dxpy 0.366.0__tar.gz → 0.368.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {dxpy-0.366.0 → dxpy-0.368.1}/PKG-INFO +3 -3
- {dxpy-0.366.0 → dxpy-0.368.1}/Readme.md +1 -1
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/dataset.py +3 -2
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/vizclient.py +1 -1
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/dataset_utilities.py +2 -2
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/filter_to_payload.py +9 -0
- dxpy-0.368.1/dxpy/nextflow/nextaur_assets.json +8 -0
- dxpy-0.368.1/dxpy/nextflow/nextaur_assets.staging.json +8 -0
- dxpy-0.368.1/dxpy/nextflow/nextflow_assets.json +8 -0
- dxpy-0.368.1/dxpy/nextflow/nextflow_assets.staging.json +8 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/nextflow/src/nextflow.sh +1 -1
- dxpy-0.368.1/dxpy/toolkit_version.py +1 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy.egg-info/PKG-INFO +3 -3
- dxpy-0.368.1/dxpy.egg-info/requires.txt +23 -0
- dxpy-0.368.1/requirements.txt +9 -0
- dxpy-0.368.1/requirements_setuptools.txt +3 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/setup.py +2 -2
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_extract_expression.py +5 -2
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_nextflow.py +1 -1
- dxpy-0.366.0/dxpy/nextflow/nextaur_assets.json +0 -8
- dxpy-0.366.0/dxpy/nextflow/nextaur_assets.staging.json +0 -8
- dxpy-0.366.0/dxpy/nextflow/nextflow_assets.json +0 -8
- dxpy-0.366.0/dxpy/nextflow/nextflow_assets.staging.json +0 -8
- dxpy-0.366.0/dxpy/toolkit_version.py +0 -1
- dxpy-0.366.0/dxpy.egg-info/requires.txt +0 -33
- dxpy-0.366.0/requirements.txt +0 -10
- dxpy-0.366.0/requirements_setuptools.txt +0 -3
- {dxpy-0.366.0 → dxpy-0.368.1}/MANIFEST.in +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/api.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/app_builder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/app_categories.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/asset_builder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/cmd_line_options_validator.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/data_transformations.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/json_validation_by_schema.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/schemas/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/schemas/assay_filtering_conditions.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/schemas/assay_filtering_json_schemas.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/schemas/input_arguments_validation_schemas.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/vizserver_filters_from_json_parser.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/apollo/vizserver_payload_builder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/auth.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/download_all_inputs.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxanalysis.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxapp.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxapp_container_functions.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxapplet.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxdatabase.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxdatabase_functions.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxdataobject_functions.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxfile.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxfile_functions.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxglobalworkflow.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxjob.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxproject.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxrecord.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/dxworkflow.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/mount_all_inputs.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/bindings/search.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/cp.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/download.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/exec_io.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/help_messages.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/org.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/output_handling.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/parsers.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/cli/workflow.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/compat.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/Homo_sapiens_genes_manifest.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/Homo_sapiens_genes_manifest_staging.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/Homo_sapiens_genes_manifest_staging_vep.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/Homo_sapiens_genes_manifest_vep.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/cohort_filter_payload.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/column_conditions.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/column_conversion.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/input_validation.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/input_validation_somatic.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/retrieve_allele_schema.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/retrieve_annotation_schema.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/retrieve_bins.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/retrieve_genotype_schema.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/return_columns_allele.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/return_columns_annotation.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/return_columns_genotype.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dx_extract_utils/somatic_filter_payload.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/dxlog.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/exceptions.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/executable_builder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/ImageRef.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/ImageRefFactory.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/collect_images.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/nextflow_builder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/nextflow_templates.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/nextflow/nextflow_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/packages/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/scripts/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/scripts/dx.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/scripts/dx_app_wizard.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/scripts/dx_build_app.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/scripts/dx_build_applet.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/ssh_tunnel_app_support.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/system_requirements.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/bash.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/python.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/Readme.md +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/bash/basic/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/bash/basic/src/code.sh +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/bash/parallelized/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/bash/parallelized/src/code.sh +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/bash/scatter-process-gather/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/bash/scatter-process-gather/src/code.sh +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/nextflow/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/basic/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/basic/src/code.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/basic/test/test.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/parallelized/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/parallelized/src/code.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/parallelized/test/test.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/scatter-process-gather/dxapp.json +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/scatter-process-gather/src/code.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/templates/python/scatter-process-gather/test/test.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/templating/utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/__init__.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/batch_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/completer.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/config.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/describe.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/exec_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/executable_unbuilder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/file_handle.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/file_load_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/genomic_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/job_log_client.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/local_exec_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/pathmatch.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/pretty_print.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/printing.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/resolver.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/utils/spelling_corrector.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy/workflow_builder.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy.egg-info/SOURCES.txt +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy.egg-info/dependency_links.txt +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy.egg-info/entry_points.txt +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy.egg-info/not-zip-safe +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/dxpy.egg-info/top_level.txt +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/requirements_test.txt +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-clone-asset +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-docker +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-download-all-inputs +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-fetch-bundled-depends +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-generate-dxapp +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-jobutil-add-output +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-jobutil-dxlink +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-jobutil-new-job +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-jobutil-parse-link +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-jobutil-report-error +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-log-stream +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-mount-all-inputs +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-notebook-reconnect +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-print-bash-vars +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/scripts/dx-upload-all-outputs +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/setup.cfg +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_batch.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_create_cohort.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_describe.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dx-docker.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dx_app_wizard.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dx_bash_helpers.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dx_completion.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dx_symlink.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dxabs.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dxasset.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dxclient.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dxpy.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dxpy_utils.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_dxunpack.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_extract_assay.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_extract_dataset.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_extract_somatic.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_nextflow_ImageRef.py +0 -0
- {dxpy-0.366.0 → dxpy-0.368.1}/test/test_nextflow_ImageRefFactory.py +0 -0
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Name: dxpy
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Summary: DNAnexus Platform API bindings for Python
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Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung
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else:
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err_message = response["error"]
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self.error_handler(str(err_message))
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return response
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return response
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@@ -1221,7 +1221,7 @@ def extract_assay_expression(args):
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)
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)
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if len(dataset.assays_info_dict
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if dataset.assays_info_dict.get("molecular_expression") is None or len(dataset.assays_info_dict.get("molecular_expression")) == 0:
|
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{
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"aws:ap-southeast-2": "record-GbqXBp05PjXYQGxJKgPzGKYJ",
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"aws:eu-central-1": "record-GbqXFGQ4Q025p587JqJgfGkb",
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"aws:eu-west-2-g": "record-GbqXJ0pK2X1pz87z51Q64QGX",
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"aws:us-east-1": "record-GbqX1Qj096VFgVYG0X1Jv4Bb",
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|
+
"azure:westeurope": "record-GbqXQGjBkq53bzV9jFb28369",
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|
+
"azure:westus": "record-GbqXY1Q99731Zxq2xQ7GxBzX"
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|
+
}
|
|
@@ -0,0 +1,8 @@
|
|
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1
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+
{
|
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+
"aws:ap-southeast-2": "record-GbqVG3j5476zQ4p994GJ2JGv",
|
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|
+
"aws:eu-central-1": "record-GbqVK484xqZkJj5v8X8QgP5Q",
|
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4
|
+
"aws:eu-west-2-g": "record-GbqVPQ2KJv5G7gpgykYxJBkp",
|
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5
|
+
"aws:us-east-1": "record-GbqV9Pj0YQg98FJq0VqjF2pZ",
|
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6
|
+
"azure:westeurope": "record-GbqVX3QBf5g471k20pKZkpYz",
|
|
7
|
+
"azure:westus": "record-GbqVZyj9vvk606j2PjfP0pBx"
|
|
8
|
+
}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
{
|
|
2
|
+
"aws:ap-southeast-2": "record-GbqXZx85YkJYkXbJGx2712B0",
|
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3
|
+
"aws:eu-central-1": "record-GbqXbKQ4f06Fb6yFVJ2jf91z",
|
|
4
|
+
"aws:eu-west-2-g": "record-GbqXffpKbPkPGyqxBKj4bkGP",
|
|
5
|
+
"aws:us-east-1": "record-GbqX3YQ0zF96QY6XkKgGj6zJ",
|
|
6
|
+
"azure:westeurope": "record-GbqXq50By9ZZF5JpzzvZVX3F",
|
|
7
|
+
"azure:westus": "record-GbqXy9Q91ggZQg52Z4Ffk84q"
|
|
8
|
+
}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
{
|
|
2
|
+
"aws:ap-southeast-2": "record-GbqVfV85P3j22G98Qk3Pbp54",
|
|
3
|
+
"aws:eu-central-1": "record-GbqVj684y262YXY4gkXP12YK",
|
|
4
|
+
"aws:eu-west-2-g": "record-GbqVkkpKqzF471k20pKZkpZJ",
|
|
5
|
+
"aws:us-east-1": "record-GbqVBJ80g9g6vzxj51xYzYj6",
|
|
6
|
+
"azure:westeurope": "record-GbqVv98B1PXF5g7GGYVqfFjx",
|
|
7
|
+
"azure:westus": "record-GbqVz1Q9K7yp85ZVKQVbVgz7"
|
|
8
|
+
}
|
|
@@ -293,7 +293,7 @@ main() {
|
|
|
293
293
|
|
|
294
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|
# If cache is used, it will be stored in the project at
|
|
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295
|
DX_CACHEDIR=$DX_PROJECT_CONTEXT_ID:/.nextflow_cache_db
|
|
296
|
-
NXF_PLUGINS_VERSION=1.
|
|
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|
+
NXF_PLUGINS_VERSION=1.7.0
|
|
297
297
|
|
|
298
298
|
# unset properties
|
|
299
299
|
cloned_job_properties=$(dx describe "$DX_JOB_ID" --json | jq -r '.properties | to_entries[] | select(.key | startswith("nextflow")) | .key')
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
version = '0.368.1'
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.1
|
|
2
2
|
Name: dxpy
|
|
3
|
-
Version: 0.
|
|
3
|
+
Version: 0.368.1
|
|
4
4
|
Summary: DNAnexus Platform API bindings for Python
|
|
5
5
|
Home-page: https://github.com/dnanexus/dx-toolkit
|
|
6
6
|
Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung
|
|
@@ -14,7 +14,7 @@ Classifier: Operating System :: POSIX
|
|
|
14
14
|
Classifier: Programming Language :: Python
|
|
15
15
|
Classifier: Programming Language :: Unix Shell
|
|
16
16
|
Classifier: Topic :: Software Development :: Libraries :: Python Modules
|
|
17
|
-
Requires-Python: >=3.
|
|
17
|
+
Requires-Python: >=3.8
|
|
18
18
|
Description-Content-Type: text/markdown
|
|
19
19
|
Provides-Extra: pandas
|
|
20
20
|
Provides-Extra: xattr
|
|
@@ -77,7 +77,7 @@ Other useful resources:
|
|
|
77
77
|
|
|
78
78
|
Python version compatibility
|
|
79
79
|
----------------------------
|
|
80
|
-
dxpy is supported on Python 3 (3.
|
|
80
|
+
dxpy is supported on Python 3 (3.8+)
|
|
81
81
|
|
|
82
82
|
Convention for Python scripts that are also modules
|
|
83
83
|
---------------------------------------------------
|
|
@@ -0,0 +1,23 @@
|
|
|
1
|
+
websocket-client==0.54.0
|
|
2
|
+
python-dateutil>=2.5
|
|
3
|
+
psutil>=5.9.3
|
|
4
|
+
certifi
|
|
5
|
+
urllib3<2.2,>=1.25
|
|
6
|
+
|
|
7
|
+
[:python_version < "3.10"]
|
|
8
|
+
argcomplete<2.0.0,>=1.9.4
|
|
9
|
+
|
|
10
|
+
[:python_version >= "3.10"]
|
|
11
|
+
argcomplete>=2.0.0
|
|
12
|
+
|
|
13
|
+
[:sys_platform == "win32"]
|
|
14
|
+
pyreadline3==3.4.1
|
|
15
|
+
colorama<=0.4.6,>=0.4.4
|
|
16
|
+
|
|
17
|
+
[pandas]
|
|
18
|
+
pandas==1.3.5
|
|
19
|
+
|
|
20
|
+
[xattr]
|
|
21
|
+
|
|
22
|
+
[xattr:sys_platform == "linux2" or sys_platform == "linux"]
|
|
23
|
+
xattr==0.10.1
|
|
@@ -0,0 +1,9 @@
|
|
|
1
|
+
argcomplete>=2.0.0; python_version >= "3.10"
|
|
2
|
+
argcomplete>=1.9.4,<2.0.0; python_version < "3.10"
|
|
3
|
+
websocket-client==0.54.0
|
|
4
|
+
python-dateutil>=2.5
|
|
5
|
+
psutil>=5.9.3
|
|
6
|
+
certifi
|
|
7
|
+
urllib3>=1.25,<2.2
|
|
8
|
+
pyreadline3==3.4.1; sys_platform == "win32"
|
|
9
|
+
colorama>=0.4.4,<=0.4.6; sys_platform == "win32"
|
|
@@ -97,10 +97,10 @@ setup(
|
|
|
97
97
|
entry_points = {
|
|
98
98
|
"console_scripts": scripts,
|
|
99
99
|
},
|
|
100
|
-
python_requires = '>=3.
|
|
100
|
+
python_requires = '>=3.8',
|
|
101
101
|
install_requires = dependencies,
|
|
102
102
|
extras_require={
|
|
103
|
-
'pandas': ["pandas==1.3.5
|
|
103
|
+
'pandas': ["pandas==1.3.5"],
|
|
104
104
|
'xattr': ["xattr==0.10.1; sys_platform == 'linux2' or sys_platform == 'linux'"]
|
|
105
105
|
},
|
|
106
106
|
tests_require = test_dependencies,
|
|
@@ -1131,7 +1131,10 @@ class TestDXExtractExpression(unittest.TestCase):
|
|
|
1131
1131
|
return process
|
|
1132
1132
|
|
|
1133
1133
|
def test_dx_extract_cmd_location_expression_sample_sql(self):
|
|
1134
|
-
expected_sql_query = [
|
|
1134
|
+
expected_sql_query = [
|
|
1135
|
+
"SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` <= 8693350 AND `expr_annotation_1`.`end` >= 67440200) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` <= 148500700 AND `expr_annotation_1`.`end` >= 148994424) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` <= 75228160 AND `expr_annotation_1`.`end` >= 75235759)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
|
|
1136
|
+
"SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
|
|
1137
|
+
]
|
|
1135
1138
|
response = self.run_dx_extract_assay_expression_cmd(
|
|
1136
1139
|
self.expression_dataset,
|
|
1137
1140
|
EXPRESSION_CLI_JSON_FILTERS["positive_test"]["location_expression_sample"],
|
|
@@ -1187,7 +1190,7 @@ class TestDXExtractExpression(unittest.TestCase):
|
|
|
1187
1190
|
self.assertEqual(len(expected_X_chrom_response), 5)
|
|
1188
1191
|
|
|
1189
1192
|
def test_dx_extract_cmd_sample_ids_with_additional_fields(self):
|
|
1190
|
-
expected_sql_query = "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start`, `expr_annotation_1`.`end` AS `end`, `expr_annotation_1`.`strand` AS `strand` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE `expression_1`.`sample_id` IN ('sample_1')"
|
|
1193
|
+
expected_sql_query = "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start`, `expr_annotation_1`.`end` AS `end`, `expr_annotation_1`.`strand` AS `strand` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE `expression_1`.`sample_id` IN ('sample_1') ORDER BY `feature_id` ASC, `sample_id` ASC"
|
|
1191
1194
|
response = self.run_dx_extract_assay_expression_cmd(
|
|
1192
1195
|
self.expression_dataset,
|
|
1193
1196
|
EXPRESSION_CLI_JSON_FILTERS["positive_test"][
|
|
@@ -99,7 +99,7 @@ class TestNextflowTemplates(DXTestCase):
|
|
|
99
99
|
|
|
100
100
|
def test_dxapp(self):
|
|
101
101
|
dxapp = get_nextflow_dxapp()
|
|
102
|
-
self.assertEqual(dxapp.get("name"), "
|
|
102
|
+
self.assertEqual(dxapp.get("name"), "python") # name is by default set to the resources directory name
|
|
103
103
|
self.assertEqual(dxapp.get("details", {}).get("repository"), "local")
|
|
104
104
|
|
|
105
105
|
@parameterized.expand([
|
|
@@ -1,8 +0,0 @@
|
|
|
1
|
-
{
|
|
2
|
-
"aws:ap-southeast-2": "record-Gb0gXQj50g6b1j928pJQ8QBj",
|
|
3
|
-
"aws:eu-central-1": "record-Gb0gQV84yZp6pzGp4JQJ53VV",
|
|
4
|
-
"aws:eu-west-2-g": "record-Gb0gZ2pK9vy1j8jk8J09qVKx",
|
|
5
|
-
"aws:us-east-1": "record-Gb0gZPj0gX4JK701KpfbBYGV",
|
|
6
|
-
"azure:westeurope": "record-Gb0gg0QBFvBx4x04gx76Xx4P",
|
|
7
|
-
"azure:westus": "record-Gb0gkx09Bb08qq5vkF1ZvJX4"
|
|
8
|
-
}
|
|
@@ -1,8 +0,0 @@
|
|
|
1
|
-
{
|
|
2
|
-
"aws:ap-southeast-2": "record-Gb53JYj5Gxk7z6xggK6qxq1K",
|
|
3
|
-
"aws:eu-central-1": "record-Gb53PJj4Q67q34JzbxK3G51g",
|
|
4
|
-
"aws:eu-west-2-g": "record-Gb53Qx2KjP0JVbQ0xVZxZYq2",
|
|
5
|
-
"aws:us-east-1": "record-Gb53Fk00VYYyFBpQjxy65jYY",
|
|
6
|
-
"azure:westeurope": "record-Gb53YF0B54bb886BZj9jv16v",
|
|
7
|
-
"azure:westus": "record-Gb53bkj9Yk85kQjfJZJKJPQ6"
|
|
8
|
-
}
|
|
@@ -1,8 +0,0 @@
|
|
|
1
|
-
{
|
|
2
|
-
"aws:ap-southeast-2": "record-GQ49JfQ5Ykz2X9X17FJ05234",
|
|
3
|
-
"aws:eu-central-1": "record-GQ49KjQ40Yp7kPpzGQXZP3Jj",
|
|
4
|
-
"aws:eu-west-2-g": "record-GQ49Q52KgBvXX9X17FJ0528Y",
|
|
5
|
-
"aws:us-east-1": "record-GQ49F900GQP33QJxYYX4YY5G",
|
|
6
|
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