Merge pull request #437 from MEDomics-UdeS/scalability

V1.5.0 merge

Author: MahdiAll99

.DS_Store

@@ -79,7 +79,7 @@ jobs:
           VERSION: ${{ steps.get-tag.outputs.VERSION }}
 
   build-linux-ubuntu:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-20.04
 
     steps:
       - name: Checkout code

.github/workflows/automaticBuilding.yml

@@ -7,7 +7,7 @@ permissions:
   contents: write
 jobs:
   build-linux-ubuntu:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-20.04
 
     steps:
       - name: Checkout code

.github/workflows/automaticBuildingLinux.yml

@@ -142,6 +142,12 @@ dmypy.json
 # submodules
 /flask_server/submodules/MEDimage/*
 /flask_server/submodules/MEDprofiles/*
+pythonCode/submodules/MEDimage/*
+pythonCode/submodules/MEDprofiles/*
+
+# Go executables 
+go_server/main
+go_server/main.exe
 
 # custom gitignore
 tmp

.gitignore

@@ -10,6 +10,8 @@ var prePath = "learning"
 // AddHandleFunc adds the specific module handle function to the server
 func AddHandleFunc() {
 	Utils.CreateHandleFunc(prePath+"/run_experiment/", handleRunExperiment)
+	Utils.CreateHandleFunc(prePath+"/get_file_content/", handleGetFileContent)
+	Utils.CreateHandleFunc(prePath+"/save_file_content/", handleSaveFileContent)
 	Utils.CreateHandleFunc(prePath+"/progress/", handleProgress)
 }
 
@@ -25,6 +27,30 @@ func handleRunExperiment(jsonConfig string, id string) (string, error) {
 	return response, nil
 }
 
+// handleGetFileContent handles the request to run an experiment
+// It returns the response from the python script
+func handleGetFileContent(jsonConfig string, id string) (string, error) {
+	log.Println("Running script get_file_content...", id)
+	response, err := Utils.StartPythonScripts(jsonConfig, "../pythonCode/modules/learning/get_file_content.py", id)
+	Utils.RemoveIdFromScripts(id)
+	if err != nil {
+		return "", err
+	}
+	return response, nil
+}
+
+// handleSaveFileContent handles the request to run an experiment
+// It returns the response from the python script
+func handleSaveFileContent(jsonConfig string, id string) (string, error) {
+	log.Println("Running script save_file_content...", id)
+	response, err := Utils.StartPythonScripts(jsonConfig, "../pythonCode/modules/learning/save_file_content.py", id)
+	Utils.RemoveIdFromScripts(id)
+	if err != nil {
+		return "", err
+	}
+	return response, nil
+}
+
 // handleProgress handles the request to get the progress of the experiment
 // It returns the progress of the experiment
 func handleProgress(jsonConfig string, id string) (string, error) {

build/.DS_Store

@@ -187,7 +187,7 @@ export function getBundledPythonEnvironment() {
 }
 
 export async function installRequiredPythonPackages(mainWindow) {
-  let requirementsFileName = process.platform === "darwin" ? "requirements_mac.txt" : "requirements.txt"
+  let requirementsFileName = "merged_requirements.txt"
   if (process.env.NODE_ENV === "production") {
     installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "resources", "pythonEnv", requirementsFileName))
   } else {
@@ -208,6 +208,12 @@ function comparePythonInstalledPackages(pythonPackages, requirements) {
       if (pythonPackage.name === requirementName && pythonPackage.version === requirementVersion) {
         found = true
         break
+      } else if (pythonPackage.name.replace('-', '_') === requirementName && pythonPackage.version === requirementVersion) {
+        found = true
+        break
+      } else if (pythonPackage.name.replace('_', '-') === requirementName && pythonPackage.version === requirementVersion) {
+        found = true
+        break
       }
     }
     if (!found) {
@@ -360,9 +366,9 @@ export async function installBundledPythonExecutable(mainWindow) {
 
       // Install the required python packages
       if (process.env.NODE_ENV === "production") {
-        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "resources", "pythonEnv", "requirements.txt"))
+        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "resources", "pythonEnv", "merged_requirements.txt"))
       } else {
-        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "pythonEnv", "requirements.txt"))
+        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "pythonEnv", "merged_requirements.txt"))
       }
       let removeCommand = `rm ${outputFileName}`
       let removePromise = exec(removeCommand, { shell: "powershell.exe" })
@@ -429,9 +435,9 @@ export async function installBundledPythonExecutable(mainWindow) {
       console.log("process.resourcesPath: ", process.resourcesPath)
       // Install the required python packages
       if (process.env.NODE_ENV === "production") {
-        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.resourcesPath, "pythonEnv", "requirements.txt"))
+        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.resourcesPath, "pythonEnv", "merged_requirements.txt"))
       } else {
-        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "pythonEnv", "requirements.txt"))
+        installPythonPackage(mainWindow, pythonExecutablePath, null, path.join(process.cwd(), "pythonEnv", "merged_requirements.txt"))
       }
     }
   }

go_server/blueprints/learning/learning.go

@@ -2,7 +2,7 @@
   "private": true,
   "name": "medomicslab-application",
   "description": "MEDomicsLab application",
-  "version": "1.0.0",
+  "version": "1.5.0",
   "author": "MEDomicsLab Team",
   "main": "app/background.js",
   "build": {
@@ -114,7 +114,7 @@
     "primeicons": "^7.0.0",
     "primereact": "^9.6.2",
     "prismjs": "^1.29.0",
-    "react-ace": "^10.1.0",
+    "react-ace": "^14.0.1",
     "react-bootstrap-icons": "^1.10.3",
     "react-bootstrap-sidebar-menu": "^2.0.3",
     "react-complex-tree": "^2.2.2",

go_server/main

@@ -0,0 +1,70 @@
+import json
+import os
+import sys
+from pathlib import Path
+
+sys.path.append(
+    str(Path(os.path.dirname(os.path.abspath(__file__))).parent.parent))
+
+from med_libs.GoExecutionScript import GoExecutionScript, parse_arguments
+from med_libs.server_utils import go_print
+
+json_params_dict, id_ = parse_arguments()
+go_print("running script.py:" + id_)
+
+
+
+class GoExecScriptMerge(GoExecutionScript):
+    """
+        This class is used to execute the merge script
+
+        Args:
+            json_params: The input json params
+            _id: The id of the page that made the request if any
+    """
+
+    def __init__(self, json_params: dict, _id: str = None):
+        super().__init__(json_params, _id)
+        self.results = {"data": "nothing to return"}
+
+    def _custom_process(self, json_config: dict) -> dict:
+        """
+        This function reads the content of a file
+
+        Args:
+            json_config: The input json params
+        """
+        go_print(json.dumps(json_config, indent=4))
+
+        try:
+            # Set local variables
+            file_path = json_config["filePath"]
+
+            # Check if the file exists
+            if not os.path.exists(file_path):
+                return {"error": "File not found"}
+
+            # Read the file content
+            with open(file_path, "r") as file:
+                content = file.read()
+
+            # Detect the file extension
+            prog_lang = os.path.splitext(file_path)[1].lower().replace(".", "")
+            if prog_lang == "py" or prog_lang == "ipynb":
+                prog_lang = "python"
+            elif prog_lang == "md":
+                prog_lang = "markdown"
+            elif prog_lang == "txt":
+                prog_lang = "text"
+
+            # Return the file content and extension
+            return {
+                "content": content,
+                "language": prog_lang
+            }
+
+        except Exception as e:
+            return {"error": str(e)}
+    
+script = GoExecScriptMerge(json_params_dict, id_)
+script.start()