fixed LoadingSpinner on features, restart on failure update, replace relative paths for cli script

Author: awolf-lib

.gitignore

@@ -28,6 +28,7 @@
 *.log
 
 **/setup_dev.sh
+**/testImport.json
 
 # VS CODE
 **/.vscode

cli/import/exampleImport.json

@@ -1,8 +1,7 @@
 [
   {
     "assembly": {
-      "assemblyID": 34,
-      "mainFile": "PATH/TO/ASSEMBLY.FASTA",
+      "mainFile": "PATH/TO/ASSEMBLY.FASTA or use assemblyID key instead",
       "label": "Assembly label"
     },
     "taxon": {

cli/import/importDataset.py

@@ -8,7 +8,7 @@
 from os import getcwd
 
 DB_NAME = "gnom_db"
-HELP_STRING = ""
+HELP_STRING = "Example call: python3 importDataset.py PATH/TO/JSON"
 BASE_PATH_TO_IMPORT = "/flask-backend/data/import/"
 
 __location__ = realpath(join(getcwd(), dirname(__file__)))
@@ -45,7 +45,7 @@ def loadDataset(datasets_path):
     print("Valid inputs...")
 
     try:
-        with open(join(__location__, "local.config")) as config_file:
+        with open(join(__location__, "../../local.config")) as config_file:
             config_params = config_file.readlines()
             config_file.close()
 
@@ -66,7 +66,8 @@ def loadDataset(datasets_path):
 def importDatasets(datasets, config):
     uuid = str(uuid1())
     try:
-        for dataset in datasets:
+        for idx, dataset in enumerate(datasets):
+            print(f"Starting {idx+1}/{len(datasets)}")
             if "assemblyID" in dataset["assembly"] and dataset["assembly"]["assemblyID"] > 0:
                 pass
             elif "mainFile" in dataset["assembly"] and exists(dataset["assembly"]["mainFile"]):
@@ -252,7 +253,7 @@ def importDatasets(datasets, config):
 
             print("Removing tmp files...")
             run(args=["rm", "-r", tmp_dir])
-
+            print(f"{idx+1}/{len(datasets)} imported!\n")
         return 1
 
     except Exception as err:

flask-backend/src/Routes/analyses.py

@@ -247,7 +247,7 @@ def analyses_bp_fetchRepeatmaskerAnalysesByAssemblyID():
         return REQUESTMETHODERROR
 
 
-# FETCH TAXON IMAGE BY TAXON ID
+# FETCH FILES BY PATH (example: Milts plot)
 @analyses_bp.route("/fetchFileByPath", methods=["GET"])
 def analyses_bp_fetchFileByPath():
     if request.method == "GET":

flask-backend/src/Routes/annotations.py

@@ -201,11 +201,12 @@ def annotations_bp_fetchFeatureTypes():
 
 
 # FETCH ALL KEYS IN ATTRIBUTE SECTION
-@annotations_bp.route("/fetchFeatureAttributeKeys", methods=["GET"])
+@annotations_bp.route("/fetchFeatureAttributeKeys", methods=["Post"])
 def annotations_bp_fetchFeatureAttributeKeys():
-    if request.method == "GET":
-        userID = request.args.get("userID", None)
-        token = request.args.get("token", None)
+    if request.method == "POST":
+        req = request.get_json(force=True)
+        userID = req.get("userID", None)
+        token = req.get("token", None)
 
         # token still active
         valid_token, error = validateActiveToken(userID, token)
@@ -214,7 +215,11 @@ def annotations_bp_fetchFeatureAttributeKeys():
             response.headers.add("Access-Control-Allow-Origin", "*")
             return response
 
-        data, notification = fetchFeatureAttributeKeys()
+        taxonIDs = req.get("taxonIDs", None)
+        assemblyID = req.get("assemblyID", None)
+        types = req.get("types", None)
+
+        data, notification = fetchFeatureAttributeKeys(assemblyID, taxonIDs, types)
 
         response = jsonify({"payload": data, "notification": notification})
         response.headers.add("Access-Control-Allow-Origin", "*")