Merge pull request #424 from mboudet/dev

Rewrite ontology management + some stuff
askomics · Oct 31, 2023 · 4569fd5 · 4569fd5
2 parents f36a977 + bc61f58
commit 4569fd5
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Showing 10 changed files with 153 additions and 136 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 This changelog was started for release 4.2.0.
 
+## [4.6.0] - Unreleased
+
+### Added
+
+- "askomics:instancesLabel" predicate can be defined at the entity-level, to set a specific attribute URI as the 'label' (ie, visible by default)
+  - Play the same role as 'askomics:instancesHaveNoLabels', except a specific attribute is visible instead of the URI attribute.
+- Added the *TIMEOUT* env variable, which will set the web workers tiemout value. Default 300s
+
+### Changed
+
+- Rewrote the ontology part. Instead of specifying 'children of' and other values, users can tick the 'recursive' button to customize the query. While this is less intuitive, this change is more flexible for the various types of ontological relations
+
 ## [4.5.0] - 2023-10-20
 
 ### **Deprecation warning**

diff --git a/Makefile b/Makefile
@@ -10,6 +10,7 @@ PYTESTOPTS=
 TESTFILE?=tests
 NTASKS?=1
 WORKERS?=1
+TIMEOUT?=300
 
 HOST?=0.0.0.0
 PORT?=5000
@@ -107,7 +108,7 @@ serve-askomics: check-venv build-config create-user
 ifeq ($(MODE), dev)
 	FLASK_ENV=development FLASK_APP=app flask run --host=$(HOST) --port $(PORT)
 else
-	FLASK_ENV=production FLASK_APP=app gunicorn -w $(WORKERS) -b $(HOST):$(PORT) app
+	FLASK_ENV=production FLASK_APP=app gunicorn --timeout $(TIMEOUT) -w $(WORKERS) -b $(HOST):$(PORT) app
 endif
 
 serve-celery: check-venv build-config create-user

diff --git a/askomics/libaskomics/FilesHandler.py b/askomics/libaskomics/FilesHandler.py
@@ -425,6 +425,8 @@ def get_type(self, file_ext):
             return 'rdf/xml'
         elif file_ext in ('.nt', ):
             return 'rdf/nt'
+        elif file_ext in ('.owl', ):
+            return 'rdf/xml'
         # Default is csv
         return 'csv/tsv'
 

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
@@ -1362,19 +1362,19 @@ def build_query_from_json(self, preview=False, for_editor=False):
                 # Classic relation
                 else:
                     # Manage ontology stuff
+                    is_inverse = link.get("reverse", False)
                     inverse = ""
-                    recurrence = ""
+                    is_recursive = link.get("recursive", False)
+                    recursive = ""
                     relation = link["uri"]
 
-                    if relation.startswith("^"):
+                    if is_inverse:
                         inverse = "^"
-                        relation = relation.lstrip("^")
 
-                    if relation.endswith("*"):
-                        recurrence = "*"
-                        relation = relation.rstrip("*")
+                    if is_recursive:
+                        recursive = "*"
 
-                    relation = inverse + "<{}>".format(relation) + recurrence
+                    relation = inverse + "<{}>".format(relation) + recursive
                     triple = {
                         "subject": source,
                         "predicate": relation,

diff --git a/askomics/libaskomics/TriplestoreExplorer.py b/askomics/libaskomics/TriplestoreExplorer.py
@@ -323,7 +323,7 @@ def get_abstraction_entities(self, single_tenant=False):
         query_builder = SparqlQuery(self.app, self.session)
 
         query = '''
-        SELECT DISTINCT ?endpoint ?graph ?entity_uri ?entity_type ?entity_faldo ?entity_label ?have_no_label
+        SELECT DISTINCT ?endpoint ?graph ?entity_uri ?entity_type ?entity_faldo ?entity_label ?have_no_label ?default_visible
         WHERE {{
             ?graph askomics:public ?public .
             ?graph dc:creator ?creator .
@@ -339,6 +339,7 @@ def get_abstraction_entities(self, single_tenant=False):
                 # Label
                 OPTIONAL {{ ?entity_uri rdfs:label ?entity_label . }}
                 OPTIONAL {{ ?entity_uri askomics:instancesHaveNoLabels ?have_no_label . }}
+                OPTIONAL {{ ?entity_uri askomics:instancesLabel ?default_visible . }}
             }}
             FILTER (
                 ?public = <true>{}
@@ -367,6 +368,7 @@ def get_abstraction_entities(self, single_tenant=False):
                     "ontology": True if result["entity_type"] == "{}ontology".format(self.settings.get("triplestore", "namespace_internal")) else False,
                     "endpoints": [result["endpoint"]],
                     "graphs": [result["graph"]],
+                    "defaultVisible": result.get("default_visible")
                 }
 
                 entities.append(entity)
@@ -519,7 +521,7 @@ def get_abstraction_relations(self, single_tenant=False):
         query_builder = SparqlQuery(self.app, self.session)
 
         query = '''
-        SELECT DISTINCT ?graph ?entity_uri ?entity_faldo ?entity_label ?attribute_uri ?attribute_faldo ?attribute_label ?attribute_range ?property_uri ?property_faldo ?property_label ?range_uri ?category_value_uri ?category_value_label ?indirect_relation
+        SELECT DISTINCT ?graph ?entity_uri ?entity_faldo ?entity_label ?attribute_uri ?attribute_faldo ?attribute_label ?attribute_range ?property_uri ?property_faldo ?property_label ?range_uri ?category_value_uri ?category_value_label ?indirect_relation ?is_recursive
         WHERE {{
             # Graphs
             ?graph askomics:public ?public .
@@ -534,6 +536,7 @@ def get_abstraction_relations(self, single_tenant=False):
                 # Retrocompatibility
                 OPTIONAL {{?node askomics:uri ?new_property_uri}}
                 BIND( IF(isBlank(?node), ?new_property_uri, ?node) as ?property_uri)
+                OPTIONAL {{?node askomics:isRecursive ?is_recursive}}
             }}
             # Relation of entity (or motherclass of entity)
             {{
@@ -565,7 +568,8 @@ def get_abstraction_relations(self, single_tenant=False):
                         "graphs": [result["graph"], ],
                         "source": result["entity_uri"],
                         "target": result["range_uri"],
-                        "indirect": result.get("indirect_relation", False)
+                        "indirect": result.get("indirect_relation", False),
+                        "recursive": result.get("is_recursive", False),
                     }
                     relations.append(relation)
                 else:

diff --git a/askomics/react/src/routes/query/ontolinkview.jsx b/askomics/react/src/routes/query/ontolinkview.jsx
@@ -11,48 +11,16 @@ import PropTypes from 'prop-types'
 export default class OntoLinkView extends Component {
   constructor (props) {
     super(props)
-    this.handleChangeOntologyType = this.props.handleChangeOntologyType.bind(this)
+    this.handleRecursiveOntology = this.props.handleRecursiveOntology.bind(this)
   }
 
-
   render () {
 
-    let content = (
-      <>
-        <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf">children of</option>
-        <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf*">descendants of</option>
-        <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf">parents of</option>
-        <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf*">ancestors of</option>
-      </>
-    )
-
-    if (this.props.link.uri.includes("http://www.w3.org/2004/02/skos/core")){
-      content = (
-        <>
-          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#broader' ? true : false} value="http://www.w3.org/2004/02/skos/core#broader">children of</option>
-          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#broader*' ? true : false} value="http://www.w3.org/2004/02/skos/core#broader*">descendants of</option>
-          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#narrower' ? true : false} value="http://www.w3.org/2004/02/skos/core#narrower">parents of</option>
-          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#narrower*' ? true : false} value="http://www.w3.org/2004/02/skos/core#narrower*">ancestors of</option>
-        </>
-      )
-    }
-
-
     return (
       <div className="container">
         <h5>Ontological Relation</h5>
         <hr />
-        <p>Search on ...</p>
-        <table>
-          <tr>
-            <td>
-             <CustomInput type="select" id={this.props.link.id} name="ontology_position" onChange={this.handleChangeOntologyType}>
-              {content}
-              </CustomInput>
-            </td>
-            <td>&nbsp;a term</td>
-          </tr>
-        </table>
+        <CustomInput disabled={!this.props.link.isRecursive} onChange={this.handleRecursiveOntology} checked={this.props.link.recursive ? true : false} value={this.props.link.recursive ? true : false} type="checkbox" id={this.props.link.id} label="Recursive" />
         <br />
       </div>
     )
@@ -61,5 +29,5 @@ export default class OntoLinkView extends Component {
 
 OntoLinkView.propTypes = {
   link: PropTypes.object,
-  handleChangeOntologyType: PropTypes.func,
+  handleRecursiveOntology: PropTypes.func
 }