fixed milts import

Author: awolf-lib

.prettierignore

@@ -0,0 +1 @@
+*.html

flask-backend/src/Routes/db.py

@@ -531,6 +531,17 @@ def removeAnalysisByAnalysisID():
         return REQUESTMETHODERROR
 
 
+# FETCH MILTS PLOT BY PATH
+@db.route("/fetchMiltsPlotByPath", methods=["GET"])
+def fetchMiltsPlotByPath():
+    if request.method == "GET":
+        path = request.args.get("path")
+        data = api.fetchMiltsPlotByPath(path)
+        return data
+    else:
+        return REQUESTMETHODERROR
+
+
 # ================== BOOKMARK ================== #
 # ADD NEW BOOKMARK
 @db.route("/addNewBookmark", methods=["GET"])

flask-backend/src/Tools/DatabaseManager.py

@@ -560,10 +560,13 @@ def fetchSpeciesProfilePictureTaxonID(self, taxonID):
             return {
                 "label": "Error",
                 "message": f"Error loading profile picture for species {taxonID}. No such file!",
-                "type": "success",
+                "type": "error",
             }
 
-        return send_file(f"{BASE_PATH_TO_STORAGE}taxa/images/" + taxonID + ".thumbnail.jpg", "image/jpg")
+        return send_file(
+            f"{BASE_PATH_TO_STORAGE}taxa/images/" + taxonID + ".thumbnail.jpg",
+            "image/jpg",
+        )
 
     # ================== ASSEMBLY ================== #
     # FETCH ALL ASSEMBLIES
@@ -1694,7 +1697,7 @@ def addNewAnalysis(self, assemblyID, name, path, userID, additionalFilesPath="")
 
         fileName = path.split("/")[-1]
 
-        if fileName == "3D_plot.html":
+        if "3D_plot.html" in fileName and fileName.endswith(".html"):
             type = "milts"
         elif "short_summary" in fileName and fileName.endswith(".txt"):
             type = "busco"
@@ -1709,6 +1712,7 @@ def addNewAnalysis(self, assemblyID, name, path, userID, additionalFilesPath="")
                 "type": "error",
             }
 
+        print(type, path, name, additionalFilesPath, assemblyName)
         path, notification = fileManager.moveFileToStorage(
             type, path, name, additionalFilesPath, assemblyName
         )
@@ -1816,6 +1820,22 @@ def removeAnalysisByAnalysisID(self, id):
             "type": "success",
         }
 
+        # FETCH MILTS 3D PLOT
+
+    def fetchMiltsPlotByPath(self, path):
+        """
+        send milts plot to frontend
+        """
+
+        if not isfile(path):
+            return {
+                "label": "Error",
+                "message": f"Error loading MILTS 3D plot. No such file!",
+                "type": "error",
+            }
+
+        return send_file(path, "text/html")
+
     def importBusco(self, analysisID, buscoData):
         """
         Imports busco analysis results

flask-backend/src/Tools/FileManager.py

@@ -5,6 +5,7 @@
 from glob import glob
 from PIL import Image
 from subprocess import run
+from re import compile
 
 # defaults
 BASE_PATH_TO_IMPORT = "/flask-backend/data/import/"
@@ -626,24 +627,37 @@ def moveFileToStorage(
             if type == "milts":
                 try:
                     with open(newPath, "r") as plotFile:
-                        lines = plotFile.readlines()
+                        plot_data = "".join(plotFile.readlines()).replace("\n", "")
+                        plot_data = plot_data.replace('"title":"taxonomic assignment"', f'"title":"{name}"')
                         plotFile.close()
 
-                    for index, line in enumerate(lines):
-                        if "3D_plot_files" in line:
-                            lines[index] = line.replace(
-                                "3D_plot_files",
-                                "../../../../../dependencies/3D_plot_files",
-                            )
-                        elif '"title":"taxonomic assignment",' in line:
-                            lines[index] = line.replace(
-                                '"title":"taxonomic assignment",', f'"title":"{name}",'
-                            )
+                    with open(
+                        "src/Tools/templates/milts_head_template.html", "r"
+                    ) as milts_template_file:
+                        milts_template = milts_template_file.readlines()
+                        milts_template_file.close()
+
+                    body_regex = compile(r"<body>.*</body>")
+                    body_match = body_regex.findall(plot_data)
+                    if len(body_match) != 1:
+                        return 0, {
+                            "label": "Error",
+                            "message": "Error using template html!",
+                            "type": "error",
+                        }
+
+                    for i in range(len(milts_template)-1, len(milts_template)-5, -1):
+                        if ("<body>REPLACE_BODY</body>" in milts_template[i]):
+                            milts_template[i] = milts_template[i].replace("<body>REPLACE_BODY</body>", body_match[0])
+                        elif ("<title>REPLACE_TITLE</title>" in milts_template[i]):
+                            milts_template[i] = milts_template[i].replace("REPLACE_TITLE", name)
+                            break
 
                     with open(newPath, "w") as plotFile:
-                        lines = plotFile.writelines(lines)
+                        plotFile.writelines(milts_template)
                         plotFile.close()
-                except:
+                except Exception as err:
+                    print(str(err))
                     self.deleteDirectories(fullPathToAnalysis)
                     return 0, STORAGEERROR
 

flask-backend/src/Tools/templates/milts_head_template.html

@@ -1,8 +1,6 @@
-import { useEffect, useState } from "react";
 import "../../App.css";
 import PropTypes from "prop-types";
 import picPlacerholder from "../../images/blankProfilePicture.png";
-import { fetchSpeciesProfilePictureTaxonID } from "../../api";
 
 const SpeciesProfilePictureViewer = ({ taxonID, imageStatus }) => {
   return (
@@ -11,7 +9,8 @@ const SpeciesProfilePictureViewer = ({ taxonID, imageStatus }) => {
       alt="Species profile"
       src={
         imageStatus
-          ? "http://localhost:3002/fetchSpeciesProfilePictureTaxonID?taxonID=" +
+          ? process.env.REACT_APP_API_ADRESS +
+            "/fetchSpeciesProfilePictureTaxonID?taxonID=" +
             taxonID
           : picPlacerholder
       }

react-frontend/src/components/SpeciesProfilePictureViewer/index.js

@@ -14,7 +14,11 @@ const TaxonomicAssignmentViewer = ({
           onLoad={() => setTaxonomicAssignmentLoading(false)}
           title="MiltsPlot"
           className="w-full h-screen"
-          src={process.env.REACT_APP_NEXTCLOUD_DOWNLOAD_ADRESS}
+          src={
+            process.env.REACT_APP_API_ADRESS +
+            "/fetchMiltsPlotByPath?path=" +
+            assemblyInformation.analyses.milts[index].path
+          }
         />
       </div>
       <div className="absolute bottom-0 right-0 z-10 opacity-50 flex items-center mx-4 my-1">
@@ -30,7 +34,7 @@ const TaxonomicAssignmentViewer = ({
         </a>
       </div>
       {assemblyInformation.analyses.milts.length > 1 && (
-        <div className="absolute bottom-0 left-0 z-10 opacity-50 flex items-center mx-4 my-1">
+        <div className="absolute bottom-0 left-0 opacity-50 flex items-center mx-4 my-1 z-10">
           <Button
             color="link"
             onClick={() =>

react-frontend/src/screens/MainRouter/components/AssemblyInformation/components/TaxonomicAssignmentViewer/index.js

@@ -211,7 +211,7 @@ const AssemblyInformation = () => {
               </div>
             )}
 
-          {/* {assemblyInformation.analyses &&
+          {assemblyInformation.analyses &&
             assemblyInformation.analyses.milts &&
             assemblyInformation.analyses.milts.length > 0 && (
               <div>
@@ -245,7 +245,7 @@ const AssemblyInformation = () => {
                 </div>
                 <hr className="shadow my-8 mx-8" />
               </div>
-            )} */}
+            )}
 
           {assemblyInformation.analyses &&
             assemblyInformation.analyses.busco &&

react-frontend/src/screens/MainRouter/components/AssemblyInformation/index.js

@@ -93,7 +93,7 @@ docker build --no-cache -t gnom/reactapp .
 # start
 echo "Start ${REACTAPP_CONTAINER_NAME} container..."
 # docker run --name $REACTAPP_CONTAINER_NAME --network gnom_app -d -p 5000:5000 gnom/reactapp
-docker run --name $REACTAPP_CONTAINER_NAME -v /home/andywolf/workspace/g-nom/react-frontend/src:/react-frontend/src --network gnom_app -d -p 3000:5000 gnom/reactapp npm start
+docker run --name $REACTAPP_CONTAINER_NAME -v /home/andywolf/workspace/g-nom/react-frontend/src:/react-frontend/src --network gnom_app -d -p 3000:3000 gnom/reactapp npm start
 cd ..
 
 # ============================================ #