mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge remote-tracking branch 'upstream/dev' into history-contents.limiting
This commit is contained in:
carlfeberhard
@@ -1,2 +1,633 @@
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contrib/
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cron/add_manual_builds.py
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cron/cleanup_datasets.py
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cron/parse_builds_3_sites.py
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cron/parse_builds.py
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lib/galaxy/actions/
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lib/galaxy/auth/__init__.py
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lib/galaxy/auth/providers/__init__.py
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lib/galaxy/config.py
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lib/galaxy/dataset_collections/builder.py
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lib/galaxy/dataset_collections/__init__.py
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lib/galaxy/dataset_collections/structure.py
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lib/galaxy/dataset_collections/subcollections.py
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lib/galaxy/dataset_collections/type_description.py
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lib/galaxy/datatypes/assembly.py
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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
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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
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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/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/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/images.py
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lib/galaxy/datatypes/__init__.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/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/generic_util.py
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lib/galaxy/datatypes/util/__init__.py
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lib/galaxy/eggs/
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lib/galaxy/exceptions/__init__.py
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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/datasets.py
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lib/galaxy/jobs/deferred/
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lib/galaxy/jobs/error_level.py
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lib/galaxy/jobs/manager.py
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lib/galaxy/jobs/metrics/collectl/__init__.py
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lib/galaxy/jobs/metrics/collectl/stats.py
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lib/galaxy/jobs/metrics/collectl/subsystems.py
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lib/galaxy/jobs/metrics/formatting.py
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lib/galaxy/jobs/metrics/instrumenters/meminfo.py
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lib/galaxy/jobs/metrics/instrumenters/uname.py
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lib/galaxy/jobs/rules/
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lib/galaxy/jobs/runners/state_handlers/
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lib/galaxy/jobs/runners/util/cli/factory.py
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lib/galaxy/jobs/runners/util/cli/job/__init__.py
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lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
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lib/galaxy/jobs/runners/util/cli/job/torque.py
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lib/galaxy/jobs/runners/util/cli/shell/__init__.py
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lib/galaxy/jobs/runners/util/drmaa/
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lib/galaxy/jobs/runners/util/env.py
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lib/galaxy/jobs/runners/util/external.py
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lib/galaxy/jobs/runners/util/__init__.py
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lib/galaxy/jobs/splitters/basic.py
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lib/galaxy/jobs/splitters/__init__.py
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lib/galaxy/jobs/stock_rules.py
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lib/galaxy/jobs/transfer_manager.py
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lib/galaxy/main.py
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lib/galaxy/managers/annotatable.py
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lib/galaxy/managers/api_keys.py
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lib/galaxy/managers/base.py
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lib/galaxy/managers/context.py
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lib/galaxy/managers/deletable.py
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lib/galaxy/managers/__init__.py
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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
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lib/galaxy/model/__init__.py
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lib/galaxy/model/migrate/__init__.py
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lib/galaxy/model/migrate/versions/0001_initial_tables.py
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lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
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lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
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lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
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lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
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lib/galaxy/model/migrate/versions/0007_sharing_histories.py
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lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
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lib/galaxy/model/migrate/versions/0009_request_table.py
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lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
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lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
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lib/galaxy/model/migrate/versions/0012_user_address.py
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lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
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lib/galaxy/model/migrate/versions/0014_pages.py
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lib/galaxy/model/migrate/versions/0015_tagging.py
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lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
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lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
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lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
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lib/galaxy/model/migrate/versions/0019_request_library_folder.py
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lib/galaxy/model/migrate/versions/0020_library_upload_job.py
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lib/galaxy/model/migrate/versions/0021_user_prefs.py
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lib/galaxy/model/migrate/versions/0022_visualization_tables.py
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lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
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lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
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lib/galaxy/model/migrate/versions/0025_user_info.py
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lib/galaxy/model/migrate/versions/0026_cloud_tables.py
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lib/galaxy/model/migrate/versions/0027_request_events.py
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lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
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lib/galaxy/model/migrate/versions/0029_user_actions.py
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lib/galaxy/model/migrate/versions/0030_history_slug_column.py
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lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
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lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
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lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
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lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
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lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
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lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
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lib/galaxy/model/migrate/versions/0037_samples_library.py
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lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
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lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
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lib/galaxy/model/migrate/versions/0040_page_annotations.py
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lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
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lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
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lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
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lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
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lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
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lib/galaxy/model/migrate/versions/0046_post_job_actions.py
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lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
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lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
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lib/galaxy/model/migrate/versions/0049_api_keys_table.py
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lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
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lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
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lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
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lib/galaxy/model/migrate/versions/0053_item_ratings.py
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lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
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lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
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lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
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lib/galaxy/model/migrate/versions/0057_request_notify.py
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lib/galaxy/model/migrate/versions/0058_history_import_export.py
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lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
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lib/galaxy/model/migrate/versions/0060_history_archive_import.py
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lib/galaxy/model/migrate/versions/0061_tasks.py
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lib/galaxy/model/migrate/versions/0062_user_openid_table.py
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lib/galaxy/model/migrate/versions/0063_sequencer_table.py
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lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
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lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
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lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
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lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
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lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
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lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
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lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
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lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
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lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
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lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
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lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
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lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
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lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
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lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
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lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
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lib/galaxy/model/migrate/versions/0080_quota_tables.py
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lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
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lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
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lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
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lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
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lib/galaxy/model/migrate/versions/0085_add_task_info.py
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lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
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lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
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lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
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lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
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lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
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lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
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lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
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lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
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lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
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lib/galaxy/model/migrate/versions/0095_hda_subsets.py
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lib/galaxy/model/migrate/versions/0096_openid_provider.py
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lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
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lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
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lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
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lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
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lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
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lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
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lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
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lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
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lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
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lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
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lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
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lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
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lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
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lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
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lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
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lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
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lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
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lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
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lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
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lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
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lib/galaxy/model/migrate/versions/0117_add_user_activation.py
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lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
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lib/galaxy/model/migrate/versions/0119_job_metrics.py
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lib/galaxy/model/migrate/versions/0120_dataset_collections.py
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lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
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lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
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lib/galaxy/model/migrate/versions/0124_job_state_history.py
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lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
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lib/galaxy/model/migrate/versions/0126_password_reset.py
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lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
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lib/galaxy/model/migrate/versions/0128_session_timeout.py
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lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
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lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
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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/objectstore/pulsar.py
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lib/galaxy/objectstore/s3_multipart_upload.py
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lib/galaxy/openid/__init__.py
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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
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lib/galaxy/security/validate_user_input.py
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lib/galaxy/tags/
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lib/galaxy/tools/actions/metadata.py
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lib/galaxy/tools/cwl/cwltool_deps.py
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lib/galaxy/tools/cwl/parser.py
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lib/galaxy/tools/cwl/runtime_actions.py
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lib/galaxy/tools/data_manager/__init__.py
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lib/galaxy/tools/deps/brew_util.py
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lib/galaxy/tools/deps/commands.py
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lib/galaxy/tools/deps/dependencies.py
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lib/galaxy/tools/deps/docker_util.py
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lib/galaxy/tools/deps/requirements.py
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lib/galaxy/tools/deps/resolvers/homebrew.py
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lib/galaxy/tools/filters/
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lib/galaxy/tools/imp_exp/export_history.py
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lib/galaxy/tools/imp_exp/__init__.py
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lib/galaxy/tools/linters/
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lib/galaxy/tools/lint.py
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lib/galaxy/tools/lint_util.py
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lib/galaxy/tools/loader_directory.py
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lib/galaxy/tools/parameters/history_query.py
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lib/galaxy/tools/parameters/input_translation.py
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lib/galaxy/tools/parameters/sanitize.py
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lib/galaxy/tools/parameters/validation.py
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lib/galaxy/tools/parameters/wrapped_json.py
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lib/galaxy/tools/parser/interface.py
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lib/galaxy/tools/parser/output_collection_def.py
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lib/galaxy/tools/parser/output_objects.py
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lib/galaxy/tools/parser/util.py
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lib/galaxy/tools/special_tools.py
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lib/galaxy/tools/test.py
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lib/galaxy/tools/toolbox/cache.py
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lib/galaxy/tools/toolbox/integrated_panel.py
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lib/galaxy/tools/toolbox/lineages/__init__.py
|
||||
lib/galaxy/tools/toolbox/lineages/interface.py
|
||||
lib/galaxy/tools/toolbox/lineages/stock.py
|
||||
lib/galaxy/tools/toolbox/lineages/tool_shed.py
|
||||
lib/galaxy/tools/toolbox/watcher.py
|
||||
lib/galaxy/tools/util/galaxyops/
|
||||
lib/galaxy/tools/util/__init__.py
|
||||
lib/galaxy/tools/verify/asserts/__init__.py
|
||||
lib/galaxy/tools/verify/asserts/tabular.py
|
||||
lib/galaxy/tools/verify/asserts/text.py
|
||||
lib/galaxy/tools/verify/__init__.py
|
||||
lib/galaxy/util/aliaspickler.py
|
||||
lib/galaxy/util/backports/
|
||||
lib/galaxy/util/bunch.py
|
||||
lib/galaxy/util/dbkeys.py
|
||||
lib/galaxy/util/dictifiable.py
|
||||
lib/galaxy/util/expressions.py
|
||||
lib/galaxy/util/inflection.py
|
||||
lib/galaxy/util/log/
|
||||
lib/galaxy/util/multi_byte.py
|
||||
lib/galaxy/util/odict.py
|
||||
lib/galaxy/util/pastescript/__init__.py
|
||||
lib/galaxy/util/plugin_config.py
|
||||
lib/galaxy/util/simplegraph.py
|
||||
lib/galaxy_utils/__init__.py
|
||||
lib/galaxy/util/sleeper.py
|
||||
lib/galaxy/util/specs.py
|
||||
lib/galaxy_utils/sequence/fasta.py
|
||||
lib/galaxy_utils/sequence/fastq.py
|
||||
lib/galaxy_utils/sequence/__init__.py
|
||||
lib/galaxy_utils/sequence/transform.py
|
||||
lib/galaxy_utils/sequence/vcf.py
|
||||
lib/galaxy/util/template.py
|
||||
lib/galaxy/util/ucsc.py
|
||||
lib/galaxy/version.py
|
||||
lib/galaxy/visualization/data_providers/basic.py
|
||||
lib/galaxy/visualization/data_providers/cigar.py
|
||||
lib/galaxy/visualization/data_providers/__init__.py
|
||||
lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
|
||||
lib/galaxy/visualization/genome/
|
||||
lib/galaxy/visualization/genomes.py
|
||||
lib/galaxy/visualization/__init__.py
|
||||
lib/galaxy/visualization/plugins/__init__.py
|
||||
lib/galaxy/visualization/plugins/utils.py
|
||||
lib/galaxy/visualization/tracks/
|
||||
lib/galaxy/webapps/galaxy/api/genomes.py
|
||||
lib/galaxy/webapps/galaxy/api/__init__.py
|
||||
lib/galaxy/webapps/galaxy/api/jobs.py
|
||||
lib/galaxy/webapps/galaxy/api/lda_datasets.py
|
||||
lib/galaxy/webapps/galaxy/api/requests.py
|
||||
lib/galaxy/webapps/galaxy/api/roles.py
|
||||
lib/galaxy/webapps/galaxy/api/samples.py
|
||||
lib/galaxy/webapps/galaxy/api/tools.py
|
||||
lib/galaxy/webapps/galaxy/api/tours.py
|
||||
lib/galaxy/webapps/galaxy/controllers/async.py
|
||||
lib/galaxy/webapps/galaxy/controllers/data_manager.py
|
||||
lib/galaxy/webapps/galaxy/controllers/error.py
|
||||
lib/galaxy/webapps/galaxy/controllers/external_services.py
|
||||
lib/galaxy/webapps/galaxy/controllers/history.py
|
||||
lib/galaxy/webapps/galaxy/controllers/__init__.py
|
||||
lib/galaxy/webapps/galaxy/controllers/mobile.py
|
||||
lib/galaxy/webapps/galaxy/controllers/page.py
|
||||
lib/galaxy/webapps/galaxy/controllers/requests.py
|
||||
lib/galaxy/webapps/galaxy/controllers/search.py
|
||||
lib/galaxy/webapps/galaxy/controllers/tool_runner.py
|
||||
lib/galaxy/webapps/galaxy/controllers/userskeys.py
|
||||
lib/galaxy/webapps/galaxy/__init__.py
|
||||
lib/galaxy/webapps/__init__.py
|
||||
lib/galaxy/webapps/reports/controllers/__init__.py
|
||||
lib/galaxy/webapps/reports/controllers/query.py
|
||||
lib/galaxy/webapps/reports/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/api/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/controllers/groups.py
|
||||
lib/galaxy/webapps/tool_shed/controllers/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/controllers/user.py
|
||||
lib/galaxy/webapps/tool_shed/framework/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
|
||||
lib/galaxy/webapps/tool_shed/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/model/mapping.py
|
||||
lib/galaxy/webapps/tool_shed/model/migrate/
|
||||
lib/galaxy/webapps/tool_shed/search/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/security/
|
||||
lib/galaxy/webapps/tool_shed/util/__init__.py
|
||||
lib/galaxy/webapps/tool_shed/util/ratings_util.py
|
||||
lib/galaxy/webapps/tool_shed/util/shed_statistics.py
|
||||
lib/galaxy/webapps/util.py
|
||||
lib/galaxy/web/base/controllers/__init__.py
|
||||
lib/galaxy/web/base/__init__.py
|
||||
lib/galaxy/web/buildapp.py
|
||||
lib/galaxy/web/formatting.py
|
||||
lib/galaxy/web/framework/decorators.py
|
||||
lib/galaxy/web/framework/helpers/grids.py
|
||||
lib/galaxy/web/framework/__init__.py
|
||||
lib/galaxy/web/framework/middleware/__init__.py
|
||||
lib/galaxy/web/framework/middleware/request_id.py
|
||||
lib/galaxy/web/framework/middleware/sentry.py
|
||||
lib/galaxy/web/framework/middleware/static.py
|
||||
lib/galaxy/web/framework/middleware/statsd.py
|
||||
lib/galaxy/web/framework/middleware/translogger.py
|
||||
lib/galaxy/web/framework/middleware/xforwardedhost.py
|
||||
lib/galaxy/web/params.py
|
||||
lib/galaxy/workflow/__init__.py
|
||||
lib/galaxy/workflow/render.py
|
||||
lib/galaxy/workflow/schedulers/__init__.py
|
||||
lib/galaxy/workflow/steps.py
|
||||
lib/galaxy/work/__init__.py
|
||||
lib/mimeparse.py
|
||||
lib/psyco_full.py
|
||||
lib/tool_shed/capsule/__init__.py
|
||||
lib/tool_shed/dependencies/__init__.py
|
||||
lib/tool_shed/dependencies/repository/__init__.py
|
||||
lib/tool_shed/dependencies/tool/
|
||||
lib/tool_shed/galaxy_install/datatypes/__init__.py
|
||||
lib/tool_shed/galaxy_install/grids/__init__.py
|
||||
lib/tool_shed/galaxy_install/__init__.py
|
||||
lib/tool_shed/galaxy_install/metadata/__init__.py
|
||||
lib/tool_shed/galaxy_install/migrate/__init__.py
|
||||
lib/tool_shed/galaxy_install/migrate/versions/
|
||||
lib/tool_shed/galaxy_install/repository_dependencies/__init__.py
|
||||
lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
|
||||
lib/tool_shed/galaxy_install/tool_dependencies/__init__.py
|
||||
lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
|
||||
lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
|
||||
lib/tool_shed/galaxy_install/tool_dependencies/recipe/__init__.py
|
||||
lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
|
||||
lib/tool_shed/galaxy_install/tools/
|
||||
lib/tool_shed/galaxy_install/utility_containers/
|
||||
lib/tool_shed/grids/__init__.py
|
||||
lib/tool_shed/grids/repository_grid_filter_manager.py
|
||||
lib/tool_shed/__init__.py
|
||||
lib/tool_shed/managers/groups.py
|
||||
lib/tool_shed/managers/__init__.py
|
||||
lib/tool_shed/metadata/__init__.py
|
||||
lib/tool_shed/repository_types/__init__.py
|
||||
lib/tool_shed/repository_types/metadata.py
|
||||
lib/tool_shed/repository_types/unrestricted.py
|
||||
lib/tool_shed/repository_types/util.py
|
||||
lib/tool_shed/tools/data_table_manager.py
|
||||
lib/tool_shed/tools/__init__.py
|
||||
lib/tool_shed/tools/tool_version_manager.py
|
||||
lib/tool_shed/util/basic_util.py
|
||||
lib/tool_shed/util/container_util.py
|
||||
lib/tool_shed/util/encoding_util.py
|
||||
lib/tool_shed/util/__init__.py
|
||||
lib/tool_shed/util/search_util.py
|
||||
lib/tool_shed/util/web_util.py
|
||||
lib/tool_shed/util/xml_util.py
|
||||
scripts/api/common.py
|
||||
scripts/api/copy_hda_to_library_folder.py
|
||||
scripts/api/create.py
|
||||
scripts/api/delete.py
|
||||
scripts/api/example_watch_folder.py
|
||||
scripts/api/filter_failed_datasets_from_collection.py
|
||||
scripts/api/form_create_from_xml.py
|
||||
scripts/api/history_create_history.py
|
||||
scripts/api/history_delete_history.py
|
||||
scripts/api/import_library_dataset_to_history.py
|
||||
scripts/api/import_workflows_from_installed_tool_shed_repository.py
|
||||
scripts/api/install_tool_shed_repositories.py
|
||||
scripts/api/library_create_folder.py
|
||||
scripts/api/library_create_library.py
|
||||
scripts/api/library_upload_dir.py
|
||||
scripts/api/library_upload_from_import_dir.py
|
||||
scripts/api/load_data_with_metadata.py
|
||||
scripts/api/repair_tool_shed_repository.py
|
||||
scripts/api/requests_update_state.py
|
||||
scripts/api/request_type_create_from_xml.py
|
||||
scripts/api/reset_metadata_on_installed_repositories.py
|
||||
scripts/api/sample_dataset_update_status.py
|
||||
scripts/api/sample_update_state.py
|
||||
scripts/api/sequencer_configuration_create.py
|
||||
scripts/api/update.py
|
||||
scripts/api/upload_to_history.py
|
||||
scripts/api/workflow_delete.py
|
||||
scripts/api/workflow_execute_parameters.py
|
||||
scripts/api/workflow_execute.py
|
||||
scripts/api/workflow_import_from_file_rpark.py
|
||||
scripts/api/workflow_import.py
|
||||
scripts/auth/
|
||||
scripts/bootstrap_history.py
|
||||
scripts/build_toolbox.py
|
||||
scripts/build_universe_config.py
|
||||
scripts/check_galaxy.py
|
||||
scripts/check_python.py
|
||||
scripts/cleanup_datasets/cleanup_datasets.py
|
||||
scripts/cleanup_datasets/populate_uuid.py
|
||||
scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
|
||||
scripts/cleanup_datasets/rename_purged_datasets.py
|
||||
scripts/cleanup_datasets/update_metadata.py
|
||||
scripts/create_db.py
|
||||
scripts/data_libraries/
|
||||
scripts/db_shell.py
|
||||
scripts/drmaa_external_killer.py
|
||||
scripts/drmaa_external_runner.py
|
||||
scripts/external_chown_script.py
|
||||
scripts/extract_dataset_part.py
|
||||
scripts/extract_toolbox_sections.py
|
||||
scripts/functional_tests.py
|
||||
scripts/get_platforms.py
|
||||
scripts/helper.py
|
||||
scripts/__init__.py
|
||||
scripts/loc_files/
|
||||
scripts/manage_db.py
|
||||
scripts/manage_tools.py
|
||||
scripts/metagenomics/
|
||||
scripts/microbes/create_bacteria_loc_file.py
|
||||
scripts/microbes/create_bacteria_table.py
|
||||
scripts/microbes/create_nib_seq_loc_file.py
|
||||
scripts/microbes/get_builds_lengths.py
|
||||
scripts/microbes/ncbi_to_ucsc.py
|
||||
scripts/microbes/util.py
|
||||
scripts/migrate_tools/
|
||||
scripts/nosetests.py
|
||||
scripts/others/
|
||||
scripts/runtime_stats.py
|
||||
scripts/set_dataset_sizes.py
|
||||
scripts/set_user_disk_usage.py
|
||||
scripts/sync_reports_config.py
|
||||
scripts/tool_shed/api/add_repository_registry_entry.py
|
||||
scripts/tool_shed/api/common.py
|
||||
scripts/tool_shed/api/create_categories.py
|
||||
scripts/tool_shed/api/create_users.py
|
||||
scripts/tool_shed/api/import_capsule.py
|
||||
scripts/tool_shed/api/remove_repository_registry_entry.py
|
||||
scripts/tool_shed/api/reset_metadata_on_repositories.py
|
||||
scripts/tool_shed/api/tool_shed_repository_revision_update.py
|
||||
scripts/tool_shed/build_ts_whoosh_index.py
|
||||
scripts/tool_shed/check_download_urls.py
|
||||
scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
|
||||
scripts/tool_shed/clean_up_tool_dependency_directory.py
|
||||
scripts/tool_shed/migrate_tools_to_repositories.py
|
||||
scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
|
||||
scripts/tools/re_escape_output.py
|
||||
test/api/__init__.py
|
||||
test/api/test_datasets.py
|
||||
test/api/test_datatypes.py
|
||||
test/api/test_framework.py
|
||||
test/api/test_histories.py
|
||||
test/api/test_history_contents_provenance.py
|
||||
test/api/test_jobs.py
|
||||
test/api/test_libraries.py
|
||||
test/api/test_search.py
|
||||
test/api/test_tours.py
|
||||
test/api/test_workflows_from_yaml.py
|
||||
test/api/workflows_format_2/interface.py
|
||||
test/api/workflows_format_2/main.py
|
||||
test/base/api_asserts.py
|
||||
test/base/api_util.py
|
||||
test/base/__init__.py
|
||||
test/base/instrument.py
|
||||
test/base/nose_util.py
|
||||
test/base/tool_shed_util.py
|
||||
test/casperjs/
|
||||
test/functional/database_contexts.py
|
||||
test/functional/__init__.py
|
||||
test/functional/tools/
|
||||
test/integration/__init__.py
|
||||
test/integration/test_pulsar_embedded.py
|
||||
test/manual/__init__.py
|
||||
test/shed_functional/base/common.py
|
||||
test/shed_functional/base/__init__.py
|
||||
test/shed_functional/functional/
|
||||
test/shed_functional/__init__.py
|
||||
test/unit/dataset_collections/__init__.py
|
||||
test/unit/datatypes/dataproviders/__init__.py
|
||||
test/unit/datatypes/__init__.py
|
||||
test/unit/datatypes/test_data.py
|
||||
test/unit/jobs/dynamic_tool_destination/__init__.py
|
||||
test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
|
||||
test/unit/jobs/dynamic_tool_destination/ymltests.py
|
||||
test/unit/jobs/__init__.py
|
||||
test/unit/jobs/test_datasets.py
|
||||
test/unit/jobs/test_rules/
|
||||
test/unit/jobs/test_runner_params.py
|
||||
test/unit/managers/__init__.py
|
||||
test/unit/managers/test_HDAManager.py
|
||||
test/unit/managers/test_HistoryContentsManager.py
|
||||
test/unit/managers/test_HistoryManager.py
|
||||
test/unit/managers/test_UserManager.py
|
||||
test/unit/shed_unit/__init__.py
|
||||
test/unit/shed_unit/test_fabric_util.py
|
||||
test/unit/test_lazy_process.py
|
||||
test/unit/test_security_helper.py
|
||||
test/unit/test_sockets.py
|
||||
test/unit/test_sqlite_utils.py
|
||||
test/unit/test_topsort.py
|
||||
test/unit/tools/filter_modules/
|
||||
test/unit/tools/__init__.py
|
||||
test/unit/tools/test_data_parameters.py
|
||||
test/unit/tools/test_tool_dependency_description.py
|
||||
test/unit/tools/test_tool_panel.py
|
||||
test/unit/unittest_utils/__init__.py
|
||||
test/unit/unittest_utils/utility.py
|
||||
test/unit/visualizations/__init__.py
|
||||
test/unit/visualizations/plugins/__init__.py
|
||||
test/unit/web/base/__init__.py
|
||||
test/unit/web/framework/__init__.py
|
||||
test/unit/web/__init__.py
|
||||
test/unit/workflows/__init__.py
|
||||
test/unit/workflows/test_extract_summary.py
|
||||
test/unit/workflows/test_modules.py
|
||||
test/unit/workflows/test_render.py
|
||||
test/unit/workflows/test_workflow_progress.py
|
||||
tool_list.py
|
||||
tools/data_source/fetch.py
|
||||
tools/data_source/genbank.py
|
||||
tools/data_source/hbvar_filter.py
|
||||
tools/data_source/import.py
|
||||
tools/data_source/microbial_import_code.py
|
||||
tools/data_source/microbial_import.py
|
||||
tools/data_source/upload.py
|
||||
tools/evolution/
|
||||
tools/extract/liftOver_wrapper.py
|
||||
tools/filters/axt_to_concat_fasta.py
|
||||
tools/filters/axt_to_fasta.py
|
||||
tools/filters/axt_to_lav_code.py
|
||||
tools/filters/axt_to_lav.py
|
||||
tools/filters/bed_to_gff_converter.py
|
||||
tools/filters/catWrapper.py
|
||||
tools/filters/convert_characters.py
|
||||
tools/filters/gff/
|
||||
tools/filters/gff_to_bed_converter.py
|
||||
tools/filters/gtf_to_bedgraph_converter.py
|
||||
tools/filters/join.py
|
||||
tools/filters/joinWrapper.py
|
||||
tools/filters/lav_to_bed_code.py
|
||||
tools/filters/lav_to_bed.py
|
||||
tools/filters/mergeCols.py
|
||||
tools/filters/randomlines.py
|
||||
tools/filters/random_lines_two_pass.py
|
||||
tools/filters/secure_hash_message_digest.py
|
||||
tools/filters/sff_extract.py
|
||||
tools/filters/sorter.py
|
||||
tools/filters/trimmer.py
|
||||
tools/filters/ucsc_gene_bed_to_exon_bed.py
|
||||
tools/filters/ucsc_gene_bed_to_intron_bed.py
|
||||
tools/filters/ucsc_gene_table_to_intervals.py
|
||||
tools/filters/uniq.py
|
||||
tools/filters/wiggle_to_simple.py
|
||||
tools/genomespace/
|
||||
tools/maf/
|
||||
tools/meme/
|
||||
tools/metag_tools/
|
||||
tools/next_gen_conversion/fastq_conversions.py
|
||||
tools/next_gen_conversion/fastq_gen_conv.py
|
||||
tools/next_gen_conversion/solid_to_fastq.py
|
||||
tools/ngs_simulation/
|
||||
tools/phenotype_association/
|
||||
tools/plotting/
|
||||
tools/solid_tools/
|
||||
tools/sr_assembly/
|
||||
tools/sr_mapping/
|
||||
tools/stats/grouping.py
|
||||
tools/stats/gsummary.py
|
||||
tools/visualization/
|
||||
|
||||
@@ -4,9 +4,16 @@ lib/galaxy/actions/
|
||||
lib/galaxy/auth/
|
||||
lib/galaxy/config.py
|
||||
lib/galaxy/dataset_collections/
|
||||
lib/galaxy/datatypes/assembly.py
|
||||
lib/galaxy/datatypes/binary.py
|
||||
lib/galaxy/datatypes/constructive_solid_geometry.py
|
||||
lib/galaxy/datatypes/converters/
|
||||
lib/galaxy/datatypes/dataproviders/
|
||||
lib/galaxy/datatypes/data.py
|
||||
lib/galaxy/datatypes/images.py
|
||||
lib/galaxy/datatypes/msa.py
|
||||
lib/galaxy/datatypes/ngsindex.py
|
||||
lib/galaxy/datatypes/proteomics.py
|
||||
lib/galaxy/datatypes/sequence.py
|
||||
lib/galaxy/datatypes/sniff.py
|
||||
lib/galaxy/datatypes/tabular.py
|
||||
|
||||
@@ -33,7 +33,11 @@ lint: ## check style using tox and flake8 for Python 2 and Python 3
|
||||
$(IN_VENV) tox -e py27-lint && tox -e py34-lint
|
||||
|
||||
release-ensure-upstream: ## Ensure upstream branch for release commands setup
|
||||
if [ ! `git remote -v | grep -q $(RELEASE_UPSTREAM)` ]; then git remote add $(RELEASE_UPSTREAM) git@github.com:galaxyproject/galaxy.git; fi
|
||||
ifeq (shell git remote -v | grep $(RELEASE_UPSTREAM), )
|
||||
git remote add $(RELEASE_UPSTREAM) git@github.com:galaxyproject/galaxy.git
|
||||
else
|
||||
@echo "Remote $(RELEASE_UPSTREAM) already exists."
|
||||
endif
|
||||
|
||||
release-merge-stable-to-next: release-ensure-upstream ## Merge last release into dev
|
||||
git fetch $(RELEASE_UPSTREAM) && git checkout dev && git merge --ff-only $(RELEASE_UPSTREAM)/dev && git merge $(RELEASE_UPSTREAM)/$(RELEASE_PREVIOUS)
|
||||
@@ -89,14 +93,16 @@ release-create-rc: release-ensure-upstream ## Create a release-candidate branch
|
||||
git push $(MY_UPSTREAM) release_$(RELEASE_CURR)
|
||||
git push $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
|
||||
git checkout -b version-$(RELEASE_CURR)
|
||||
sed -i "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_CURR)\"/" lib/galaxy/version.py
|
||||
sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = \"rc1\"/" lib/galaxy/version.py
|
||||
sed -i.bak -e "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_CURR)\"/" lib/galaxy/version.py
|
||||
sed -i.bak -e "s/^VERSION_MINOR = .*/VERSION_MINOR = \"rc1\"/" lib/galaxy/version.py
|
||||
rm -f lib/galaxy/version.py.bak
|
||||
git add lib/galaxy/version.py
|
||||
git commit -m "Update version to $(RELEASE_CURR).rc1"
|
||||
git checkout dev
|
||||
|
||||
git checkout -b version-$(RELEASE_NEXT).dev
|
||||
sed -i "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_NEXT)\"/" lib/galaxy/version.py
|
||||
sed -i.bak -e "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_NEXT)\"/" lib/galaxy/version.py
|
||||
rm -f lib/galaxy/version.py.bak
|
||||
git add lib/galaxy/version.py
|
||||
git commit -m "Update version to $(RELEASE_NEXT).dev"
|
||||
|
||||
@@ -106,6 +112,7 @@ release-create-rc: release-ensure-upstream ## Create a release-candidate branch
|
||||
git commit -m "Merge branch 'version-$(RELEASE_CURR)' into version-$(RELEASE_NEXT).dev"
|
||||
git push $(MY_UPSTREAM) version-$(RELEASE_CURR):version-$(RELEASE_CURR)
|
||||
git push $(MY_UPSTREAM) version-$(RELEASE_NEXT).dev:version-$(RELEASE_NEXT).dev
|
||||
git checkout dev
|
||||
git branch -d version-$(RELEASE_CURR)
|
||||
git branch -d version-$(RELEASE_NEXT).dev
|
||||
# TODO: Use hub to automate these PR creations or push directly.
|
||||
@@ -125,7 +132,8 @@ release-create: release-ensure-upstream ## Create a release branch
|
||||
# Test run of merging. If there are conflicts, it will fail here.
|
||||
git merge release_$(RELEASE_CURR)
|
||||
git checkout release_$(RELEASE_CURR)
|
||||
sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = None/" lib/galaxy/version.py
|
||||
sed -i.bak -e "s/^VERSION_MINOR = .*/VERSION_MINOR = None/" lib/galaxy/version.py
|
||||
rm -f lib/galaxy/version.py.bak
|
||||
git add lib/galaxy/version.py
|
||||
git commit -m "Update version to $(RELEASE_CURR)"
|
||||
git tag -m "Tag version $(RELEASE_CURR)" v$(RELEASE_CURR)
|
||||
@@ -153,7 +161,8 @@ release-create-point: ## Create a point release
|
||||
#git push $(MY_UPSTREAM) $(RELEASE_NEXT_BRANCH)
|
||||
git merge release_$(RELEASE_CURR)
|
||||
git checkout release_$(RELEASE_CURR)
|
||||
sed -i "s/^VERSION_MINOR = .*/VERSION_MINOR = \"$(RELEASE_CURR_MINOR_NEXT)\"/" lib/galaxy/version.py
|
||||
sed -i.bak -e "s/^VERSION_MINOR = .*/VERSION_MINOR = \"$(RELEASE_CURR_MINOR_NEXT)\"/" lib/galaxy/version.py
|
||||
rm -f lib/galaxy/version.py.bak
|
||||
git add lib/galaxy/version.py
|
||||
git commit -m "Update version to $(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)"
|
||||
git tag -m "Tag version $(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)" v$(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)
|
||||
|
||||
+2
-1
@@ -29,7 +29,8 @@
|
||||
"wymeditor": "~1.0.0-rc.1",
|
||||
"jstree": "~3.0.9",
|
||||
"jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2",
|
||||
"threedubmedia.jquery.event": "*",
|
||||
"jquery.complexify": "git://github.com/danpalmer/jquery.complexify.js.git#~0.5.1",
|
||||
"threedubmedia.jquery.event": "*",
|
||||
"jquery-migrate": "~1.4",
|
||||
"requirejs": "~2"
|
||||
},
|
||||
|
||||
@@ -0,0 +1,192 @@
|
||||
/*
|
||||
http://github.com/danpalmer/jquery.complexify.js
|
||||
|
||||
This code is distributed under the WTFPL v2:
|
||||
*/
|
||||
(function ($) {
|
||||
|
||||
$.fn.extend({
|
||||
complexify: function(options, callback) {
|
||||
|
||||
var MIN_COMPLEXITY = 49; // 12 chars with Upper, Lower and Number
|
||||
var MAX_COMPLEXITY = 120; // 25 chars, all charsets
|
||||
var CHARSETS = [
|
||||
// Commonly Used
|
||||
////////////////////
|
||||
[0x0020, 0x0020], // Space
|
||||
[0x0030, 0x0039], // Numbers
|
||||
[0x0041, 0x005A], // Uppercase
|
||||
[0x0061, 0x007A], // Lowercase
|
||||
[0x0021, 0x002F], // Punctuation
|
||||
[0x003A, 0x0040], // Punctuation
|
||||
[0x005B, 0x0060], // Punctuation
|
||||
[0x007B, 0x007E], // Punctuation
|
||||
// Everything Else
|
||||
////////////////////
|
||||
[0x0080, 0x00FF], // Latin-1 Supplement
|
||||
[0x0100, 0x017F], // Latin Extended-A
|
||||
[0x0180, 0x024F], // Latin Extended-B
|
||||
[0x0250, 0x02AF], // IPA Extensions
|
||||
[0x02B0, 0x02FF], // Spacing Modifier Letters
|
||||
[0x0300, 0x036F], // Combining Diacritical Marks
|
||||
[0x0370, 0x03FF], // Greek
|
||||
[0x0400, 0x04FF], // Cyrillic
|
||||
[0x0530, 0x058F], // Armenian
|
||||
[0x0590, 0x05FF], // Hebrew
|
||||
[0x0600, 0x06FF], // Arabic
|
||||
[0x0700, 0x074F], // Syriac
|
||||
[0x0780, 0x07BF], // Thaana
|
||||
[0x0900, 0x097F], // Devanagari
|
||||
[0x0980, 0x09FF], // Bengali
|
||||
[0x0A00, 0x0A7F], // Gurmukhi
|
||||
[0x0A80, 0x0AFF], // Gujarati
|
||||
[0x0B00, 0x0B7F], // Oriya
|
||||
[0x0B80, 0x0BFF], // Tamil
|
||||
[0x0C00, 0x0C7F], // Telugu
|
||||
[0x0C80, 0x0CFF], // Kannada
|
||||
[0x0D00, 0x0D7F], // Malayalam
|
||||
[0x0D80, 0x0DFF], // Sinhala
|
||||
[0x0E00, 0x0E7F], // Thai
|
||||
[0x0E80, 0x0EFF], // Lao
|
||||
[0x0F00, 0x0FFF], // Tibetan
|
||||
[0x1000, 0x109F], // Myanmar
|
||||
[0x10A0, 0x10FF], // Georgian
|
||||
[0x1100, 0x11FF], // Hangul Jamo
|
||||
[0x1200, 0x137F], // Ethiopic
|
||||
[0x13A0, 0x13FF], // Cherokee
|
||||
[0x1400, 0x167F], // Unified Canadian Aboriginal Syllabics
|
||||
[0x1680, 0x169F], // Ogham
|
||||
[0x16A0, 0x16FF], // Runic
|
||||
[0x1780, 0x17FF], // Khmer
|
||||
[0x1800, 0x18AF], // Mongolian
|
||||
[0x1E00, 0x1EFF], // Latin Extended Additional
|
||||
[0x1F00, 0x1FFF], // Greek Extended
|
||||
[0x2000, 0x206F], // General Punctuation
|
||||
[0x2070, 0x209F], // Superscripts and Subscripts
|
||||
[0x20A0, 0x20CF], // Currency Symbols
|
||||
[0x20D0, 0x20FF], // Combining Marks for Symbols
|
||||
[0x2100, 0x214F], // Letterlike Symbols
|
||||
[0x2150, 0x218F], // Number Forms
|
||||
[0x2190, 0x21FF], // Arrows
|
||||
[0x2200, 0x22FF], // Mathematical Operators
|
||||
[0x2300, 0x23FF], // Miscellaneous Technical
|
||||
[0x2400, 0x243F], // Control Pictures
|
||||
[0x2440, 0x245F], // Optical Character Recognition
|
||||
[0x2460, 0x24FF], // Enclosed Alphanumerics
|
||||
[0x2500, 0x257F], // Box Drawing
|
||||
[0x2580, 0x259F], // Block Elements
|
||||
[0x25A0, 0x25FF], // Geometric Shapes
|
||||
[0x2600, 0x26FF], // Miscellaneous Symbols
|
||||
[0x2700, 0x27BF], // Dingbats
|
||||
[0x2800, 0x28FF], // Braille Patterns
|
||||
[0x2E80, 0x2EFF], // CJK Radicals Supplement
|
||||
[0x2F00, 0x2FDF], // Kangxi Radicals
|
||||
[0x2FF0, 0x2FFF], // Ideographic Description Characters
|
||||
[0x3000, 0x303F], // CJK Symbols and Punctuation
|
||||
[0x3040, 0x309F], // Hiragana
|
||||
[0x30A0, 0x30FF], // Katakana
|
||||
[0x3100, 0x312F], // Bopomofo
|
||||
[0x3130, 0x318F], // Hangul Compatibility Jamo
|
||||
[0x3190, 0x319F], // Kanbun
|
||||
[0x31A0, 0x31BF], // Bopomofo Extended
|
||||
[0x3200, 0x32FF], // Enclosed CJK Letters and Months
|
||||
[0x3300, 0x33FF], // CJK Compatibility
|
||||
[0x3400, 0x4DB5], // CJK Unified Ideographs Extension A
|
||||
[0x4E00, 0x9FFF], // CJK Unified Ideographs
|
||||
[0xA000, 0xA48F], // Yi Syllables
|
||||
[0xA490, 0xA4CF], // Yi Radicals
|
||||
[0xAC00, 0xD7A3], // Hangul Syllables
|
||||
[0xD800, 0xDB7F], // High Surrogates
|
||||
[0xDB80, 0xDBFF], // High Private Use Surrogates
|
||||
[0xDC00, 0xDFFF], // Low Surrogates
|
||||
[0xE000, 0xF8FF], // Private Use
|
||||
[0xF900, 0xFAFF], // CJK Compatibility Ideographs
|
||||
[0xFB00, 0xFB4F], // Alphabetic Presentation Forms
|
||||
[0xFB50, 0xFDFF], // Arabic Presentation Forms-A
|
||||
[0xFE20, 0xFE2F], // Combining Half Marks
|
||||
[0xFE30, 0xFE4F], // CJK Compatibility Forms
|
||||
[0xFE50, 0xFE6F], // Small Form Variants
|
||||
[0xFE70, 0xFEFE], // Arabic Presentation Forms-B
|
||||
[0xFEFF, 0xFEFF], // Specials
|
||||
[0xFF00, 0xFFEF], // Halfwidth and Fullwidth Forms
|
||||
[0xFFF0, 0xFFFD] // Specials
|
||||
];
|
||||
|
||||
var defaults = {
|
||||
minimumChars: 8,
|
||||
strengthScaleFactor: 1,
|
||||
bannedPasswords: window.COMPLEXIFY_BANLIST || [],
|
||||
banMode: 'strict' // (strict|loose)
|
||||
};
|
||||
|
||||
if($.isFunction(options) && !callback) {
|
||||
callback = options;
|
||||
options = {};
|
||||
}
|
||||
|
||||
options = $.extend(defaults, options);
|
||||
|
||||
function additionalComplexityForCharset(str, charset) {
|
||||
for (var i = str.length - 1; i >= 0; i--) {
|
||||
if (charset[0] <= str.charCodeAt(i) && str.charCodeAt(i) <= charset[1]) {
|
||||
return charset[1] - charset[0] + 1;
|
||||
}
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
function inBanlist(str) {
|
||||
if (options.banMode === 'strict') {
|
||||
for (var i = 0; i < options.bannedPasswords.length; i++) {
|
||||
if (str.toLowerCase().indexOf(options.bannedPasswords[i].toLowerCase()) !== -1) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
} else {
|
||||
return $.inArray(str, options.bannedPasswords) > -1 ? true : false;
|
||||
}
|
||||
}
|
||||
|
||||
function evaluateSecurity() {
|
||||
var password = $(this).val();
|
||||
var complexity = 0, valid = false;
|
||||
|
||||
// Reset complexity to 0 when banned password is found
|
||||
if (!inBanlist(password)) {
|
||||
|
||||
// Add character complexity
|
||||
for (var i = CHARSETS.length - 1; i >= 0; i--) {
|
||||
complexity += additionalComplexityForCharset(password, CHARSETS[i]);
|
||||
}
|
||||
|
||||
} else {
|
||||
complexity = 1;
|
||||
}
|
||||
|
||||
// Use natural log to produce linear scale
|
||||
complexity = Math.log(Math.pow(complexity, password.length)) * (1/options.strengthScaleFactor);
|
||||
|
||||
valid = (complexity > MIN_COMPLEXITY && password.length >= options.minimumChars);
|
||||
|
||||
// Scale to percentage, so it can be used for a progress bar
|
||||
complexity = (complexity / MAX_COMPLEXITY) * 100;
|
||||
complexity = (complexity > 100) ? 100 : complexity;
|
||||
|
||||
callback.call(this, valid, complexity);
|
||||
}
|
||||
|
||||
this.each(function () {
|
||||
if($(this).val()) {
|
||||
evaluateSecurity.apply(this);
|
||||
}
|
||||
});
|
||||
|
||||
return this.each(function () {
|
||||
$(this).bind('keyup focus input propertychange mouseup', evaluateSecurity);
|
||||
});
|
||||
|
||||
}
|
||||
});
|
||||
|
||||
})(jQuery);
|
||||
+9
-16
@@ -1,5 +1,5 @@
|
||||
/*!
|
||||
* jQuery JavaScript Library v1.12.3
|
||||
* jQuery JavaScript Library v1.12.4
|
||||
* http://jquery.com/
|
||||
*
|
||||
* Includes Sizzle.js
|
||||
@@ -9,7 +9,7 @@
|
||||
* Released under the MIT license
|
||||
* http://jquery.org/license
|
||||
*
|
||||
* Date: 2016-04-05T19:16Z
|
||||
* Date: 2016-05-20T17:17Z
|
||||
*/
|
||||
|
||||
(function( global, factory ) {
|
||||
@@ -65,7 +65,7 @@ var support = {};
|
||||
|
||||
|
||||
var
|
||||
version = "1.12.3",
|
||||
version = "1.12.4",
|
||||
|
||||
// Define a local copy of jQuery
|
||||
jQuery = function( selector, context ) {
|
||||
@@ -6672,6 +6672,7 @@ var documentElement = document.documentElement;
|
||||
if ( reliableHiddenOffsetsVal ) {
|
||||
div.style.display = "";
|
||||
div.innerHTML = "<table><tr><td></td><td>t</td></tr></table>";
|
||||
div.childNodes[ 0 ].style.borderCollapse = "separate";
|
||||
contents = div.getElementsByTagName( "td" );
|
||||
contents[ 0 ].style.cssText = "margin:0;border:0;padding:0;display:none";
|
||||
reliableHiddenOffsetsVal = contents[ 0 ].offsetHeight === 0;
|
||||
@@ -6996,19 +6997,6 @@ function getWidthOrHeight( elem, name, extra ) {
|
||||
isBorderBox = support.boxSizing &&
|
||||
jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
|
||||
|
||||
// Support: IE11 only
|
||||
// In IE 11 fullscreen elements inside of an iframe have
|
||||
// 100x too small dimensions (gh-1764).
|
||||
if ( document.msFullscreenElement && window.top !== window ) {
|
||||
|
||||
// Support: IE11 only
|
||||
// Running getBoundingClientRect on a disconnected node
|
||||
// in IE throws an error.
|
||||
if ( elem.getClientRects().length ) {
|
||||
val = Math.round( elem.getBoundingClientRect()[ name ] * 100 );
|
||||
}
|
||||
}
|
||||
|
||||
// some non-html elements return undefined for offsetWidth, so check for null/undefined
|
||||
// svg - https://bugzilla.mozilla.org/show_bug.cgi?id=649285
|
||||
// MathML - https://bugzilla.mozilla.org/show_bug.cgi?id=491668
|
||||
@@ -9999,6 +9987,11 @@ function getDisplay( elem ) {
|
||||
}
|
||||
|
||||
function filterHidden( elem ) {
|
||||
|
||||
// Disconnected elements are considered hidden
|
||||
if ( !jQuery.contains( elem.ownerDocument || document, elem ) ) {
|
||||
return true;
|
||||
}
|
||||
while ( elem && elem.nodeType === 1 ) {
|
||||
if ( getDisplay( elem ) === "none" || elem.type === "hidden" ) {
|
||||
return true;
|
||||
|
||||
+107
-111
@@ -1,4 +1,4 @@
|
||||
/*! Raven.js 3.0.3 (3738576) | github.com/getsentry/raven-js */
|
||||
/*! Raven.js 3.3.0 (74c6c03) | github.com/getsentry/raven-js */
|
||||
|
||||
/*
|
||||
* Includes TraceKit
|
||||
@@ -11,6 +11,35 @@
|
||||
*/
|
||||
|
||||
(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}g.Raven = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(_dereq_,module,exports){
|
||||
exports = module.exports = stringify
|
||||
exports.getSerialize = serializer
|
||||
|
||||
function stringify(obj, replacer, spaces, cycleReplacer) {
|
||||
return JSON.stringify(obj, serializer(replacer, cycleReplacer), spaces)
|
||||
}
|
||||
|
||||
function serializer(replacer, cycleReplacer) {
|
||||
var stack = [], keys = []
|
||||
|
||||
if (cycleReplacer == null) cycleReplacer = function(key, value) {
|
||||
if (stack[0] === value) return "[Circular ~]"
|
||||
return "[Circular ~." + keys.slice(0, stack.indexOf(value)).join(".") + "]"
|
||||
}
|
||||
|
||||
return function(key, value) {
|
||||
if (stack.length > 0) {
|
||||
var thisPos = stack.indexOf(this)
|
||||
~thisPos ? stack.splice(thisPos + 1) : stack.push(this)
|
||||
~thisPos ? keys.splice(thisPos, Infinity, key) : keys.push(key)
|
||||
if (~stack.indexOf(value)) value = cycleReplacer.call(this, key, value)
|
||||
}
|
||||
else stack.push(value)
|
||||
|
||||
return replacer == null ? value : replacer.call(this, key, value)
|
||||
}
|
||||
}
|
||||
|
||||
},{}],2:[function(_dereq_,module,exports){
|
||||
'use strict';
|
||||
|
||||
function RavenConfigError(message) {
|
||||
@@ -22,7 +51,7 @@ RavenConfigError.prototype.constructor = RavenConfigError;
|
||||
|
||||
module.exports = RavenConfigError;
|
||||
|
||||
},{}],2:[function(_dereq_,module,exports){
|
||||
},{}],3:[function(_dereq_,module,exports){
|
||||
'use strict';
|
||||
|
||||
var wrapMethod = function(console, level, callback) {
|
||||
@@ -61,13 +90,14 @@ module.exports = {
|
||||
wrapMethod: wrapMethod
|
||||
};
|
||||
|
||||
},{}],3:[function(_dereq_,module,exports){
|
||||
},{}],4:[function(_dereq_,module,exports){
|
||||
/*global XDomainRequest:false*/
|
||||
'use strict';
|
||||
|
||||
var TraceKit = _dereq_(6);
|
||||
var RavenConfigError = _dereq_(1);
|
||||
var utils = _dereq_(5);
|
||||
var TraceKit = _dereq_(7);
|
||||
var RavenConfigError = _dereq_(2);
|
||||
var utils = _dereq_(6);
|
||||
var stringify = _dereq_(1);
|
||||
|
||||
var isFunction = utils.isFunction;
|
||||
var isUndefined = utils.isUndefined;
|
||||
@@ -84,7 +114,7 @@ var htmlTreeAsString = utils.htmlTreeAsString;
|
||||
var parseUrl = utils.parseUrl;
|
||||
var isString = utils.isString;
|
||||
|
||||
var wrapConsoleMethod = _dereq_(2).wrapMethod;
|
||||
var wrapConsoleMethod = _dereq_(3).wrapMethod;
|
||||
|
||||
var dsnKeys = 'source protocol user pass host port path'.split(' '),
|
||||
dsnPattern = /^(?:(\w+):)?\/\/(?:(\w+)(:\w+)?@)?([\w\.-]+)(?::(\d+))?(\/.*)/;
|
||||
@@ -150,7 +180,7 @@ Raven.prototype = {
|
||||
// webpack (using a build step causes webpack #1617). Grunt verifies that
|
||||
// this value matches package.json during build.
|
||||
// See: https://github.com/getsentry/raven-js/issues/465
|
||||
VERSION: '3.0.3',
|
||||
VERSION: '3.3.0',
|
||||
|
||||
debug: false,
|
||||
|
||||
@@ -210,14 +240,6 @@ Raven.prototype = {
|
||||
this._globalEndpoint = this._globalServer +
|
||||
'/' + path + 'api/' + this._globalProject + '/store/';
|
||||
|
||||
if (this._globalOptions.fetchContext) {
|
||||
TraceKit.remoteFetching = true;
|
||||
}
|
||||
|
||||
if (this._globalOptions.linesOfContext) {
|
||||
TraceKit.linesOfContext = this._globalOptions.linesOfContext;
|
||||
}
|
||||
|
||||
TraceKit.collectWindowErrors = !!this._globalOptions.collectWindowErrors;
|
||||
|
||||
// return for chaining
|
||||
@@ -500,7 +522,20 @@ Raven.prototype = {
|
||||
*/
|
||||
getContext: function() {
|
||||
// lol javascript
|
||||
return JSON.parse(JSON.stringify(this._globalContext));
|
||||
return JSON.parse(stringify(this._globalContext));
|
||||
},
|
||||
|
||||
|
||||
/*
|
||||
* Set environment of application
|
||||
*
|
||||
* @param {string} environment Typically something like 'production'.
|
||||
* @return {Raven}
|
||||
*/
|
||||
setEnvironment: function(environment) {
|
||||
this._globalOptions.environment = environment;
|
||||
|
||||
return this;
|
||||
},
|
||||
|
||||
/*
|
||||
@@ -523,7 +558,10 @@ Raven.prototype = {
|
||||
* @return {Raven}
|
||||
*/
|
||||
setDataCallback: function(callback) {
|
||||
this._globalOptions.dataCallback = callback;
|
||||
var original = this._globalOptions.dataCallback;
|
||||
this._globalOptions.dataCallback = isFunction(callback)
|
||||
? function (data) { return callback(data, original); }
|
||||
: callback;
|
||||
|
||||
return this;
|
||||
},
|
||||
@@ -536,7 +574,10 @@ Raven.prototype = {
|
||||
* @return {Raven}
|
||||
*/
|
||||
setShouldSendCallback: function(callback) {
|
||||
this._globalOptions.shouldSendCallback = callback;
|
||||
var original = this._globalOptions.shouldSendCallback;
|
||||
this._globalOptions.shouldSendCallback = isFunction(callback)
|
||||
? function (data) { return callback(data, original); }
|
||||
: callback;
|
||||
|
||||
return this;
|
||||
},
|
||||
@@ -778,9 +819,9 @@ Raven.prototype = {
|
||||
// Use only the path component of the URL if the URL matches the current
|
||||
// document (almost all the time when using pushState)
|
||||
if (parsedLoc.protocol === parsedTo.protocol && parsedLoc.host === parsedTo.host)
|
||||
to = parsedTo.path;
|
||||
to = parsedTo.relative;
|
||||
if (parsedLoc.protocol === parsedFrom.protocol && parsedLoc.host === parsedFrom.host)
|
||||
from = parsedFrom.path;
|
||||
from = parsedFrom.relative;
|
||||
|
||||
this.captureBreadcrumb({
|
||||
category: 'navigation',
|
||||
@@ -885,8 +926,15 @@ Raven.prototype = {
|
||||
// Capture breadcrubms from any click that is unhandled / bubbled up all the way
|
||||
// to the document. Do this before we instrument addEventListener.
|
||||
if (this._hasDocument) {
|
||||
document.addEventListener('click', self._breadcrumbEventHandler('click'));
|
||||
document.addEventListener('keypress', self._keypressEventHandler());
|
||||
if (document.addEventListener) {
|
||||
document.addEventListener('click', self._breadcrumbEventHandler('click'), false);
|
||||
document.addEventListener('keypress', self._keypressEventHandler(), false);
|
||||
}
|
||||
else {
|
||||
// IE8 Compatibility
|
||||
document.attachEvent('onclick', self._breadcrumbEventHandler('click'));
|
||||
document.attachEvent('onkeypress', self._keypressEventHandler());
|
||||
}
|
||||
}
|
||||
|
||||
// event targets borrowed from bugsnag-js:
|
||||
@@ -954,7 +1002,13 @@ Raven.prototype = {
|
||||
}
|
||||
|
||||
// record navigation (URL) changes
|
||||
if ('history' in window && history.pushState) {
|
||||
// NOTE: in Chrome App environment, touching history.pushState, *even inside
|
||||
// a try/catch block*, will cause Chrome to output an error to console.error
|
||||
// borrowed from: https://github.com/angular/angular.js/pull/13945/files
|
||||
var chrome = window.chrome;
|
||||
var isChromePackagedApp = chrome && chrome.app && chrome.app.runtime;
|
||||
var hasPushState = !isChromePackagedApp && window.history && history.pushState;
|
||||
if (hasPushState) {
|
||||
// TODO: remove onpopstate handler on uninstall()
|
||||
var oldOnPopState = window.onpopstate;
|
||||
window.onpopstate = function () {
|
||||
@@ -1106,13 +1160,7 @@ Raven.prototype = {
|
||||
lineno: frame.line,
|
||||
colno: frame.column,
|
||||
'function': frame.func || '?'
|
||||
}, context = this._extractContextFromFrame(frame), i;
|
||||
|
||||
if (context) {
|
||||
var keys = ['pre_context', 'context_line', 'post_context'];
|
||||
i = 3;
|
||||
while (i--) normalized[keys[i]] = context[i];
|
||||
}
|
||||
};
|
||||
|
||||
normalized.in_app = !( // determine if an exception came from outside of our app
|
||||
// first we check the global includePaths list.
|
||||
@@ -1126,55 +1174,12 @@ Raven.prototype = {
|
||||
return normalized;
|
||||
},
|
||||
|
||||
_extractContextFromFrame: function(frame) {
|
||||
// immediately check if we should even attempt to parse a context
|
||||
if (!frame.context || !this._globalOptions.fetchContext) return;
|
||||
|
||||
var context = frame.context,
|
||||
pivot = ~~(context.length / 2),
|
||||
i = context.length, isMinified = false;
|
||||
|
||||
while (i--) {
|
||||
// We're making a guess to see if the source is minified or not.
|
||||
// To do that, we make the assumption if *any* of the lines passed
|
||||
// in are greater than 300 characters long, we bail.
|
||||
// Sentry will see that there isn't a context
|
||||
if (context[i].length > 300) {
|
||||
isMinified = true;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if (isMinified) {
|
||||
// The source is minified and we don't know which column. Fuck it.
|
||||
if (isUndefined(frame.column)) return;
|
||||
|
||||
// If the source is minified and has a frame column
|
||||
// we take a chunk of the offending line to hopefully shed some light
|
||||
return [
|
||||
[], // no pre_context
|
||||
context[pivot].substr(frame.column, 50), // grab 50 characters, starting at the offending column
|
||||
[] // no post_context
|
||||
];
|
||||
}
|
||||
|
||||
return [
|
||||
context.slice(0, pivot), // pre_context
|
||||
context[pivot], // context_line
|
||||
context.slice(pivot + 1) // post_context
|
||||
];
|
||||
},
|
||||
|
||||
_processException: function(type, message, fileurl, lineno, frames, options) {
|
||||
var stacktrace, fullMessage;
|
||||
var stacktrace;
|
||||
|
||||
if (!!this._globalOptions.ignoreErrors.test && this._globalOptions.ignoreErrors.test(message)) return;
|
||||
|
||||
message += '';
|
||||
message = truncate(message, this._globalOptions.maxMessageLength);
|
||||
|
||||
fullMessage = (type ? type + ': ' : '') + message;
|
||||
fullMessage = truncate(fullMessage, this._globalOptions.maxMessageLength);
|
||||
|
||||
if (frames && frames.length) {
|
||||
fileurl = frames[0].filename || fileurl;
|
||||
@@ -1204,8 +1209,7 @@ Raven.prototype = {
|
||||
stacktrace: stacktrace
|
||||
}]
|
||||
},
|
||||
culprit: fileurl,
|
||||
message: fullMessage
|
||||
culprit: fileurl
|
||||
}, options);
|
||||
|
||||
// Fire away!
|
||||
@@ -1216,7 +1220,9 @@ Raven.prototype = {
|
||||
// For now, we only want to truncate the two different messages
|
||||
// but this could/should be expanded to just trim everything
|
||||
var max = this._globalOptions.maxMessageLength;
|
||||
data.message = truncate(data.message, max);
|
||||
if (data.message) {
|
||||
data.message = truncate(data.message, max);
|
||||
}
|
||||
if (data.exception) {
|
||||
var exception = data.exception.values[0];
|
||||
exception.value = truncate(exception.value, max);
|
||||
@@ -1286,6 +1292,9 @@ Raven.prototype = {
|
||||
data.user = this._globalContext.user;
|
||||
}
|
||||
|
||||
// Include the environment if it's defined in globalOptions
|
||||
if (globalOptions.environment) data.environment = globalOptions.environment;
|
||||
|
||||
// Include the release if it's defined in globalOptions
|
||||
if (globalOptions.release) data.release = globalOptions.release;
|
||||
|
||||
@@ -1327,10 +1336,14 @@ Raven.prototype = {
|
||||
auth.sentry_secret = this._globalSecret;
|
||||
}
|
||||
|
||||
var exception = data.exception && data.exception.values[0];
|
||||
this.captureBreadcrumb({
|
||||
category: 'sentry',
|
||||
message: data.message,
|
||||
event_id: data.event_id
|
||||
message: exception
|
||||
? (exception.type ? exception.type + ': ' : '') + exception.message
|
||||
: data.message,
|
||||
event_id: data.event_id,
|
||||
level: data.level || 'error' // presume error unless specified
|
||||
});
|
||||
|
||||
var url = this._globalEndpoint;
|
||||
@@ -1357,9 +1370,6 @@ Raven.prototype = {
|
||||
_makeRequest: function(opts) {
|
||||
var request = new XMLHttpRequest();
|
||||
|
||||
if (request.send.toString() === 'function send() { [native code] }') {
|
||||
throw new Error('shouldnt get here');
|
||||
}
|
||||
// if browser doesn't support CORS (e.g. IE7), we are out of luck
|
||||
var hasCORS =
|
||||
'withCredentials' in request ||
|
||||
@@ -1398,14 +1408,7 @@ Raven.prototype = {
|
||||
// NOTE: auth is intentionally sent as part of query string (NOT as custom
|
||||
// HTTP header) so as to avoid preflight CORS requests
|
||||
request.open('POST', url + '?' + urlencode(opts.auth));
|
||||
request.send(JSON.stringify(opts.data));
|
||||
},
|
||||
|
||||
// Note: this is shitty, but I can't figure out how to get
|
||||
// sinon to stub document.createElement without breaking everything
|
||||
// so this wrapper is just so I can stub it for tests.
|
||||
_newImage: function() {
|
||||
return document.createElement('img');
|
||||
request.send(stringify(opts.data));
|
||||
},
|
||||
|
||||
_logDebug: function(level) {
|
||||
@@ -1434,7 +1437,7 @@ Raven.prototype.setReleaseContext = Raven.prototype.setRelease;
|
||||
|
||||
module.exports = Raven;
|
||||
|
||||
},{"1":1,"2":2,"5":5,"6":6}],4:[function(_dereq_,module,exports){
|
||||
},{"1":1,"2":2,"3":3,"6":6,"7":7}],5:[function(_dereq_,module,exports){
|
||||
/**
|
||||
* Enforces a single instance of the Raven client, and the
|
||||
* main entry point for Raven. If you are a consumer of the
|
||||
@@ -1443,7 +1446,7 @@ module.exports = Raven;
|
||||
|
||||
'use strict';
|
||||
|
||||
var RavenConstructor = _dereq_(3);
|
||||
var RavenConstructor = _dereq_(4);
|
||||
|
||||
var _Raven = window.Raven;
|
||||
|
||||
@@ -1464,7 +1467,7 @@ Raven.afterLoad();
|
||||
|
||||
module.exports = Raven;
|
||||
|
||||
},{"3":3}],5:[function(_dereq_,module,exports){
|
||||
},{"4":4}],6:[function(_dereq_,module,exports){
|
||||
/*eslint no-extra-parens:0*/
|
||||
'use strict';
|
||||
|
||||
@@ -1581,10 +1584,15 @@ function urlencode(o) {
|
||||
function parseUrl(url) {
|
||||
var match = url.match(/^(([^:\/?#]+):)?(\/\/([^\/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?$/);
|
||||
if (!match) return {};
|
||||
|
||||
// coerce to undefined values to empty string so we don't get 'undefined'
|
||||
var query = match[6] || '';
|
||||
var fragment = match[8] || '';
|
||||
return {
|
||||
protocol: match[2],
|
||||
host: match[4],
|
||||
path: match[5]
|
||||
path: match[5],
|
||||
relative: match[5] + query + fragment // everything minus origin
|
||||
};
|
||||
}
|
||||
function uuid4() {
|
||||
@@ -1717,10 +1725,10 @@ module.exports = {
|
||||
parseUrl: parseUrl
|
||||
};
|
||||
|
||||
},{}],6:[function(_dereq_,module,exports){
|
||||
},{}],7:[function(_dereq_,module,exports){
|
||||
'use strict';
|
||||
|
||||
var utils = _dereq_(5);
|
||||
var utils = _dereq_(6);
|
||||
|
||||
var hasKey = utils.hasKey;
|
||||
var isString = utils.isString;
|
||||
@@ -1732,10 +1740,7 @@ var isUndefined = utils.isUndefined;
|
||||
*/
|
||||
|
||||
var TraceKit = {
|
||||
remoteFetching: false,
|
||||
collectWindowErrors: true,
|
||||
// 3 lines before, the offending line, 3 lines after
|
||||
linesOfContext: 7,
|
||||
debug: false
|
||||
};
|
||||
|
||||
@@ -1895,7 +1900,6 @@ TraceKit.report = (function reportModuleWrapper() {
|
||||
}
|
||||
|
||||
location.func = UNKNOWN_FUNCTION;
|
||||
location.context = null;
|
||||
|
||||
stack = {
|
||||
'name': name,
|
||||
@@ -1998,7 +2002,6 @@ TraceKit.report = (function reportModuleWrapper() {
|
||||
* s.stack[i].args - arguments passed to the function, if known
|
||||
* s.stack[i].line - line number, if known
|
||||
* s.stack[i].column - column number, if known
|
||||
* s.stack[i].context - an array of source code lines; the middle element corresponds to the correct line#
|
||||
*
|
||||
* Supports:
|
||||
* - Firefox: full stack trace with line numbers and unreliable column
|
||||
@@ -2107,7 +2110,7 @@ TraceKit.computeStackTrace = (function computeStackTraceWrapper() {
|
||||
|
||||
var chrome = /^\s*at (.*?) ?\(((?:file|https?|blob|chrome-extension|native|eval|<anonymous>).*?)(?::(\d+))?(?::(\d+))?\)?\s*$/i,
|
||||
gecko = /^\s*(.*?)(?:\((.*?)\))?(?:^|@)((?:file|https?|blob|chrome|\[native).*?)(?::(\d+))?(?::(\d+))?\s*$/i,
|
||||
winjs = /^\s*at (?:((?:\[object object\])?.+) )?\(?((?:ms-appx|https?|blob):.*?):(\d+)(?::(\d+))?\)?\s*$/i,
|
||||
winjs = /^\s*at (?:((?:\[object object\])?.+) )?\(?((?:file|ms-appx|https?|blob):.*?):(\d+)(?::(\d+))?\)?\s*$/i,
|
||||
lines = ex.stack.split('\n'),
|
||||
stack = [],
|
||||
parts,
|
||||
@@ -2148,10 +2151,6 @@ TraceKit.computeStackTrace = (function computeStackTraceWrapper() {
|
||||
element.func = UNKNOWN_FUNCTION;
|
||||
}
|
||||
|
||||
if (element.line) {
|
||||
element.context = null;
|
||||
}
|
||||
|
||||
stack.push(element);
|
||||
}
|
||||
|
||||
@@ -2217,7 +2216,6 @@ TraceKit.computeStackTrace = (function computeStackTraceWrapper() {
|
||||
if (!element.func && element.line) {
|
||||
element.func = UNKNOWN_FUNCTION;
|
||||
}
|
||||
element.context = [lines[line + 1]];
|
||||
|
||||
stack.push(element);
|
||||
}
|
||||
@@ -2305,7 +2303,6 @@ TraceKit.computeStackTrace = (function computeStackTraceWrapper() {
|
||||
if (!item.func) {
|
||||
item.func = UNKNOWN_FUNCTION;
|
||||
}
|
||||
item.context = [lines[line + 1]];
|
||||
|
||||
stack.push(item);
|
||||
}
|
||||
@@ -2355,7 +2352,6 @@ TraceKit.computeStackTrace = (function computeStackTraceWrapper() {
|
||||
return false; // already in stack trace
|
||||
} else if (!stackInfo.stack[0].line && stackInfo.stack[0].func === initial.func) {
|
||||
stackInfo.stack[0].line = initial.line;
|
||||
stackInfo.stack[0].context = initial.context;
|
||||
return false;
|
||||
}
|
||||
}
|
||||
@@ -2510,5 +2506,5 @@ TraceKit.computeStackTrace = (function computeStackTraceWrapper() {
|
||||
|
||||
module.exports = TraceKit;
|
||||
|
||||
},{"5":5}]},{},[4])(4)
|
||||
},{"6":6}]},{},[5])(5)
|
||||
});
|
||||
@@ -55,15 +55,23 @@ var menu = [
|
||||
},
|
||||
{
|
||||
html : _l( 'Delete' ),
|
||||
confirm : _l( 'Really delete the current history?' ),
|
||||
href : 'history/delete_current',
|
||||
anon : true,
|
||||
func : function() {
|
||||
if( Galaxy && Galaxy.currHistoryPanel && confirm( _l( 'Really delete the current history?' ) ) ){
|
||||
galaxy_main.window.location.href = 'history/delete?id=' + Galaxy.currHistoryPanel.model.id;
|
||||
}
|
||||
},
|
||||
},
|
||||
{
|
||||
html : _l( 'Delete Permanently' ),
|
||||
confirm : _l( 'Really delete the current history permanently? This cannot be undone.' ),
|
||||
href : 'history/delete_current?purge=True',
|
||||
purge : true,
|
||||
anon : true,
|
||||
func : function() {
|
||||
if( Galaxy && Galaxy.currHistoryPanel
|
||||
&& confirm( _l( 'Really delete the current history permanently? This cannot be undone.' ) ) ){
|
||||
galaxy_main.window.location.href = 'history/delete?purge=True&id=' + Galaxy.currHistoryPanel.model.id;
|
||||
}
|
||||
},
|
||||
},
|
||||
|
||||
|
||||
|
||||
@@ -1750,3 +1750,16 @@ div.toolTitleNoSection
|
||||
font-size: 12px;
|
||||
margin-left: 93.2%;
|
||||
}
|
||||
|
||||
// password complexity monitor
|
||||
#change_password,#registrationForm {
|
||||
.progress {
|
||||
width:200px;
|
||||
margin-left: 20px;
|
||||
}
|
||||
.progress-bar {
|
||||
color:black;
|
||||
text-align:left;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -22,6 +22,7 @@ module.exports = function( grunt ){
|
||||
'farbtastic': [ 'src/farbtastic.js', 'farbtastic.js' ],
|
||||
'jQTouch': [ 'src/reference/jqtouch.js', 'jquery/jqtouch.js' ],
|
||||
'bootstrap-tour': [ 'build/js/bootstrap-tour.js', 'bootstrap-tour.js' ],
|
||||
'jquery.complexify': [ 'jquery.complexify.js', 'jquery.complexify.js' ],
|
||||
|
||||
// these need to be updated and tested
|
||||
//'jquery-form': [ 'jquery.form.js', 'jquery/jquery.form.js' ],
|
||||
|
||||
@@ -20,6 +20,7 @@ var webpack = require( 'webpack' ),
|
||||
'libs/jquery/jquery-ui',
|
||||
'libs/bootstrap',
|
||||
'libs/bootstrap-tour',
|
||||
'libs/jquery.complexify',
|
||||
// mvc
|
||||
'libs/underscore',
|
||||
'libs/backbone',
|
||||
|
||||
@@ -230,7 +230,7 @@
|
||||
</datatype>
|
||||
<datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/>
|
||||
<datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true" description="A binary file archive format from the NCBI Sequence Read Archive with a '.sra' file extension." description_url="http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure"/>
|
||||
<datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
|
||||
<datatype extension="svg" type="galaxy.datatypes.xml:GenericXml" mimetype="image/svg+xml" subclass="True"/>
|
||||
<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
|
||||
<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/>
|
||||
<datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
|
||||
|
||||
@@ -5,14 +5,15 @@ for velvet assembler tool in galaxy
|
||||
"""
|
||||
from __future__ import absolute_import
|
||||
|
||||
from galaxy.datatypes import data
|
||||
import logging
|
||||
import os
|
||||
import re
|
||||
import sys
|
||||
|
||||
from galaxy.datatypes import data
|
||||
from galaxy.datatypes import sequence
|
||||
from galaxy.datatypes.text import Html
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
from galaxy.datatypes.text import Html
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -149,7 +150,7 @@ class Velvet( Html ):
|
||||
MetadataElement( name="short2_reads", desc="has 2nd short reads", default="False", readonly=False, set_in_upload=True)
|
||||
composite_type = 'auto_primary_file'
|
||||
allow_datatype_change = False
|
||||
file_ext = 'html'
|
||||
file_ext = 'velvet'
|
||||
|
||||
def __init__( self, **kwd ):
|
||||
Html.__init__( self, **kwd )
|
||||
@@ -161,7 +162,7 @@ class Velvet( Html ):
|
||||
log.debug( "Velvet log info %s %s" % ('JJ generate_primary_file', dataset))
|
||||
rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
|
||||
rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
|
||||
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():
|
||||
fn = composite_name
|
||||
log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file', fn, composite_file))
|
||||
opt_text = ''
|
||||
@@ -208,7 +209,7 @@ class Velvet( Html ):
|
||||
# rval.append('<div>Generated:<p/><code> %s </code></div>' %(re.sub('\n','<br>',log_msg)))
|
||||
rval.append('<div>Generated:<p/> %s </div>' % (gen_msg))
|
||||
rval.append('<div>Velveth dataset:<p/><ul>')
|
||||
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():
|
||||
fn = composite_name
|
||||
log.debug( "Velvet log info %s %s %s" % ('JJ regenerate_primary_file', fn, composite_file))
|
||||
if re.search('Log', fn) is None:
|
||||
|
||||
@@ -1,12 +1,14 @@
|
||||
"""
|
||||
Constructive Solid Geometry file formats.
|
||||
"""
|
||||
import abc
|
||||
|
||||
from galaxy import util
|
||||
from galaxy.datatypes import data
|
||||
from galaxy.datatypes.binary import Binary
|
||||
from galaxy.datatypes.data import get_file_peek
|
||||
from galaxy.datatypes.data import nice_size
|
||||
from galaxy.datatypes.metadata import MetadataElement
|
||||
from galaxy import util
|
||||
|
||||
MAX_HEADER_LINES = 500
|
||||
MAX_LINE_LEN = 2000
|
||||
@@ -20,6 +22,7 @@ class Ply(object):
|
||||
normal direction that can be attached to these elements. A PLY
|
||||
file contains the description of exactly one object.
|
||||
"""
|
||||
subtype = ''
|
||||
# Add metadata elements.
|
||||
MetadataElement(name="file_format", default=None, desc="File format",
|
||||
readonly=True, optional=True, visible=True, no_value=None)
|
||||
@@ -30,13 +33,17 @@ class Ply(object):
|
||||
MetadataElement(name="other_elements", default=[], desc="Other elements",
|
||||
readonly=True, optional=True, visible=True, no_value=[])
|
||||
|
||||
def sniff(self, filename, subtype):
|
||||
@abc.abstractmethod
|
||||
def __init__(self, **kwd):
|
||||
raise NotImplementedError
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
The structure of a typical PLY file:
|
||||
Header, Vertex List, Face List, (lists of other elements)
|
||||
"""
|
||||
with open(filename, "r") as fh:
|
||||
if not self._is_ply_header(fh, subtype):
|
||||
if not self._is_ply_header(fh, self.subtype):
|
||||
return False
|
||||
return True
|
||||
return False
|
||||
@@ -109,26 +116,20 @@ class Ply(object):
|
||||
|
||||
|
||||
class PlyAscii(Ply, data.Text):
|
||||
|
||||
file_ext = "plyascii"
|
||||
subtype = 'ascii'
|
||||
|
||||
def __init__(self, **kwd):
|
||||
data.Text.__init__(self, **kwd)
|
||||
|
||||
def sniff(self, filename):
|
||||
return super(PlyAscii, self).sniff(filename, subtype='ascii')
|
||||
|
||||
|
||||
class PlyBinary(Ply, Binary):
|
||||
|
||||
file_ext = "plybinary"
|
||||
subtype = 'binary'
|
||||
|
||||
def __init__(self, **kwd):
|
||||
Binary.__init__(self, **kwd)
|
||||
|
||||
def sniff(self, filename):
|
||||
return super(PlyBinary, self).sniff(filename, subtype='binary')
|
||||
|
||||
Binary.register_sniffable_binary_format("plybinary", "plybinary", PlyBinary)
|
||||
|
||||
|
||||
@@ -156,6 +157,7 @@ class Vtk(object):
|
||||
TODO: only legacy formats are currently supported and support for XML formats
|
||||
should be added.
|
||||
"""
|
||||
subtype = ''
|
||||
# Add metadata elements.
|
||||
MetadataElement(name="vtk_version", default=None, desc="Vtk version",
|
||||
readonly=True, optional=True, visible=True, no_value=None)
|
||||
@@ -196,14 +198,18 @@ class Vtk(object):
|
||||
MetadataElement(name="field_components", default={}, desc="Field names and components",
|
||||
readonly=True, optional=True, visible=True, no_value={})
|
||||
|
||||
def sniff(self, filename, subtype):
|
||||
@abc.abstractmethod
|
||||
def __init__(self, **kwd):
|
||||
raise NotImplementedError
|
||||
|
||||
def sniff(self, filename):
|
||||
"""
|
||||
VTK files can be either ASCII or binary, with two different
|
||||
styles of file formats: legacy or XML. We'll assume if the
|
||||
file contains a valid VTK header, then it is a valid VTK file.
|
||||
"""
|
||||
with open(filename, "r") as fh:
|
||||
if self._is_vtk_header(fh, subtype):
|
||||
if self._is_vtk_header(fh, self.subtype):
|
||||
return True
|
||||
return False
|
||||
return False
|
||||
@@ -436,26 +442,20 @@ class Vtk(object):
|
||||
|
||||
|
||||
class VtkAscii(Vtk, data.Text):
|
||||
|
||||
file_ext = "vtkascii"
|
||||
subtype = 'ASCII'
|
||||
|
||||
def __init__(self, **kwd):
|
||||
data.Text.__init__(self, **kwd)
|
||||
|
||||
def sniff(self, filename):
|
||||
return super(VtkAscii, self).sniff(filename, subtype='ASCII')
|
||||
|
||||
|
||||
class VtkBinary(Vtk, Binary):
|
||||
|
||||
file_ext = "vtkbinary"
|
||||
subtype = 'BINARY'
|
||||
|
||||
def __init__(self, **kwd):
|
||||
Binary.__init__(self, **kwd)
|
||||
|
||||
def sniff(self, filename):
|
||||
return super(VtkBinary, self).sniff(filename, subtype='BINARY')
|
||||
|
||||
Binary.register_sniffable_binary_format("vtkbinary", "vtkbinary", VtkBinary)
|
||||
|
||||
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
from __future__ import absolute_import
|
||||
|
||||
import abc
|
||||
import logging
|
||||
import mimetypes
|
||||
import os
|
||||
@@ -7,9 +9,10 @@ import tempfile
|
||||
import zipfile
|
||||
from cgi import escape
|
||||
from inspect import isclass
|
||||
from six import string_types
|
||||
|
||||
from . import metadata
|
||||
import paste
|
||||
import six
|
||||
|
||||
from galaxy import util
|
||||
from galaxy.datatypes.metadata import MetadataElement # import directly to maintain ease of use in Datatype class definitions
|
||||
from galaxy.util import inflector
|
||||
@@ -19,8 +22,7 @@ from galaxy.util.odict import odict
|
||||
from galaxy.util.sanitize_html import sanitize_html
|
||||
|
||||
from . import dataproviders
|
||||
|
||||
import paste
|
||||
from . import metadata
|
||||
|
||||
XSS_VULNERABLE_MIME_TYPES = [
|
||||
'image/svg+xml', # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
|
||||
@@ -35,7 +37,7 @@ col1_startswith = ['chr', 'chl', 'groupun', 'reftig_', 'scaffold', 'super_', 'vc
|
||||
valid_strand = ['+', '-', '.']
|
||||
|
||||
|
||||
class DataMeta( type ):
|
||||
class DataMeta( abc.ABCMeta ):
|
||||
"""
|
||||
Metaclass for Data class. Sets up metadata spec.
|
||||
"""
|
||||
@@ -47,6 +49,7 @@ class DataMeta( type ):
|
||||
metadata.Statement.process( cls )
|
||||
|
||||
|
||||
@six.add_metaclass(DataMeta)
|
||||
@dataproviders.decorators.has_dataproviders
|
||||
class Data( object ):
|
||||
"""
|
||||
@@ -72,7 +75,6 @@ class Data( object ):
|
||||
#: dictionary of metadata fields for this datatype::
|
||||
metadata_spec = None
|
||||
|
||||
__metaclass__ = DataMeta
|
||||
# Add metadata elements
|
||||
MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.DBKeyParameter, multiple=False, no_value="?" )
|
||||
# Stores the set of display applications, and viewing methods, supported by this datatype
|
||||
@@ -158,7 +160,7 @@ class Data( object ):
|
||||
Specifying a list of 'skip' items will return True even when a named metadata value is missing
|
||||
"""
|
||||
if check:
|
||||
to_check = [ ( to_check, dataset.metadata.get( to_check ) ) for to_check in check ]
|
||||
to_check = ( ( to_check, dataset.metadata.get( to_check ) ) for to_check in check )
|
||||
else:
|
||||
to_check = dataset.metadata.items()
|
||||
for key, value in to_check:
|
||||
@@ -327,7 +329,7 @@ class Data( object ):
|
||||
# Prevent IE8 from sniffing content type since we're explicit about it. This prevents intentionally text/plain
|
||||
# content from being rendered in the browser
|
||||
trans.response.headers['X-Content-Type-Options'] = 'nosniff'
|
||||
if isinstance( data, string_types ):
|
||||
if isinstance( data, six.string_types ):
|
||||
return data
|
||||
if filename and filename != "index":
|
||||
# For files in extra_files_path
|
||||
@@ -454,7 +456,7 @@ class Data( object ):
|
||||
|
||||
def get_display_applications_by_dataset( self, dataset, trans ):
|
||||
rval = odict()
|
||||
for key, value in self.display_applications.iteritems():
|
||||
for key, value in self.display_applications.items():
|
||||
value = value.filter_by_dataset( dataset, trans )
|
||||
if value.links:
|
||||
rval[key] = value
|
||||
@@ -462,7 +464,7 @@ class Data( object ):
|
||||
|
||||
def get_display_types(self):
|
||||
"""Returns display types available"""
|
||||
return self.supported_display_apps.keys()
|
||||
return list(self.supported_display_apps.keys())
|
||||
|
||||
def get_display_label(self, type):
|
||||
"""Returns primary label for display app"""
|
||||
@@ -525,7 +527,7 @@ class Data( object ):
|
||||
if len(params) > 0:
|
||||
trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id )
|
||||
if not visible:
|
||||
for value in converted_dataset.itervalues():
|
||||
for value in converted_dataset.values():
|
||||
value.visible = False
|
||||
if return_output:
|
||||
return converted_dataset
|
||||
@@ -571,7 +573,7 @@ class Data( object ):
|
||||
files = odict()
|
||||
if self.composite_type != 'auto_primary_file':
|
||||
files[ self.primary_file_name ] = self.__new_composite_file( self.primary_file_name )
|
||||
for key, value in self.get_composite_files( dataset=dataset ).iteritems():
|
||||
for key, value in self.get_composite_files( dataset=dataset ).items():
|
||||
files[ key ] = value
|
||||
return files
|
||||
|
||||
@@ -585,7 +587,7 @@ class Data( object ):
|
||||
return key % meta_value
|
||||
return key
|
||||
files = odict()
|
||||
for key, value in self.composite_files.iteritems():
|
||||
for key, value in self.composite_files.items():
|
||||
files[ substitute_composite_key( key, value ) ] = value
|
||||
return files
|
||||
|
||||
|
||||
@@ -7,9 +7,13 @@ Base class(es) for all DataProviders.
|
||||
# also, this shouldn't be a replacement/re-implementation of the tool layer
|
||||
# (which provides traceability/versioning/reproducibility)
|
||||
|
||||
from collections import deque
|
||||
import exceptions
|
||||
import logging
|
||||
from collections import deque
|
||||
|
||||
import six
|
||||
|
||||
from . import exceptions
|
||||
|
||||
log = logging.getLogger( __name__ )
|
||||
|
||||
_TODO = """
|
||||
@@ -60,7 +64,8 @@ class HasSettings( type ):
|
||||
|
||||
|
||||
# ----------------------------------------------------------------------------- base classes
|
||||
class DataProvider( object ):
|
||||
@six.add_metaclass(HasSettings)
|
||||
class DataProvider( six.Iterator ):
|
||||
"""
|
||||
Base class for all data providers. Data providers:
|
||||
(a) have a source (which must be another file-like object)
|
||||
@@ -71,7 +76,6 @@ class DataProvider( object ):
|
||||
# a definition of expected types for keyword arguments sent to __init__
|
||||
# useful for controlling how query string dictionaries can be parsed into correct types for __init__
|
||||
# empty in this base class
|
||||
__metaclass__ = HasSettings
|
||||
settings = {}
|
||||
|
||||
def __init__( self, source, **kwargs ):
|
||||
@@ -130,8 +134,8 @@ class DataProvider( object ):
|
||||
for datum in self.source:
|
||||
yield datum
|
||||
|
||||
def next( self ):
|
||||
return self.source.next()
|
||||
def __next__( self ):
|
||||
return next(self.source)
|
||||
|
||||
# context manager interface
|
||||
def __enter__( self ):
|
||||
|
||||
@@ -1,15 +1,13 @@
|
||||
"""
|
||||
Image classes
|
||||
"""
|
||||
|
||||
import imghdr
|
||||
import logging
|
||||
import zipfile
|
||||
from urllib import quote_plus
|
||||
from six.moves.urllib.parse import quote_plus
|
||||
|
||||
from galaxy.datatypes.binary import Binary
|
||||
from galaxy.datatypes.text import Html as HtmlFromText
|
||||
from galaxy.datatypes.sniff import get_headers
|
||||
from galaxy.datatypes.text import Html as HtmlFromText
|
||||
from galaxy.datatypes.util.image_util import check_image_type
|
||||
from galaxy.util import nice_size
|
||||
from . import data
|
||||
@@ -39,6 +37,11 @@ class Image( data.Data ):
|
||||
"""Class describing an image"""
|
||||
edam_data = 'data_2968'
|
||||
edam_format = "format_3547"
|
||||
file_ext = ''
|
||||
|
||||
def __init__(self, **kwd):
|
||||
super(Image, self).__init__(**kwd)
|
||||
self.image_formats = [self.file_ext.upper()]
|
||||
|
||||
def set_peek( self, dataset, is_multi_byte=False ):
|
||||
if not dataset.dataset.purged:
|
||||
@@ -49,173 +52,98 @@ class Image( data.Data ):
|
||||
dataset.blurb = 'file purged from disk'
|
||||
|
||||
def sniff( self, filename ):
|
||||
# First check if we can use PIL
|
||||
if PIL is not None:
|
||||
try:
|
||||
im = PIL.open( filename )
|
||||
im.close()
|
||||
return True
|
||||
except:
|
||||
return False
|
||||
else:
|
||||
if imghdr.what( filename ) is not None:
|
||||
return True
|
||||
else:
|
||||
return False
|
||||
"""Determine if the file is in this format"""
|
||||
return check_image_type( filename, self.image_formats )
|
||||
|
||||
|
||||
class Jpg( Image ):
|
||||
edam_format = "format_3579"
|
||||
file_ext = "jpg"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in jpg format."""
|
||||
return check_image_type( filename, ['JPEG'], image )
|
||||
def __init__(self, **kwd):
|
||||
super(Jpg, self).__init__(**kwd)
|
||||
self.image_formats = ['JPEG']
|
||||
|
||||
|
||||
class Png( Image ):
|
||||
edam_format = "format_3603"
|
||||
file_ext = "png"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in png format."""
|
||||
return check_image_type( filename, ['PNG'], image )
|
||||
|
||||
|
||||
class Tiff( Image ):
|
||||
edam_format = "format_3591"
|
||||
file_ext = "tiff"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in tiff format."""
|
||||
return check_image_type( filename, ['TIFF'], image )
|
||||
|
||||
|
||||
class Bmp( Image ):
|
||||
edam_format = "format_3592"
|
||||
file_ext = "bmp"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in bmp format."""
|
||||
return check_image_type( filename, ['BMP'], image )
|
||||
|
||||
|
||||
class Gif( Image ):
|
||||
edam_format = "format_3467"
|
||||
file_ext = "gif"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in gif format."""
|
||||
return check_image_type( filename, ['GIF'], image )
|
||||
|
||||
|
||||
class Im( Image ):
|
||||
edam_format = "format_3593"
|
||||
file_ext = "im"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in im format."""
|
||||
return check_image_type( filename, ['IM'], image )
|
||||
|
||||
|
||||
class Pcd( Image ):
|
||||
edam_format = "format_3594"
|
||||
file_ext = "pcd"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in pcd format."""
|
||||
return check_image_type( filename, ['PCD'], image )
|
||||
|
||||
|
||||
class Pcx( Image ):
|
||||
edam_format = "format_3595"
|
||||
file_ext = "pcx"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in pcx format."""
|
||||
return check_image_type( filename, ['PCX'], image )
|
||||
|
||||
|
||||
class Ppm( Image ):
|
||||
edam_format = "format_3596"
|
||||
file_ext = "ppm"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in ppm format."""
|
||||
return check_image_type( filename, ['PPM'], image )
|
||||
|
||||
|
||||
class Psd( Image ):
|
||||
edam_format = "format_3597"
|
||||
file_ext = "psd"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in psd format."""
|
||||
return check_image_type( filename, ['PSD'], image )
|
||||
|
||||
|
||||
class Xbm( Image ):
|
||||
edam_format = "format_3598"
|
||||
file_ext = "xbm"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in XBM format."""
|
||||
return check_image_type( filename, ['XBM'], image )
|
||||
|
||||
|
||||
class Xpm( Image ):
|
||||
edam_format = "format_3599"
|
||||
file_ext = "xpm"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in XPM format."""
|
||||
return check_image_type( filename, ['XPM'], image )
|
||||
|
||||
|
||||
class Rgb( Image ):
|
||||
edam_format = "format_3600"
|
||||
file_ext = "rgb"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in RGB format."""
|
||||
return check_image_type( filename, ['RGB'], image )
|
||||
|
||||
|
||||
class Pbm( Image ):
|
||||
edam_format = "format_3601"
|
||||
file_ext = "pbm"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in PBM format"""
|
||||
return check_image_type( filename, ['PBM'], image )
|
||||
|
||||
|
||||
class Pgm( Image ):
|
||||
edam_format = "format_3602"
|
||||
file_ext = "pgm"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in PGM format"""
|
||||
return check_image_type( filename, ['PGM'], image )
|
||||
|
||||
|
||||
class Eps( Image ):
|
||||
edam_format = "format_3466"
|
||||
file_ext = "eps"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in eps format."""
|
||||
return check_image_type( filename, ['EPS'], image )
|
||||
|
||||
|
||||
class Rast( Image ):
|
||||
edam_format = "format_3605"
|
||||
file_ext = "rast"
|
||||
|
||||
def sniff(self, filename, image=None):
|
||||
"""Determine if the file is in rast format"""
|
||||
return check_image_type( filename, ['RAST'], image )
|
||||
|
||||
|
||||
class Pdf( Image ):
|
||||
edam_format = "format_3508"
|
||||
@@ -241,14 +169,14 @@ def create_applet_tag_peek( class_name, archive, params ):
|
||||
type="application/x-java-applet"
|
||||
height="30" width="200" align="center" >
|
||||
<param name="archive" value="%s"/>""" % ( class_name, archive )
|
||||
for name, value in params.iteritems():
|
||||
for name, value in params.items():
|
||||
text += """<param name="%s" value="%s"/>""" % ( name, value )
|
||||
text += """
|
||||
<object classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93"
|
||||
height="30" width="200" >
|
||||
<param name="code" value="%s" />
|
||||
<param name="archive" value="%s"/>""" % ( class_name, archive )
|
||||
for name, value in params.iteritems():
|
||||
for name, value in params.items():
|
||||
text += """<param name="%s" value="%s"/>""" % ( name, value )
|
||||
text += """<div class="errormessage">You must install and enable Java in your browser in order to access this applet.<div></object>
|
||||
</object>
|
||||
@@ -271,7 +199,7 @@ class Gmaj( data.Data ):
|
||||
"nobutton": "false",
|
||||
"urlpause": "100",
|
||||
"debug": "false",
|
||||
"posturl": "history_add_to?%s" % "&".join( map( lambda x: "%s=%s" % ( x[0], quote_plus( str( x[1] ) ) ), [ ( 'copy_access_from', dataset.id), ( 'history_id', dataset.history_id ), ( 'ext', 'maf' ), ( 'name', 'GMAJ Output on data %s' % dataset.hid ), ( 'info', 'Added by GMAJ' ), ( 'dbkey', dataset.dbkey ) ] ) )
|
||||
"posturl": "history_add_to?%s" % "&".join( "%s=%s" % ( x[0], quote_plus( str( x[1] ) ) ) for x in [ ( 'copy_access_from', dataset.id), ( 'history_id', dataset.history_id ), ( 'ext', 'maf' ), ( 'name', 'GMAJ Output on data %s' % dataset.hid ), ( 'info', 'Added by GMAJ' ), ( 'dbkey', dataset.dbkey ) ] )
|
||||
}
|
||||
class_name = "edu.psu.bx.gmaj.MajApplet.class"
|
||||
archive = "/static/gmaj/gmaj.jar"
|
||||
@@ -331,7 +259,7 @@ class Laj( data.Text ):
|
||||
"alignfile1": "display?id=%s" % dataset.id,
|
||||
"buttonlabel": "Launch LAJ",
|
||||
"title": "LAJ in Galaxy",
|
||||
"posturl": quote_plus( "history_add_to?%s" % "&".join( [ "%s=%s" % ( key, value ) for key, value in { 'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id }.items() ] ) ),
|
||||
"posturl": quote_plus( "history_add_to?%s" % "&".join( "%s=%s" % ( key, value ) for key, value in { 'history_id': dataset.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': dataset.dbkey, 'copy_access_from': dataset.id }.items() ) ),
|
||||
"noseq": "true"
|
||||
}
|
||||
class_name = "edu.psu.cse.bio.laj.LajApplet.class"
|
||||
|
||||
@@ -1,3 +1,4 @@
|
||||
import abc
|
||||
import logging
|
||||
import os
|
||||
|
||||
@@ -13,7 +14,6 @@ log = logging.getLogger(__name__)
|
||||
class Hmmer( Text ):
|
||||
edam_data = "data_1364"
|
||||
edam_format = "format_1370"
|
||||
file_ext = "hmm"
|
||||
|
||||
def set_peek(self, dataset, is_multi_byte=False):
|
||||
if not dataset.dataset.purged:
|
||||
@@ -29,9 +29,14 @@ class Hmmer( Text ):
|
||||
except:
|
||||
return "HMMER database (%s)" % ( nice_size( dataset.get_size() ) )
|
||||
|
||||
@abc.abstractmethod
|
||||
def sniff(self, filename):
|
||||
raise NotImplementedError
|
||||
|
||||
|
||||
class Hmmer2( Hmmer ):
|
||||
edam_format = "format_3328"
|
||||
file_ext = "hmm2"
|
||||
|
||||
def sniff(self, filename):
|
||||
"""HMMER2 files start with HMMER2.0
|
||||
@@ -43,6 +48,7 @@ class Hmmer2( Hmmer ):
|
||||
|
||||
class Hmmer3( Hmmer ):
|
||||
edam_format = "format_3329"
|
||||
file_ext = "hmm3"
|
||||
|
||||
def sniff(self, filename):
|
||||
"""HMMER3 files start with HMMER3/f
|
||||
|
||||
@@ -1,11 +1,11 @@
|
||||
"""
|
||||
NGS indexes
|
||||
"""
|
||||
import os
|
||||
import logging
|
||||
import os
|
||||
|
||||
from metadata import MetadataElement
|
||||
from text import Html
|
||||
from .metadata import MetadataElement
|
||||
from .text import Html
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -18,7 +18,6 @@ class BowtieIndex( Html ):
|
||||
MetadataElement( name="base_name", desc="base name for this index set", default='galaxy_generated_bowtie_index', set_in_upload=True, readonly=True )
|
||||
MetadataElement( name="sequence_space", desc="sequence_space for this index set", default='unknown', set_in_upload=True, readonly=True )
|
||||
|
||||
file_ext = 'bowtie_index'
|
||||
is_binary = True
|
||||
composite_type = 'auto_primary_file'
|
||||
allow_datatype_change = False
|
||||
@@ -59,9 +58,6 @@ class BowtieIndex( Html ):
|
||||
except:
|
||||
return "Bowtie index file"
|
||||
|
||||
def sniff( self, filename ):
|
||||
return False
|
||||
|
||||
|
||||
class BowtieColorIndex( BowtieIndex ):
|
||||
"""
|
||||
|
||||
@@ -40,7 +40,7 @@ class Wiff(Binary):
|
||||
def generate_primary_file(self, dataset=None):
|
||||
rval = ['<html><head><title>Wiff Composite Dataset </title></head><p/>']
|
||||
rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
|
||||
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():
|
||||
fn = composite_name
|
||||
opt_text = ''
|
||||
if composite_file.optional:
|
||||
@@ -58,7 +58,7 @@ Binary.register_sniffable_binary_format("wiff", "wiff", Wiff )
|
||||
class PepXmlReport(Tabular):
|
||||
"""pepxml converted to tabular report"""
|
||||
edam_data = "data_2536"
|
||||
file_ext = "tsv"
|
||||
file_ext = "pepxml.tsv"
|
||||
|
||||
def __init__(self, **kwd):
|
||||
Tabular.__init__(self, **kwd)
|
||||
@@ -72,7 +72,7 @@ class PepXmlReport(Tabular):
|
||||
class ProtXmlReport(Tabular):
|
||||
"""protxml converted to tabular report"""
|
||||
edam_data = "data_2536"
|
||||
file_ext = "tsv"
|
||||
file_ext = "protxml.tsv"
|
||||
comment_lines = 1
|
||||
|
||||
def __init__(self, **kwd):
|
||||
@@ -351,7 +351,7 @@ class SPLib(Msp):
|
||||
def generate_primary_file(self, dataset=None):
|
||||
rval = ['<html><head><title>Spectral Library Composite Dataset </title></head><p/>']
|
||||
rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
|
||||
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():
|
||||
fn = composite_name
|
||||
opt_text = ''
|
||||
if composite_file.optional:
|
||||
|
||||
@@ -3,6 +3,7 @@ Tabular datatype
|
||||
"""
|
||||
from __future__ import absolute_import
|
||||
|
||||
import abc
|
||||
import csv
|
||||
import gzip
|
||||
import logging
|
||||
@@ -44,6 +45,10 @@ class TabularData( data.Text ):
|
||||
MetadataElement( name="column_names", default=[], desc="Column names", readonly=True, visible=False, optional=True, no_value=[] )
|
||||
MetadataElement( name="delimiter", default='\t', desc="Data delimiter", readonly=True, visible=False, optional=True, no_value=[] )
|
||||
|
||||
@abc.abstractmethod
|
||||
def set_meta( self, dataset, **kwd ):
|
||||
raise NotImplementedError
|
||||
|
||||
def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None ):
|
||||
super(TabularData, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False )
|
||||
if dataset.metadata.comment_lines:
|
||||
@@ -395,7 +400,7 @@ class Tabular( TabularData ):
|
||||
class Taxonomy( Tabular ):
|
||||
def __init__(self, **kwd):
|
||||
"""Initialize taxonomy datatype"""
|
||||
Tabular.__init__( self, **kwd )
|
||||
super(Taxonomy, self).__init__( **kwd )
|
||||
self.column_names = ['Name', 'TaxId', 'Root', 'Superkingdom', 'Kingdom', 'Subkingdom',
|
||||
'Superphylum', 'Phylum', 'Subphylum', 'Superclass', 'Class', 'Subclass',
|
||||
'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily',
|
||||
@@ -404,7 +409,7 @@ class Taxonomy( Tabular ):
|
||||
|
||||
def display_peek( self, dataset ):
|
||||
"""Returns formated html of peek"""
|
||||
return Tabular.make_html_table( self, dataset, column_names=self.column_names )
|
||||
return super(Taxonomy, self).make_html_table( dataset, column_names=self.column_names )
|
||||
|
||||
|
||||
@dataproviders.decorators.has_dataproviders
|
||||
@@ -417,14 +422,14 @@ class Sam( Tabular ):
|
||||
|
||||
def __init__(self, **kwd):
|
||||
"""Initialize taxonomy datatype"""
|
||||
Tabular.__init__( self, **kwd )
|
||||
super( Sam, self ).__init__( **kwd )
|
||||
self.column_names = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR',
|
||||
'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT'
|
||||
]
|
||||
|
||||
def display_peek( self, dataset ):
|
||||
"""Returns formated html of peek"""
|
||||
return Tabular.make_html_table( self, dataset, column_names=self.column_names )
|
||||
return super( Sam, self ).make_html_table( dataset, column_names=self.column_names )
|
||||
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
@@ -606,11 +611,11 @@ class Pileup( Tabular ):
|
||||
MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter )
|
||||
|
||||
def init_meta( self, dataset, copy_from=None ):
|
||||
Tabular.init_meta( self, dataset, copy_from=copy_from )
|
||||
super( Pileup, self ).init_meta( dataset, copy_from=copy_from )
|
||||
|
||||
def display_peek( self, dataset ):
|
||||
"""Returns formated html of peek"""
|
||||
return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'} )
|
||||
return super( Pileup, self ).make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'} )
|
||||
|
||||
def repair_methods( self, dataset ):
|
||||
"""Return options for removing errors along with a description"""
|
||||
@@ -686,10 +691,10 @@ class Vcf( Tabular ):
|
||||
|
||||
def display_peek( self, dataset ):
|
||||
"""Returns formated html of peek"""
|
||||
return Tabular.make_html_table( self, dataset, column_names=self.column_names )
|
||||
return super( Vcf, self ).make_html_table( dataset, column_names=self.column_names )
|
||||
|
||||
def set_meta( self, dataset, **kwd ):
|
||||
Tabular.set_meta( self, dataset, **kwd )
|
||||
super( Vcf, self ).set_meta( dataset, **kwd )
|
||||
source = open( dataset.file_name )
|
||||
|
||||
# Skip comments.
|
||||
@@ -741,7 +746,7 @@ class Eland( Tabular ):
|
||||
|
||||
def __init__(self, **kwd):
|
||||
"""Initialize taxonomy datatype"""
|
||||
Tabular.__init__( self, **kwd )
|
||||
super( Eland, self ).__init__( **kwd )
|
||||
self.column_names = ['MACHINE', 'RUN_NO', 'LANE', 'TILE', 'X', 'Y',
|
||||
'INDEX', 'READ_NO', 'SEQ', 'QUAL', 'CHROM', 'CONTIG',
|
||||
'POSITION', 'STRAND', 'DESC', 'SRAS', 'PRAS', 'PART_CHROM'
|
||||
@@ -883,11 +888,10 @@ class BaseCSV( TabularData ):
|
||||
Delimiter-separated table data.
|
||||
This includes CSV, TSV and other dialects understood by the
|
||||
Python 'csv' module https://docs.python.org/2/library/csv.html
|
||||
Must be extended to define the dialect to use, strict_width: and file_ext.
|
||||
See Python module csv for documentation of dialect settings
|
||||
Must be extended to define the dialect to use, strict_width and file_ext.
|
||||
See the Python module csv for documentation of dialect settings
|
||||
"""
|
||||
delimiter = ','
|
||||
file_ext = 'csv' # File extension
|
||||
peek_size = 1024 # File chunk used for sniffing CSV dialect
|
||||
big_peek_size = 10240 # Large File chunk used for sniffing CSV dialect
|
||||
|
||||
@@ -1004,12 +1008,9 @@ class CSV( BaseCSV ):
|
||||
Comma-separated table data.
|
||||
Only sniffs comma-separated files with at least 2 rows and 2 columns.
|
||||
"""
|
||||
|
||||
def __init__(self, **kwd):
|
||||
BaseCSV.__init__( self, **kwd )
|
||||
self.dialect = csv.excel # This is the default
|
||||
self.file_ext = 'csv' # File extension
|
||||
self.strict_width = False # Previous csv type did not check column width
|
||||
file_ext = 'csv'
|
||||
dialect = csv.excel # This is the default
|
||||
strict_width = False # Previous csv type did not check column width
|
||||
|
||||
|
||||
@dataproviders.decorators.has_dataproviders
|
||||
@@ -1026,12 +1027,9 @@ class TSV( BaseCSV ):
|
||||
column less to indicate first column is row names. This kind of file is
|
||||
handled fine by the tabular datatype.
|
||||
"""
|
||||
|
||||
def __init__(self, **kwd):
|
||||
BaseCSV.__init__( self, **kwd )
|
||||
self.dialect = csv.excel_tab
|
||||
self.file_ext = 'tsv' # File extension
|
||||
self.strict_width = True # Leave files with different width to tabular
|
||||
file_ext = 'tsv'
|
||||
dialect = csv.excel_tab
|
||||
strict_width = True # Leave files with different width to tabular
|
||||
|
||||
|
||||
class ConnectivityTable( Tabular ):
|
||||
@@ -1042,7 +1040,7 @@ class ConnectivityTable( Tabular ):
|
||||
structure_regexp = re.compile( "^[0-9]+" + "(?:\t|[ ]+)" + "[ACGTURYKMSWBDHVN]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+" + "(?:\t|[ ]+)" + "[^\t]+")
|
||||
|
||||
def __init__(self, **kwd):
|
||||
Tabular.__init__( self, **kwd )
|
||||
super( ConnectivityTable, self ).__init__( **kwd )
|
||||
self.columns = 6
|
||||
self.column_names = ['base_index', 'base', 'neighbor_left', 'neighbor_right', 'partner', 'natural_numbering']
|
||||
self.column_types = ['int', 'str', 'int', 'int', 'int', 'int']
|
||||
|
||||
@@ -19,6 +19,7 @@ from ..objectstore import ObjectStore, convert_bytes
|
||||
try:
|
||||
from azure.storage import CloudStorageAccount
|
||||
from azure.storage.blob import BlockBlobService
|
||||
from azure.storage.blob.models import Blob
|
||||
from azure.common import AzureHttpError
|
||||
except ImportError:
|
||||
BlockBlobService = None
|
||||
@@ -170,6 +171,11 @@ class AzureBlobObjectStore(ObjectStore):
|
||||
def _get_size_in_azure(self, rel_path):
|
||||
try:
|
||||
properties = self.service.get_blob_properties(self.container_name, rel_path)
|
||||
# Currently this returns a blob and not a BlobProperties object
|
||||
# Similar issue for the ruby https://github.com/Azure/azure-storage-ruby/issues/13
|
||||
# The typecheck is an attempt at future-proofing this when/if the bug is fixed.
|
||||
if type(properties) is Blob:
|
||||
properties = properties.properties
|
||||
if properties:
|
||||
size_in_bytes = properties.content_length
|
||||
return size_in_bytes
|
||||
|
||||
@@ -1,3 +1,3 @@
|
||||
VERSION_MAJOR = "16.07"
|
||||
VERSION_MAJOR = "16.10"
|
||||
VERSION_MINOR = "dev"
|
||||
VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '')
|
||||
|
||||
@@ -482,9 +482,10 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
|
||||
if prev_galaxy_session:
|
||||
self.sa_session.add( prev_galaxy_session )
|
||||
self.sa_session.flush()
|
||||
# If the old session was invalid, get a new history with our new session
|
||||
# If the old session was invalid, get a new (or existing default,
|
||||
# unused) history with our new session
|
||||
if invalidate_existing_session:
|
||||
self.new_history()
|
||||
self.get_or_create_default_history()
|
||||
|
||||
def _ensure_logged_in_user( self, environ, session_cookie ):
|
||||
# The value of session_cookie can be one of
|
||||
@@ -719,7 +720,7 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
|
||||
if hasattr( self.galaxy_session, 'current_history' ):
|
||||
history = self.galaxy_session.current_history
|
||||
if not history and util.string_as_bool( create ):
|
||||
history = self.new_history()
|
||||
history = self.get_or_create_default_history()
|
||||
return history
|
||||
|
||||
def set_history( self, history ):
|
||||
|
||||
@@ -1091,61 +1091,36 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
count += 1
|
||||
return trans.show_ok_message( "%d datasets have been deleted permanently" % count, refresh_frames=['history'] )
|
||||
|
||||
# TODO: use api instead
|
||||
@web.expose
|
||||
def delete_current( self, trans, purge=False ):
|
||||
"""Delete just the active history -- this does not require a logged in user."""
|
||||
history = trans.get_history()
|
||||
if history.users_shared_with:
|
||||
return trans.show_error_message( "History (%s) has been shared with others, unshare it before deleting it. " % history.name )
|
||||
if not history.deleted:
|
||||
history.deleted = True
|
||||
trans.sa_session.add( history )
|
||||
trans.sa_session.flush()
|
||||
trans.log_event( "History id %d marked as deleted" % history.id )
|
||||
if purge and trans.app.config.allow_user_dataset_purge:
|
||||
for hda in history.datasets:
|
||||
if trans.user:
|
||||
trans.user.adjust_total_disk_usage(-hda.quota_amount(trans.user))
|
||||
hda.purged = True
|
||||
trans.sa_session.add( hda )
|
||||
trans.log_event( "HDA id %s has been purged" % hda.id )
|
||||
trans.sa_session.flush()
|
||||
if hda.dataset.user_can_purge:
|
||||
try:
|
||||
hda.dataset.full_delete()
|
||||
trans.log_event( "Dataset id %s has been purged upon the the purge of HDA id %s" % ( hda.dataset.id, hda.id ) )
|
||||
trans.sa_session.add( hda.dataset )
|
||||
except:
|
||||
log.exception( 'Unable to purge dataset (%s) on purge of hda (%s):' % ( hda.dataset.id, hda.id ) )
|
||||
history.purged = True
|
||||
self.sa_session.add( history )
|
||||
self.sa_session.flush()
|
||||
for hda in history.datasets:
|
||||
# Not all datasets have jobs associated with them (e.g., datasets imported from libraries).
|
||||
if hda.creating_job_associations:
|
||||
# HDA has associated job, so try marking it deleted.
|
||||
job = hda.creating_job_associations[0].job
|
||||
if job.history_id == history.id and not job.finished:
|
||||
# No need to check other outputs since the job's parent history is this history
|
||||
job.mark_deleted( trans.app.config.track_jobs_in_database )
|
||||
trans.app.job_manager.job_stop_queue.put( job.id )
|
||||
def delete( self, trans, id, purge=False ):
|
||||
"""Delete the history -- this does not require a logged in user."""
|
||||
# TODO: use api instead
|
||||
try:
|
||||
# get the history with the given id, delete and optionally purge
|
||||
current_history = self.history_manager.get_current( trans )
|
||||
history = self.history_manager.get_owned( self.decode_id( id ), trans.user, current_history=current_history )
|
||||
if history.users_shared_with:
|
||||
raise exceptions.ObjectAttributeInvalidException(
|
||||
"History has been shared with others. Unshare it before deleting it."
|
||||
)
|
||||
self.history_manager.delete( history, flush=( not purge ) )
|
||||
if purge:
|
||||
self.history_manager.purge( history )
|
||||
|
||||
# Regardless of whether it was previously deleted, get the most recent history or create a new one.
|
||||
most_recent_history = self.history_manager.most_recent(
|
||||
user=trans.user,
|
||||
filters=[
|
||||
model.History.deleted == false(),
|
||||
model.History.purged == false(),
|
||||
]
|
||||
)
|
||||
if most_recent_history:
|
||||
trans.set_history( most_recent_history )
|
||||
return trans.show_ok_message( "History deleted, your most recent history is now active",
|
||||
refresh_frames=['history'] )
|
||||
# if this history is the current history for this session,
|
||||
# - attempt to find the most recently used, undeleted history and switch to it.
|
||||
# - If no suitable recent history is found, create a new one and switch
|
||||
if history == current_history:
|
||||
not_deleted_or_purged = [ model.History.deleted == false(), model.History.purged == false() ]
|
||||
most_recent_history = self.history_manager.most_recent( user=trans.user, filters=not_deleted_or_purged )
|
||||
if most_recent_history:
|
||||
self.history_manager.set_current( trans, most_recent_history )
|
||||
else:
|
||||
trans.get_or_create_default_history()
|
||||
|
||||
trans.get_or_create_default_history()
|
||||
return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] )
|
||||
except Exception as exc:
|
||||
return trans.show_error_message( exc )
|
||||
return trans.show_ok_message( "History deleted", refresh_frames=['history'] )
|
||||
|
||||
@web.expose
|
||||
def resume_paused_jobs( self, trans, current=False, ids=None ):
|
||||
|
||||
@@ -510,7 +510,9 @@ if [ "$driver" = "python" ]; then
|
||||
export GALAXY_TEST_TOOL_CONF
|
||||
fi
|
||||
python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args
|
||||
exit_status=$?
|
||||
echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
|
||||
exit ${exit_status}
|
||||
else
|
||||
ensure_grunt
|
||||
if [ -n "$watch" ]; then
|
||||
|
||||
@@ -176,6 +176,8 @@ RELEASE_ISSUE_TEMPLATE = string.Template("""
|
||||
|
||||
- [ ] Open PRs from your fork of branch ``version-${version}`` to upstream ``release_${version}`` and of ``version-${next_version}.dev`` to ``dev``.
|
||||
|
||||
- [ ] Update ``next_milestone`` in [P4's configuration](https://github.com/galaxyproject/p4) to `{version}` so it properly tags new PRs.
|
||||
|
||||
- [ ] **Deploy and Test Release**
|
||||
|
||||
- [ ] Update test to ensure it is running a dev at or past branch point (${freeze_date} + 1 day).
|
||||
|
||||
@@ -5,6 +5,7 @@ import sys
|
||||
|
||||
from pkg_resources import load_entry_point
|
||||
|
||||
assert sys.version_info[:2] >= ( 2, 4 )
|
||||
assert sys.version_info[:2] >= ( 2, 7 )
|
||||
|
||||
sys.exit( load_entry_point('nose', 'console_scripts', 'nosetests')() )
|
||||
nose_core_TestProgram = load_entry_point('nose', 'console_scripts', 'nosetests')
|
||||
nose_core_TestProgram()
|
||||
|
||||
@@ -0,0 +1 @@
|
||||
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|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
|
||||
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|
||||
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|
||||
File diff suppressed because one or more lines are too long
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@@ -0,0 +1,2 @@
|
||||
!function(a){a.fn.extend({complexify:function(b,c){function d(a,b){for(var c=a.length-1;c>=0;c--)if(b[0]<=a.charCodeAt(c)&&a.charCodeAt(c)<=b[1])return b[1]-b[0]+1;return 0}function e(c){if("strict"===b.banMode){for(var d=0;d<b.bannedPasswords.length;d++)if(-1!==c.toLowerCase().indexOf(b.bannedPasswords[d].toLowerCase()))return!0;return!1}return a.inArray(c,b.bannedPasswords)>-1?!0:!1}function f(){var f=a(this).val(),j=0,k=!1;if(e(f))j=1;else for(var l=i.length-1;l>=0;l--)j+=d(f,i[l]);j=Math.log(Math.pow(j,f.length))*(1/b.strengthScaleFactor),k=j>g&&f.length>=b.minimumChars,j=j/h*100,j=j>100?100:j,c.call(this,k,j)}var g=49,h=120,i=[[32,32],[48,57],[65,90],[97,122],[33,47],[58,64],[91,96],[123,126],[128,255],[256,383],[384,591],[592,687],[688,767],[768,879],[880,1023],[1024,1279],[1328,1423],[1424,1535],[1536,1791],[1792,1871],[1920,1983],[2304,2431],[2432,2559],[2560,2687],[2688,2815],[2816,2943],[2944,3071],[3072,3199],[3200,3327],[3328,3455],[3456,3583],[3584,3711],[3712,3839],[3840,4095],[4096,4255],[4256,4351],[4352,4607],[4608,4991],[5024,5119],[5120,5759],[5760,5791],[5792,5887],[6016,6143],[6144,6319],[7680,7935],[7936,8191],[8192,8303],[8304,8351],[8352,8399],[8400,8447],[8448,8527],[8528,8591],[8592,8703],[8704,8959],[8960,9215],[9216,9279],[9280,9311],[9312,9471],[9472,9599],[9600,9631],[9632,9727],[9728,9983],[9984,10175],[10240,10495],[11904,12031],[12032,12255],[12272,12287],[12288,12351],[12352,12447],[12448,12543],[12544,12591],[12592,12687],[12688,12703],[12704,12735],[12800,13055],[13056,13311],[13312,19893],[19968,40959],[40960,42127],[42128,42191],[44032,55203],[55296,56191],[56192,56319],[56320,57343],[57344,63743],[63744,64255],[64256,64335],[64336,65023],[65056,65071],[65072,65103],[65104,65135],[65136,65278],[65279,65279],[65280,65519],[65520,65533]],j={minimumChars:8,strengthScaleFactor:1,bannedPasswords:window.COMPLEXIFY_BANLIST||[],banMode:"strict"};return a.isFunction(b)&&!c&&(c=b,b={}),b=a.extend(j,b),this.each(function(){a(this).val()&&f.apply(this)}),this.each(function(){a(this).bind("keyup focus input propertychange mouseup",f)})}})}(jQuery);
|
||||
//# sourceMappingURL=../../maps/libs/jquery.complexify.js.map
|
||||
Vendored
+3
-4
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@@ -1,2 +1,2 @@
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization"],function(a,b,c,d){"use strict";function e(a,b,c){return _.clone(f).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var f=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("History Actions"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),confirm:d("Really delete the current history?"),href:"history/delete_current"},{html:d("Delete Permanently"),confirm:d("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:!0,anon:!0},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy.currHistoryPanel.unhideHidden()}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy.currHistoryPanel.deleteHidden()}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}],g=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,f=c.purgeAllowed||!1,g=e(d,f,Galaxy.root);return new a(b,g)};return g});
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization"],function(a,b,c,d){"use strict";function e(a,b,c){return _.clone(f).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var f=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("History Actions"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy.currHistoryPanel.unhideHidden()}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy.currHistoryPanel.deleteHidden()}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}],g=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,f=c.purgeAllowed||!1,g=e(d,f,Galaxy.root);return new a(b,g)};return g});
|
||||
//# sourceMappingURL=../../../maps/mvc/history/options-menu.js.map
|
||||
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@@ -16,6 +16,18 @@
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script>
|
||||
$(function() {
|
||||
$("[name='password']").complexify({'minimumChars':6}, function(valid, complexity){
|
||||
var progressBar = $('.progress-bar');
|
||||
var color = valid ? 'lightgreen' : 'red';
|
||||
|
||||
progressBar.css('background-color', color);
|
||||
progressBar.css({'width': complexity + '%'});
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
<div class="toolForm">
|
||||
<form name="change_password" id="change_password" action="${h.url_for( controller='user', action='change_password' )}" method="post" >
|
||||
<input type="hidden" name="display_top" value="${display_top}"/>
|
||||
@@ -32,6 +44,11 @@
|
||||
<label>New password:</label>
|
||||
<input type="password" name="password" value="" size="40"/>
|
||||
</div>
|
||||
<div class="progress">
|
||||
<div id="complexity-bar" class="progress-bar" role="progressbar">
|
||||
Strength
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Confirm:</label>
|
||||
<input type="password" name="confirm" value="" size="40"/>
|
||||
|
||||
@@ -86,7 +86,15 @@ def inherit(context):
|
||||
$(".errormessage").html(message);
|
||||
}
|
||||
|
||||
$('#registration').bind('submit', function(e) {
|
||||
$("[name='password']").complexify({'minimumChars':6}, function(valid, complexity){
|
||||
var progressBar = $('.progress-bar');
|
||||
var color = valid ? 'lightgreen' : 'red';
|
||||
|
||||
progressBar.css('background-color', color);
|
||||
progressBar.css({'width': complexity + '%'});
|
||||
});
|
||||
|
||||
$('#registration').bind('submit', function(e) {
|
||||
$('#send').attr('disabled', 'disabled');
|
||||
|
||||
// we need this value to detect submitting at backend
|
||||
@@ -130,6 +138,11 @@ def inherit(context):
|
||||
<label>Password:</label>
|
||||
<input id="password_input" type="password" name="password" value="" size="40"/>
|
||||
</div>
|
||||
<div class="progress">
|
||||
<div id="complexity-bar" class="progress-bar" role="progressbar">
|
||||
Strength
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Confirm password:</label>
|
||||
<input id="password_check_input" type="password" name="confirm" value="" size="40"/>
|
||||
|
||||
@@ -3,7 +3,8 @@ import os.path
|
||||
from stat import S_IXUSR
|
||||
from os import makedirs, stat, symlink, chmod, environ
|
||||
from shutil import rmtree
|
||||
from galaxy.tools.deps import DependencyManager, INDETERMINATE_DEPENDENCY
|
||||
from galaxy.tools.deps import DependencyManager
|
||||
from galaxy.tools.deps.resolvers import NullDependency
|
||||
from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency
|
||||
from galaxy.tools.deps.resolvers.modules import ModuleDependencyResolver, ModuleDependency
|
||||
from galaxy.util.bunch import Bunch
|
||||
@@ -141,7 +142,7 @@ advisor/2013/update3 intel/12.0 mkl/10.2.7.041
|
||||
assert module.module_version == "3.0.1"
|
||||
|
||||
module = resolver.resolve( name="R", version="3.0.4", type="package" )
|
||||
assert module == INDETERMINATE_DEPENDENCY
|
||||
assert isinstance(module, NullDependency)
|
||||
|
||||
|
||||
def test_module_dependency():
|
||||
|
||||
@@ -35,21 +35,21 @@ deps =
|
||||
# include list is reduced to just the inverse of Galaxy's linting
|
||||
# blacklist these can both just be removed and flake8-import-order can
|
||||
# be added as a dependency to Galaxy's main linting task.
|
||||
[testenv:py27-lint-imports]
|
||||
[testenv:py27-lint-imports]
|
||||
commands = bash .ci/flake8_wrapper.sh
|
||||
whitelist_externals = bash
|
||||
skip_install = True
|
||||
deps =
|
||||
flake8<3
|
||||
flake8-import-order
|
||||
flake8
|
||||
flake8-import-order>=0.9
|
||||
|
||||
[testenv:py27-lint-imports-include-list]
|
||||
commands = bash .ci/flake8_wrapper_imports.sh
|
||||
whitelist_externals = bash
|
||||
skip_install = True
|
||||
deps =
|
||||
flake8<3
|
||||
flake8-import-order
|
||||
flake8
|
||||
flake8-import-order>=0.9
|
||||
|
||||
[testenv:qunit]
|
||||
commands = bash run_tests.sh -q
|
||||
|
||||
Reference in New Issue
Block a user