Merge pull request #595 from ISA-tools/develop

closes #598, #591

Author: proccaserra

isatools/convert/experimental/nih_dcc_flux.py

@@ -281,7 +281,7 @@ def nihdcc2isa_convert(json_path, output_path):
                 material_out.characteristics.append(material_type)
 
                 study.assays[0].samples.append(material_in)
-                study.assays[0].materials["other_material"].append(material_in)
+                study.assays[0].other_material.append(material_in)
                 try:
                     material_separation_process
                 except NameError:
@@ -300,7 +300,7 @@ def nihdcc2isa_convert(json_path, output_path):
                     value=OntologyAnnotation(term=sample_json["type"], term_source=obi),
                 )
                 material_in.characteristics.append(material_type)
-                study.assays[0].materials["other_material"].append(material_in)
+                study.assays[0].other_material.append(material_in)
 
                 data_acq_process = Process(executes_protocol=study.get_prot(sample_json["protocol.id"]))
                 data_acq_process.name = sample_json["id"]

isatools/database/models/ontology_annotation.py

@@ -82,12 +82,14 @@ def to_sql(self, session):
         if oa:
             return oa
         term_source_id = self.term_source.to_sql(session) if self.term_source else None
+        comments_objs = [c.to_sql(session) for c in self.comments]
+
         oa = OntologyAnnotation(
             ontology_annotation_id=self.id,
             annotation_value=self.term,
             term_accession=self.term_accession,
             term_source_id=term_source_id.ontology_source_id if term_source_id else None,
-            comments=[comment.to_sql() for comment in self.comments],
+            comments=comments_objs,
         )
         session.add(oa)
         return oa

isatools/net/ols.py

@@ -23,7 +23,7 @@
 
 def get_ols_ontologies():
     """Returns a list of OntologySource objects according to what's in OLS"""
-    ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE)
+    ontologiesUri = OLS_API_BASE_URI + "/ontologies?" + str(OLS_PAGINATION_SIZE)
     log.debug(ontologiesUri)
     J = json.loads(urlopen(ontologiesUri).read().decode("utf-8"))
     ontology_sources = []
@@ -43,28 +43,24 @@ def get_ols_ontologies():
     return ontology_sources
 
 
-def get_ols_ontology(ontology_name):
+def get_ols_ontology(ontology_name, page: int):
     """Returns a single OntologySource objects according to what's in OLS"""
-    ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE)
+    ontologiesUri = OLS_API_BASE_URI + "/ontologies?page=" + str(page) + "&size=" + str(OLS_PAGINATION_SIZE)
     log.debug(ontologiesUri)
     J = json.loads(urlopen(ontologiesUri).read().decode("utf-8"))
-    print("EMBEDDED: ", J["_embedded"]["ontologies"])
     ontology_sources = []
     for ontology_source_json in J["_embedded"]["ontologies"]:
-        ontology_sources.append(
-            OntologySource(
-                name=ontology_source_json["ontologyId"],
-                version=ontology_source_json["config"]["version"] if ontology_source_json["config"]["version"] else "",
-                description=ontology_source_json["config"]["title"] if ontology_source_json["config"]["title"] else "",
-                file=ontology_source_json["_links"]["self"]["href"],
+        if ontology_source_json["ontologyId"] == ontology_name:
+            ontology_sources.append(
+                OntologySource(
+                    name=ontology_source_json["ontologyId"],
+                    version=ontology_source_json["config"]["version"] if ontology_source_json["config"]["version"] else "",
+                    description=ontology_source_json["config"]["title"] if ontology_source_json["config"]["title"] else "",
+                    file=ontology_source_json["_links"]["self"]["href"],
+                )
             )
-        )
-    print("NAME: ", ontology_name)
-    print("SOURCES: ", [o.name for o in ontology_sources])
-    hits = [o for o in ontology_sources if o.name == ontology_name]
-    print("HITS: ", hits)
-    if len(hits) == 1:
-        return hits[0]
+    if len(ontology_sources) == 1:
+        return ontology_sources[0]
     return None
 
 
@@ -80,6 +76,8 @@ def search_ols(term, ontology_source):
 
     query = "{0}&queryFields=label&ontology={1}&exact=True".format(term, os_search)
     url += "?q={}".format(query)
+
+    #print("OLS_URL", url)
     log.debug(url)
     import requests