Implements create new ontology

cropontology/config/routes.py

@@ -47,7 +47,7 @@
     SectionRemoveUserView,
 )
 
-from ..views.ontology import OntologyView, JSONDataView, OntologyRDFView
+from ..views.ontology import OntologyView, JSONDataView, CreateOntology
 from ..views.api import APIDocView
 from ..views.brapi import (
     BRAPITraitsView,
@@ -251,6 +251,15 @@ def load_routes(config):
         )
     )
 
+    routes.append(
+        add_route(
+            "create_ontology",
+            "/ontologies/create",
+            CreateOntology,
+            "ontology/add_ontology.jinja2",
+        )
+    )
+
     routes.append(
         add_route(
             "ontology_owl",

cropontology/templates/ontology/add_ontology.jinja2

@@ -0,0 +1,39 @@
+{% extends 'page.jinja2' %}
+{% import 'macros/form.jinja2' as form %}
+
+{% block breadcrums %}
+    {% include 'ontology/snippets/breadcrums_add.jinja2' %}
+{% endblock breadcrums %}
+
+{% block main_container %}
+<div class="row">
+    <div class="col-lg-12">
+        <div class="card">
+            <div class="card-header">
+                <h5 class="card-title m-0">{{ _('Information for the new ontology') }}</h5>
+            </div>
+            {{ form.display_errors(errors) }}
+            <form role="form" method="post" action="{{ request.url }}">
+                {{ form.secure_form(request) }}
+                <div class="card-body">
+                    <div class="form-group">
+                        <label for="exampleInputEmail1">{{ _('ID') }}</label>
+                        <input type="text" class="form-control" name="ontology_id" value="{{ form_data.ontology_id }}" placeholder="{{ _('Enter ontology ID') }}">
+                    </div>
+                    <div class="form-group">
+                        <label for="exampleInputEmail1">{{ _('Name') }}</label>
+                        <input type="text" class="form-control" name="ontology_name" value="{{ form_data.ontology_name }}" placeholder="{{ _('Enter a description') }}">
+                    </div>
+                    <div class="form-group">
+                        <label for="exampleInputEmail1">{{ _('Description') }}</label>
+                        <textarea class="form-control" name="ontology_desc">{{ form_data.ontology_desc }}</textarea>
+                    </div>
+                </div>
+                <div class="card-footer">
+                    <button type="submit" class="btn btn-primary">{{ _('Add ontology') }}</button>
+                </div>
+            </form>
+        </div>
+    </div>
+</div>
+{% endblock main_container %}

cropontology/templates/ontology/snippets/breadcrums_add.jinja2

@@ -0,0 +1,13 @@
+<div class="container">
+    <div class="row mb-2">
+        <div class="col-sm-6">
+            <h1 class="m-0 text-dark"> {{ _('Ontologies') }} <br><small>{{ _('Add new ontology') }}</small></h1>
+        </div>
+        <div class="col-sm-6">
+            <ol class="breadcrumb float-sm-right">
+                <li class="breadcrumb-item"><a href="{{ request.route_url('home') }}">{{ _('Home') }}</a></li>
+                <li class="breadcrumb-item active">{{ _('Add new ontology') }}</li>
+            </ol>
+        </div>
+    </div>
+</div>

cropontology/templates/pages/add_page.jinja2

@@ -12,6 +12,7 @@
             <div class="card-header">
                 <h5 class="card-title m-0">{{ _('Information for the new page') }}</h5>
             </div>
+            {{ form.display_errors(errors) }}
             <form role="form" method="post" action="{{ request.url }}">
                 {{ form.secure_form(request) }}
                 <div class="card-body">

cropontology/templates/pages/edit_page.jinja2

@@ -12,6 +12,7 @@
             <div class="card-header">
                 <h5 class="card-title m-0">{{ _('Current content of ') }} {{ form_data.page_desc }}</h5>
             </div>
+            {{ form.display_errors(errors) }}
             <form role="form" method="post" action="{{ request.url }}">
                 {{ form.secure_form(request) }}
                 <div class="card-body">

cropontology/templates/sections/add_section.jinja2

@@ -12,6 +12,7 @@
             <div class="card-header">
                 <h5 class="card-title m-0">{{ _('Information for the new section') }}</h5>
             </div>
+            {{ form.display_errors(errors) }}
             <form role="form" method="post" action="{{ request.url }}">
                 {{ form.secure_form(request) }}
                 <div class="card-body">

cropontology/templates/sections/edit_section.jinja2

@@ -12,6 +12,7 @@
             <div class="card-header">
                 <h5 class="card-title m-0">{{ _('Current content of ') }} {{ form_data.section_desc }}</h5>
             </div>
+            {{ form.display_errors(errors) }}
             <form role="form" method="post" action="{{ request.url }}">
                 {{ form.secure_form(request) }}
                 <div class="card-body">

cropontology/templates/snippets/navbar_main.jinja2

@@ -28,6 +28,9 @@
                 <li class="nav-item dropdown">
                     <a id="dropdownSubMenu1" href="#" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false" class="nav-link dropdown-toggle">{{ _('Site maintenance') }}</a>
                     <ul aria-labelledby="dropdownSubMenu1" class="dropdown-menu border-0 shadow">
+                        {% if activeUser.super %}
+                            <li><a href="{{ request.route_url('create_ontology') }}" class="dropdown-item">{{ _('Create new ontology') }}</a></li>
+                        {% endif %}
                         {% if activeUser.super %}
                             <li><a href="{{ request.route_url('page_list') }}" class="dropdown-item">{{ _('Pages') }}</a></li>
                         {% endif %}

cropontology/views/ontology.py

@@ -1,11 +1,60 @@
-from .classes import PublicView
+from .classes import PublicView, PrivateView
 from pyramid.httpexceptions import HTTPNotFound, HTTPFound
 import pymongo
 import json
-from webhelpers2.html import literal
 from neo4j import GraphDatabase
 import requests
 from pyramid.response import Response
+import datetime
+
+
+class CreateOntology(PrivateView):
+    def process_view(self):
+        if self.request.method == "POST":
+            form_data = self.get_post_dict()
+            if form_data["ontology_id"] != "":
+                if form_data["ontology_desc"] != "":
+                    if form_data["ontology_name"] != "":
+                        mongo_url = self.request.registry.settings.get("mongo.url")
+                        mongo_client = pymongo.MongoClient(mongo_url)
+                        ontology_db = mongo_client["ontologies"]
+                        ontology_collection = ontology_db["ontologies"]
+                        res = ontology_collection.find_one(
+                            {"ontology_id": form_data["ontology_id"]}
+                        )
+                        if res is None:
+                            ontology_data = {
+                                "ontology_summary": form_data["ontology_desc"],
+                                "ontology_id": form_data["ontology_id"],
+                                "created_at": datetime.datetime.now(),
+                                "user_key": self.userID,
+                                "ontology_name": form_data["ontology_name"],
+                                "category": "300-499 Phenotype and Trait Ontology",
+                                "ontology_type": "trait",
+                            }
+                            ontology_collection.insert_one(ontology_data)
+                            self.request.session.flash(
+                                self._("The ontology was created successfully")
+                            )
+                            self.returnRawViewResult = True
+                            return HTTPFound(location=self.request.route_url("home"))
+                        else:
+                            self.append_to_errors(
+                                self._("The ontology ID already exists")
+                            )
+                    else:
+                        self.append_to_errors(
+                            self._("The ontology name cannot be empty")
+                        )
+                else:
+                    self.append_to_errors(
+                        self._("The ontology description cannot be empty")
+                    )
+            else:
+                self.append_to_errors(self._("The ontology ID cannot be empty"))
+        else:
+            form_data = {}
+        return {"form_data": form_data}
 
 
 class OntologyView(PublicView):

cropontology/views/public_views.py

@@ -51,7 +51,10 @@ def process_view(self):
             roots = []
             for an_item in cursor:
                 roots.append(an_item["p.id"])
-            an_ontology["root"] = roots[0]
+            if len(roots) > 0:
+                an_ontology["root"] = roots[0]
+            else:
+                an_ontology["root"] = "None"
             if an_ontology["category"] not in categories:
                 categories.append(an_ontology["category"])
         result = []

cropontology/views/template.py

@@ -152,6 +152,7 @@ def process_view(self):
                         "created_at": date,
                         "language": row["Language"],
                         "term_type": "term",
+                        "term_id": ontology_id + ":ROOT",
                     }  # Root
                     if not term_index.term_exists(ontology_id + ":ROOT"):
                         term_index.add_term(ontology_id + ":ROOT", es_data)
@@ -271,6 +272,7 @@ def process_view(self):
                     "created_at": date,
                     "language": row["Language"],
                     "term_type": "variable",
+                    "term_id": var_id,
                 }  # Root
                 if row["Variable synonyms"]:
                     es_data["variable_synonyms"] = row["Variable synonyms"]
@@ -425,6 +427,7 @@ def process_view(self):
                     "created_at": date,
                     "language": row["Language"],
                     "term_type": "trait",
+                    "term_id": trait_id,
                 }
                 if row["Trait class"]:
                     es_data["trait_class"] = row["Trait class"]
@@ -549,6 +552,7 @@ def process_view(self):
                     "created_at": date,
                     "language": row["Language"],
                     "term_type": "method",
+                    "term_id": method_id,
                 }
                 if row["Method class"]:
                     es_data["method_class"] = row["Method class"]
@@ -684,6 +688,7 @@ def process_view(self):
                     "created_at": date,
                     "language": row["Language"],
                     "term_type": "scale",
+                    "term_id": scale_id,
                 }
                 if row["Scale class"]:
                     es_data["scale_class"] = row["Scale class"]
@@ -801,6 +806,7 @@ def process_view(self):
                     "created_at": date,
                     "language": row["Language"],
                     "term_type": "term",
+                    "term_id": ontology_id + ":" + row["Trait class"],
                 }
 
                 if not term_index.term_exists(ontology_id + ":" + row["Trait class"]):

cropontology/views/term.py

@@ -45,6 +45,9 @@ def process_view(self):
         es_query = {"query": {"match_phrase": {"term_id": term_id}}}
         res, hits = index_manager.free_query(es_query)
         if hits == 0:
+            print("****************************1111")
+            print("Not hits for {}".format(term_id))
+            print("****************************1111")
             raise HTTPNotFound()
         results = []
         ontology_id = None