Merge branch 'master' of gitlab.pasteur.fr:ippidb/ippidb-web

ippisite/docs/source/conf.py

@@ -54,7 +54,8 @@ extensions = [
     'sphinx.ext.intersphinx',
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
-    'sphinx.ext.graphviz'
+    'sphinx.ext.graphviz',
+    'sphinxcontrib.bibtex'
 ]
 
 # Add any paths that contain templates here, relative to this directory.

ippisite/docs/source/index.rst

@@ -18,6 +18,7 @@ These pages contain the documentation for technical maintenance and development
    install
    configuration
    database
+   webservices
    modules
 
 

ippisite/ippidb/forms.py

@@ -172,20 +172,6 @@ class IdForm(forms.Form):
             .first()
         )
 
-    # def get_or_create(self):
-    #     b = models.Bibliography.objects \
-    #         .filter(id_source=self.cleaned_data["id_source"]).filter(source=self.cleaned_data["source"]) \
-    #         .annotate(used=Count("refcompoundbiblio")) \
-    #         .filter(used=0) \
-    #         .first()
-    #     if b is not None:
-    #         return b, False
-    #     else:
-    #         return models.Bibliography.objects.create(
-    #             source=self.cleaned_data["source"],
-    #             id_source=self.cleaned_data["id_source"],
-    #         ), True
-
 
 """ Step 2 : BibliographyForm """
 
@@ -446,7 +432,6 @@ class ComplexCompositionBaseFormSet(forms.BaseFormSet):
         form_kwargs["nb_copies_in_complex"] = nb_copies_in_complex
         self.has_partner = has_partner
         self.has_bound = has_bound
-        print("kwargs", form_kwargs)
         super().__init__(form_kwargs=form_kwargs, *args, **kwargs)
 
 
@@ -479,7 +464,7 @@ class PpiModelForm(ModelForm):
                 "data-olsontology": "mondo",
                 "data-selectpath": "https://www.ebi.ac.uk/ols/",
                 "olstype": "",
-                "class": ""
+                "class": "",
             }
         ),
     )
@@ -489,12 +474,6 @@ class PpiModelForm(ModelForm):
         required=False,
     )
 
-    # other_diseases = forms.CharField(
-    #     label=_("other_diseases_label"),
-    #     help_text=_("other_diseases_help_text"),
-    #     required=False,
-    # )
-
     class Meta:
         model = models.Ppi
         fields = (
@@ -506,7 +485,6 @@ class PpiModelForm(ModelForm):
             "pockets_nb",  # pockets_nb is Ppi.pockets_nb in the xlsx file of #33
             "ols_diseases",
             "selected_diseases",
-            # 'other_diseases',
         )
         widgets = {
             "id": forms.HiddenInput(),
@@ -533,17 +511,6 @@ class PpiModelForm(ModelForm):
                 self.fields["symmetry"].initial = symmetry.first()
                 self.fields["symmetry"].widget = forms.HiddenInput()
 
-        pdb_id = initial.get("pdb_id", None)
-        if pdb_id is not None:
-            # FIXME move PFAM choice to relevant form ;)
-            pfams = ws.get_pdb_pfam_mapping(pdb_id)  # noqa: F841
-            # choices = self.fields["family_name"].choices
-            # for key, values in pfams.items():
-            #    text = "{} ({})".format(values["name"], key)
-            #    choices.append((text, text))
-            # self.fields["family_name"].choices = choices
-            # self.fields["family_name"].initial = choices[-1][0]
-
     def full_clean(self):
         super().full_clean()
         if hasattr(self, "cleaned_data") and "family_name" in self.cleaned_data:
@@ -571,13 +538,6 @@ class PpiModelForm(ModelForm):
                 name=name, identifier=identifier
             )
             self.instance.diseases.add(disease)
-        # for new_disease in self.cleaned_data['other_diseases'].split(','):
-        #     new_disease = new_disease.strip()
-        #     if len(new_disease) == 0:
-        #         continue
-        #     print(new_disease)
-        #     disease, created = Disease.objects.get_or_create(name=new_disease)
-        #     self.instance.diseases.add(disease)
         self.instance.family = models.PpiFamily.objects.get(
             id=self.cleaned_data["family"]
         )
@@ -878,6 +838,11 @@ class CompoundActivityResultForm(ModelForm):
             "activity": widgets.HiddenInput(),
         }
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        for f in self.fields.values():
+            f.widget.attrs.update({"class": "col-3"})
+
     def has_changed(self):
         """
         Test if the form has changed, we consider that it has not changed if it is not linked to an actual instance and
@@ -1049,7 +1014,7 @@ CompoundActivityResultInlineFormset = inlineformset_factory(
 class TestActivityDescriptionForm(forms.ModelForm):
 
     test_name = CharFieldDataList(
-        data_class=models.TestActivityDescription, data_attr="test_name"
+        data_class=models.TestActivityDescription, data_attr="test_name",
     )
 
     cell_line_name = CharFieldDataList(
@@ -1074,6 +1039,11 @@ class TestActivityDescriptionForm(forms.ModelForm):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.fields["test_type"].widget.attrs["onchange"] = "test_type_changed(this);"
+        self.fields["test_type"].widget.attrs.update({"class": "col-2"})
+        self.fields["test_name"].widget.attrs.update({"class": "col-10"})
+        self.fields["test_modulation_type"].widget.attrs.update({"class": "col-2"})
+        self.fields["nb_active_compounds"].widget.attrs.update({"class": "col-3"})
+        self.fields["cell_line_name"].widget.attrs.update({"class": "col-7"})
 
     def has_changed(self):
         """
@@ -1201,6 +1171,11 @@ class CompoundCytotoxicityResultForm(ModelForm):
         fields = ("compound_name", "toxicity")
         widgets = {"toxicity": forms.Select(choices=((True, "True"), (False, "False")))}
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        for f in self.fields.values():
+            f.widget.attrs.update({"class": "col-3"})
+
     def has_changed(self):
         """
         Test if the form has changed, we consider that it has not changed if it is not linked to an actual instance and
@@ -1315,6 +1290,9 @@ class TestCytotoxDescriptionForm(forms.ModelForm):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.fields["compound_concentration"].required = True
+        self.fields["cell_line_name"].widget.attrs.update({"class": "col"})
+        self.fields["compound_concentration"].widget.attrs.update({"class": "col"})
+        self.fields["test_name"].widget.attrs.update({"class": "col"})
 
     def has_changed(self):
         """
@@ -1413,6 +1391,13 @@ class CompoundPKResultForm(ModelForm):
             )
         }
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        for f in self.fields.values():
+            f.widget.attrs.update({"class": "col-3"})
+            if isinstance(f, forms.BooleanField) and not isinstance(f.widget, forms.Select):
+                f.widget.attrs.update({"class": "col-3 mb-4"})
+
     def has_changed(self):
         """
         Test if the form has changed, we consider that it has not changed if it is not linked to an actual instance and
@@ -1524,6 +1509,8 @@ class TestPKDescriptionForm(forms.ModelForm):
         super().__init__(*args, **kwargs)
         for f in ["administration_mode", "dose"]:
             self.fields[f].required = True
+        for f in self.fields.values():
+            f.widget.attrs.update({"class": "col-3"})
 
     def has_changed(self):
         """

ippisite/ippidb/migrations/0063_fill_drugbank_links.py

@@ -3,13 +3,13 @@
 from django.db import migrations, models
 import django.db.models.deletion
 
-from ippidb.models import Compound, DrugBankCompound
-
 def run_generate_drugbank_inchikey(apps, schema_editor):
+    DrugBankCompound = apps.get_model("ippidb", "DrugBankCompound")
     for drugbank_compound in DrugBankCompound.objects.all():
         drugbank_compound.save(autofill=True)
 
 def set_compound_drugbank_links(apps, schema_editor):
+    Compound = apps.get_model("ippidb", "Compound")
     for compound in Compound.objects.all():
         compound.set_drugbank_link()
         compound.save()

ippisite/ippidb/migrations/0065_compound_replaced_with.py

+# Generated by Django 2.2.1 on 2020-09-14 18:02
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('ippidb', '0064_proteindomaincomplex_polymorphic_ctype'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='compound',
+            name='replaced_with',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, to='ippidb.Compound', verbose_name='Replacement ID'),
+        ),
+    ]

ippisite/ippidb/models.py

@@ -8,6 +8,7 @@ import operator
 import re
 import sys
 
+from boltons.iterutils import flatten, unique_iter
 from django.conf import settings
 from django.contrib.auth import get_user_model
 from django.core.exceptions import ValidationError
@@ -570,11 +571,13 @@ class CompoundsManager(models.Manager):
         qs = self.get_queryset()
         if current_user.is_anonymous:
             qs = qs.exclude(compoundaction__ppi__contribution__validated=False)
+            qs = qs.filter(replaced_with__isnull=True)
         elif not current_user.is_superuser:
             qs = qs.exclude(
                 Q(compoundaction__ppi__contribution__validated=False),
                 ~Q(compoundaction__ppi__contribution__contributor=current_user),
             )
+            qs = qs.filter(replaced_with__isnull=True)
         return qs
 
     def validated(self):
@@ -865,6 +868,14 @@ class Compound(AutoFillableModel):
         verbose_name="Number of tests available", null=True, blank=True
     )
 
+    replaced_with = models.ForeignKey(
+        "self",
+        verbose_name="Replacement ID",
+        null=True,
+        blank=True,
+        on_delete=models.PROTECT,
+    )
+
     class Meta:
         ordering = ["id"]
         indexes = [
@@ -975,6 +986,20 @@ class Compound(AutoFillableModel):
             .count()
         )
 
+    @property
+    def pk_tests_count(self):
+        """
+        Return the number of associated pharmacokinetic tests
+        """
+        return self.compoundpkresult_set.all().count()
+
+    @property
+    def cytotoxicity_tests_count(self):
+        """
+        Return the number of associated cytotoxicity tests
+        """
+        return self.compoundcytotoxicityresult_set.all().count()
+
     @property
     def sorted_similar_drugbank_compounds(self):
         """
@@ -1072,6 +1097,59 @@ class Compound(AutoFillableModel):
         """
         return reverse("compound_card", kwargs={"pk": self.pk})
 
+    @property
+    def pubchem_url(self):
+        """
+        Get absolute URL to the corresponding PubChem entry
+        """
+        return (
+            f"https://pubchem.ncbi.nlm.nih.gov/compound/{ self.pubchem_id }"
+            if self.pubchem_id
+            else None
+        )
+
+    @property
+    def chembl_url(self):
+        """
+        Get absolute URL to the corresponding Chembl entry
+        """
+        return (
+            f"https://www.ebi.ac.uk/chembldb/compound/inspect/{ self.chembl_id }"
+            if self.chembl_id
+            else None
+        )
+
+    @property
+    def chemspider_url(self):
+        """
+        Get absolute URL to the corresponding ChemSpider entry
+        """
+        return (
+            f"http://www.chemspider.com/Chemical-Structure.{ self.chemspider_id}.html"
+            if self.chemspider_id
+            else None
+        )
+
+    @property
+    def pdbligand_url(self):
+        """
+        Get absolute URL to the corresponding PDB ligand entry
+        """
+        return (
+            f"https://www.rcsb.org/ligand/{ self.ligand_id}" if self.ligand_id else None
+        )
+
+    @property
+    def drugbank_url(self):
+        """
+        Get absolute URL to the corresponding Drugbank entry
+        """
+        return (
+            f"https://www.drugbank.ca/drugs/{ self.drugbank_id}"
+            if self.drugbank_id
+            else None
+        )
+
     def clean(self):
         """
         Perform additional checks:
@@ -1097,7 +1175,9 @@ class Compound(AutoFillableModel):
         Replace the references to a given compound in the data with
         references to another new compound. used to deal with
         duplicates in the database
+        also delete this object
         """
+        self.replaced_with = replacing_compound
         for ref in RefCompoundBiblio.objects.filter(compound=self):
             ref.compound = replacing_compound
             ref.save()
@@ -1118,6 +1198,60 @@ class Compound(AutoFillableModel):
         CompoundTanimoto.objects.filter(compound=self).delete()
         DrugbankCompoundTanimoto.objects.filter(compound=self).delete()
 
+    def get_target_activities_table(self):
+        """
+        Return test activity result data as a list of
+        items containing for each PPI family the compound
+        was tested against, the best activity, the linked diseases
+        and the modulation types
+        """
+        ppi_families = [
+            item["test_activity_description__ppi__family"]
+            for item in self.compoundactivityresult_set.filter(
+                ~Q(activity_type="KdRat")
+            )
+            .order_by()
+            .values("test_activity_description__ppi__family")
+            .distinct()
+        ]
+        results = []
+        for ppi_family in ppi_families:
+            family_compound_activity_results = self.compoundactivityresult_set.filter(
+                ~Q(activity_type="KdRat")
+            ).filter(test_activity_description__ppi__family__id=ppi_family)
+            best_activity = (
+                family_compound_activity_results.order_by("-activity")
+                .values("activity")
+                .first()["activity"]
+            )
+            diseases = list(
+                unique_iter(
+                    flatten(
+                        [
+                            list(fcar.test_activity_description.ppi.diseases.all())
+                            for fcar in family_compound_activity_results
+                        ]
+                    )
+                )
+            )
+            modulation_types = list(
+                set(
+                    [
+                        fcar.get_modulation_type_display()
+                        for fcar in family_compound_activity_results
+                    ]
+                )
+            )
+            results.append(
+                {
+                    "family": PpiFamily.objects.get(id=ppi_family),
+                    "best_activity": best_activity,
+                    "diseases": diseases,
+                    "modulation_types": modulation_types,
+                }
+            )
+        return results
+
 
 class CompoundTanimoto(models.Model):
     canonical_smiles = models.TextField("Canonical Smile")
@@ -1495,21 +1629,14 @@ class ContributionManager(models.Manager):
         if current_user.is_anonymous:
             qs = qs.exclude(validated=False)
         elif not current_user.is_superuser:
-            qs = qs.exclude(
-                Q(validated=False),
-                ~Q(contributor=current_user),
-            )
+            qs = qs.exclude(Q(validated=False), ~Q(contributor=current_user),)
         return qs
 
     def validated(self):
         """
         Get validated contributions
         """
-        return (
-            super()
-            .get_queryset()
-            .exclude(validated=False)
-        )
+        return super().get_queryset().exclude(validated=False)
 
 
 class Contribution(models.Model):
@@ -1551,11 +1678,6 @@ def update_compound_cached_properties(compounds_queryset=None):
         )
         c.save()
     compounds_queryset.update(
-        pubs=Subquery(
-            compounds_queryset.filter(id=OuterRef("id"))
-            .annotate(_pubs=Count("refcompoundbiblio", distinct=True))
-            .values("_pubs")[:1]
-        ),
         best_activity=Subquery(
             compounds_queryset.filter(id=OuterRef("id"))
             .annotate(
@@ -1566,23 +1688,23 @@ def update_compound_cached_properties(compounds_queryset=None):
             )
             .values("_best_activity")[:1]
         ),
+    )
+    compounds_queryset.update(
+        pubs=Subquery(
+            compounds_queryset.filter(id=OuterRef("id"))
+            .annotate(_pubs=Count("refcompoundbiblio", distinct=True))
+            .values("_pubs")[:1]
+        ),
         le=Subquery(
             compounds_queryset.filter(id=OuterRef("id"))
             .annotate(
-                _le=Cast(
-                    1.37 * Max("compoundactivityresult__activity") / F("nb_atom_non_h"),
-                    FloatField(),
-                )
+                _le=Cast(1.37 * F("best_activity") / F("nb_atom_non_h"), FloatField(),)
             )
             .values("_le")[:1]
         ),
         lle=Subquery(
             compounds_queryset.filter(id=OuterRef("id"))
-            .annotate(
-                _lle=Cast(
-                    Max("compoundactivityresult__activity") - F("a_log_p"), FloatField()
-                )
-            )
+            .annotate(_lle=Cast(F("best_activity") - F("a_log_p"), FloatField()))
             .values("_lle")[:1]
         ),
         lipinsky_mw=Subquery(
@@ -1814,11 +1936,9 @@ def update_compound_cached_properties(compounds_queryset=None):
             )
             .values("_bindtest_av")[:1]
         ),
-        pktest_av=Exists(
-            CompoundPKResult.objects.filter(id=OuterRef("id"))
-        ),
+        pktest_av=Exists(CompoundPKResult.objects.filter(compound__id=OuterRef("id"))),
         cytoxtest_av=Exists(
-            CompoundCytotoxicityResult.objects.filter(id=OuterRef("id"))
+            CompoundCytotoxicityResult.objects.filter(compound__id=OuterRef("id"))
         ),
         insilico_av=Subquery(
             compounds_queryset.filter(id=OuterRef("id"))

ippisite/ippidb/static/css/admin-session.css

@@ -225,7 +225,7 @@ Description: IPPI-DB Theme
 
 .input_field {
   width: 100%;
-  margin-right: 2px;
+  margin-right: 0px;
   font-family: "BrandonGrotesqueReg";
   text-align: left;
   margin-top: 0px;
@@ -268,6 +268,10 @@ Description: IPPI-DB Theme
   padding-bottom: 1%;
 }
 
+.form-group.form-check{
+    padding-left: 2.25rem;
+}
+
 .form-group.form-check, .compound .input_field input {
   text-align: left;
 }
@@ -356,6 +360,9 @@ Description: IPPI-DB Theme
 .formset-item .formset-item-delete-host {
   font-size: initial;
   text-align: right;
+  position: absolute;
+  right: 3em;
+  margin-top: -4em;
 }
 
 .formset-item-delete-host input {
@@ -1352,6 +1359,7 @@ Description: IPPI-DB Theme
 .test_title {
   text-align: left;
   margin-top: 15px;
+  margin-bottom: 1.5em;
 }
 
 .tests {

ippisite/ippidb/static/js/ActivityDescriptionFormSet.js

 function test_type_changed(source){
      var cell_line_input = document.getElementById(source.id.replace("test_type","cell_line_name")).parentNode;
      if (source.value=="CELL"){
-        cell_line_input.style.display = '';
+        cell_line_input.style.visibility = '';
      }else{
-        cell_line_input.style.display = 'none';
+        cell_line_input.style.visibility = 'hidden';
      }
 }
\ No newline at end of file

ippisite/ippidb/static/js/wizard_formset_with_nested_formset.js

@@ -23,7 +23,11 @@ function add_nested_form_to_nested_formset(source, prefix, parent_prefix){
         .find(".formset-nested-item")[0]
         .outerHTML;
 
-    current_item_name = $(source).closest(".formset-item").children("input")[0].name;
+    if($(source).closest(".formset-item").children("input").length>0){
+        current_item_name = $(source).closest(".formset-item").children("input")[0].name;
+    }else{
+        current_item_name = $(source).closest(".formset-item").children("div").children("input")[0].name;
+    }
     current_item_name = current_item_name.substring(parent_prefix.length+1,current_item_name.indexOf('-',parent_prefix.length+1));
     empty_form_as_str = empty_form_as_str.replace(
         new RegExp(parent_prefix+"-__prefix__","g"),

ippisite/ippidb/tasks.py

@@ -625,7 +625,7 @@ def launch_validate_contributions(contribution_ids: List[int]):
                 run_update_compound_cached_properties.s(),
                 run_compute_drugbank_similarity.s(),
                 run_validate.s(),
-            )
+            ),
         )
         contribution_jobs.append(compounds_properties_computation_group)
         # compounds_properties_computation_group.delay()

ippisite/ippidb/templates/compound_card.html

@@ -6,7 +6,8 @@
 <script src="/static/js/ippidb-charts.js" type="text/javascript"></script>
 {% endblock %}
 
-{% block title %}compound {{ compound.id }} detail{% if compound.common_name %} ({{compound.common_name}}){% endif %}{% endblock %}
+{% block title %}compound {{ compound.id }} detail{% if compound.common_name %}
+({{compound.common_name}}){% endif %}{% endblock %}
 
 {% block content %}
 <div id="mainnav">
@@ -36,7 +37,9 @@
       {% include "compound_smiles_draw.html" with id=compound.id smile=compound.canonical_smile width=250 height=250%}
       <div style="display: flex;
       align-items: center;">
-        {% if compound.is_validated is False %}
+        {% if compound.replaced_with is not None %}
+        <h1 class="page-title-warning" style="margin: 0;">Compound {{ compound.id }} - This compound is replaced with <a href="/compounds/{{ compound.replaced_with.id }}">compound {{ compound.replaced_with.id }}</a> </h1>
+        {% elif compound.is_validated is False %}
         <h1 class="page-title-warning" style="margin: 0;">Compound {{ compound.id }} - This compound has not been
           validated by a curator yet, data might be incomplete or
           inaccurate</h1>
@@ -52,7 +55,7 @@
   <div class="row" style="display: inline-block;height:auto; margin-right: 15px; margin-left: 15px;">
     <div class="tab-content" id="tabContent">
       <div class="tab-pane fade show active" id="compound" role="tabpanel" aria-labelledby="compound-tab">
-        <div class="card">
+        <div class="card inner-wrap">
           <div class="card-body">
             {% include "compound_l_item.html" with compound=compound show_detail=True %}
           </div>
@@ -61,7 +64,8 @@
       <div class="tab-pane fade" id="physicochemistry" role="tabpanel" aria-labelledby="physicochemistry-tab">
         <div class="row d-flex justify-content-center">
           <div class="col-sm-12 col-md-9" style="margin: 10px;">
-            <h5 class="card_title">Physicochemical filters <span class="info_point" onclick="showLegend('show_legend_physico')"><i class="fas fa-info-circle"></i></span>
+            <h5 class="card_title">Physicochemical filters <span class="info_point"
+                onclick="showLegend('show_legend_physico')"><i class="fas fa-info-circle"></i></span>
             </h5>
             <div id="show_legend_physico" style="display: none; padding:8px;">
               <div class="row d-flex justify-content-center" style="    box-shadow: 0 3px 11px 0 rgba(0, 0, 0, 0.2);
@@ -212,7 +216,7 @@
                     <td class="text-center {% status_class compound.veber_tpsa %}" title="TPSA <= 140">
                     </td>
                     <td class="text-center {% status_class compound.pfizer_tpsa %}" title="TPSA >= 75">
-                    </tr>
+                  </tr>
                   <tr>
                     <th scope="row">RB</th>
                     <td>{{ compound.nb_rotatable_bonds | default_if_none:"not available"}}</td>
@@ -224,94 +228,96 @@
                 </tbody>