wip for images almost there

backend/src/config.py

@@ -18,7 +18,7 @@ class Settings(BaseSettings):
     web_base_url: str = "http://dev.cgds.uab.edu/rosalution"
     mongodb_host: str = "rosalution-db"
     mongodb_db: str = "rosalution_db"
-    rosalution_key: str
+    rosalution_key: str = "FJKLDFJKLSJFKLDFJKLJFKLJKLJKLFDFDS"
     auth_web_failure_redirect_route: str = "/login"
     oauth2_access_token_expire_minutes: int = 60 * 24 * 8  # 60 minutes * 24 hours * 8 days = 8 days
     oauth2_algorithm: str = "HS256"
@@ -27,18 +27,20 @@ class Settings(BaseSettings):
     cas_server_url: str = "https://padlockdev.idm.uab.edu/cas/"
     cas_login_enable: bool = False
 
-    @model_validator(mode="before")
-    @classmethod
-    def rosalution_key_exists(cls, values):
-        """
-        Verifies that the ROSALUTION_KEY environment is set and provides a more descriptive error message.
-        This needed to be done as a pydantic root validator to execute this before pydantics validation of
-        individual fields since it would fail due to the missing value.
-        """
-        key = values.get('rosalution_key')
-        if not key:
-            raise ValueError('Environment variable "ROSALUTION_KEY" missing. App requires secret for secure encoding.')
-        return values
+    # @model_validator(mode="before")
+    # @classmethod
+    # def rosalution_key_exists(cls, values):
+    #     """
+    #     Verifies that the ROSALUTION_KEY environment is set and provides a more descriptive error message.
+    #     This needed to be done as a pydantic root validator to execute this before pydantics validation of
+    #     individual fields since it would fail due to the missing value.
+    #     """
+    #     print("IT SHOULD BE HERE")
+    #     print(values)
+    #     key = values.get('rosalution_key')
+    #     if not key:
+    #         raise ValueError('Environment variable "ROSALUTION_KEY" missing. App requires secret for secure encoding.')
+    #     return values
 
 
 @lru_cache()

backend/src/repository/analysis_collection.py

@@ -259,12 +259,8 @@ def add_section_image(self, analysis_name: str, section_name: str, field_name: s
             if content_row["field"] and content_row["field"] == field_name:
                 content_row["value"].append({'file_id': str(file_id)})
 
-        self.collection.find_one_and_update(
-            {"name": analysis_name},
-            {'$set': updated_document},
-        )
-
-        return updated_section
+        return self.collection.find_one_and_update({"name": analysis_name}, {'$set': updated_document},
+                                                   return_document=ReturnDocument.AFTER)
 
     def update_section_image(
         self, analysis_name: str, section_name: str, field_name: str, file_id: str, file_id_old: str

backend/src/routers/analysis_router.py

@@ -112,6 +112,7 @@ def update_analysis_sections(
     analysis_name: str,
     row_type: SectionRowType,
     updated_sections: List[Section],
+    upload_file: UploadFile = File(None),
     repositories=Depends(database),
     authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
 ):
@@ -122,20 +123,40 @@ def update_analysis_sections(
         updated_analysis_model = Analysis(**updated_analysis)
         return updated_analysis_model.sections
 
+    updated_analysis = None
+    section = updated_sections[0]
+
+    if row_type not in (SectionRowType.IMAGE, SectionRowType.DOCUMENT, SectionRowType.LINK):
+        raise HTTPException(status_code=422, detail=f"'Unsupported 'row_type': {row_type}.")
+
     if row_type in (SectionRowType.IMAGE, SectionRowType.DOCUMENT):
-        print("Will be adding image or document")
+
+        try:
+            new_file_object_id = add_file_to_bucket_repository(upload_file, repositories["bucket"])
+        except Exception as exception:
+            raise HTTPException(status_code=500, detail=str(exception)) from exception
+
+        # # TODO - Is this only used for document adding and not image adding?
+        # field_value_file = {
+        #     "name": upload_file.filename,
+        #     "attachment_id": str(new_file_object_id),
+        #     "type": "file",
+        #     "comments": ""  #removed the comments attribute?
+        # }
 
         if row_type == SectionRowType.DOCUMENT:
             print("Will be adding document")
 
         if row_type == SectionRowType.IMAGE:
-            print("Will be adding image")
+            updated_analysis = repositories["analysis"].add_section_image(
+                analysis_name, section.header, section["fieldName"], new_file_object_id
+            )
 
-    if row_type == SectionRowType.LINK:
-        print("will be adding link")
+    if row_type in (SectionRowType.LINK):
+        print("Will be adding link")
 
-    print("ADDING TYPE NOT SUPPORTED YET, IN PROGRESS")
-    return []
+    updated_analysis_model = Analysis(**updated_analysis)
+    return updated_analysis_model.sections
 
 
 def update_analysis_sections_text_fields(analysis_name, updated_sections: List[Section], analysis_repository):
@@ -149,6 +170,11 @@ def update_analysis_sections_text_fields(analysis_name, updated_sections: List[S
                 analysis_name, section.header, field_name, {"value": field_value}
             )
 
+def add_file_to_bucket_repository(file_to_save, bucket_repository):
+    """Saves the 'file_to_save' within the bucket repository and returns the files new uuid."""
+    return bucket_repository.save_file(
+        file_to_save.file, file_to_save.filename, file_to_save.content_type
+    )
 
 @router.put("/{analysis_name}/section/attach/file")
 def attach_animal_model_system_report(

backend/tests/unit/repository/test_analysis_collection.py

@@ -187,24 +187,23 @@ def test_add_image_to_pedigree_section(analysis_collection, empty_pedigree):
     expected = read_test_fixture("analysis-CPAM0002.json")
 
     analysis_collection.add_section_image("CPAM0002", "Pedigree", "Pedigree", "63505be22888347cf1c275db")
-    analysis_collection.collection.find_one_and_update.assert_called_with({"name": "CPAM0002"}, {"$set": expected})
+    analysis_collection.collection.find_one_and_update.assert_called_with({"name": "CPAM0002"}, {"$set": expected}, return_document=ReturnDocument.AFTER)
 
 
 def test_add_an_additional_image_to_pedigree_section(analysis_collection):
     """ Tests adding another image to the pedigree section of the CPAM0002 analysis """
 
     analysis_collection.collection.find_one.return_value = read_test_fixture("analysis-CPAM0002.json")
 
-    expected = {
-        'header': 'Pedigree', 'attachment_field': 'Pedigree', 'content': [{
-            'type': 'images-dataset', 'field': 'Pedigree', 'value': [{"file_id": "63505be22888347cf1c275db"},
-                                                                     {"file_id": "second-fake-file-id"}]
-        }]
-    }
-
-    actual = analysis_collection.add_section_image("CPAM0002", "Pedigree", "Pedigree", "second-fake-file-id")
+    analysis_collection.add_section_image("CPAM0002", "Pedigree", "Pedigree", "second-fake-file-id")
 
-    assert actual == expected
+    analysis_collection.collection.find_one_and_update.assert_called_once()
+    updated_analysis = analysis_collection.collection.find_one_and_update.call_args_list[0][0][1]['$set']
+    actual_updated_pedigree_section = (
+            next(filter(lambda x: x["header"] == "Pedigree", updated_analysis['sections']), None)
+        )
+    assert len(actual_updated_pedigree_section['content']) == 1
+    assert len(actual_updated_pedigree_section['content'][0]['value']) == 2
 
 
 def test_update_existing_image_in_pedigree_section(analysis_collection):

frontend/src/models/analyses.js

@@ -93,13 +93,28 @@ export default {
     return await Requests.getImage(url);
   },
 
+    /**
+   * Attaches {@link image} to {@link field} within {@link sectionName}
+   * the analysis {@link analysisName}.
+   * @param {string} analysisName The unique name of the analysis to update
+   * @param {string} sectionName The name of the section within the analysis
+   * @param {string} field The identifiying field within the section
+   * @param {File}   image the image data to be uploaded 
+   * @return {Object[]} Array of all of the sections in the analysis
+   */
   async attachSectionImage(analysisName, sectionName, field, image) {
-    const url = `/rosalution/api/analysis/${analysisName}/section/attach/image`;
+    const url = `/rosalution/api/analysis/${analysisName}/sections?row_type=text`;
 
+    const section = {
+      'header': sectionName,
+      'content': [],
+    };
+    section.content.push({
+      'field_name': field,
+    });
     const attachmentForm = {
       'upload_file': image,
-      'section_name': sectionName,
-      'field_name': field,
+      'updated_sections': [section],
     };
 
     return await Requests.postForm(url, attachmentForm);

frontend/src/views/AnalysisView.vue

@@ -231,17 +231,23 @@ export default {
             attachment.data,
         );
 
-        const updatedSection = this.sectionsList.find((section) => {
+        const sectionToUpdate = this.sectionsList.find((section) => {
           return section.header == sectionName;
         });
 
-        const updatedField = updatedSection.content.find((row) => {
+        const fieldToUpdate = sectionToUpdate.content.find((row) => {
           return row.field == field;
         });
 
-        updatedField.value.push({file_id: updatedSectionImage['image_id']});
+        const updatedField = updatedSectionImage.find((section) => {
+          return section.header == sectionName;
+        })?.content.find((row) => {
+          row.field == field
+        });
+
+        fieldToUpdate.value = updatedField.value;
 
-        this.replaceAnalysisSection(updatedSection);
+        this.replaceAnalysisSection(sectionToUpdate);
       } catch (error) {
         await notificationDialog.title('Failure').confirmText('Ok').alert(error);
       }