Merge pull request #266 from EBI-Metagenomics/bugfix/missing-dependencies-and-deployments

Missing deps and deps

Author: SandyRogers

deployment/ebi-wp-k8s-hl/Taskfile.yaml

@@ -33,7 +33,7 @@ tasks:
   deploy-all:
     desc: "Deploy all flows defined in the production prefect.yaml file."
     cmds:
-      - kubectl --context=emgapiv2-hl-exp exec -it $(task get-api-pod-name) -- python manage.py prefectcli --no-prompt deploy --all --prefect-file {{.YAML}}
+      - kubectl --context=emgapiv2-hl-exp exec $(task get-api-pod-name) -- python manage.py prefectcli --no-prompt deploy --all --prefect-file {{.YAML}}
     vars:
       YAML: '{{.YAML | default "workflows/prefect_deployments/prefect-ebi-codon.yaml"}}'
 

requirements.txt

@@ -6,6 +6,7 @@ Pillow~=11.3.0  # imagefield requirement
 typing_extensions~=4.14.1
 tzdata
 pendulum
+pandas
 
 # Django and plugins
 django==5.2.7

workflows/prefect_deployments/prefect-ebi-codon.yaml

@@ -290,3 +290,15 @@ deployments:
   entrypoint: workflows.prefect_utils.datamovers:move_data
   work_pool:
     name: slurm
+
+- name: import_v5_analyses_deployment
+  description: |-
+    This flow will iteratively import analyses (made with MGnify V5 pipeline)
+    into the EMG DB.
+
+    It connects to the legacy EMG MySQL and Mongo DBs, but not through Django.
+
+    :param mgys: accession of the study to import (with its analyses)
+  entrypoint: workflows/flows/legacy/flows/import_v5_analyses.py:import_v5_analyses
+  work_pool:
+    name: slurm