Script to add site

README.md

@@ -316,3 +316,13 @@ python scripts/toggle_queue.py close
 # This will give submit permissions for the NLP sandbox users
 python scripts/toggle_queue.py open
 ```
+
+### Add centers/datasets
+
+When we add centers and their datasets, use this [code](scripts/add_center.py). The steps are:
+
+1. Create center Synapse service account?
+1. Create internal queues
+1. Add to configuration table
+1. Make sure orchestrator configured to accept submissions from internal queues {"queue_id": "syn25582656"...}
+1. Add to submission view

scripts/add_center.py

@@ -0,0 +1,81 @@
+"""Adds a center's dataset
+
+1. Create center bot?
+2. Create internal queues
+3. Add to configuration table
+4. Make sure orchestrator configured to accept submissions from
+internal queues {"queue_id": "syn25582656"...}
+5. Add to submission view
+"""
+import argparse
+
+import challengeutils
+import pandas as pd
+import synapseclient
+
+
+# List of annotator types
+ANNOTATORS = ["Id", "Date", "Covid Symptom", "Contact", "Person Name", "Location"]
+
+
+def create_evaluation_queues(syn, center, annotator_types):
+    queue_mapping = {}
+    for annotator_type in annotator_types:
+        queue_name = f"{center} - {annotator_type} Annotator"
+        queue_ent = synapseclient.Evaluation(
+            name=queue_name,
+            contentSource="syn22277123"
+        )
+        queue_ent = syn.store(queue_ent)
+        challengeutils.permissions.set_evaluation_permissions(
+            syn=syn,
+            evaluation=queue_ent,
+            principalid=3413389,
+            permission_level="admin"
+        )
+        queue_mapping[queue_name] = queue_ent.id
+    return queue_mapping
+
+
+def main():
+    # Build cli
+    parser = argparse.ArgumentParser(description='Add center')
+    parser.add_argument('center', type=str, help="Center to add")
+    args = parser.parse_args()
+
+    center = args.center
+    syn = synapseclient.login()
+
+    # Create evaluation queues for internal queue
+    queue_mapping = create_evaluation_queues(
+        syn=syn,
+        center=center,
+        annotator_types=ANNOTATORS
+    )
+
+    # Create submission view
+    view_columns = list(syn.getTableColumns("syn25582644"))
+    submission_view_ent = synapseclient.SubmissionViewSchema(
+        name=center,
+        parent="syn22277124",
+        scopes=list(queue_mapping.values()),
+        columns=view_columns,
+        addAnnotationColumns=False,
+        addDefaultViewColumns=False
+    )
+    submission_view_ent = syn.store(submission_view_ent)
+
+    # Update queue config
+    queue_config_syn_id = "syn25952454"
+    queue_config = {
+        "queue_name": list(queue_mapping.keys()),
+        "queue_id": list(queue_mapping.values()),
+        "center": [center]*len(queue_mapping),
+        "submission_viewid": [submission_view_ent.id]* len(queue_mapping)
+    }
+    queue_config_df = pd.DataFrame(queue_config)
+    syn.store(synapseclient.Table(queue_config_syn_id, queue_config_df))
+
+
+if __name__ == "__main__":
+    main()