Animal model section backend (#145)

* First push of the animal model systems script to insert sections into the analysis for the intercenter meeting

* changed supporting-evidence values to be arrays not objects

* Updating the analysis fixtures to include a mouse model system in CPAM0002, fixed some wording in the migration script, and updated the supplemental-evidence section to be an array instead of an object

* First push for the endpoints to attach imaging and reports

* Re-structured endpoints and collection functions to adding supporting evidence to section fields, linting and tests

* yapf formatting for python

* Fixed a test for adding a link to an analysis section

* Renamed endpoints to be consistent

backend/src/repository/analysis_collection.py

@@ -7,7 +7,7 @@
 from ..models.event import Event
 from ..enums import EventType
 
-# pylint: disable=too-few-public-methods
+# pylint: disable=too-many-public-methods
 # Disabling too few public metods due to utilizing Pydantic/FastAPI BaseSettings class
 
 
@@ -374,3 +374,115 @@ def update_event(self, analysis_name: str, username: str, event_type: EventType)
         # remove the _id field from the returned document since it is not JSON serializable
         updated_document.pop("_id", None)
         return updated_document
+
+    def attach_section_supporting_evidence_file(
+        self, analysis_name: str, section_name: str, field_name: str, field_value_file: object
+    ):
+        """
+        Attaches a file to a field within an analysis section and returns only the updated field within that section
+        """
+
+        updated_document = self.collection.find_one({"name": analysis_name})
+
+        if "_id" in updated_document:
+            updated_document.pop("_id", None)
+
+        updated_section = None
+        for section in updated_document['sections']:
+            if section_name == section['header']:
+                updated_section = section
+
+        if None is updated_section:
+            raise ValueError(
+                f"'{section_name}' does not exist within '{analysis_name}'. Unable to attach report to '{section_name}'\
+                section."
+            )
+
+        updated_field = None
+        for field in updated_section['content']:
+            if field['field'] == field_name:
+                field['value'] = [field_value_file]
+                updated_field = field
+
+        self.collection.find_one_and_update(
+            {"name": analysis_name},
+            {'$set': updated_document},
+            return_document=ReturnDocument.AFTER,
+        )
+
+        return_field = {"header": section_name, "field": field_name, "updated_row": updated_field}
+
+        return return_field
+
+    def attach_section_supporting_evidence_link(
+        self, analysis_name: str, section_name: str, field_name: str, field_value_link: object
+    ):
+        """
+        Attaches a link to a section field within an analysis and returns only the updated field for that section
+        """
+        updated_document = self.collection.find_one({"name": analysis_name})
+
+        if "_id" in updated_document:
+            updated_document.pop("_id", None)
+
+        updated_section = None
+        for section in updated_document['sections']:
+            if section_name == section['header']:
+                updated_section = section
+
+        if None is updated_section:
+            raise ValueError(
+                f"'{section_name}' does not exist within '{analysis_name}'. Unable to attach report to '{section_name}'\
+                section."
+            )
+
+        new_uuid = str(uuid4())
+        field_value_link['attachment_id'] = new_uuid
+
+        updated_field = None
+        for field in updated_section['content']:
+            if field['field'] == 'Veterinary Pathology Imaging':
+                field['value'] = [field_value_link]
+                updated_field = field
+
+        self.collection.find_one_and_update(
+            {"name": analysis_name},
+            {'$set': updated_document},
+            return_document=ReturnDocument.AFTER,
+        )
+
+        return_updated_field = {"header": section_name, "field": field_name, "updated_row": updated_field}
+
+        return return_updated_field
+
+    def remove_section_supporting_evidence(self, analysis_name: str, section_name: str, field_name: str):
+        """ Removes a section field's supporting evidence """
+        updated_document = self.collection.find_one({"name": analysis_name})
+
+        if "_id" in updated_document:
+            updated_document.pop("_id", None)
+
+        updated_section = None
+        for section in updated_document['sections']:
+            if section_name == section['header']:
+                updated_section = section
+
+        if None is updated_section:
+            raise ValueError(
+                f"'{section_name}' does not exist within '{analysis_name}'. Unable to attach report to '{section_name}'\
+                section."
+            )
+
+        for field in updated_section['content']:
+            if field['field'] == field_name:
+                field['value'] = []
+
+        self.collection.find_one_and_update(
+            {"name": analysis_name},
+            {'$set': updated_document},
+            return_document=ReturnDocument.AFTER,
+        )
+
+        return_field = {"header": section_name, "field": field_name}
+
+        return return_field

backend/src/routers/analysis_router.py

@@ -124,6 +124,84 @@ def update_analysis_sections(
     return repositories["analysis"].find_by_name(analysis_name)
 
 
+@router.put("/{analysis_name}/section/attach/file")
+def attach_animal_model_system_report(
+    analysis_name: str,
+    section_name: str = Form(...),
+    field_name: str = Form(...),
+    comments: str = Form(...),
+    upload_file: UploadFile = File(...),
+    repositories=Depends(database),
+    authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
+):
+    """ Attaches a file as supporting evidence to a section in an Analysis  """
+
+    try:
+        new_file_object_id = repositories["bucket"].save_file(
+            upload_file.file, upload_file.filename, upload_file.content_type
+        )
+    except Exception as exception:
+        raise HTTPException(status_code=500, detail=str(exception)) from exception
+
+    field_value_file = {
+        "name": upload_file.filename, "attachment_id": str(new_file_object_id), "type": "file", "comments": comments
+    }
+
+    return repositories['analysis'].attach_section_supporting_evidence_file(
+        analysis_name, section_name, field_name, field_value_file
+    )
+
+
+@router.put("/{analysis_name}/section/remove/file")
+def remove_animal_model_system_report(
+    analysis_name: str,
+    section_name: str = Form(...),
+    field_name: str = Form(...),
+    attachment_id: str = Form(...),
+    repositories=Depends(database),
+    authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
+):
+    """ Removes a supporting evidence file from an analysis section """
+
+    if repositories["bucket"].id_exists(attachment_id):
+        repositories["bucket"].delete_file(attachment_id)
+
+    return repositories['analysis'].remove_section_supporting_evidence(analysis_name, section_name, field_name)
+
+
+@router.put("/{analysis_name}/section/attach/link")
+def attach_animal_model_system_imaging(
+    analysis_name: str,
+    section_name: str = Form(...),
+    field_name: str = Form(...),
+    link_name: str = Form(...),
+    link: str = Form(...),
+    comments: str = Form(...),
+    repositories=Depends(database),
+    authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
+):
+    """ Attaches a link as supporting evidence to an analysis section """
+
+    field_value_link = {"name": link_name, "data": link, "type": "link", "comments": comments}
+
+    return repositories["analysis"].attach_section_supporting_evidence_link(
+        analysis_name, section_name, field_name, field_value_link
+    )
+
+
+@router.put("/{analysis_name}/section/remove/link")
+def remove_animal_model_system_imaging(
+    analysis_name: str,
+    section_name: str = Form(...),
+    field_name: str = Form(...),
+    repositories=Depends(database),
+    authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
+):
+    """ Removes a supporting evidence link from an analysis section """
+
+    return repositories["analysis"].remove_section_supporting_evidence(analysis_name, section_name, field_name)
+
+
 @router.get("/download/{file_id}")
 def download_file_by_id(file_id: str, repositories=Depends(database)):
     """ Returns a file from GridFS using the file's id """

backend/tests/fixtures/analysis-CPAM0002.json

@@ -87,6 +87,61 @@
         }
       ]
     },
+    {
+      "header":"Mus musculus (Mouse) Model System",
+      "content":[
+         {
+            "type":"section-text",
+            "field":"Mutation",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"Pathogenicity Test",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"Design",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"Founder Screening/Expansion",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"Screening",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"History",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"Diagnoses",
+            "value":[]
+         },
+         {
+            "type":"section-text",
+            "field":"Remarks",
+            "value":[]
+         },
+         {
+            "type":"supporting-evidence",
+            "field":"Veterinary Histology Report",
+            "value":[]
+         },
+         {
+            "type":"supporting-evidence",
+            "field":"Veterinary Pathology Imaging",
+            "value":[]
+         }
+      ]
+   },
     {
       "header": "Medical Summary",
       "content": [

backend/tests/fixtures/empty-pedigree.json

@@ -87,6 +87,61 @@
                 }
             ]
         },
+        {
+            "header":"Mus musculus (Mouse) Model System",
+            "content":[
+               {
+                  "type":"section-text",
+                  "field":"Mutation",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"Pathogenicity Test",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"Design",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"Founder Screening/Expansion",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"Screening",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"History",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"Diagnoses",
+                  "value":[]
+               },
+               {
+                  "type":"section-text",
+                  "field":"Remarks",
+                  "value":[]
+               },
+               {
+                  "type":"supporting-evidence",
+                  "field":"Veterinary Histology Report",
+                  "value":[]
+               },
+               {
+                  "type":"supporting-evidence",
+                  "field":"Veterinary Pathology Imaging",
+                  "value":[]
+               }
+            ]
+         },
         {
             "header": "Medical Summary",
             "content": [

backend/tests/unit/repository/test_analysis_collection.py

@@ -323,6 +323,63 @@ def test_mark_ready_analysis_does_not_exist(analysis_collection):
         assert str(error) == "Analysis with name CPAM2222 does not exist."
 
 
+def test_attach_section_supporting_evidence_file(analysis_collection):
+    """ Tests adding a file as supporting evidence to an analysis section field"""
+    analysis_collection.collection.find_one.return_value = read_test_fixture("analysis-CPAM0002.json")
+
+    expected = {
+        "header": "Mus musculus (Mouse) Model System", "field": "Veterinary Histology Report", "updated_row": {
+            'type': 'supporting-evidence', 'field': 'Veterinary Histology Report', 'value': [{
+                'name': 'fake-cpam0002-histology-report.pdf', 'attachment_id': 'fake-file-report-id', 'type': 'file',
+                'comments': 'These are comments'
+            }]
+        }
+    }
+
+    field_value_file = {
+        "name": "fake-cpam0002-histology-report.pdf", "attachment_id": "fake-file-report-id", "type": "file",
+        "comments": "These are comments"
+    }
+
+    actual = analysis_collection.attach_section_supporting_evidence_file(
+        "CPAM0002", "Mus musculus (Mouse) Model System", "Veterinary Histology Report", field_value_file
+    )
+
+    assert expected == actual
+
+
+def test_attach_section_supporting_evidence_link(analysis_collection):
+    """ Tests adding a link as supporting evidence to an analysis section field """
+    analysis_collection.collection.find_one.return_value = read_test_fixture("analysis-CPAM0002.json")
+
+    field_value_link = {
+        "name": "Google Link", "data": "https://www.google.com", "type": "link", "comments": "nothing to do with google"
+    }
+
+    actual = analysis_collection.attach_section_supporting_evidence_link(
+        "CPAM0002", "Mus musculus (Mouse) Model System", "Veterinary Pathology Imaging", field_value_link
+    )
+
+    new_evidence = next((evidence for evidence in actual['updated_row']['value'] if evidence['name'] == "Google Link"),
+                        None)
+    assert new_evidence['type'] == 'link'
+    assert 'attachment_id' in new_evidence
+    assert new_evidence['data'] == 'https://www.google.com'
+
+
+def test_remove_section_supporting_evidence(analysis_collection):
+    """ Tests removing supporting evidence from an analysis section field """
+    analysis_collection.collection.find_one.return_value = read_test_fixture("analysis-CPAM0002.json")
+
+    expected = {"header": "Mus musculus (Mouse) Model System", "field": "Veterinary Histology Report"}
+
+    actual = analysis_collection.remove_section_supporting_evidence(
+        "CPAM0002", "Mus musculus (Mouse) Model System", "Veterinary Histology Report"
+    )
+
+    assert expected == actual
+
+
 @pytest.fixture(name="analysis_with_no_p_dot")
 def fixture_analysis_with_no_p_dot():
     """Returns an analysis with no p. in the genomic unit"""