increase robustesse of generation identifier for pmid reference. use …

…rdf4j streaming and ammonite scala command

app/build/pmid_to_identifier_rdf4j.sc

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+// Ammonite 2.5.2, scala 2.13
+// JAVA_OPTS="-Xmx16g -Xms16g" amm app/build/pmid_to_identifier.sc pmid_identifiers.tsv data-test/pc_reference_identifier_000001.ttl.gz
+
+import $ivy.`org.eclipse.rdf4j:rdf4j-storage:4.3.11`
+
+import java.io._
+import java.nio.file.{Files, Paths}
+import java.util.zip.GZIPInputStream
+import scala.util.{Try,Success,Failure}
+
+import scala.concurrent._
+import scala.concurrent.duration._
+
+import java.io.InputStream
+import java.net.URI
+import org.eclipse.rdf4j.model.Statement
+import org.eclipse.rdf4j.rio.RDFFormat
+import org.eclipse.rdf4j.rio.Rio
+import org.eclipse.rdf4j.query._;
+
+def uncompressed(infile: String): InputStream = {
+  new GZIPInputStream(new FileInputStream(new File(infile)))
+}
+
+//https://rdf4j.org/documentation/programming/rio/
+@main
+def main(outfile : String,pc_reference_identifier_files : String*) : Unit = {
+
+
+    if (new File(outfile).exists()) {
+      System.err.println(s"$outfile exists !")
+      new File(outfile).delete()
+    }
+
+    /* to avoid error read from reference */
+    System.setProperty("org.eclipse.rdf4j.rio.verify_uri_syntax","false")
+
+    val fileWriter = new FileWriter(new File(outfile))
+
+    pc_reference_identifier_files.foreach  {
+        case (filePath : String) => {
+            println(s"---  $filePath --- ")
+           val is : InputStream = if (filePath.endsWith(".gz")) {
+              println(" -- gunzip -- ")
+              uncompressed(filePath)
+            } else {
+              new FileInputStream(filePath)
+            }
+
+        val baseURI: String = new File(filePath).toURI.toString
+        val format: RDFFormat = RDFFormat.TURTLE
+
+        try {
+          val res: GraphQueryResult = QueryResults.parseGraphBackground(is, baseURI, format,null)
+          try {
+            while (res.hasNext()) {
+              val st: Statement = res.next()
+
+              val objUri = st.getObject().toString()
+              if (objUri.contains("pubmed.ncbi.nlm.nih.gov") && !objUri.contains("PMC")) {
+                val sub = st.getSubject().toString().split("/").last.trim
+                val obj = objUri.split("/").last.trim
+                fileWriter.write(sub+"\t"+obj+"\n")
+              }
+
+            }
+          } finally {
+            res.close()
+          }
+        } catch {
+          case e: Exception =>
+            // Gérer l'erreur irrécupérable ici
+        } finally {
+          is.close()
+        }
+        }
+
+    }
+    fileWriter.close()
+}