||
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
from galaxy.managers.context import (
|
||||
ProvidesAppContext,
|
||||
ProvidesUserContext,
|
||||
ProvidesHistoryContext
|
||||
ProvidesHistoryContext,
|
||||
ProvidesUserContext
|
||||
)
|
||||
|
||||
|
||||
|
||||
@@ -3,34 +3,44 @@ Modules used in building workflows
|
||||
"""
|
||||
import logging
|
||||
from json import loads
|
||||
from xml.etree.ElementTree import Element
|
||||
from xml.etree.ElementTree import XML
|
||||
from xml.etree.ElementTree import (
|
||||
Element,
|
||||
XML
|
||||
)
|
||||
|
||||
from galaxy import exceptions, model, web
|
||||
from galaxy.exceptions import ToolMissingException
|
||||
from galaxy import (
|
||||
exceptions,
|
||||
model,
|
||||
web
|
||||
)
|
||||
from galaxy.dataset_collections import matching
|
||||
from galaxy.exceptions import ToolMissingException
|
||||
from galaxy.jobs.actions.post import ActionBox
|
||||
from galaxy.model import PostJobAction
|
||||
from galaxy.tools import (
|
||||
DefaultToolState,
|
||||
ToolInputsNotReadyException
|
||||
)
|
||||
from galaxy.tools.execute import execute
|
||||
from galaxy.tools.parameters import check_param
|
||||
from galaxy.tools.parameters import params_to_incoming
|
||||
from galaxy.tools.parameters import visit_input_values
|
||||
from galaxy.tools.parameters import (
|
||||
check_param,
|
||||
params_to_incoming,
|
||||
visit_input_values
|
||||
)
|
||||
from galaxy.tools.parameters.basic import (
|
||||
parameter_types,
|
||||
BooleanToolParameter,
|
||||
TextToolParameter,
|
||||
SelectToolParameter,
|
||||
DataCollectionToolParameter,
|
||||
DataToolParameter,
|
||||
parameter_types,
|
||||
RuntimeValue,
|
||||
SelectToolParameter,
|
||||
TextToolParameter,
|
||||
workflow_building_modes
|
||||
)
|
||||
from galaxy.tools.parameters.wrapped import make_dict_copy
|
||||
from galaxy.tools import DefaultToolState
|
||||
from galaxy.tools import ToolInputsNotReadyException
|
||||
from galaxy.util.odict import odict
|
||||
from galaxy.util.bunch import Bunch
|
||||
from galaxy.util.json import safe_loads
|
||||
from galaxy.util.odict import odict
|
||||
from tool_shed.util import common_util
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
@@ -346,7 +356,7 @@ class InputModule( WorkflowModule ):
|
||||
# Web controller may set copy_inputs_to_history, API controller always sets
|
||||
# inputs.
|
||||
if invocation.copy_inputs_to_history:
|
||||
for input_dataset_hda in step_outputs.values():
|
||||
for input_dataset_hda in list(step_outputs.values()):
|
||||
content_type = input_dataset_hda.history_content_type
|
||||
if content_type == "dataset":
|
||||
new_hda = input_dataset_hda.copy( copy_children=True )
|
||||
@@ -362,7 +372,7 @@ class InputModule( WorkflowModule ):
|
||||
# so do that now so dependent steps can be recalculated. In the future
|
||||
# everything should come in from the API and this can be eliminated.
|
||||
if not invocation.has_input_for_step( step.id ):
|
||||
content = step_outputs.values()[ 0 ]
|
||||
content = next(iter(step_outputs.values()))
|
||||
if content:
|
||||
invocation.add_input( content, step.id )
|
||||
progress.set_outputs_for_input( step, step_outputs )
|
||||
@@ -610,7 +620,7 @@ class ToolModule( WorkflowModule ):
|
||||
super( ToolModule, self ).save_to_step( step )
|
||||
step.tool_id = self.tool_id
|
||||
step.tool_version = self.get_version()
|
||||
for k, v in self.post_job_actions.iteritems():
|
||||
for k, v in self.post_job_actions.items():
|
||||
pja = self.__to_pja( k, v, step )
|
||||
self.trans.sa_session.add( pja )
|
||||
|
||||
@@ -666,7 +676,7 @@ class ToolModule( WorkflowModule ):
|
||||
def get_data_outputs( self ):
|
||||
data_outputs = []
|
||||
if self.tool:
|
||||
for name, tool_output in self.tool.outputs.iteritems():
|
||||
for name, tool_output in self.tool.outputs.items():
|
||||
extra_kwds = {}
|
||||
if tool_output.collection:
|
||||
extra_kwds["collection"] = True
|
||||
@@ -907,7 +917,7 @@ class ToolModule( WorkflowModule ):
|
||||
# job actions for this execution.
|
||||
flush_required = False
|
||||
effective_post_job_actions = step.post_job_actions[:]
|
||||
for key, value in self.runtime_post_job_actions.iteritems():
|
||||
for key, value in self.runtime_post_job_actions.items():
|
||||
effective_post_job_actions.append( self.__to_pja( key, value, None ) )
|
||||
for pja in effective_post_job_actions:
|
||||
if pja.action_type in ActionBox.immediate_actions:
|
||||
|
||||
@@ -96,8 +96,8 @@ class WorkflowCanvas( object ):
|
||||
else:
|
||||
# Take any key / value pair available in out_conn_index_dict.
|
||||
# A problem will result if the dictionary is empty.
|
||||
if out_conn_index_dict.keys():
|
||||
key = out_conn_index_dict.keys()[0]
|
||||
if out_conn_index_dict:
|
||||
key = next(iter(out_conn_index_dict.keys()))
|
||||
out_conn_pos = self.out_pos[ out_pos_index ][ key ]
|
||||
adjusted = ( out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
|
||||
self.text.append( svgwrite.shapes.Circle(center=(out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ] - MARGIN,
|
||||
@@ -130,7 +130,7 @@ class WorkflowCanvas( object ):
|
||||
fill = "#EBD9B2"
|
||||
width = self.widths[ step_dict[ 'id' ] ]
|
||||
self.add_boxes( step_dict, width, fill )
|
||||
for conn, output_dict in step_dict[ 'input_connections' ].iteritems():
|
||||
for conn, output_dict in step_dict[ 'input_connections' ].items():
|
||||
self.add_connection( step_dict, conn, output_dict )
|
||||
|
||||
def populate_data_for_step( self, step, module_name, module_data_inputs, module_data_outputs, tool_errors=None ):
|
||||
|
||||
@@ -1,14 +1,15 @@
|
||||
import logging
|
||||
import uuid
|
||||
|
||||
from galaxy import exceptions
|
||||
from galaxy import model
|
||||
|
||||
from galaxy import (
|
||||
exceptions,
|
||||
model
|
||||
)
|
||||
from galaxy.managers import histories
|
||||
from galaxy.tools.parameters.meta import expand_workflow_inputs
|
||||
|
||||
INPUT_STEP_TYPES = [ 'data_input', 'data_collection_input', 'parameter_input' ]
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
@@ -147,8 +148,7 @@ def _flatten_step_params( param_dict, prefix="" ):
|
||||
# a complex value object versus something that maps to child parameters
|
||||
# better than the hack or searching for src and id here.
|
||||
new_params = {}
|
||||
keys = param_dict.keys()[:]
|
||||
for key in keys:
|
||||
for key in list(param_dict.keys()):
|
||||
if prefix:
|
||||
effective_key = "%s|%s" % ( prefix, key )
|
||||
else:
|
||||
@@ -244,7 +244,7 @@ def build_workflow_run_configs( trans, workflow, payload ):
|
||||
|
||||
steps_by_id = workflow.steps_by_id
|
||||
# Set workflow inputs.
|
||||
for key, input_dict in normalized_inputs.iteritems():
|
||||
for key, input_dict in normalized_inputs.items():
|
||||
step = steps_by_id[key]
|
||||
if step.type == 'parameter_input':
|
||||
continue
|
||||
@@ -353,13 +353,13 @@ def workflow_run_config_to_request( trans, run_config, workflow ):
|
||||
)
|
||||
|
||||
replacement_dict = run_config.replacement_dict
|
||||
for name, value in replacement_dict.iteritems():
|
||||
for name, value in replacement_dict.items():
|
||||
add_parameter(
|
||||
name=name,
|
||||
value=value,
|
||||
type=param_types.REPLACEMENT_PARAMETERS,
|
||||
)
|
||||
for step_id, content in run_config.inputs.iteritems():
|
||||
for step_id, content in run_config.inputs.items():
|
||||
workflow_invocation.add_input( content, step_id )
|
||||
|
||||
add_parameter( "copy_inputs_to_history", "true" if run_config.copy_inputs_to_history else "false", param_types.META_PARAMETERS )
|
||||
|
||||
@@ -1,16 +1,14 @@
|
||||
import os
|
||||
import time
|
||||
import logging
|
||||
import os
|
||||
import threading
|
||||
|
||||
import time
|
||||
from xml.etree import ElementTree
|
||||
|
||||
import galaxy.workflow.schedulers
|
||||
from galaxy import model
|
||||
from galaxy.util import plugin_config
|
||||
from galaxy.util.handlers import ConfiguresHandlers
|
||||
|
||||
import galaxy.workflow.schedulers
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
DEFAULT_SCHEDULER_ID = "default" # well actually this should be called DEFAULT_DEFAULT_SCHEDULER_ID...
|
||||
@@ -77,7 +75,7 @@ class WorkflowSchedulingManager( object, ConfiguresHandlers ):
|
||||
return self.__has_handlers.get_handler( None, index=random_index )
|
||||
|
||||
def shutdown( self ):
|
||||
for workflow_scheduler in self.workflow_schedulers.itervalues():
|
||||
for workflow_scheduler in self.workflow_schedulers.values():
|
||||
try:
|
||||
workflow_scheduler.shutdown()
|
||||
except Exception:
|
||||
@@ -103,7 +101,7 @@ class WorkflowSchedulingManager( object, ConfiguresHandlers ):
|
||||
return workflow_invocation
|
||||
|
||||
def __start_schedulers( self ):
|
||||
for workflow_scheduler in self.workflow_schedulers.itervalues():
|
||||
for workflow_scheduler in self.workflow_schedulers.values():
|
||||
workflow_scheduler.startup( self.app )
|
||||
|
||||
def __plugins_dict( self ):
|
||||
@@ -185,7 +183,7 @@ class WorkflowRequestMonitor( object ):
|
||||
def __monitor( self ):
|
||||
to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
|
||||
while self.active:
|
||||
for workflow_scheduler_id, workflow_scheduler in to_monitor.iteritems():
|
||||
for workflow_scheduler_id, workflow_scheduler in to_monitor.items():
|
||||
if not self.active:
|
||||
return
|
||||
|
||||
|
||||
+1
-2
@@ -1,9 +1,8 @@
|
||||
# override tempfile methods for debugging
|
||||
|
||||
import logging
|
||||
import tempfile
|
||||
import traceback
|
||||
|
||||
import logging
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
|
||||
|
||||
@@ -4,6 +4,7 @@ Class encapsulating the management of repositories installed into Galaxy from th
|
||||
import copy
|
||||
import logging
|
||||
import os
|
||||
import shutil
|
||||
|
||||
from sqlalchemy import and_, false, true
|
||||
|
||||
@@ -78,11 +79,11 @@ class InstalledRepositoryManager( object ):
|
||||
|
||||
def activate_repository( self, repository ):
|
||||
"""Activate an installed tool shed repository that has been marked as deactivated."""
|
||||
repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository )
|
||||
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( self.app, repository )
|
||||
repository.deleted = False
|
||||
repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED
|
||||
if repository.includes_tools_for_display_in_tool_panel:
|
||||
repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository )
|
||||
tpm = tool_panel_manager.ToolPanelManager( self.app )
|
||||
irmm = InstalledRepositoryMetadataManager( app=self.app,
|
||||
tpm=tpm,
|
||||
@@ -749,6 +750,75 @@ class InstalledRepositoryManager( object ):
|
||||
if installed_repository_dict[ 'display_path' ]:
|
||||
cdl.load_installed_display_applications( installed_repository_dict, deactivate=deactivate )
|
||||
|
||||
def uninstall_repository(self, repository, remove_from_disk=True):
|
||||
errors = ''
|
||||
shed_tool_conf, tool_path, relative_install_dir = \
|
||||
suc.get_tool_panel_config_tool_path_install_dir( app=self.app, repository=repository )
|
||||
if relative_install_dir:
|
||||
if tool_path:
|
||||
relative_install_dir = os.path.join( tool_path, relative_install_dir )
|
||||
repository_install_dir = os.path.abspath( relative_install_dir )
|
||||
else:
|
||||
repository_install_dir = None
|
||||
if repository.includes_tools_for_display_in_tool_panel:
|
||||
# Handle tool panel alterations.
|
||||
tpm = tool_panel_manager.ToolPanelManager(app=self.app)
|
||||
tpm.remove_repository_contents(repository,
|
||||
shed_tool_conf,
|
||||
uninstall=remove_from_disk)
|
||||
if repository.includes_data_managers:
|
||||
dmh = data_manager.DataManagerHandler(app=self.app)
|
||||
dmh.remove_from_data_manager(repository)
|
||||
if repository.includes_datatypes:
|
||||
# Deactivate proprietary datatypes.
|
||||
cdl = custom_datatype_manager.CustomDatatypeLoader(app=self.app)
|
||||
installed_repository_dict = cdl.load_installed_datatypes( repository,
|
||||
repository_install_dir,
|
||||
deactivate=True )
|
||||
if installed_repository_dict:
|
||||
converter_path = installed_repository_dict.get( 'converter_path' )
|
||||
if converter_path is not None:
|
||||
cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True )
|
||||
display_path = installed_repository_dict.get( 'display_path' )
|
||||
if display_path is not None:
|
||||
cdl.load_installed_display_applications( installed_repository_dict, deactivate=True )
|
||||
if remove_from_disk:
|
||||
try:
|
||||
# Remove the repository from disk.
|
||||
shutil.rmtree( repository_install_dir )
|
||||
log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) )
|
||||
removed = True
|
||||
except Exception as e:
|
||||
log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) )
|
||||
if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ):
|
||||
removed = True
|
||||
log.debug( "Repository directory does not exist on disk, marking as uninstalled." )
|
||||
else:
|
||||
removed = False
|
||||
if removed:
|
||||
repository.uninstalled = True
|
||||
# Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any
|
||||
# repository dependencies.
|
||||
tool_dependencies_to_uninstall = repository.tool_dependencies_installed_or_in_error
|
||||
tool_dependencies_to_uninstall.extend( repository.tool_dependencies_being_installed )
|
||||
for tool_dependency in tool_dependencies_to_uninstall:
|
||||
uninstalled, error_message = tool_dependency_util.remove_tool_dependency( self.app, tool_dependency )
|
||||
if error_message:
|
||||
errors = '%s %s' % ( errors, error_message )
|
||||
repository.deleted = True
|
||||
if remove_from_disk:
|
||||
repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
|
||||
repository.error_message = None
|
||||
if self.app.config.manage_dependency_relationships:
|
||||
# Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
|
||||
# installed_repository_manager.
|
||||
self.handle_repository_uninstall( repository )
|
||||
else:
|
||||
repository.status = self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED
|
||||
self.app.install_model.context.current.add( repository )
|
||||
self.app.install_model.context.current.flush()
|
||||
return errors
|
||||
|
||||
def purge_repository( self, repository ):
|
||||
"""Purge a repository with status New (a white ghost) from the database."""
|
||||
sa_session = self.app.model.context.current
|
||||
|
||||
@@ -2,7 +2,6 @@ import logging
|
||||
|
||||
from sqlalchemy import and_, or_
|
||||
|
||||
from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
|
||||
from tool_shed.util import hg_util
|
||||
from tool_shed.util import metadata_util
|
||||
from tool_shed.util import repository_util
|
||||
@@ -112,4 +111,3 @@ class ToolVersionManager( object ):
|
||||
parent_id=tool_version_using_parent_id.id )
|
||||
context.add( tool_version_association )
|
||||
context.flush()
|
||||
self.app.tool_version_cache = ToolVersionCache(self.app)
|
||||
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
|
||||
{"version":3,"file":"history-list.js","sources":["../../../src/mvc/history/history-list.js"],"names":["define","Utils","GridView","HistoryModel","historyCopyDialog","View","Backbone","extend","initialize","self","this","setElement","$","model","Model","get","url","Galaxy","root","success","response","_","each","operation","label","onclick","id","_showCopyDialog","set","render","grid","attributes","$el","empty","append","history","History","fetch","fail","alert","done","window","parent","currHistoryPanel","loadCurrentHistory","location","reload"],"mappings":"AACAA,QAAU,cAAe,qBAAsB,4BAA6B,2BAA6B,SAAUC,EAAOC,EAAUC,EAAcC,GAE9I,GAAIC,GAAOC,SAASD,KAAKE,QACrBC,WAAY,WACR,GAAIC,GAAOC,IACXA,MAAKC,WAAYC,EAAG,WACpBF,KAAKG,MAAQ,GAAIP,UAASQ,MAC1Bb,EAAMc,KACFC,IAAUC,OAAOC,KAAO,eACxBC,QAAU,SAAUC,GAChBA,EAAwB,aAAI,EAC5BC,EAAEC,KAAMF,EAAuB,WAAG,SAAUG,GAChB,QAAnBA,EAAUC,QACXD,EAAUE,QAAU,SAAUC,GAAOjB,EAAKkB,gBAAiBD,OAGnEjB,EAAKI,MAAMe,IAAKR,GAChBX,EAAKoB,aAKjBA,OAAQ,WACJ,GAAIC,GAAO,GAAI5B,GAAUQ,KAAKG,MAAMkB,WACpCrB,MAAKsB,IAAIC,QAAQC,OAAQJ,EAAKE,MAGlCL,gBAAiB,SAAUD,GACvB,GAAIS,GAAU,GAAIhC,GAAaiC,SAAWV,GAAKA,GAC/CS,GAAQE,QACAC,KAAM,WACHC,MAAO,mEAEVC,KAAM,WACHpC,EAAmB+B,MAAcK,KAAM,WAC/BC,OAAOC,QAAUD,OAAOC,OAAOzB,QAAUwB,OAAOC,OAAOzB,OAAO0B,kBAC9DF,OAAOC,OAAOzB,OAAO0B,iBAAiBC,qBAE1CH,OAAOI,SAASC,QAAQ,SAM/C,QACIzC,KAAMA"}
|
||||
{"version":3,"file":"history-list.js","sources":["../../../src/mvc/history/history-list.js"],"names":["define","Utils","GridView","HistoryModel","historyCopyDialog","View","Backbone","extend","initialize","options","self","this","setElement","$","model","Model","get","url","Galaxy","root","action_id","success","response","_","each","operation","label","onclick","id","_showCopyDialog","set","render","grid","attributes","$el","empty","append","history","History","fetch","fail","alert","done","window","parent","currHistoryPanel","loadCurrentHistory","location","reload"],"mappings":"AACAA,QAAU,cAAe,qBAAsB,4BAA6B,2BAA6B,SAAUC,EAAOC,EAAUC,EAAcC,GAE9I,GAAIC,GAAOC,SAASD,KAAKE,QACrBC,WAAY,SAAUC,GAClB,GAAIC,GAAOC,IACXA,MAAKC,WAAYC,EAAG,WACpBF,KAAKG,MAAQ,GAAIR,UAASS,MAC1Bd,EAAMe,KACFC,IAAUC,OAAOC,KAAO,WAAaV,EAAQW,UAC7CC,QAAU,SAAUC,GAChBA,EAAwB,aAAI,EAC5BC,EAAEC,KAAMF,EAAuB,WAAG,SAAUG,GAChB,QAAnBA,EAAUC,QACXD,EAAUE,QAAU,SAAUC,GAAOlB,EAAKmB,gBAAiBD,OAGnElB,EAAKI,MAAMgB,IAAKR,GAChBZ,EAAKqB,aAKjBA,OAAQ,WACJ,GAAIC,GAAO,GAAI9B,GAAUS,KAAKG,MAAMmB,WACpCtB,MAAKuB,IAAIC,QAAQC,OAAQJ,EAAKE,MAGlCL,gBAAiB,SAAUD,GACvB,GAAIS,GAAU,GAAIlC,GAAamC,SAAWV,GAAKA,GAC/CS,GAAQE,QACAC,KAAM,WACHC,MAAO,mEAEVC,KAAM,WACHtC,EAAmBiC,MAAcK,KAAM,WAC/BC,OAAOC,QAAUD,OAAOC,OAAO1B,QAAUyB,OAAOC,OAAO1B,OAAO2B,kBAC9DF,OAAOC,OAAO1B,OAAO2B,iBAAiBC,qBAE1CH,OAAOI,SAASC,QAAQ,SAM/C,QACI3C,KAAMA"}
|
||||
@@ -1 +1 @@
|
||||
{"version":3,"file":"options-menu.js","sources":["../../../src/mvc/history/options-menu.js"],"names":["define","PopupMenu","historyCopyDialog","BASE_MVC","_l","Webhooks","buildMenu","isAnon","purgeAllowed","urlRoot","_","clone","menu","filter","menuOption","anon","purge","href","target","confirm","func","galaxy_main","location","html","header","Galaxy","currHistoryPanel","createNewHistory","model","done","loadCurrentHistory","window","id","collapseAll","$","post","root","user_action","add","url","async","callback","webhooks","webhooks_menu","each","models","index","webhook","toJSON","activate","push","config","title","length","unshift","merge","create","$button","options","undefined","anonymous"],"mappings":"AAAAA,QACI,oBACA,0BACA,eACA,qBACA,gBACD,SAAUC,EAAWC,EAAmBC,EAAUC,EAAIC,GAEzD,YA6LA,SAASC,GAAWC,EAAQC,EAAcC,GACtC,MAAOC,GAAEC,MAAOC,GAAOC,OAAQ,SAAUC,GACrC,MAAIP,KAAWO,EAAWC,MACf,GAENP,GAAgBM,EAAWE,OACrB,GAIPF,EAAWG,OACXH,EAAWG,KAAOR,EAAUK,EAAWG,KACvCH,EAAWI,OAASJ,EAAWI,QAAU,eAGzCJ,EAAWK,UACXL,EAAWM,KAAO,WACVD,QAASL,EAAWK,WACpBE,YAAYC,SAAWR,EAAWG,SAIvC,KAhNf,GAAIL,KAEIW,KAAUnB,EAAI,iBACdoB,QAAU,IAGVD,KAAUnB,EAAI,mBACda,KAAU,iBACVC,OAAU,SAIVK,KAAUnB,EAAI,4BACda,KAAU,wBAIVM,KAAUnB,EAAI,mBACdoB,QAAU,EACVT,MAAU,IAGVQ,KAAUnB,EAAI,cACdgB,KAAU,WACFK,QAAUA,OAAOC,kBACjBD,OAAOC,iBAAiBC,sBAKhCJ,KAAUnB,EAAI,gBACdgB,KAAU,WACNlB,EAAmBuB,OAAOC,iBAAiBE,OACtCC,KAAM,WACHJ,OAAOC,iBAAiBI,0BAKpCP,KAAUnB,EAAI,oBACda,KAAU,oBAGVM,KAAUnB,EAAI,kBACda,KAAU,6BACVF,MAAU,IAGVQ,KAAUnB,EAAI,oBACda,KAAU,wCAGVM,KAAUnB,EAAI,UACdW,MAAU,EACVK,KAAU,WACFK,QAAUA,OAAOC,kBAAoBP,QAASf,EAAI,yCAClDiB,YAAYU,OAAOT,SAASL,KAAO,qBAAuBQ,OAAOC,iBAAiBE,MAAMI,OAKhGT,KAAUnB,EAAI,sBACdY,OAAU,EACVD,MAAU,EACVK,KAAU,WACFK,QAAUA,OAAOC,kBACjBP,QAASf,EAAI,4EACbiB,YAAYU,OAAOT,SAASL,KAAO,gCAAkCQ,OAAOC,iBAAiBE,MAAMI,OAO3GT,KAAUnB,EAAI,mBACdoB,QAAU,EACVT,MAAU,IAGVQ,KAAUnB,EAAI,iBACda,KAAU,0BAGVM,KAAUnB,EAAI,oBACda,KAAU,yCAGVM,KAAUnB,EAAI,sBACda,KAAU,0CACVF,MAAU,IAGVQ,KAAUnB,EAAI,8BACdgB,KAAU,WACFK,QAAUA,OAAOC,kBACjBD,OAAOC,iBAAiBO,iBAKhCV,KAAUnB,EAAI,0BACdW,MAAU,EACVK,KAAU,WAEFK,QAAUA,OAAOC,kBAAoBP,QAASf,EAAI,wCAClD8B,EAAEC,KAAKV,OAAOW,KAAO,yBACZC,YAAgB,UAClB,WAAWZ,OAAOC,iBAAiBI,0BAKlDP,KAAUnB,EAAI,0BACdW,MAAU,EACVK,KAAU,WAEFK,QAAUA,OAAOC,kBAAoBP,QAASf,EAAI,wCAClD8B,EAAEC,KAAKV,OAAOW,KAAO,yBACZC,YAAgB,UAClB,WAAWZ,OAAOC,iBAAiBI,0BAKlDP,KAAUnB,EAAI,0BACde,QAAUf,EAAI,0EACda,KAAU,iCACVD,OAAU,EACVD,MAAU,IAKVQ,KAAUnB,EAAI,aACdoB,QAAU,IAGVD,KAAUnB,EAAI,yBACda,KAAU,oBACVF,MAAU,IAGVQ,KAAUnB,EAAI,0BACda,KAAU,sCACVF,MAAU,IAIVQ,KAAUnB,EAAI,iBACdoB,QAAU,IAGVD,KAAUnB,EAAI,oBACda,KAAU,0BAKlBZ,GAASiC,KACLC,IAAK,gCACLC,OAAO,EACPC,SAAU,SAASC,GACf,GAAIC,KAEJT,GAAEU,KAAKF,EAASG,OAAQ,SAASC,EAAOlB,GACpC,GAAImB,GAAUnB,EAAMoB,QAChBD,GAAQE,UACRN,EAAcO,MACV3B,KAAOnB,EAAI2C,EAAQI,OAAOC,OAE1BrC,MAAO,MAKf4B,EAAcU,OAAS,IACvBV,EAAcW,SACV/B,KAASnB,EAAI,YACboB,QAAS,IAEbU,EAAEqB,MAAM3C,EAAM+B,MAgC1B,IAAIa,GAAS,SAAUC,EAASC,GAC5BA,EAAUA,KACV,IAAInD,GAA+BoD,SAAtBD,EAAQE,WAAyB,EAAOF,EAAQE,UACzDpD,EAAekD,EAAQlD,eAAgB,EACvCI,EAAON,EAAWC,EAAQC,EAAciB,OAAOW,KAEnD,OAAO,IAAInC,GAAWwD,EAAS7C,GAK/B,OAAO4C"}
|
||||
{"version":3,"file":"options-menu.js","sources":["../../../src/mvc/history/options-menu.js"],"names":["define","PopupMenu","historyCopyDialog","BASE_MVC","_l","Webhooks","buildMenu","isAnon","purgeAllowed","urlRoot","_","clone","menu","filter","menuOption","anon","purge","href","target","confirm","func","galaxy_main","location","html","header","Galaxy","currHistoryPanel","createNewHistory","model","done","loadCurrentHistory","window","id","collapseAll","$","post","root","user_action","add","url","async","callback","webhooks","webhooks_menu","each","models","index","webhook","toJSON","activate","push","config","title","length","unshift","merge","create","$button","options","undefined","anonymous"],"mappings":"AAAAA,QACI,oBACA,0BACA,eACA,qBACA,gBACD,SAAUC,EAAWC,EAAmBC,EAAUC,EAAIC,GAEzD,YA6LA,SAASC,GAAWC,EAAQC,EAAcC,GACtC,MAAOC,GAAEC,MAAOC,GAAOC,OAAQ,SAAUC,GACrC,MAAIP,KAAWO,EAAWC,MACf,GAENP,GAAgBM,EAAWE,OACrB,GAIPF,EAAWG,OACXH,EAAWG,KAAOR,EAAUK,EAAWG,KACvCH,EAAWI,OAASJ,EAAWI,QAAU,eAGzCJ,EAAWK,UACXL,EAAWM,KAAO,WACVD,QAASL,EAAWK,WACpBE,YAAYC,SAAWR,EAAWG,SAIvC,KAhNf,GAAIL,KAEIW,KAAUnB,EAAI,iBACdoB,QAAU,IAGVD,KAAUnB,EAAI,mBACda,KAAU,iBACVC,OAAU,SAIVK,KAAUnB,EAAI,4BACda,KAAU,wBACVC,OAAU,SAGVK,KAAUnB,EAAI,mBACdoB,QAAU,EACVT,MAAU,IAGVQ,KAAUnB,EAAI,cACdgB,KAAU,WACFK,QAAUA,OAAOC,kBACjBD,OAAOC,iBAAiBC,sBAKhCJ,KAAUnB,EAAI,gBACdgB,KAAU,WACNlB,EAAmBuB,OAAOC,iBAAiBE,OACtCC,KAAM,WACHJ,OAAOC,iBAAiBI,0BAKpCP,KAAUnB,EAAI,oBACda,KAAU,oBAGVM,KAAUnB,EAAI,kBACda,KAAU,6BACVF,MAAU,IAGVQ,KAAUnB,EAAI,oBACda,KAAU,wCAGVM,KAAUnB,EAAI,UACdW,MAAU,EACVK,KAAU,WACFK,QAAUA,OAAOC,kBAAoBP,QAASf,EAAI,yCAClDiB,YAAYU,OAAOT,SAASL,KAAO,qBAAuBQ,OAAOC,iBAAiBE,MAAMI,OAKhGT,KAAUnB,EAAI,sBACdY,OAAU,EACVD,MAAU,EACVK,KAAU,WACFK,QAAUA,OAAOC,kBACjBP,QAASf,EAAI,4EACbiB,YAAYU,OAAOT,SAASL,KAAO,gCAAkCQ,OAAOC,iBAAiBE,MAAMI,OAO3GT,KAAUnB,EAAI,mBACdoB,QAAU,EACVT,MAAU,IAGVQ,KAAUnB,EAAI,iBACda,KAAU,0BAGVM,KAAUnB,EAAI,oBACda,KAAU,yCAGVM,KAAUnB,EAAI,sBACda,KAAU,0CACVF,MAAU,IAGVQ,KAAUnB,EAAI,8BACdgB,KAAU,WACFK,QAAUA,OAAOC,kBACjBD,OAAOC,iBAAiBO,iBAKhCV,KAAUnB,EAAI,0BACdW,MAAU,EACVK,KAAU,WAEFK,QAAUA,OAAOC,kBAAoBP,QAASf,EAAI,wCAClD8B,EAAEC,KAAKV,OAAOW,KAAO,yBACZC,YAAgB,UAClB,WAAWZ,OAAOC,iBAAiBI,0BAKlDP,KAAUnB,EAAI,0BACdW,MAAU,EACVK,KAAU,WAEFK,QAAUA,OAAOC,kBAAoBP,QAASf,EAAI,wCAClD8B,EAAEC,KAAKV,OAAOW,KAAO,yBACZC,YAAgB,UAClB,WAAWZ,OAAOC,iBAAiBI,0BAKlDP,KAAUnB,EAAI,0BACde,QAAUf,EAAI,0EACda,KAAU,iCACVD,OAAU,EACVD,MAAU,IAKVQ,KAAUnB,EAAI,aACdoB,QAAU,IAGVD,KAAUnB,EAAI,yBACda,KAAU,oBACVF,MAAU,IAGVQ,KAAUnB,EAAI,0BACda,KAAU,sCACVF,MAAU,IAIVQ,KAAUnB,EAAI,iBACdoB,QAAU,IAGVD,KAAUnB,EAAI,oBACda,KAAU,0BAKlBZ,GAASiC,KACLC,IAAK,gCACLC,OAAO,EACPC,SAAU,SAASC,GACf,GAAIC,KAEJT,GAAEU,KAAKF,EAASG,OAAQ,SAASC,EAAOlB,GACpC,GAAImB,GAAUnB,EAAMoB,QAChBD,GAAQE,UACRN,EAAcO,MACV3B,KAAOnB,EAAI2C,EAAQI,OAAOC,OAE1BrC,MAAO,MAKf4B,EAAcU,OAAS,IACvBV,EAAcW,SACV/B,KAASnB,EAAI,YACboB,QAAS,IAEbU,EAAEqB,MAAM3C,EAAM+B,MAgC1B,IAAIa,GAAS,SAAUC,EAASC,GAC5BA,EAAUA,KACV,IAAInD,GAA+BoD,SAAtBD,EAAQE,WAAyB,EAAOF,EAAQE,UACzDpD,EAAekD,EAAQlD,eAAgB,EACvCI,EAAON,EAAWC,EAAQC,EAAciB,OAAOW,KAEnD,OAAO,IAAInC,GAAWwD,EAAS7C,GAK/B,OAAO4C"}
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user