Merge pull request #124 from ssi-dk/feat/116101-always-send-resfinder…

…version-to-lims feat: always add resfinder_version to lims approvals
ssi-dk · Dec 5, 2024 · 1c18b58 · 1c18b58
2 parents 1b3551e + 1685c1a
commit 1c18b58
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Showing 11 changed files with 106 additions and 5 deletions.
diff --git a/app/src/app/analysis/judgement/judgement.tsx b/app/src/app/analysis/judgement/judgement.tsx
@@ -150,10 +150,15 @@ export const Judgement = <T extends NotEmpty>(props: Props<T>) => {
       setError(true);
     } else {
       const matrix = {};
+      const required_values = {};
       Object.keys(selection).forEach((key) => {
         matrix[key] = selection[key].cells;
+        required_values[key] = {}
+        required_values[key]["resfinder_version"] =
+          selection[key].original.resfinder_version ?? "";
       });
-      doApproval({ matrix });
+
+      doApproval({ matrix, required_values });
     }
   }, [selection, doApproval, setNeedsApproveNotify, getDependentColumns]);
 

diff --git a/app/src/sap-client/models/ApprovalRequest.ts b/app/src/sap-client/models/ApprovalRequest.ts
@@ -30,11 +30,18 @@ export interface ApprovalRequest  {
      * @memberof ApprovalRequest
      */
     matrix: { [key: string]: { [key: string]: ApprovalStatus; }; };
+    /**
+     * 
+     * @type {{ [key: string]: { [key: string]: string; }; }}
+     * @memberof ApprovalRequest
+     */
+    required_values?: { [key: string]: { [key: string]: string; }; };
 }
 
 export function ApprovalRequestFromJSON(json: any): ApprovalRequest {
     return {
         'matrix': json['matrix'],
+        'required_values': !exists(json, 'required_values') ? undefined : json['required_values'],
     };
 }
 
@@ -44,6 +51,7 @@ export function ApprovalRequestToJSON(value?: ApprovalRequest): any {
     }
     return {
         'matrix': value.matrix,
+        'required_values': value.required_values,
     };
 }
 

diff --git a/bifrost/bifrost_queue_broker/brokers/request/lims_request_broker.py b/bifrost/bifrost_queue_broker/brokers/request/lims_request_broker.py
@@ -119,6 +119,9 @@ def approve_fields(self, request):
                 for k, v in fields.items()
                 if reverse_column_mapping.normal_get(k) and v
             }
+            # add edge-case columns that always should be sent
+            mapped_request["ResfinderVersion"] = fields["resfinder_version"]
+
             logging.debug(f"Reverse-mapped request: {mapped_request}")
             conn_id, lms_cfg = create_lims_conn_config()
 

diff --git a/openapi_specs/SOFI/SOFI.yaml b/openapi_specs/SOFI/SOFI.yaml
@@ -1031,6 +1031,12 @@ components:
       properties:
         matrix:
           $ref: "#/components/schemas/ApprovalMatrix"
+        required_values:
+          type: object
+          additionalProperties:
+            type: object
+            additionalProperties:
+              type: string
 
     Approval:
       allOf:

diff --git a/web/openapi_specs/SOFI/SOFI.yaml b/web/openapi_specs/SOFI/SOFI.yaml
@@ -1031,6 +1031,12 @@ components:
       properties:
         matrix:
           $ref: "#/components/schemas/ApprovalMatrix"
+        required_values:
+          type: object
+          additionalProperties:
+            type: object
+            additionalProperties:
+              type: string
 
     Approval:
       allOf:

diff --git a/web/src/SAP/generated/models/approval.py b/web/src/SAP/generated/models/approval.py
@@ -23,11 +23,13 @@ class Approval(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, matrix=None, id=None, approver=None, timestamp=None, sequence_ids=None, status=None):  # noqa: E501
+    def __init__(self, matrix=None, required_values=None, id=None, approver=None, timestamp=None, sequence_ids=None, status=None):  # noqa: E501
         """Approval - a model defined in OpenAPI
 
         :param matrix: The matrix of this Approval.  # noqa: E501
         :type matrix: Dict[str, Dict[str, ApprovalStatus]]
+        :param required_values: The required_values of this Approval.  # noqa: E501
+        :type required_values: Dict[str, Dict[str, str]]
         :param id: The id of this Approval.  # noqa: E501
         :type id: str
         :param approver: The approver of this Approval.  # noqa: E501
@@ -41,6 +43,7 @@ def __init__(self, matrix=None, id=None, approver=None, timestamp=None, sequence
         """
         self.openapi_types = {
             'matrix': Dict[str, Dict[str, ApprovalStatus]],
+            'required_values': Dict[str, Dict[str, str]],
             'id': str,
             'approver': str,
             'timestamp': datetime,
@@ -50,6 +53,7 @@ def __init__(self, matrix=None, id=None, approver=None, timestamp=None, sequence
 
         self.attribute_map = {
             'matrix': 'matrix',
+            'required_values': 'required_values',
             'id': 'id',
             'approver': 'approver',
             'timestamp': 'timestamp',
@@ -58,6 +62,7 @@ def __init__(self, matrix=None, id=None, approver=None, timestamp=None, sequence
         }
 
         self._matrix = matrix
+        self._required_values = required_values
         self._id = id
         self._approver = approver
         self._timestamp = timestamp
@@ -98,6 +103,27 @@ def matrix(self, matrix):
 
         self._matrix = matrix
 
+    @property
+    def required_values(self):
+        """Gets the required_values of this Approval.
+
+
+        :return: The required_values of this Approval.
+        :rtype: Dict[str, Dict[str, str]]
+        """
+        return self._required_values
+
+    @required_values.setter
+    def required_values(self, required_values):
+        """Sets the required_values of this Approval.
+
+
+        :param required_values: The required_values of this Approval.
+        :type required_values: Dict[str, Dict[str, str]]
+        """
+
+        self._required_values = required_values
+
     @property
     def id(self):
         """Gets the id of this Approval.

diff --git a/web/src/SAP/generated/models/approval_request.py b/web/src/SAP/generated/models/approval_request.py
@@ -19,21 +19,26 @@ class ApprovalRequest(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, matrix=None):  # noqa: E501
+    def __init__(self, matrix=None, required_values=None):  # noqa: E501
         """ApprovalRequest - a model defined in OpenAPI
 
         :param matrix: The matrix of this ApprovalRequest.  # noqa: E501
         :type matrix: Dict[str, Dict[str, ApprovalStatus]]
+        :param required_values: The required_values of this ApprovalRequest.  # noqa: E501
+        :type required_values: Dict[str, Dict[str, str]]
         """
         self.openapi_types = {
             'matrix': Dict[str, Dict[str, ApprovalStatus]],
+            'required_values': Dict[str, Dict[str, str]],
         }
 
         self.attribute_map = {
             'matrix': 'matrix',
+            'required_values': 'required_values',
         }
 
         self._matrix = matrix
+        self._required_values = required_values
 
     @classmethod
     def from_dict(cls, dikt):
@@ -68,3 +73,24 @@ def matrix(self, matrix):
             raise ValueError("Invalid value for `matrix`, must not be `None`")  # noqa: E501
 
         self._matrix = matrix
+
+    @property
+    def required_values(self):
+        """Gets the required_values of this ApprovalRequest.
+
+
+        :return: The required_values of this ApprovalRequest.
+        :rtype: Dict[str, Dict[str, str]]
+        """
+        return self._required_values
+
+    @required_values.setter
+    def required_values(self, required_values):
+        """Sets the required_values of this ApprovalRequest.
+
+
+        :param required_values: The required_values of this ApprovalRequest.
+        :type required_values: Dict[str, Dict[str, str]]
+        """
+
+        self._required_values = required_values
diff --git a/web/src/SAP/generated/openapi/openapi.yaml b/web/src/SAP/generated/openapi/openapi.yaml
@@ -1215,6 +1215,9 @@ components:
       type: object
     ApprovalRequest:
       example:
+        required_values:
+          key:
+            key: required_values
         matrix:
           key:
             key: matrix
@@ -1225,6 +1228,12 @@ components:
               $ref: '#/components/schemas/ApprovalStatus'
             type: object
           type: object
+        required_values:
+          additionalProperties:
+            additionalProperties:
+              type: string
+            type: object
+          type: object
       required:
       - matrix
       type: object

diff --git a/web/src/SAP/generated/test/test_approval_controller.py b/web/src/SAP/generated/test/test_approval_controller.py
@@ -34,6 +34,11 @@ def test_create_approval(self):
         
         """
         body = {
+  "required_values" : {
+    "key" : {
+      "key" : "required_values"
+    }
+  },
   "matrix" : {
     "key" : {
       "key" : "matrix"

diff --git a/web/src/SAP/src/controllers/ApprovalController.py b/web/src/SAP/src/controllers/ApprovalController.py
@@ -44,6 +44,7 @@ def create_approval(user, token_info, body: ApprovalRequest):
 
     appr = Approval()
     appr.matrix = body.matrix
+    appr.required_values = body.required_values
     appr.approver = user
     appr.timestamp = datetime.datetime.now()
     appr.status = "submitted"
@@ -82,6 +83,7 @@ def create_approval(user, token_info, body: ApprovalRequest):
         for f in time_fields:
             analysis_timestamp_reverts[error_seq_id] = {f: None}
         del appr.matrix[error_seq_id]
+        del appr.required_values[error_seq_id]
         errors.append(error)
 
     # If any sequences errored out on the metadata service, revert their
@@ -101,7 +103,9 @@ def create_approval(user, token_info, body: ApprovalRequest):
 def handle_approvals(approvals: Approval, institution: str):
     errors = []
     for sequence_id, field_mask in approvals.matrix.items():
-        if error := post_and_await_approval(sequence_id, field_mask, institution):
+        if sequence_id in approvals.required_values:
+            required_values = approvals.required_values[sequence_id]
+        if error := post_and_await_approval(sequence_id, field_mask, institution, required_values):
             errors.append(error)
 
     return errors

diff --git a/web/src/SAP/src/services/queue_service.py b/web/src/SAP/src/services/queue_service.py
@@ -35,7 +35,7 @@ def post_and_await_reload(isolate_id, institution):
         return {"error": f"Could not reload isolate {isolate_id} due to an error."}, 500
 
 
-def post_and_await_approval(sequence_id, field_mask, user_institution):
+def post_and_await_approval(sequence_id, field_mask, user_institution, required_values):
     data = get_analysis_with_metadata(sequence_id)
     internal_fields = internal_approval_fields()
 
@@ -51,6 +51,9 @@ def post_and_await_approval(sequence_id, field_mask, user_institution):
     # For LIMS, date_analysis_sofi should always be implicitly included
     if institution == "FVST":
         fields["date_analysis_sofi"] = data.get("date_analysis_sofi")
+
+    for field, val in required_values.items():
+        fields[field] = val  
 
     print(data, file=sys.stderr)
     # TODO UNDO