moved the infering of the file type into its own function

Author: IvoLeist

convertPheno_client/src/code/views/conversion/ components/submission/components/submissionForms/components/fileUpload/components/inputFilesPond/InputFilesPond.jsx

@@ -120,6 +120,39 @@ export default function InputFilesPond(props) {
     }
   }, [files]);
 
+  const inferPotentialFileType = (file) => {
+    /*
+    inferPotentialFileType function
+
+    Props:
+      - filename (string): name of the file that was uploaded
+
+    Functionality:
+      - tries to infer based on the file name and extension the file type
+        (input file, dictionary, mapping file)
+
+    Purpose:
+      - To update the state uploadedFiles with the file that was uploaded
+    */
+    const { filename, fileExtension } = file;
+
+    if (
+      filename.includes("dictionary") &&
+      ["csv", "tsv", "txt"].includes(fileExtension)
+    ) {
+      return "redcap-dictionary";
+    }
+
+    if (
+      filename.includes("mapping") &&
+      ["yaml", "yml", "json"].includes(fileExtension)
+    ) {
+      return "mapping-file";
+    }
+
+    return "input-file";
+  };
+
   const handleFileUploadFinished = (_, file) => {
     /*
     handleFileUploadFinished function
@@ -131,25 +164,20 @@ export default function InputFilesPond(props) {
       - tries to infer based on the file name and extension the file type
         (input file, dictionary, mapping file)
 
-        Purpose:
-        - To update the state uploadedFiles with the file that was uploaded
+    Purpose:
+    - To update the state uploadedFiles with the file that was uploaded
     */
 
     const returnedFileName = JSON.parse(file.serverId).tempFilename;
-    const { filename, fileExtension } = file;
+    const { filename } = file;
 
     if (filename in uploadedFiles) {
       toast.error("File already uploaded");
       file.setMetadata("processingAborted", true);
       file.abortProcessing();
       return;
     }
-
-    const fileType = filename.includes("dictionary") && fileExtension === "csv"
-      ? "redcap-dictionary"
-      : filename.includes("mapping") && ["yaml", "yml", "json"].includes(fileExtension)
-        ? "mapping-file"
-        : "input-file"
+    const fileType = inferPotentialFileType(file);
 
     setUploadedFiles((prev) => {
       return {

convertPheno_server/docker-compose.yml

@@ -47,7 +47,7 @@ services:
   convert-pheno:
     user: ${UID}
     image: manuelrueda/convert-pheno:0.15
-    container_name: convert-pheno
+    container_name: convert-pheno-container
     restart: unless-stopped
     tty: true
     volumes:

convertPheno_server/example.env

@@ -14,3 +14,5 @@ API_SECURITY=true
 # you can get the public Keycloak key in the admin view or by running
 # bash get_public_kc_key.sh https://<yourDomain>/auth/ <yourRealm>
 KC_PUBLIC_KEY=MII..
+
+CP_CONTAINER_NAME=convert-pheno-container

convertPheno_server/server/config/config.py

@@ -19,6 +19,15 @@
 db_name = environ.get("API_DB_NAME")
 security = environ.get("API_SECURITY")
 vscode_debugger = environ.get("DEBUGGER")
+cp_container_name = environ.get("CP_CONTAINER_NAME")
+
+# check if all environment variables are set
+if None in [db_user, db_pw, db_host, db_port, db_name, security, cp_container_name]:
+    raise ValueError(
+        "Please set the environment variables:"
+        "API_DB_USER, API_DB_PW, API_DB_HOST, API_DB_PORT, API_DB_NAME"
+        "API_SECURITY, CP_CONTAINER_NAME"
+    )
 
 # throw an error if security is not "true" or "false"
 if security not in ["true", "false"]:
@@ -44,3 +53,5 @@ class Config:
         FLASK_UPLOAD_DIR = Path("../data/uploads/")
         FLASK_EXAMPLE_DIR = Path("../data/example_in/").resolve()
         FLASK_OUT_DIR = Path("../data/output/").resolve()
+
+    CP_CONTAINER_NAME = cp_container_name

convertPheno_server/server/utils/convert_pheno.py

@@ -26,10 +26,11 @@ def get_docker_container():
     """
     # TODO: add error handling
     client = docker.from_env()
+    container_name = cfg["CP_CONTAINER_NAME"]
     try:
-        container_obj = client.containers.get("convert-pheno")
+        container_obj = client.containers.get(container_name)
     except docker.errors.NotFound:
-        raise ValueError("Docker container convert-pheno not found")
+        raise ValueError(f"Docker container {container_name} not found")
 
     return container_obj
 

docker-compose.prod.yml

@@ -29,6 +29,7 @@ services:
       UID: ${UID}
       GID: ${GID}
       API_SECURITY: true
+      CP_CONTAINER_NAME: convert-pheno
     restart: unless-stopped
     healthcheck:
       test: curl -f http://0.0.0.0:5000/api/curltest

docker-compose.yml

@@ -26,6 +26,7 @@ services:
       UID: ${UID}
       GID: ${GID}
       API_SECURITY: ${API_SECURITY}
+      CP_CONTAINER_NAME: convert-pheno
     restart: unless-stopped
     healthcheck:
       test: curl -f http://0.0.0.0:5000/api/curltest

example.env

@@ -23,3 +23,5 @@ API_DB_NAME=postgres
 # API configuration
 ## enable/disable keycloak security
 API_SECURITY=true
+
+CONVERT_PHENO_CONTAINER_NAME=convert-pheno