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add(FOHM and GSAID to upload API) #4028

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merged 4 commits into from
Dec 17, 2024
Merged

add(FOHM and GSAID to upload API) #4028

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99a3f47
add fohm and gsaid to mutant uploadAPI
ChrOertlin Dec 16, 2024
948a880
add general exception handling and error raise
ChrOertlin Dec 17, 2024
efcd012
remove try except
ChrOertlin Dec 17, 2024
5b7492a
remove logger
ChrOertlin Dec 17, 2024
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10 changes: 7 additions & 3 deletions cg/meta/upload/fohm/fohm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -368,9 +368,13 @@ def parse_and_write_pangolin_report(self) -> list[FohmPangolinReport]:
self.create_pangolin_report(sars_cov_pangolin_reports)
return sars_cov_pangolin_reports

def aggregate_delivery(self, cases: list[str]) -> None:
"""Aggregate and hardlink reports."""
self.set_cases_to_aggregate(cases)
def aggregate_delivery(self, case_ids: list[str]) -> None:
"""
Aggregate and hardlink reports.
args:
case_ids: The internal ids for cases to aggregate.
"""
self.set_cases_to_aggregate(case_ids)
self.create_daily_delivery_folders()
sars_cov_complementary_reports: list[FohmComplementaryReport] = (
self.parse_and_write_complementary_report()
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8 changes: 8 additions & 0 deletions cg/meta/upload/mutant/mutant.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
from click import Context

from cg.meta.upload.fohm.fohm import FOHMUploadAPI
from cg.meta.upload.gisaid import GisaidAPI
from cg.meta.upload.upload_api import UploadAPI
from cg.meta.workflow.mutant import MutantAnalysisAPI
from cg.models.cg_config import CGConfig
Expand All @@ -10,10 +12,16 @@ class MutantUploadAPI(UploadAPI):

def __init__(self, config: CGConfig):
self.analysis_api: MutantAnalysisAPI = MutantAnalysisAPI(config)
self.fohm_api = FOHMUploadAPI(config)
self.gsaid_api = GisaidAPI(config)

super().__init__(config=config, analysis_api=self.analysis_api)

def upload(self, ctx: Context, case: Case, restart: bool) -> None:
latest_analysis: Analysis = case.analyses[0]
self.update_upload_started_at(latest_analysis)
self.upload_files_to_customer_inbox(case)
self.gsaid_api.upload(case.internal_id)
self.fohm_api.aggregate_delivery(case_ids=[case.internal_id])
self.fohm_api.sync_files_sftp()
self.update_uploaded_at(latest_analysis)
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