Fixed encoding and launch page issues

Cloud_dockerfile

@@ -8,7 +8,7 @@ ENV CALCUS_CLOUD True
 
 ADD ./cloud_requirements.txt /calcus/cloud_requirements.txt
 RUN pip install -r /calcus/cloud_requirements.txt
-RUN apt update && apt install openbabel postgresql-client dos2unix nwchem libxm4 libgl1 -y
+RUN apt update && apt install openbabel postgresql-client dos2unix nwchem libxm4 libgl1 libmagic1 -y
 
 COPY calcus /calcus/calcus
 COPY frontend /calcus/frontend

Dockerfile

@@ -20,7 +20,7 @@ ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/binaries/orca"
 ENV PATH=$PATH:$XTB4STDAHOME/xtb/bin:$XTB4STDAHOME:$EBROOTORCA:$GAUSS_EXEDIR
 ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/binaries/orca:/usr/lib/openmpi/
 
-RUN apt update && apt install openbabel sshpass postgresql-client dos2unix python3-dev gfortran mpi-default-bin mpi-default-dev libxm4 libgl1 -y
+RUN apt update && apt install openbabel sshpass postgresql-client dos2unix python3-dev gfortran mpi-default-bin mpi-default-dev libxm4 libgl1 libmagic1 -y
 RUN curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-data_7.2.0-2_all.debian_bullseye.deb
 RUN curl -LJO https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem_7.2.0-2_amd64.debian_bullseye.deb
 RUN dpkg -i nwchem*7.2.0*.deb

cloud_requirements.txt

@@ -23,6 +23,7 @@ periodictable
 psutil==5.7.2
 psycopg2
 pysisyphus
+python-magic
 rdkit
 requests
 scipy

frontend/management/commands/init_static_obj.py

@@ -211,25 +211,24 @@ def handle(self, *args, **options):
                 title=title, page_path="nmr_prediction_quick.html"
             )
 
-        if not settings.IS_TEST:
-            if self.is_absent_property("mo"):
-                molden = get_showcase("mo_molden")
-                mo_diagram = get_showcase("mo_diagram")
-                prop = ShowcaseProperty.objects.create(
-                    name="mo", molden=molden, mo_diagram=mo_diagram
-                )
+        if self.is_absent_property("mo"):
+            molden = get_showcase("mo_molden")
+            mo_diagram = get_showcase("mo_diagram")
+            prop = ShowcaseProperty.objects.create(
+                name="mo", molden=molden, mo_diagram=mo_diagram
+            )
 
-            if self.is_absent_ensemble("acetylsalicylic_acid"):
-                e = ShowcaseEnsemble.objects.create(label="acetylsalicylic_acid")
-                params = Parameters.objects.create(charge=0, multiplicity=1)
-                multixyz, E = parse_multixyz_from_file(
-                    os.path.join(showcase_dir, "Acetylsalicylic_Acid.xyz")
+        if self.is_absent_ensemble("acetylsalicylic_acid"):
+            e = ShowcaseEnsemble.objects.create(label="acetylsalicylic_acid")
+            params = Parameters.objects.create(charge=0, multiplicity=1)
+            multixyz, E = parse_multixyz_from_file(
+                os.path.join(showcase_dir, "Acetylsalicylic_Acid.xyz")
+            )
+            for ind, (xyz, ener) in enumerate(zip(multixyz, E)):
+                _xyz = format_xyz(xyz)
+                s = Structure.objects.create(
+                    parent_ensemble=e, xyz_structure=_xyz, number=ind + 1
+                )
+                prop = ShowcaseProperty.objects.create(
+                    energy=ener, parent_structure=s, parameters=params
                 )
-                for ind, (xyz, ener) in enumerate(zip(multixyz, E)):
-                    _xyz = format_xyz(xyz)
-                    s = Structure.objects.create(
-                        parent_ensemble=e, xyz_structure=_xyz, number=ind + 1
-                    )
-                    prop = ShowcaseProperty.objects.create(
-                        energy=ener, parent_structure=s, parameters=params
-                    )

frontend/test_views.py

@@ -625,8 +625,8 @@ def setUp(self):
         self.client.force_login(self.user)
 
     def test_single_file(self):
-        with open(os.path.join(tests_dir, "Cl.xyz")) as f:
-            xyz = bytes(f.read(), "UTF-8")
+        with open(os.path.join(tests_dir, "Cl.xyz"), "rb") as f:
+            xyz = f.read()
 
         f = SimpleUploadedFile("Cl.xyz", xyz, content_type="chemical/x-xyz")
 
@@ -645,6 +645,48 @@ def test_single_file(self):
         self.assertEqual(Molecule.objects.count(), 1)
         self.assertEqual(Ensemble.objects.count(), 1)
 
+    def test_iso_8859_1(self):
+        with open(os.path.join(tests_dir, "ethanol_iso-8859-1.xyz"), "rb") as f:
+            xyz = f.read()
+
+        f = SimpleUploadedFile("ethanol.xyz", xyz, content_type="chemical/x-xyz")
+
+        params = basic_params.copy()
+        params["structure"] = ""
+        params["calc_charge"] = "0"
+        params["file_structure"] = [f]
+        params["calc_combine_files"] = ("",)
+        params["calc_parse_filenames"] = ""
+
+        response = self.client.post("/submit_calculation/", data=params, follow=True)
+        self.assertEqual(response.status_code, 200)
+        self.assertNotContains(response, "Error while submitting your calculation")
+
+        self.assertEqual(CalculationOrder.objects.count(), 1)
+        self.assertEqual(Molecule.objects.count(), 1)
+        self.assertEqual(Ensemble.objects.count(), 1)
+
+    def test_utf_16(self):
+        with open(os.path.join(tests_dir, "ethanol_utf-16.xyz"), "rb") as f:
+            xyz = f.read()
+
+        f = SimpleUploadedFile("ethanol.xyz", xyz, content_type="chemical/x-xyz")
+
+        params = basic_params.copy()
+        params["structure"] = ""
+        params["calc_charge"] = "0"
+        params["file_structure"] = [f]
+        params["calc_combine_files"] = ("",)
+        params["calc_parse_filenames"] = ""
+
+        response = self.client.post("/submit_calculation/", data=params, follow=True)
+        self.assertEqual(response.status_code, 200)
+        self.assertNotContains(response, "Error while submitting your calculation")
+
+        self.assertEqual(CalculationOrder.objects.count(), 1)
+        self.assertEqual(Molecule.objects.count(), 1)
+        self.assertEqual(Ensemble.objects.count(), 1)
+
     def test_parse_charge_no_filename(self):
         with open(os.path.join(tests_dir, "Cl.xyz")) as f:
             xyz = bytes(f.read(), "UTF-8")
@@ -2008,3 +2050,69 @@ def test_refill_busted(self):
         self.assertEqual(
             self.user.allocated_seconds, settings.FREE_DEFAULT_COMP_SECONDS + 100
         )
+
+
+class LaunchPageTests(TestCase):
+    def setUp(self):
+        call_command("init_static_obj")
+        self.email = "Tester@test.com"
+        self.password = "test1234"
+
+        self.user = User.objects.create_superuser(
+            email=self.email,
+            password=self.password,
+        )
+        self.proj = Project.objects.create(author=self.user)
+        self.group = ResearchGroup.objects.create(name="Test group", PI=self.user)
+        self.client = Client()
+        self.client.force_login(self.user)
+
+    def test_basic(self):
+        response = self.client.get("/launch/")
+        self.assertEqual(response.status_code, 200)
+
+    def test_ensemble_does_not_exist(self):
+        response = self.client.post("/launch/", data={"ensemble": 2})
+        self.assertEqual(response.status_code, 302)
+
+    def test_ensemble_no_structure(self):
+        mol = Molecule.objects.create(project=self.proj)
+        e = Ensemble.objects.create(parent_molecule=mol)
+        response = self.client.post("/launch/", data={"ensemble": e.id})
+        self.assertEqual(response.status_code, 200)
+
+    def test_ensemble_no_prop(self):
+        mol = Molecule.objects.create(project=self.proj)
+        e = Ensemble.objects.create(parent_molecule=mol)
+        struct = Structure.objects.create(parent_ensemble=e, number=1)
+        response = self.client.post("/launch/", data={"ensemble": e.id})
+        self.assertEqual(response.status_code, 200)
+
+    def test_ensemble_prop(self):
+        mol = Molecule.objects.create(project=self.proj)
+        e = Ensemble.objects.create(parent_molecule=mol)
+        struct = Structure.objects.create(parent_ensemble=e, number=1)
+        prop = Property.objects.create(parent_structure=struct)
+        response = self.client.post("/launch/", data={"ensemble": e.id})
+        self.assertEqual(response.status_code, 200)
+
+    def test_ensemble_structure_with_prop(self):
+        mol = Molecule.objects.create(project=self.proj)
+        e = Ensemble.objects.create(parent_molecule=mol)
+        struct = Structure.objects.create(parent_ensemble=e, number=1)
+        prop = Property.objects.create(parent_structure=struct)
+
+        response = self.client.post(
+            "/launch/", data={"ensemble": e.id, "structures": [1]}
+        )
+        self.assertEqual(response.status_code, 200)
+
+    def test_ensemble_structure_without_prop(self):
+        mol = Molecule.objects.create(project=self.proj)
+        e = Ensemble.objects.create(parent_molecule=mol)
+        struct = Structure.objects.create(parent_ensemble=e, number=1)
+
+        response = self.client.post(
+            "/launch/", data={"ensemble": e.id, "structures": [1]}
+        )
+        self.assertEqual(response.status_code, 200)

frontend/tests/ethanol_iso-8859-1.xyz

@@ -0,0 +1,11 @@
+9
+Title
+C         -1.31970       -0.64380        0.00000
+H         -0.96310       -1.65260        0.00000
+H         -0.96310       -0.13940       -0.87370
+H         -2.38970       -0.64380        0.00000
+C         -0.80640        0.08220        1.25740
+H         -1.16150        1.09160        1.25640
+H         -1.16470       -0.42110        2.13110
+O          0.62360        0.07990        1.25870
+H          0.94410        0.53240        2.04240

frontend/views.py

@@ -34,6 +34,7 @@
 import base64, gzip
 import copy
 import itertools
+import magic
 
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric import rsa
@@ -1620,7 +1621,13 @@ def set_project_default(request):
 
 
 def handle_file_upload(ff, is_local, verify=False):
-    in_file = clean(ff.read().decode("utf-8"))
+    blob = ff.read()
+
+    m = magic.open(magic.MAGIC_MIME_ENCODING)
+    m.load()
+    encoding = m.buffer(blob)
+
+    in_file = clean(blob.decode(encoding))
     fname = clean(ff.name)
     filename = ".".join(fname.split(".")[:-1])
     ext = fname.split(".")[-1]
@@ -4549,9 +4556,11 @@ def launch(request):
         params["interface"] = "simple"
 
     if "ensemble" in request.POST.keys():
+        e_id = clean(request.POST["ensemble"])
         try:
-            e = Ensemble.objects.get(pk=clean(request.POST["ensemble"]))
+            e = Ensemble.objects.get(pk=e_id)
         except Ensemble.DoesNotExist:
+            logger.info(f"Ensemble with id {e_id} requested, but not found")
             return redirect("/")
 
         if not can_view_ensemble(e, request.user):
@@ -4585,16 +4594,20 @@ def launch(request):
                 if s_num not in avail_nums:
                     return HttpResponse(status=404)
 
-            # TODO: catch possible edge cases
-            init_params = struct.properties.all()[0].parameters
+            if struct.properties.count() > 0:
+                init_params = struct.properties.first().parameters
+                if init_params is not None:
+                    params["init_params_id"] = init_params.id
 
             params["structures"] = s_str
             params["structure"] = struct
-            params["init_params_id"] = init_params.id
         else:
-            init_params = e.structure_set.all()[0].properties.all()[0].parameters
-
-            params["init_params_id"] = init_params.id
+            if e.structure_set.count() > 0:
+                example_struct = e.structure_set.first()
+                if example_struct.properties.count() > 0:
+                    init_params = example_struct.properties.first().parameters
+                    if init_params is not None:
+                        params["init_params_id"] = init_params.id
     elif "calc_id" in request.POST.keys():
         calc_id = clean(request.POST["calc_id"])
 

requirements.txt

@@ -24,6 +24,7 @@ pre-commit
 psutil==5.7.2
 psycopg2
 pysisyphus
+python-magic
 rdkit
 requests
 scipy