feature(dev-branch-pacbio) #3453
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ChrOertlin
commented
Jul 23, 2024
ChrOertlin
commented
Jul 23, 2024
ChrOertlin
commented
Jul 23, 2024
ChrOertlin
commented
Jul 23, 2024
diitaz93
reviewed
Jul 24, 2024
# Descriptions Adds the implementation of the RunDataGenerator interface for the Pacbio post processing.
diitaz93
reviewed
Jul 24, 2024
cg/services/post_processing/pacbio/run_data_generator/run_data.py
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## Description Closes Clinical-Genomics/add-new-tech#67 Add PacBioRunFileManager, fixture and tests --------- Co-authored-by: Christian Oertlin <[email protected]>
seallard
reviewed
Jul 24, 2024
## Description Refactor PacBio metrics parser to compile with the post-processing flow ### Changed - Condensed all individual parsers into one - Refactored tests
## Description Closes Clinical-Genomics/add-new-tech#64 The read metrics we parsed came from a file containing only HiFi data. It is important to parse the failed read metrics too. There is a file containing both HiFi and failed metrics (`m84202_240522_135641_s1.ccs_report.json`). It is, however, generated by **another software** so the values are not exactly the same as the metrics parsed before. @J35P312 assured that the difference was negligible. ### Added - New parameters to parse from ccs file: - [x] <Q20 Reads - [x] <Q20 Yield (bp) - [x] <Q20 Read Length (mean, bp) ### Changed - Renamed `HiFiMetrics` model to `ReadMetrics` - The path to the ccs file ### Fixed - Removed old ccs file usage and fixture
diitaz93
reviewed
Jul 26, 2024
cg/services/post_processing/pacbio/run_file_manager/run_file_manager.py
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# Description implement housekeeper service for pacbio
# description add sample dto
Test on stage: Non-existent smrt cell should fail with correct error message$ cg -l DEBUG post-process run r84202_20241119_150802/1_A01
Running cg post-processing.
Instantiating post-processing services
Instantiating PacBio post-processing service
Instantiating status db
Instantiating housekeeper api
Initializing Store
Starting PacBio post-processing for run: r84202_20241119_150802/1_A01
File or directory /home/proj/stage/sequencing_data/pacbio/r84202_20241119_150802/1_A01 does not exist
Traceback (most recent call last):
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 16, in wrapper
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/pacbio/run_file_manager/run_file_manager.py", line 21, in get_files_to_parse
validate_files_or_directories_exist([run_path])
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/validators.py", line 25, in validate_files_or_directories_exist
raise FileNotFoundError("Some of the provided paths do not exist")
FileNotFoundError: Some of the provided paths do not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 16, in wrapper
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/pacbio/metrics_parser/metrics_parser.py", line 41, in parse_metrics
metrics_files: list[Path] = self.file_manager.get_files_to_parse(run_data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 18, in wrapper
raise to_raise(error) from error
cg.services.run_devices.exc.PostProcessingRunFileManagerError: Some of the provided paths do not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 16, in wrapper
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py", line 35, in get_post_processing_dtos
metrics: PacBioMetrics = self.metrics_service.parse_metrics(run_data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 18, in wrapper
raise to_raise(error) from error
cg.services.run_devices.exc.PostProcessingParsingError: Some of the provided paths do not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 16, in wrapper
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py", line 55, in store_post_processing_data
dtos: PacBioDTOs = self.data_transfer_service.get_post_processing_dtos(run_data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 20, in wrapper
raise CgError(f"{error}") from error
cg.exc.CgError: Some of the provided paths do not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 16, in wrapper
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/pacbio/post_processing_service.py", line 53, in post_process
self.store_service.store_post_processing_data(run_data=run_data, dry_run=dry_run)
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 20, in wrapper
raise CgError(f"{error}") from error
cg.exc.CgError: Some of the provided paths do not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/proj/stage/bin/miniconda3/envs/S_cg/bin/cg", line 8, in <module>
sys.exit(base())
^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/click/decorators.py", line 45, in new_func
return f(get_current_context().obj, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/cli/post_process/post_process.py", line 35, in post_process_sequencing_run
post_processing_service.post_process(run_name=run_name, dry_run=dry_run)
File "/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages/cg/services/run_devices/error_handler.py", line 20, in wrapper
raise CgError(f"{error}") from error
cg.exc.CgError: Some of the provided paths do not exist |
Test on stage: Dry run$ cg -l DEBUG post-process run r84202_20240319_150802/1_A01 --dry-run
Running cg post-processing.
Instantiating post-processing services
Instantiating PacBio post-processing service
Instantiating status db
Instantiating housekeeper api
Initializing Store
Starting PacBio post-processing for run: r84202_20240319_150802/1_A01
Dry run, no entries will be added to database for SMRT cell /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01.
Dry run: would have added /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/control.report.json to Housekeeper.
Dry run: would have added /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/loading.report.json to Housekeeper.
Dry run: would have added /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/raw_data.report.json to Housekeeper.
Dry run: would have added /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/smrtlink-datasets.json to Housekeeper.
Dry run: would have added /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/m84202_240319_154410_s1.ccs_report.json to Housekeeper.
Dry run: would have added /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/hifi_reads/m84202_240319_154410_s1.hifi_reads.bam to Housekeeper. |
Test on stage: post-processing a PacBio run cellCheck that post-processing finishes succesfully$ cg -l DEBUG post-process run r84202_20240319_150802/1_A01
Running cg post-processing.
Instantiating post-processing services
Instantiating PacBio post-processing service
Instantiating status db
Instantiating housekeeper api
Initializing Store
Starting PacBio post-processing for run: r84202_20240319_150802/1_A01
Fetching bundle with name: EA094816
Bundle with name EA094816 already exists
Fetching tag with name: EA094816
Fetch latest version from bundle EA094816
Found Housekeeper version object for EA094816: <housekeeper.store.models.Version object at 0x7fa351cf3450>
Bundle EA094816 already has a file with the same name as /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/control.report.json
Fetching bundle with name: EA094816
Bundle with name EA094816 already exists
Fetching tag with name: EA094816
Fetch latest version from bundle EA094816
Found Housekeeper version object for EA094816: <housekeeper.store.models.Version object at 0x7fa351d10cd0>
Bundle EA094816 already has a file with the same name as /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/loading.report.json
Fetching bundle with name: EA094816
Bundle with name EA094816 already exists
Fetching tag with name: EA094816
Fetch latest version from bundle EA094816
Found Housekeeper version object for EA094816: <housekeeper.store.models.Version object at 0x7fa351d11bd0>
Bundle EA094816 already has a file with the same name as /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/raw_data.report.json
Fetching bundle with name: EA094816
Bundle with name EA094816 already exists
Fetching tag with name: EA094816
Fetch latest version from bundle EA094816
Found Housekeeper version object for EA094816: <housekeeper.store.models.Version object at 0x7fa351d12150>
Bundle EA094816 already has a file with the same name as /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/unzipped_reports/smrtlink-datasets.json
Fetching bundle with name: EA094816
Bundle with name EA094816 already exists
Fetching tag with name: EA094816
Fetch latest version from bundle EA094816
Found Housekeeper version object for EA094816: <housekeeper.store.models.Version object at 0x7fa351d122d0>
Fetch latest version from bundle EA094816
Fetching tag with name: ccs-report
Fetching tag with name: EA094816
Fetching tag with name: ccs-report
Fetching tag with name: EA094816
Created new bundle version dir: /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14
Linked file: /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/statistics/m84202_240319_154410_s1.ccs_report.json -> /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14/m84202_240319_154410_s1.ccs_report.json
File added to Housekeeper bundle EA094816
Fetching bundle with name: 2023-41693-02
Created new bundle: 2023-41693-02
Created new version
New bundle created with name 2023-41693-02
Fetching tag with name: 2023-41693-02
Fetch latest version from bundle 2023-41693-02
Found Housekeeper version object for 2023-41693-02: <housekeeper.store.models.Version object at 0x7fa351d2ad10>
Fetch latest version from bundle 2023-41693-02
Fetching tag with name: bam
Fetching tag with name: 2023-41693-02
Fetching tag with name: bam
Fetching tag with name: 2023-41693-02
Created new bundle version dir: /home/proj/stage/housekeeper-bundles/2023-41693-02/2024-08-14
Linked file: /home/proj/stage/sequencing_data/pacbio/r84202_20240319_150802/1_A01/hifi_reads/m84202_240319_154410_s1.hifi_reads.bam -> /home/proj/stage/housekeeper-bundles/2023-41693-02/2024-08-14/m84202_240319_154410_s1.hifi_reads.bam
File added to Housekeeper bundle 2023-41693-02Check that files were added to Housekeeper in the sample bundle and in the smart cell bundle:$ housekeeper get bundle EA094816
2024-08-14 15:24:36 hasta.scilifelab.se housekeeper.cli.core[119715] INFO Use root path /home/proj/stage/housekeeper-bundles
📦 Bundle table 📦
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┃ ID ┃ Bundle name ┃ Version IDs ┃ Created ┃
┡━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
│ 190806 │ EA094816 │ 195684 │ 2024-08-14 │
└────────┴─────────────┴─────────────┴────────────┘
📕 Version table 📕
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┃ ID ┃ Bundle name ┃ Nr files ┃ Included ┃ Archived ┃ Created ┃ Expires ┃
┡━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━┩
│ 195684 │ EA094816 │ 5 │ │ │ 2024-08-14 │ │
└────────┴─────────────┴──────────┴──────────┴──────────┴────────────┴─────────┘
📜 Local files 📜
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│ 6502566 │ /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14/control.report.json │ EA094816, control-report │
│ 6502567 │ /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14/loading.report.json │ EA094816, loading-report │
│ 6502568 │ /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14/raw_data.report.json │ EA094816, raw-data-report │
│ 6502569 │ /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14/smrtlink-datasets.json │ EA094816, datasets-report │
│ 6502571 │ /home/proj/stage/housekeeper-bundles/EA094816/2024-08-14/m84202_240319_154410_s1.ccs_report.json │ EA094816, ccs-report │
└─────────┴──────────────────────────────────────────────────────────────────────────────────────────────────┴───────────────────────────┘
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└────┴───────────┴──────┘
[15:24] [hiseq.clinical@hasta:/home/proj/stage/sequencing_data/pacbio] [S_base] $ housekeeper get bundle 2023-41693-02
2024-08-14 15:25:02 hasta.scilifelab.se housekeeper.cli.core[120146] INFO Use root path /home/proj/stage/housekeeper-bundles
📦 Bundle table 📦
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┃ ID ┃ Bundle name ┃ Version IDs ┃ Created ┃
┡━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
│ 190807 │ 2023-41693-02 │ 195685 │ 2024-08-14 │
└────────┴───────────────┴─────────────┴────────────┘
📕 Version table 📕
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┃ ID ┃ Bundle name ┃ Nr files ┃ Included ┃ Archived ┃ Created ┃ Expires ┃
┡━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━┩
│ 195685 │ 2023-41693-02 │ 1 │ │ │ 2024-08-14 │ │
└────────┴───────────────┴──────────┴──────────┴──────────┴────────────┴─────────┘
📜 Local files 📜
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│ 6502572 │ /home/proj/stage/housekeeper-bundles/2023-41693-02/2024-08-14/m84202_240319_154410_s1.hifi_reads.bam │ bam, 2023-41693-02 │
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* Add cell tag to bam file * patch to fix tag accumulation
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diitaz93
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Aug 15, 2024
Vince-janv
approved these changes
Aug 15, 2024
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| device: str = get_item_by_pattern_in_source( | ||
| source=run_name, pattern_map=PATTERN_TO_DEVICE_MAP | ||
| ) |
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I'm not sure we want to use the same function for mapping files to tags as we do to map directories to post-process classes. I feel like that function might be too general. I don't think having a helper function that only applies PATTERN_TO_DEVICE_MAP is problematic
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I think we can wrap the map plus the function that returns the device.
tests/services/run_devices/pacbio/run_data_generator/test_pacbio_run_data_generator.py
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## Description Address last comments of #3453 regarding PacBio post-processing
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Description
This PR introduces a new structure for the run devices post-processing:
flowchart TD X([sequencing_dir]) --> B[Run Data Generator] A([run_name]) --> B B --> C([Run Data]) C --> D[Run File Manager] D --> E(["list[path]"]) D --> F(["list[path]"]) E --> G[Metrics Parser] G --> H([Metrics]) H --> I[Transfer Service] I --> J([DTOs]) J --> K[Store Service] F --> L[HK Service] K --> M[Post-processing Service] L --> M[Post-processing Service]Added
cg post-process run <run-name>which currently works with PacBio SMRT cells but will work for any run in the futureChanged
store_fastq_path_in_housekeeperin housekeeper modified intocreate_bundle_and_add_file_with_tagsso that it works in a more general way (not only for fastqs)How to prepare for test
uspaxaHow to test
See below
Review
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Implementation Plan
INFO [alembic.runtime.migration] Context impl MySQLImpl. INFO [alembic.runtime.migration] Will assume non-transactional DDL. fatal: Not a git repository (or any parent up to mount point /home) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). repository is clean Logging deploy ... Getting deployer... done. Getting last commit message and SHA... done. Getting version of deploy scripts... /home/js.diazboada done. Log deploy... done. cg, version 62.1.0 [js.diazboada@hasta:~] [S_base] $ up