Metamist¶
Helpers to communicate with the metamist
database.
cpg_flow.metamist.get_metamist
¶
get_metamist()
Return the cohort object
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.Metamist
¶
Metamist()
Communication with metamist.
Source code in src/cpg_flow/metamist.py
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make_retry_aapi_call
¶
make_retry_aapi_call(api_func, **kwargv)
Make a generic API call to self.aapi with retries. Retry only if ServiceException is thrown
TODO: How many retries? e.g. try 3 times, wait 2^3: 8, 16, 24 seconds
Source code in src/cpg_flow/metamist.py
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make_aapi_call
¶
make_aapi_call(api_func, **kwargv)
Make a generic API call to self.aapi. This is a wrapper around retry of API call to handle exceptions and logger.
Source code in src/cpg_flow/metamist.py
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get_sg_entries
¶
get_sg_entries(dataset_name)
Retrieve sequencing group entries for a dataset, in the context of access level and filtering options.
Source code in src/cpg_flow/metamist.py
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update_analysis
¶
update_analysis(analysis, status)
Update "status" of an Analysis entry.
Source code in src/cpg_flow/metamist.py
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get_analyses_by_sgid
¶
get_analyses_by_sgid(
analysis_type, analysis_status=COMPLETED, dataset=None
)
Query the DB to find the last completed analysis for the type, sequencing group ids, and sequencing type, one Analysis object per sequencing group. Assumes the analysis is defined for a single sequencing group (that is, analysis_type=cram|gvcf|qc).
Source code in src/cpg_flow/metamist.py
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create_analysis
¶
create_analysis(
output,
type_,
status,
cohort_ids=None,
sequencing_group_ids=None,
dataset=None,
meta=None,
)
Tries to create an Analysis entry, returns its id if successful.
Source code in src/cpg_flow/metamist.py
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get_ped_entries
¶
get_ped_entries(dataset=None)
Retrieve PED lines for a specified SM project, with external participant IDs.
Source code in src/cpg_flow/metamist.py
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get_metamist_proj
¶
get_metamist_proj(dataset=None)
Return the Metamist project name, appending '-test' if the access level is 'test'.
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.AnalysisStatus
¶
Bases: Enum
Corresponds to metamist Analysis statuses: https://github.com/populationgenomics/sample-metadata/blob/dev/models/enums/analysis.py#L14-L21
parse
staticmethod
¶
parse(name)
Parse str and create a AnalysisStatus object
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.AnalysisType
¶
Bases: Enum
Corresponds to metamist Analysis types: https://github.com/populationgenomics/sample-metadata/blob/dev/models/enums /analysis.py#L4-L11
Re-defined in a separate module to decouple from the main metamist module,
so decorators can use @stage(analysis_type=AnalysisType.QC)
without importing
the metamist package.
parse
staticmethod
¶
parse(val)
Parse str and create a AnalysisStatus object
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.Analysis
dataclass
¶
Analysis(
id, type, status, sequencing_group_ids, output, meta
)
Metamist DB Analysis entry.
See the metamist package for more details: https://github.com/populationgenomics/sample-metadata
parse
staticmethod
¶
parse(data)
Parse data to create an Analysis object.
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.Assay
dataclass
¶
Assay(
id,
sequencing_group_id,
meta,
assay_type,
alignment_input=None,
)
Metamist "Assay" entry.
See metamist for more details: https://github.com/populationgenomics/sample-metadata
parse
staticmethod
¶
parse(
data, sg_id, check_existence=False, run_parse_reads=True
)
Create from a dictionary.
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.get_cohort_sgs
¶
get_cohort_sgs(cohort_id)
Retrieve sequencing group entries for a single cohort.
Source code in src/cpg_flow/metamist.py
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cpg_flow.metamist.parse_reads
¶
parse_reads(
sequencing_group_id, assay_meta, check_existence
)
Parse a AlignmentInput object from the meta dictionary.
check_existence
: check if fastq/crams exist on buckets.
Default value is pulled from self.metamist and can be overridden.
Source code in src/cpg_flow/metamist.py
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