Update local

README.md

@@ -19,6 +19,10 @@ Development in python3.12 with
 - OPERA2.3_CL (https://github.com/kmansouri/OPERA/releases), fix the minor error in the install folder add a "/" at the path beginning
 - OPERA will install PADEL in the same folder
 
+## install OPERA --> install command line
+$sudo ./OPERA2.6_XXX_mcr.install -mode silent -agreeToLicense yes
+
+
 ## run the server
 $python manage makemigrations
 $python migrate

bodymap/templates/bodymap/index.html

@@ -26,7 +26,7 @@ <h1>Tox21BodyMap</h1>
 
 <br>
 <h2>Please cite</h2>
-<p style="text-align:  center; font-size: 25px">
+<p style="text-align:  center; font-size: 20px">
    <a href="https://doi.org/10.1093/nar/gkaa433" style="color: darkred">Tox21BodyMap: a webtool to map chemical effects on the human body, <i>NAR webserver</i></a><br>
 </p>
 <p>* This website is free and open to all users and there is no login requirement.</p>
@@ -46,12 +46,14 @@ <h2>Visualization</h2>
     Visualization includes three parts: 
     <ul style="margin-left:40px">
 
-        <li style="font-size: 20px;">chemical information, linked to the <a class = "aurl" href="https://comptox.epa.gov/dashboard">EPA chemical dashboard</a></li>
-        <li style="font-size: 20px;">body-mapping based on a consensus of assay AC50 (µM) and gene expression cutoffs</li>
-        <li style="font-size: 20px;">network representation integrating gene expression, body mapping and chemical activity by assay</li>
+        <li style="font-size: 15px;">chemical information, linked to the <a class = "aurl" href="https://comptox.epa.gov/dashboard">EPA chemical dashboard</a></li>
+        <li style="font-size: 15px;">body-mapping based on a consensus of assay AC50 (µM) and gene expression cutoffs</li>
+        <li style="font-size: 15px;">network representation integrating gene expression, body mapping and chemical activity by assay</li>
     </ul>
 </p>
 
+<br><br>
+
 
 <div class="row">
     <div class="column">

bodymap/views.py

@@ -7,6 +7,7 @@
 from .loadMapping import assaysMapping
 from .mapChem import mapChem
 from .prepInputChem import prepChem
+from django.views.decorators.csrf import csrf_exempt
 
 
 # Create your views here.
@@ -20,7 +21,7 @@ def help(request):
     return render(request, 'bodymap/help.html', {
     })
 
-
+@csrf_exempt 
 def mappingChemicalToBody(request):
 
     # form for bodypart

chemmaps/DSSToxPrep.py

@@ -187,7 +187,7 @@ def loadChemMapAddMap(self):
         if nbChemAdd == 1:
             center_map = 1
         else:
-            center_map =0
+            center_map = 0
 
 
         for chem in self.input["SMILESClass"].keys():
@@ -226,8 +226,10 @@ def loadChemMapAddMap(self):
                 else:
                     self.coord[chem] = deepcopy(self.input["coord"][chem])
                 self.dinfo[chem] = {}
-                for desc in self.input["info"][chem]:
-                    self.dinfo[chem][DDESCDSSTOX[desc]] = self.input["info"][chem][desc]
+
+
+                for desc in list(self.input["info"][chem].keys()):
+                    self.dinfo[chem][desc] = self.input["info"][chem][desc]
                 self.dneighbor[chem] = deepcopy(self.input["neighbor"][chem])
                 self.dSMILES[chem] = {}
                 self.dSMILES[chem]["SMILES"] = deepcopy(self.input["SMILESClass"][chem]["SMILES"])

chemmaps/JSbuilder.py

@@ -51,7 +51,7 @@ def __init__(self, nameMap, ldescMap = [], prout = ""):
         self.prout = prout
         self.ldescMap = ldescMap
         self.cDB = DBrequest()
-        self.pMap = path.abspath("./static/chemmaps/map/" + self.nameMap + "/") + "/"
+        self.pMap = path.abspath(path.dirname(__file__) + "/../static/chemmaps/map/" + self.nameMap + "/") + "/"
         self.cDB.verbose = 0
         self.err = 0
 
@@ -382,7 +382,7 @@ def generateCoords(self, p1D2D, p3D):
 
             # run R script
             ## add Rscript for  windows install!
-            cmd = "Rscript %s/addonMap.R %s %s %s1D2Dscaling.csv %s3Dscaling.csv %sCP1D2D.csv %sCP3D.csv %s"%(path.abspath("./chemmaps/Rscripts"), p1D2D, p3D, self.pMap, self.pMap, self.pMap, self.pMap, self.prout)
+            cmd = "%s/addonMap.R %s %s %s1D2Dscaling.csv %s3Dscaling.csv %sCP1D2D.csv %sCP3D.csv %s"%(path.abspath(path.dirname(__file__) + "/Rscripts"), p1D2D, p3D, self.pMap, self.pMap, self.pMap, self.pMap, self.prout)
             system(cmd)
 
             if path.exists(p1D2Dcoord) and path.exists(p3Dcoord):

chemmaps/urls.py

@@ -1,6 +1,5 @@
 from django.urls import re_path as url
 from django.views.generic import TemplateView
-from django.conf.urls.static import static
 from django.conf import settings
 from . import views
 
@@ -225,4 +224,4 @@
         r'^lowestAC50.csv',
         views.download, {"name": "lowestAC50"}, name="lowestAC50",
     )
-]
+]

chemmaps/views.py

@@ -3,6 +3,7 @@
 from django.views.generic import TemplateView
 from django.core.files.storage import default_storage
 from django.template import RequestContext
+from django.views.decorators.csrf import csrf_exempt
 from random import randint
 import json
 from re import search
@@ -52,6 +53,7 @@ def download(request, name):
             return response
     raise Http404
 
+@csrf_exempt 
 def launchMap(request, map, *args, **kwargs):
 
     name_session = request.session.get("name_session")
@@ -155,10 +157,12 @@ def launchMap(request, map, *args, **kwargs):
                     build.err = 1
                 else:
                     build.loadChemMapCenterChem(chemIn, center = 1, nbChem = 10000)
+
                 if build.err == 1:
                     reponse = render(request, 'chemmaps/launchMap.html', {"form_info": formDesc, "form_smiles": form_smiles,
                                                                     "from_upload": formUpload, "Error": "0", "map": map,
                                                                     "ErrorDSSTox":"1", "dassays":d_assays})
+                    return reponse
                 dcoord = json.dumps(build.coord)
                 dinfo = json.dumps(build.dinfo)
                 dneighbor = json.dumps(build.dneighbor)
@@ -190,6 +194,7 @@ def launchMap(request, map, *args, **kwargs):
                                                            "from_upload": formUpload, "Error": "0", "map":map, "dassays":d_assays})
     return reponse
 
+@csrf_exempt
 def launchTox21AssayMap(request, assay):
 
     cloadAssays = loadTox21AssayMap(assay)
@@ -237,7 +242,7 @@ def launchTox21TagetMap(request, target):
     return render(request, 'chemmaps/Map3D.html', {"dcoord": dcoord, "dinfo": dinfo, "dneighbor": dneighbor,
                                                              "dSMILESClass":dSMILESClass,
                                                              "ldesc":ldescJS, "map":"Tox21Target", "mapJS": mapJS, "prSessionJS":prSessionJS, "target":target, "assay":"", "nb_assays": cloadAssays.nb_assays})#, "nb_active": cloadAssays.nb_active, "nb_tested":  cloadAssays.nb_tested })
-
+@csrf_exempt
 def launchTox21MostPotent(request):
 
 
@@ -261,7 +266,7 @@ def launchTox21MostPotent(request):
     return render(request, 'chemmaps/Map3D.html', {"dcoord": dcoord, "dinfo": dinfo, "dneighbor": dneighbor,
                                                              "dSMILESClass":dSMILESClass,
                                                              "ldesc":ldescJS, "map":"Tox21Target", "mapJS": mapJS, "prSessionJS":prSessionJS, "target":"Most active", "assay":"", "nb_assays": cloadAssays.nb_assays})#, "nb_active": cloadAssays.nb_active, "nb_tested":  cloadAssays.nb_tested })
-
+@csrf_exempt
 def browseChemicals(request):
 
     name_session = request.session.get("name_session")
@@ -302,6 +307,7 @@ def launchDSSToxMap(request, DTXSID):
 
         return render(request, 'chemmaps/Map3D.html', {"dcoord": dcoord, "dinfo": dinfo, "dneighbor": dneighbor, "dSMILESClass":dSMILESClass, "ldesc":ldescJS, "map":"dsstox", "mapJS": mapJS,"prSessionJS":prSessionJS, "center_map":DTXSID, "assay":"" })
 
+@csrf_exempt 
 def computeDescriptor(request, map):
 
 
@@ -381,11 +387,6 @@ def computeDescriptor(request, map):
             mapJS = json.dumps(map)
 
 
-        print(len(list(dJS["coord"].keys())))
-        print(len(list(dJS["info"].keys())))
-        print(len(list(dJS["neighbor"].keys())))
-        print(len(list(dJS["SMILESClass"].keys())))
-        print(len(ldesc))
         return render(request, 'chemmaps/Map3D.html', {"dcoord": dcoord, "dinfo": dinfo, "dneighbor": dneighbor,
                                                            "dSMILESClass": dSMILESClass, "ldesc": ldesc,
                                                             "map": map, "mapJS": mapJS, "prSessionJS":prSessionJS,

django_server/urls.py

@@ -17,6 +17,7 @@
 from django.urls import path
 from django.conf.urls import include
 from .views import Home
+from django.conf.urls.static import static
 from django.urls import re_path as url
 
 urlpatterns = [

django_server/wsgi.py

@@ -19,7 +19,5 @@
 #    print ('%-30s %s' % (k,v[:70]))
 
 
-os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'django_server.settings')
-
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'django_server.settings.production')
 application = get_wsgi_application()
-#application = "FUCK"

interferences/content.py

@@ -131,6 +131,8 @@ def computeDesc(self):
         filout2D.write("ID\tSMILES\tinchikey\t" + "\t".join(ldesc1D2D) + "\n")
         filoutOPERA.write("ID\tSMILES\t" + "\t".join(ldescOPERA) + "\n")
 
+        print("HERE2")
+        print(self.dclean)
         for k in self.dclean["IN"].keys():
             dout[k] = {}
             SMICLEAN = self.dclean["OUT"][k]["SMILES"]
@@ -150,7 +152,7 @@ def computeDesc(self):
 
                 # check if chemical is in DB for 1D2D
                 lval1D2D_OPERA = downloadDescFromDB(self.cDB, ldesc1D2D, ldescOPERA, inch)
-                
+
                 # case of error in computation
                 if lval1D2D_OPERA == []:
                     dout[k]["desc"] = "checkNo.png"
@@ -243,13 +245,16 @@ def downloadDescFromDB(cDB, ldesc1D2D, ldescOPERA, inchikey):
 
     else:
         nb_userDB = cDB.execCMD("SELECT COUNT(*) FROM chemical_description_user WHERE inchikey='%s' AND status != 'update'"%(inchikey))[0][0]
+        print(nb_userDB)
+        print("SELECT COUNT(*) FROM chemical_description_user WHERE inchikey='%s' AND status != 'update'"%(inchikey))
         if nb_userDB > 0:
             lval1D2D = cDB.extractColoumn("chemical_description_user", "desc_1d2d","where inchikey='%s' and status != 'update' limit(1)"%(inchikey))
             lvalOPERA = cDB.extractColoumn("chemical_description_user", "desc_opera", "where inchikey='%s' and status != 'update' limit(1)"%(inchikey))
 
         else:
             return 0
 
+    # break if one descriptor error
     if lval1D2D == "ERROR" or lval1D2D == [] or lvalOPERA == "ERROR" or lvalOPERA == [] or lvalOPERA == [(None)]:
         return []
 

interferences/predictInterference.py

@@ -8,7 +8,10 @@
 
 import subprocess
 
-PMODEL = path.abspath("./static/interferences/models") + "/"
+
+#PMODEL = path.abspath("./static/interferences/models") + "/"
+PMODEL = path.abspath(path.dirname(__file__) + "/../static/interferences/models/") + "/"
+
 
 
 class Predict:
@@ -18,6 +21,7 @@ def __init__(self, lmodels, noDB, prSession):
         self.pdes2D = prSession + "2D.csv"
         self.pOpera = prSession + "OPERA.csv"
         self.prSession = prSession
+
         self.err = 0
         self.cDB = DBrequest()
         self.noDB = noDB
@@ -45,7 +49,6 @@ def predictAll(self):
 
             if type(lpred) == list and lpred != []: 
                 #lpred = self.cDB.extractColoumn("interference_chemicals", "interference_prediction", "WHERE inchikey='%s'"%(inch))
-                print(lpred)
                 lpred = lpred[0]
                 if lpred[0] == None:
                     i = i + 1
@@ -111,14 +114,14 @@ def predictAll(self):
     def predictRmodel(self, pmodel, pdesc2D, pOPERA, pout):
 
         if os.name == "nt":
-            pRpredict = path.abspath("./interferences/Rscripts") + "/predictfromModel.R"
+            pRpredict = path.abspath(path.dirname(__file__) + "/Rscripts") + "/predictfromModel.R"
 
             cmd = f'"C:\\Program Files\\R\\R-4.2.1\\bin\\Rscript.exe" "{pRpredict}" "{pdesc2D}" "{pOPERA}" "{pmodel}" "{pout}"'
             print(cmd)
             subprocess.run(cmd, shell=True, check=True)
 
         else:
-            pRpredict = path.abspath("./interferences/Rscripts") + "/predictfromModel.R"
+            pRpredict = path.abspath(path.dirname(__file__) + "/Rscripts") + "/predictfromModel.R"
             cmd = "%s %s %s %s %s" % (pRpredict, pdesc2D, pOPERA, pmodel, pout)
             print(cmd)
             system(cmd)

interferences/templates/interferences/cleanSMILES.html

@@ -20,7 +20,7 @@ <h1>QSAR-ready SMILES</h1>
 {% endif %}
 
 
-<div class="row">
+<div class="row" style="margin: auto;">
         <div class="column" style="background-color:#004400;">
             <h3 style="color:#ffffff">Inputs</h3>
             <div class="divTable">

interferences/templates/interferences/computeDESC.html

@@ -18,7 +18,7 @@ <h1>Chemical descriptors</h1>
     <p class = "Errorform" style="margin-right: 0px"> No descriptor computed.</p>
 {% endif %}
 
-<div class="row">
+<div class="row" style="margin: auto;">
         <div class="column" style="background-color:#004400;">
             <h3 style="color:#ffffff">Inputs</h3>
             <div class="divTable">

interferences/views.py

@@ -1,5 +1,6 @@
 from django.shortcuts import render
 from django.http import HttpResponseRedirect, HttpResponse, Http404
+from django.views.decorators.csrf import csrf_exempt
 from random import randint
 from os import path
 import json
@@ -24,9 +25,11 @@ def help(request):
     return render(request, 'interferences/help.html', {
     })
 
-def uploadSMILES(request):
+@csrf_exempt 
+def uploadSMILES(request, *args, **kwargs):
 
     name_session = request.session.get("name_session")
+    print(name_session)
 
     if request.method == 'GET':
         form_smiles = UploadChemList()
@@ -47,7 +50,7 @@ def uploadSMILES(request):
             return render(request, 'interferences/uploadSMILES.html', {"form_smiles":form_smiles,
                                                            "from_upload": formUpload, "ErrorLine": "1"})
 
-        prSession = path.abspath("./temp") + "/" + str(name_session) + "/"
+        prSession = path.abspath(path.dirname(__file__) + "/../temp") + "/" + str(name_session) + "/"
         createFolder(prSession, 1)
 
         cinput = formatSMILES(content, prSession)
@@ -60,7 +63,7 @@ def uploadSMILES(request):
 
     elif formUpload.is_valid() == True:
 
-        prSession = path.abspath("./temp") + "/" + str(name_session) + "/"
+        prSession = path.abspath(path.dirname(__file__) + "/../temp") + "/" + str(name_session) + "/"
         createFolder(prSession, 1)
 
         pfileserver = prSession + "upload.txt"
@@ -94,13 +97,13 @@ def uploadSMILES(request):
 
     return render(request, 'interferences/uploadSMILES.html', {"form_smiles":form_smiles,
                                                            "from_upload": formUpload, "ErrorLine": "0"})
-
+@csrf_exempt 
 def computeDesc(request):
 
     name_session = request.session.get("name_session")
 
     # open file with
-    prsession = path.abspath("./temp") + "/" + str(name_session) + "/"
+    prsession = path.abspath(path.dirname(__file__) + "/../temp") + "/" + str(name_session) + "/"
     dSMI = loadMatrixToDict(prsession + "smiClean.csv", sep="\t")
 
     cinput = formatSMILES(dSMI, prsession)

settings/local.py

@@ -29,7 +29,7 @@
 DEBUG = True
 
 
-ALLOWED_HOSTS = ['localhost']#,'152.1.45.108', 'www.chemmaps.com', "www.alexborrel.com"]
+ALLOWED_HOSTS = ['localhost', '192.168.167.131']#,'152.1.45.108', 'www.chemmaps.com', "www.alexborrel.com"]
 
 # CORS
 CORS_ORIGIN_ALLOW_ALL = False
@@ -156,4 +156,4 @@
 
 
 # manage cookies
-CSRF_COOKIE_SECURE = True
+CSRF_COOKIE_SECURE = True

todo.md

@@ -43,6 +43,8 @@ pip install git+https://github.com/jazzband/django-cookie-consent@master#egg=dja
 
 ### BodyMap
 #### Priority high
+- redone chemsum with proper chemical name
+
 
 ### Priority low
 

toolchem/computeCoords.py

@@ -28,7 +28,7 @@ def computeCoordForOnlyNewChem(self):
         self.cDBresquest.closeConnection()
 
         # run R script
-        cmd = "%s/addonMap.R %s %s %s1D2Dscaling.csv %s3Dscaling.csv %sCP1D2D.csv %sCP3D.csv %s"%(path.abspath("./chemmaps/Rscripts"), p_desc1D2D, p_desc1D3D, self.p_staticMap, self.p_staticMap, self.p_staticMap, self.p_staticMap, self.pr_session)
+        cmd = "%s/addonMap.R %s %s %s1D2Dscaling.csv %s3Dscaling.csv %sCP1D2D.csv %sCP3D.csv %s"%(path.abspath(path.dirname(__file__) + "/Rscripts"), p_desc1D2D, p_desc1D3D, self.p_staticMap, self.p_staticMap, self.p_staticMap, self.p_staticMap, self.pr_session)
         system(cmd)
 
         p_coords1D2D = self.pr_session + "coord1D2D.csv"