test delete broken or incomplete jsons

return 404 if the file does not exist
h2020charisma · Mar 28, 2024 · 6bedd4a · 6bedd4a
1 parent 062214d
commit 6bedd4a
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Showing 5 changed files with 302 additions and 26 deletions.
diff --git a/src/rcapi/api/templates.py b/src/rcapi/api/templates.py
@@ -212,6 +212,8 @@ async def get_template(request : Request, response : Response,
 
     if format in format_supported:
         json_blueprint ,file_path = template_service.get_template_json(uuid) 
+        if file_path is None:
+            raise HTTPException(status_code=404, detail="Not found")
         last_modified_time = get_last_modified(file_path)
         custom_headers = {  "Last-Modified":  last_modified_time.strftime(DATE_FORMAT) }
         if format=="json":
@@ -243,7 +245,7 @@ async def get_template(request : Request, response : Response,
             except Exception as err:
                 raise HTTPException(status_code=400, detail="The blueprint may not be complete. {}".format(err))
     else:
-            raise HTTPException(status_code=400, detail="Format not supported")
+        raise HTTPException(status_code=400, detail="Format not supported")
 
 
 @router.get("/template")

diff --git a/src/rcapi/services/template_service.py b/src/rcapi/services/template_service.py
@@ -52,6 +52,8 @@ def get_template_json(uuid):
     if os.path.exists(file_path):
         with open(file_path, "r") as file:
             json_data = json.load(file)
+    else:
+        file_path = None
     return json_data ,file_path
 
 

diff --git a/tests/resources/templates/dose_response_noname.json b/tests/resources/templates/dose_response_noname.json
@@ -0,0 +1,236 @@
+{
+    "newtemplate": "create_new",
+    "PROTOCOL_TOP_CATEGORY": "TOX",
+    "pageNo": 0,
+    "user_role": [
+        "role_lab"
+    ],
+    "templates": "c5dd3ac9-9340-44b0-9be8-6724c5e34c99",
+    "METHOD": "Dose response ",
+    "EXPERIMENT": "Generic dose response template",
+    "conditions": [
+        {
+            "conditon_name": "concentration",
+            "condition_unit": "ug/ml",
+            "condition_type": "c_concentration "
+        },
+        {
+            "conditon_name": "time",
+            "condition_unit": "h",
+            "condition_type": "c_time "
+        },
+        {
+            "conditon_name": "Replicate",
+            "condition_type": "c_replicate_tech "
+        },
+        {
+            "conditon_name": "Experiment",
+            "condition_type": "c_replicate_bio "
+        }
+    ],
+    "PROTOCOL_CATEGORY_CODE": "ENM_0000068_SECTION",
+    "raw_data": true,
+    "RESULTS": "raw data ( absorbance) \ncell viability  (%)",
+    "raw_data_report": [
+        {
+            "raw_conditions": [
+                "concentration",
+                "time",
+                "Experiment",
+                "Replicate"
+            ],
+            "raw_endpoint": "Absorbance",
+            "raw_unit": "A.U.",
+            "raw_type": "value_num"
+        }
+    ],
+    "question3": [
+        {
+            "results_conditions": [
+                "concentration",
+                "time",
+                "Experiment"
+            ],
+            "result_name": "Cell viability",
+            "result_unit": "%",
+            "result_type": "value_num"
+        }
+    ],
+    "METADATA_PARAMETERS": [
+        {
+            "param_name": "Serum concentration in culture medium"
+        },
+        {
+            "param_name": "Detailed cell type/line specification",
+            "param_group": "CELL LINE DETAILS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Cell line short-name",
+            "param_group": "CELL LINE DETAILS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Supplier",
+            "param_group": "CELL LINE DETAILS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Passage no",
+            "param_group": "CELL LINE DETAILS",
+            "param_type": "value_num"
+        },
+        {
+            "param_name": "Plate details as applic.",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Make / type",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Number of cells per well",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_num"
+        },
+        {
+            "param_name": "Total volume per well",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_num"
+        },
+        {
+            "param_name": "Medium (Supplier/Lot No.)",
+            "param_group": "MEDIUM",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Serum (inc. supplier/Lot No.)",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Serum concentration in treatment medium",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_num"
+        },
+        {
+            "param_name": "Was serum heat inactivated? If app.",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Submerged, ALI, or semi-ALI",
+            "param_group": "CULTURE CONDITIONS",
+            "param_type": "value_text "
+        },
+        {
+            "param_name": "Exposure method",
+            "param_group": "ENVIRONMENT",
+            "param_type": "value_text "
+        }
+    ],
+    "METADATA_SAMPLE_INFO": [
+        {
+            "param_sample_name": "ID",
+            "param_sample_group": "ID"
+        },
+        {
+            "param_sample_name": "Name",
+            "param_sample_group": "NAME"
+        },
+        {
+            "param_sample_name": "CAS No",
+            "param_sample_group": "CASRN"
+        },
+        {
+            "param_sample_name": "Nanomaterial Supplier",
+            "param_sample_group": "SUPPLIER"
+        },
+        {
+            "param_sample_name": "Material State",
+            "param_sample_group": "OTHER_METADATA"
+        },
+        {
+            "param_sample_name": "Batch",
+            "param_sample_group": "BATCH"
+        },
+        {
+            "param_sample_name": "Vial",
+            "param_sample_group": "BATCH"
+        }
+    ],
+    "METADATA_SAMPLE_PREP": [
+        {
+            "param_sampleprep_name": "Date of preparation (YYYY-MM-DD)",
+            "param_sampleprep_group": "OTHER_METADATA",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Endotoxin confirmed as absent?",
+            "param_sampleprep_group": "OTHER_METADATA",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Effective concentration range used lowest-to-highest, inc units",
+            "param_sampleprep_group": "OTHER_METADATA",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Specify standard dispersion protocol used",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Dispersion agent",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": " Additives used? If yes, specify which & conc. used:",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Dispersed in cell culture medium",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Aids used to disperse",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Sonication-Bath",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Sonication-tip",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Vortexing",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Stirring",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Specify time-duration",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        },
+        {
+            "param_sampleprep_name": "Energy (for sonication)",
+            "param_sampleprep_group": "DISPERSION",
+            "param_type": "value_text "
+        }
+    ]
+}
diff --git a/tests/resources/templates/null.json b/tests/resources/templates/null.json
@@ -0,0 +1 @@
+null