fixed label issue of sample and assay metadata fields

ngtax_to_biom.py

@@ -106,7 +106,7 @@ def process_rdf_files(rdf_file):
     }""")
 
     for row in qres:
-        predicate = row.predicate.split("/")[-1]
+        predicate = "assay_"+row.predicate.split("/")[-1]
         identifier = "Sample1_" + row.id + "_1.fastq.gz"
         print(identifier + "\t"+predicate + f"\t{row.object}", file=output)
 
@@ -118,18 +118,21 @@ def process_rdf_files(rdf_file):
     PREFIX unlock: <http://m-unlock.nl/ontology/>
     PREFIX jerm: <http://jermontology.org/ontology/JERMOntology#>
     PREFIX schema: <http://schema.org/>
-    SELECT DISTINCT ?id ?predicate ?object
+    SELECT DISTINCT ?id ?predicate ?object ?predicate_label
     WHERE {
         ?sample a jerm:Sample .
         ?sample ?predicate ?object .
-        ?sample unlock:assay ?assay .
+        OPTIONAL { ?predicate rdfs:label ?predicate_label}
+        ?sample jerm:hasPart ?assay .
         ?assay a unlock:AmpliconAssay .
         ?assay schema:identifier ?id .
         FILTER(!ISIRI(?object))
     }""")
 
     for row in qres:
-        predicate = row.predicate.split("/")[-1]
+        predicate = "sample_" + row.predicate.split("/")[-1]
+        if type(row.predicate_label) == rdflib.term.Literal:
+            predicate = "sample_" + row.predicate_label.replace(" ","_")
         identifier = "Sample1_" + row.id + "_1.fastq.gz"
         print(identifier + "\t"+predicate + f"\t{row.object}", file=output)