From b6a121e7992c414f84d600f98d4c77620a667156 Mon Sep 17 00:00:00 2001 From: qlands Date: Mon, 16 Aug 2021 18:21:41 -0600 Subject: [PATCH] Implements create new ontology --- cropontology/config/routes.py | 11 +++- .../templates/ontology/add_ontology.jinja2 | 39 ++++++++++++++ .../ontology/snippets/breadcrums_add.jinja2 | 13 +++++ cropontology/templates/pages/add_page.jinja2 | 1 + cropontology/templates/pages/edit_page.jinja2 | 1 + .../templates/sections/add_section.jinja2 | 1 + .../templates/sections/edit_section.jinja2 | 1 + .../templates/snippets/navbar_main.jinja2 | 3 ++ cropontology/views/ontology.py | 53 ++++++++++++++++++- cropontology/views/public_views.py | 5 +- cropontology/views/template.py | 6 +++ cropontology/views/term.py | 3 ++ 12 files changed, 133 insertions(+), 4 deletions(-) create mode 100644 cropontology/templates/ontology/add_ontology.jinja2 create mode 100644 cropontology/templates/ontology/snippets/breadcrums_add.jinja2 diff --git a/cropontology/config/routes.py b/cropontology/config/routes.py index 6c51c04..8a12d34 100644 --- a/cropontology/config/routes.py +++ b/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", diff --git a/cropontology/templates/ontology/add_ontology.jinja2 b/cropontology/templates/ontology/add_ontology.jinja2 new file mode 100644 index 0000000..a8bd773 --- /dev/null +++ b/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 %} +
+
+
+
+
{{ _('Information for the new ontology') }}
+
+ {{ form.display_errors(errors) }} +
+ {{ form.secure_form(request) }} +
+
+ + +
+
+ + +
+
+ + +
+
+
+ +
+
+
+
+
+{% endblock main_container %} \ No newline at end of file diff --git a/cropontology/templates/ontology/snippets/breadcrums_add.jinja2 b/cropontology/templates/ontology/snippets/breadcrums_add.jinja2 new file mode 100644 index 0000000..2ec00da --- /dev/null +++ b/cropontology/templates/ontology/snippets/breadcrums_add.jinja2 @@ -0,0 +1,13 @@ +
+
+
+

{{ _('Ontologies') }}
{{ _('Add new ontology') }}

+
+
+
    +
  1. {{ _('Home') }}
    2. +
  2. {{ _('Add new ontology') }}
    3. +
+
+
+
\ No newline at end of file diff --git a/cropontology/templates/pages/add_page.jinja2 b/cropontology/templates/pages/add_page.jinja2 index 647c076..f3e4716 100644 --- a/cropontology/templates/pages/add_page.jinja2 +++ b/cropontology/templates/pages/add_page.jinja2 @@ -12,6 +12,7 @@
{{ _('Information for the new page') }}
+ {{ form.display_errors(errors) }}
{{ form.secure_form(request) }}
diff --git a/cropontology/templates/pages/edit_page.jinja2 b/cropontology/templates/pages/edit_page.jinja2 index 0b632cf..2d9d95e 100644 --- a/cropontology/templates/pages/edit_page.jinja2 +++ b/cropontology/templates/pages/edit_page.jinja2 @@ -12,6 +12,7 @@
{{ _('Current content of ') }} {{ form_data.page_desc }}
+ {{ form.display_errors(errors) }} {{ form.secure_form(request) }}
diff --git a/cropontology/templates/sections/add_section.jinja2 b/cropontology/templates/sections/add_section.jinja2 index 1e2228a..6912a69 100644 --- a/cropontology/templates/sections/add_section.jinja2 +++ b/cropontology/templates/sections/add_section.jinja2 @@ -12,6 +12,7 @@
{{ _('Information for the new section') }}
+ {{ form.display_errors(errors) }} {{ form.secure_form(request) }}
diff --git a/cropontology/templates/sections/edit_section.jinja2 b/cropontology/templates/sections/edit_section.jinja2 index fd90841..9d68467 100644 --- a/cropontology/templates/sections/edit_section.jinja2 +++ b/cropontology/templates/sections/edit_section.jinja2 @@ -12,6 +12,7 @@
{{ _('Current content of ') }} {{ form_data.section_desc }}
+ {{ form.display_errors(errors) }} {{ form.secure_form(request) }}
diff --git a/cropontology/templates/snippets/navbar_main.jinja2 b/cropontology/templates/snippets/navbar_main.jinja2 index b3bbc70..ff18f8c 100644 --- a/cropontology/templates/snippets/navbar_main.jinja2 +++ b/cropontology/templates/snippets/navbar_main.jinja2 @@ -28,6 +28,9 @@
    • + {% if activeUser.super %} +
    • {{ _('Create new ontology') }}
      • + {% endif %} {% if activeUser.super %}
    • {{ _('Pages') }}
      • {% endif %} diff --git a/cropontology/views/ontology.py b/cropontology/views/ontology.py index 44a38c1..f890cb5 100644 --- a/cropontology/views/ontology.py +++ b/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): diff --git a/cropontology/views/public_views.py b/cropontology/views/public_views.py index eb1cba2..dc5175c 100644 --- a/cropontology/views/public_views.py +++ b/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 = [] diff --git a/cropontology/views/template.py b/cropontology/views/template.py index a2534d8..92afb95 100644 --- a/cropontology/views/template.py +++ b/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"]): diff --git a/cropontology/views/term.py b/cropontology/views/term.py index 11ab861..e56d0c8 100644 --- a/cropontology/views/term.py +++ b/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