add fohm and gsaid to mutant uploadAPI

Author: ChrOertlin

cg/meta/upload/fohm/fohm.py

@@ -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()

cg/meta/upload/mutant/mutant.py

@@ -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
@@ -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)