Merge branch 'master' into 'release'

Prepare for v1.1.1

See merge request !30

.gitlab-ci.yml

@@ -18,6 +18,7 @@ test-ansible:
       - pip3.5 install ansible
       - cd ansible
       - whoami
+      - ansible-galaxy collection install ansible.posix
       - ansible-playbook system.yaml --syntax-check 
       - ansible-playbook deploy.yaml --syntax-check 
 
@@ -98,6 +99,7 @@ deploy-webserver-targetcentric:
     - pip3.5 install ansible
     - cd ansible
     - whoami
+    - ansible-galaxy collection install ansible.posix
     - ansible-playbook -vvv -i ./hosts_master deploy.yaml 
       --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_targetcentric galaxy_base_url=$GALAXY_BASE_URL_targetcentric galaxy_apikey=$GALAXY_APIKEY_targetcentric galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_targetcentric secret_key=$SECRET_KEY_targetcentric dbname=$DBNAME_targetcentric dbuser=$DBUSER_targetcentric dbpassword=$DBPASSWORD_targetcentric dbhost=$DBHOST_targetcentric dbport=$DBPORT_targetcentric http_port=$HTTP_PORT_targetcentric branch=$CI_COMMIT_REF_NAME gacode=$GACODE_targetcentric ippidb_media=$IPPIDB_MEDIA_targetcentric"
   only:
@@ -121,6 +123,7 @@ deploy-webserver-test:
     - pip3.5 install ansible
     - cd ansible
     - whoami
+    - ansible-galaxy collection install ansible.posix
     - ansible-playbook -vvv -i ./hosts_master deploy.yaml 
       --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_master galaxy_base_url=$GALAXY_BASE_URL_master galaxy_apikey=$GALAXY_APIKEY_master galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_master secret_key=$SECRET_KEY_master dbname=$DBNAME_master dbuser=$DBUSER_master dbpassword=$DBPASSWORD_master dbhost=$DBHOST_master dbport=$DBPORT_master http_port=$HTTP_PORT_master branch=$CI_COMMIT_REF_NAME gacode=$GACODE_master ippidb_media=$IPPIDB_MEDIA_master"
   only:
@@ -144,6 +147,7 @@ deploy-webserver-production:
     - pip3.5 install ansible
     - cd ansible
     - whoami
+    - ansible-galaxy collection install ansible.posix
     - ansible-playbook -vvv -i ./hosts_release deploy.yaml 
       --extra-vars "deploy_user_name=ippidb repo_api_token=JZS-4cH7bWkFkHa2rAVf marvinjs_apikey=$MARVINJS_APIKEY_release galaxy_base_url=$GALAXY_BASE_URL_release galaxy_apikey=$GALAXY_APIKEY_release galaxy_compoundproperties_workflowid=$GALAXY_COMPOUNDPROPERTIES_WORKFLOWID_release secret_key=$SECRET_KEY_release dbname=$DBNAME_release dbuser=$DBUSER_release dbpassword=$DBPASSWORD_release dbhost=$DBHOST_release dbport=$DBPORT_release http_port=$HTTP_PORT_release branch=$CI_COMMIT_REF_NAME  gacode=$GACODE_release ippidb_media=$IPPIDB_MEDIA_release"
   only:

ansible/deploy.yaml

@@ -7,7 +7,7 @@
   gather_facts: yes
   tasks:
     - name: Disable SELinux
-      selinux:
+      ansible.posix.selinux:
         state: disabled
     - name: Create celery user
       user: name=celery-{{ http_port }} groups={{ deploy_user_name }} append=yes state=present createhome=yes 
@@ -350,14 +350,14 @@
     - name: Enable firewalld
       service: name=firewalld state=started enabled=yes
     - name: open http firewall service
-      firewalld:
+      ansible.posix.firewalld:
         service: http
         zone: public
         immediate: yes
         permanent: true
         state: enabled
     - name: open http firewall port
-      firewalld:
+      ansible.posix.firewalld:
         port: "{{ http_port }}/tcp"
         zone: public
         permanent: true

ansible/system.yaml

@@ -42,16 +42,16 @@
     # disable SELinux, and open firewall to incoming http 
     - name: disable SELinux
       become: true
-      selinux:
+      ansible.posix.selinux:
         state: disabled
     - name: Open firewall to HTTP traffic
-      firewalld:
+      ansible.posix.firewalld:
         service: http
         permanent: true
         state: enabled
       become: true
     - name: Open firwall to port 80 81 traffic
-      firewalld:
+      ansible.posix.firewalld:
         port: "{{ http_port }}/tcp"
         permanent: true
         state: enabled

ippisite/ippidb/management/commands/update_mrc_files.py

@@ -18,6 +18,17 @@ def dir_path(string):
         raise NotADirectoryError(string)
 
 
+def isolevel_float(arg):
+    """ Type function for argparse - a float within some predefined bounds """
+    try:
+        f = float(arg)
+    except ValueError:
+        raise CommandError("Must be a floating point number")
+    if f < 0 or f > 1.0:
+        raise CommandError("Argument must be < 1.0 and > 0")
+    return f
+
+
 class Command(AppCommand):
     """
     Command to update mrc files
@@ -26,7 +37,12 @@ class Command(AppCommand):
     help = "liste all mrc files in a directory and update files in the database"
 
     def __init__(
-        self, stdout=None, stderr=None, no_color=False, force_color=False, task=None,
+        self,
+        stdout=None,
+        stderr=None,
+        no_color=False,
+        force_color=False,
+        task=None,
     ):
         super(Command, self).__init__(
             stdout=stdout, stderr=stderr, no_color=no_color, force_color=force_color
@@ -38,7 +54,10 @@ class Command(AppCommand):
 
     def add_arguments(self, parser):
         parser.add_argument(
-            "-mp", "--mrcpath", type=dir_path, help="root directory with all mrc files",
+            "-mp",
+            "--mrcpath",
+            type=dir_path,
+            help="root directory with all mrc files",
         )
         parser.add_argument(
             "-pa",
@@ -61,6 +80,14 @@ class Command(AppCommand):
             dest="label",
             help="label for files, used as label in the interface",
         )
+        parser.add_argument(
+            "-di",
+            "--default_isolevel",
+            dest="default_isolevel",
+            help="isolevel default value",
+            default=0.7,
+            type=isolevel_float,
+        )
 
     def handle(self, *args, **options):
         """
@@ -75,7 +102,9 @@ class Command(AppCommand):
         if typefile == "druggability":
             storage_path = Chain.mrc_file.field.storage.path("content/mrc_files")
         else:
-            storage_path = InteractFile.interact_file.field.storage.path("content/interact_files")
+            storage_path = InteractFile.interact_file.field.storage.path(
+                "content/interact_files"
+            )
         if not os.path.exists(storage_path):
             os.makedirs(storage_path)
         list_files = glob.glob(os.path.join(mrcpath, pattern))
@@ -108,13 +137,18 @@ class Command(AppCommand):
                     with open(data, "rb") as f:
                         dbchains[0].mrc_file.delete()
                         dbchains[0].mrc_file.save(os.path.basename(data), File(f))
+                        dbchains[0].default_isolevel = options["default_isolevel"]
+                        dbchains[0].save()
                 else:
                     interactfile, created = InteractFile.objects.get_or_create(
-                        chain=dbchains[0], label=label
+                        chain=dbchains[0],
+                        label=label,
                     )
                     with open(data, "rb") as f:
                         interactfile.interact_file.delete()
                         interactfile.interact_file.save(os.path.basename(data), File(f))
+                    interactfile.default_isolevel = options["default_isolevel"]
+                    interactfile.save()
                 self.stdout.write(
                     self.style.SUCCESS(
                         "File mrc {}, have been saved in Chain, pdb: {}, chain: {}".format(
@@ -126,7 +160,8 @@ class Command(AppCommand):
                 self.stdout.write(
                     self.style.WARNING(
                         "WARNING: Chain, pdb: {}, chain: {} doesn't exist".format(
-                            pdb, chain,
+                            pdb,
+                            chain,
                         )
                     )
                 )

ippisite/ippidb/migrations/0068_auto_20210310_1052.py

+# Generated by Django 2.2.1 on 2021-03-10 10:52
+
+from django.db import migrations, models
+
+
+def init_isolevel(apps, schema_editor):
+    Chain = apps.get_model("ippidb", "Chain")
+    InteractFile = apps.get_model("ippidb", "InteractFile")
+    Chain.objects.all().update(default_isolevel=0.5)
+
+    InteractFile.objects.filter(label="all").update(default_isolevel=0.7)
+    InteractFile.objects.filter(label="hydrophobic").update(default_isolevel=0.3)
+    InteractFile.objects.filter(label="hbond donor-acceptor").update(
+        default_isolevel=0.3
+    )
+    InteractFile.objects.filter(label="negative").update(default_isolevel=0.08)
+    InteractFile.objects.filter(label="positive").update(default_isolevel=0.05)
+    InteractFile.objects.filter(label="backbone").update(default_isolevel=0.18)
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("ippidb", "0067_metainformation_normalize_factor"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="chain",
+            name="default_isolevel",
+            field=models.FloatField(default=0.7, verbose_name="Default isolevel value"),
+        ),
+        migrations.AddField(
+            model_name="interactfile",
+            name="default_isolevel",
+            field=models.FloatField(default=0.7, verbose_name="Default isolevel value"),
+        ),
+        migrations.RunPython(init_isolevel, reverse_code=migrations.RunPython.noop),
+    ]

ippisite/ippidb/models/targetcentric.py

@@ -132,9 +132,13 @@ class Chain(models.Model):
         verbose_name="pdb file content with only one chain", default="no pdb file"
     )
     mrc_file = models.FileField(upload_to=content, blank=True)
+    default_isolevel = models.FloatField(
+        default=0.7, verbose_name="Default isolevel value"
+    )
 
     class Meta:
         unique_together = ("pdb", "pdb_chain_id")
+        ordering = ["pdb", "pdb_chain_id"]
 
     def is_partner(self):
         return self.partner_set.count()
@@ -156,6 +160,9 @@ class InteractFile(models.Model):
     chain = models.ForeignKey(Chain, on_delete=models.CASCADE)
     label = models.CharField(max_length=250, blank=False, null=False)
     interact_file = models.FileField(upload_to=contentinteract, blank=True)
+    default_isolevel = models.FloatField(
+        default=0.7, verbose_name="Default isolevel value"
+    )
 
     def __unicode__(self):
         return "{}".format(self.interact_file)
@@ -356,6 +363,7 @@ class Cavity(models.Model):
     class Meta:
         unique_together = ("full_name", "chain", "cavity_number", "partner")
         verbose_name_plural = "Cavities"
+        ordering = ["chain", "cavity_number"]
 
     @property
     def near_cavities(self):
@@ -415,22 +423,35 @@ class MetaInformation(models.Model):
     """
 
     average = models.DecimalField(
-        verbose_name="Average", max_digits=11, decimal_places=8
+        verbose_name="Average",
+        max_digits=11,
+        decimal_places=8,
+        help_text="partial matrix mean value",
     )
     std = models.DecimalField(
-        verbose_name="Standard Deviation", max_digits=11, decimal_places=8
+        verbose_name="Standard Deviation",
+        max_digits=11,
+        decimal_places=8,
+        help_text="partial matrix standard deviation",
     )
     maximum = models.DecimalField(
-        verbose_name="Maximum", max_digits=11, decimal_places=8
+        verbose_name="Maximum",
+        max_digits=11,
+        decimal_places=8,
+        help_text="partial matrix maximum value",
     )
     minimum = models.DecimalField(
-        verbose_name="Minimum", max_digits=11, decimal_places=8
+        verbose_name="Minimum",
+        max_digits=11,
+        decimal_places=8,
+        help_text="partial matrix minimum value",
     )
     normalize_factor = models.DecimalField(
         blank=True,
         null=True,
         default=4.58599730,
         verbose_name="Normalize Factor",
+        help_text="complet matrix standard deviation",
         max_digits=11,
         decimal_places=8,
     )

ippisite/ippidb/serializer.py

@@ -57,7 +57,7 @@ class ChainDistanceSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Chain
-        fields = ("id", "pdb_chain_id", "protein", "pdb")
+        fields = ("id", "pdb_chain_id", "protein", "pdb", "default_isolevel")
 
 
 class PartnerDistanceSerializer(serializers.ModelSerializer):
@@ -121,6 +121,7 @@ class ChainSerializer(serializers.ModelSerializer):
             "cavity_set",
             "partner_set",
             "mrc_file",
+            "default_isolevel",
             "interactfile_set",
         )
 

ippisite/ippidb/static/css/main.css

@@ -356,10 +356,47 @@ div.hidden {
 
 /* -- Home page choices -- */
 
-.background_choices {
-    margin: 40px;
+.compound_choices {
     position: relative;
-    background: #e3e9eb url(/static/images/Other/cross.png) 50px 100px no-repeat;
+    background: #E3E9EB url(/static/images/Other/cross.png) 50px 100px no-repeat;
+    text-align: center;
+    height: fit-content;
+    box-shadow:  0 3px 11px 0 rgb(0 0 0 / 20%);
+}
+
+.compound_background {
+    position: relative;
+    background: #E3E9EB url(/static/images/Other/cross.png) 50px 100px no-repeat;
+    text-align: center;
+    height: fit-content;
+}
+
+.compound_choices:hover{
+    background: #D1DBDE url(/static/images/Other/cross.png) 50px 100px no-repeat;
+}
+
+.pocket_choices {
+    position: relative;
+    background: #AABDC3 url(/static/images/Other/cross.png) 50px 100px no-repeat;
+    text-align: center;
+    height: fit-content;
+    box-shadow:  0 3px 11px 0 rgb(0 0 0 / 20%);
+}
+
+.pocket_choices:hover {
+    background: #97ADB5 url(/static/images/Other/cross.png) 50px 100px no-repeat;
+}
+
+.pocket_background {
+    position: relative;
+    background: #AABDC3 url(/static/images/Other/cross.png) 50px 100px no-repeat;
+    text-align: center;
+    height: fit-content;
+}
+
+.icons {
+    padding: 10%;
+    font-size: 1.5em;
 }
 
 .choices_background {
@@ -448,6 +485,15 @@ div.hidden {
     display:block;
   }
 
+  .front-vertical-align {
+      padding-top: 80px;
+  }
+
+  .back-vertical-align {
+      padding-top: 25px;
+  }
+
+
 /* -- Breadcrumb -- */
 
 .breadNav {
@@ -1221,3 +1267,47 @@ div.hidden {
 .btn.float-right+.btn.float-right {
     margin-right: 5px
 }
+
+/* Modal */
+
+.modal-xl {
+    width:  100%;
+    max-width:1200px;
+    height: fit-content;
+    max-height: 1200px;
+}
+
+.close_choices_modal {
+    margin: 0px !important;
+    right: 32px !important;
+    top: 32px !important;
+    width: 32px !important;
+    height: 32px !important;
+    opacity: 0.5;
+    border: none !important;
+    color: #495057 !important;
+    cursor: pointer;
+    float: right;
+    text-align: right;
+    font-size: 2em;
+    background-color: white !important;
+}
+
+.close_choices_modal:hover {
+    opacity: 1;
+}
+
+.align_modal {
+    display: inline-block;
+}
+
+.modal_choices_title {
+    float: left;
+    text-align: right;
+    font-family: "PlayfairDisplayReg";
+    font-size: 2em;
+}
+
+.fade_index {
+    transition: opacity 1s linear;
+  }
\ No newline at end of file

ippisite/ippidb/static/css/targetcentric.css

@@ -134,7 +134,18 @@ Description: IPPI-DB targetcentric Theme
 
 .dropbtn {
   font-size: 14px;
-  color: #007bff
+  color: #2D96FA;
+  border-radius: 5px;
+  border-color: #97ADB5;
+  background-color: #eff3f5;
+  padding-right: 3px;
+  padding-left: 3px;
+  padding-bottom: 1px;
+  padding-top: 1px;
+  border-style: solid;
+  border-width: 2px;
+  min-width: 25px;
+  text-align: center;
 }
 
 .dropdown {
@@ -145,12 +156,16 @@ Description: IPPI-DB targetcentric Theme
 .dropdown-content {
   display: none;
   position: absolute;
-  bottom: 24px; 
-  left: 14px;
-  background-color: #f1f1f1;
+  bottom: 22px; 
+  left: 12px;
+  background-color: #eff3f5;
   min-width: 100px;
-  box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2);
+  box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.4);
   z-index: 3;
+  border-radius: 5px;
+  border-color: #97adb5 !important;
+  border: 2px;
+  border-style: solid;
 }
 
 .dropdown-content a {
@@ -161,25 +176,28 @@ Description: IPPI-DB targetcentric Theme
   display: block;
 }
 
-.dropdown-content a:hover {background-color: #ddd;}
+.dropdown-content a:hover {
+  background-color: #d3dee2; 
+  color: black;
+  border-radius: 5px;
+}
 
 .dropdown:hover .dropdown-content {display: block;}
 
-.dropdown:hover .dropbtn {background-color: #ddd;}
-
-a.infobulle{
-  color:#ccc;               
+.dropdown:hover .dropbtn {
+  background-color: #d3dee2; 
+  color: black;
 }
 
-a.infobulle:hover, a.infobulle:focus{
-  color:#17a2b8;
+
+.infobulle svg{
+  color: rgb(45, 150, 250);
 }
 
-a.infobulle span{
+.infobulle span{
   position:absolute;
   color:white;
-  margin-top:23px;
-  margin-left:0px;
+  bottom: 100%;
   background:rgba(0,0,0,.9);
   padding:15px;
   border-radius:3px;
@@ -190,7 +208,7 @@ a.infobulle span{
   z-index: 3;
 }
 
-a.infobulle:hover span, a.infobulle:focus span{
+.infobulle:hover span, .infobulle:focus span{
   transform:scale(1) rotate(0);
   opacity:1;
 }
@@ -207,3 +225,12 @@ table.gradiant td{
   white-space: nowrap;
   text-align: left;
 }
+
+.fa-plus-square {
+  box-shadow: 0 0 2px rgba(0,0,0,.5);
+}
+
+th .fa-plus-square:hover {
+  background-color: black;
+  color: rgb(255, 255, 255);
+}
\ No newline at end of file

ippisite/ippidb/static/js/ippidb.js

@@ -278,3 +278,10 @@ var toggleCheckBox = function (id) {
         queryUrl.changeSelection(id, null);
     }
 }
+
+$(document).ready(function () {
+    $(".modalhref").click(function(e){
+        $(".modal").modal('hide');
+        window.open($(this).find("a").last()[0].href, '_self');
+    });
+});
\ No newline at end of file

ippisite/ippidb/static/js/targetcentric.js

@@ -366,20 +366,29 @@ function loadNGL(url, callback){
             // Handle window resizing
             var divflex = createElement("div",{},{},"d-flex justify-content-between flex-row-reverse bd-highlight");
             var divmultiButtonright = createElement("div",{role: "group"},{},"d-flex align-items-end flex-column");
-            var divcavitiesButton  = createElement("div",{role: "group"},{},"btn-group-vertical btn-group-sm btn-group-toggle p-2");
+            var divcavitiesButton  = createElement("div",{role: "group"},{},"infobulle btn-group-vertical btn-group-sm btn-group-toggle p-2");
+            var spaninfocav = createElement("span", {}, {}, '');
+            spaninfocav.innerHTML = "Load a pocket detected with Volsite (Desaphy et al., 2012).";
+            divcavitiesButton.appendChild(spaninfocav);
             divmultiButtonright.appendChild(divcavitiesButton);
             var divmultiButtoncenter = createElement("div",{},{}, "btn-group-vertical align-self-start");
             var divmultiButtonleft = createElement("div", {}, {}, "btn-group align-self-start");
             divflex.appendChild(divmultiButtonright);
             divflex.appendChild(divmultiButtoncenter);
             divflex.appendChild(divmultiButtonleft);
-            var divslider = createElement("div", {}, {}, 'form-group border border-info rounded p-2');
+            var divslider = createElement("div", {}, {}, 'infobulle form-group border border-info rounded p-2');
+            var spaninfodrug = createElement("span", {}, {}, '');
+            spaninfodrug.innerHTML = "Druggability has been determined by our Deep Learning tool InDeep trained on protein/ligand interactions. They are represented as isolevel probabilities, which you can adjust with the slider (0,1)."
+            divslider.appendChild(spaninfodrug);
             titledruggable = createElement("strong", {}, {}, '');
-            titledruggable.innerHTML = "Predictive Druggability";
+            titledruggable.innerHTML = "Predicted druggability";
             divslider.appendChild(titledruggable);
-            var divsliderinteractibility = createElement("div", {}, {}, 'form-group border border-info rounded p-2 mr-2');
+            var divsliderinteractibility = createElement("div", {}, {}, 'infobulle form-group border border-info rounded p-2 mr-2');
+            var spaninfoint = createElement("span", {}, {"right":"50%"}, '');
+            spaninfoint.innerHTML = "Interactability has been determined by our Deep Learning tool InDeep trained on protein-protein interactions. They are represented as isolevel probabilities, which you can adjust with the slider (0,1)."
+            divsliderinteractibility.appendChild(spaninfoint);
             titleinteractible = createElement("strong", {}, {}, '');
-            titleinteractible.innerHTML = "Predictive Interactibility";
+            titleinteractible.innerHTML = "Predicted Interactability";
             divsliderinteractibility.appendChild(titleinteractible);
             divmultiButtonleft.appendChild(divsliderinteractibility);
             divmultiButtonleft.appendChild(divslider);
@@ -388,7 +397,7 @@ function loadNGL(url, callback){
                 }, false );
             var hasmrc = 0
             var hasinteract = 0
-            pdb.chain_set.reverse().forEach(function(chain, indexchain){
+            pdb.chain_set.forEach(function(chain, indexchain){
                 var blobchain = new Blob( [ chain.file_content ], {type: 'text/plain'} );
                 var componentname = pdb.code +  '_' + chain.pdb_chain_id;
                 stage.loadFile( blobchain, {ext:"pdb", name: componentname}).then( function( o ){
@@ -410,7 +419,7 @@ function loadNGL(url, callback){
 
                     hasinteract = 1;
                     var labelsliderinterac = createElement("label", {}, {}, "", {'for':'isolevel' + chain.pdb_chain_id});
-                    labelsliderinterac.innerHTML = 'Adjust predictive interactibility surface on chain ' + chain.pdb_chain_id;
+                    labelsliderinterac.innerHTML = 'Adjust predicted interactability surface on chain ' + chain.pdb_chain_id;
                     divchain.appendChild(labelsliderinterac);
                     divchain.appendChild(createElement('br'));
                     var divdropdowninterac = createElement("div",{},{},"dropdown");
@@ -419,7 +428,7 @@ function loadNGL(url, callback){
                                                                   "data-toggle":"dropdown", 
                                                                   "aria-haspopup":"true", 
                                                                   "aria-expanded":"false"});
-                    buttondorpdowninterac.append("Select interactibility model, chain ".concat(chain.pdb_chain_id ));
+                    buttondorpdowninterac.append("Select interactability model, chain ".concat(chain.pdb_chain_id ));
                     divdropdowninterac.appendChild(buttondorpdowninterac);
                     var dropdowninteracmenu = createElement("div",{},{},"dropdown-menu",{'aria-labelledby': componentname + "_interact"});
                     divdropdowninterac.appendChild(dropdowninteracmenu);
@@ -448,13 +457,13 @@ function loadNGL(url, callback){
                                                                                         opaqueBack: false,
                                                                                         smooth: 2,
                                                                                         color: filecolor(indexchain, indexfile),
-                                                                                        isolevel: 0.7,
+                                                                                        isolevel: interactfile.default_isolevel,
                                                                                         isolevelType: 'value',});