Create db schema on start

.gitignore

 data
+db
 
 # Eclipse
 .project

src/main/java/ibb/api/geneinfo/loader/DrosophilaGeneLoader.java

@@ -25,38 +25,39 @@ public class DrosophilaGeneLoader {
 	@PostConstruct
 	@Transactional
     public void load() {
-		if (DrosophilaGene.count() > 0) return;
+		if (DrosophilaGene.count() == 0) {
 		
-		LOG.info("Attempting to initialize Drosophila data...");
-        Set<String> idSet = new HashSet<>();
+			LOG.info("Attempting to initialize Drosophila data...");
+	        Set<String> idSet = new HashSet<>();
+	        
+	        Parser.parseTSV(geneSetPath, List.of(
+	                "organism",
+	                "gene_type",
+	                "gene_ID",
+	                "gene_symbol",
+	                "gene_fullname",
+	                "annotation_ID",
+	                "transcript_type",
+	                "transcript_ID",
+	                "transcript_symbol",
+	                "polypeptide_ID",
+	                "polypeptide_symbol"), record -> {
+	            
+	            if (!"Dmel".equals(record.get("organism"))) return;
+	            
+	            String id = record.get("gene_ID");
+	            if (idSet.contains(id)) return;
+	            
+	            DrosophilaGene gene = new DrosophilaGene();
+	            gene.id = id;
+	            gene.symbol = record.get("gene_symbol");
+	            gene.fullname = record.get("gene_fullname");
+	            gene.annotationId = record.get("annotation_ID");
+	            gene.persist();
+	            idSet.add(id);
+	        });
+		}
         
-        Parser.parseTSV(geneSetPath, List.of(
-                "organism",
-                "gene_type",
-                "gene_ID",
-                "gene_symbol",
-                "gene_fullname",
-                "annotation_ID",
-                "transcript_type",
-                "transcript_ID",
-                "transcript_symbol",
-                "polypeptide_ID",
-                "polypeptide_symbol"), record -> {
-            
-            if (!"Dmel".equals(record.get("organism"))) return;
-            
-            String id = record.get("gene_ID");
-            if (idSet.contains(id)) return;
-            
-            DrosophilaGene gene = new DrosophilaGene();
-            gene.id = id;
-            gene.symbol = record.get("gene_symbol");
-            gene.fullname = record.get("gene_fullname");
-            gene.annotationId = record.get("annotation_ID");
-            gene.persist();
-            idSet.add(id);
-        });
-        
-        LOG.infov("Loaded {0} Drosophila genes", DrosophilaGene.count());
+        LOG.infov("Drosophila gene count: {0}", DrosophilaGene.count());
 	}
 }

src/main/java/ibb/api/geneinfo/loader/TriboliumGeneLoader.java

@@ -14,6 +14,7 @@ import javax.annotation.PostConstruct;
 import javax.transaction.Transactional;
 
 import org.eclipse.microprofile.config.inject.ConfigProperty;
+import org.jboss.logging.Logger;
 
 import ibb.api.geneinfo.model.TriboliumGene;
 import ibb.api.geneinfo.parser.FastaRecord;
@@ -24,6 +25,7 @@ import io.quarkus.runtime.Startup;
 @Deprecated
 @Startup
 public class TriboliumGeneLoader {
+	private static final Logger LOG = Logger.getLogger(TriboliumGeneLoader.class);
 	private static final Pattern TC_PATTERN = Pattern.compile("(TC[0-9]{6})");
     
     @ConfigProperty(name = "data.tribolium.gene.gff")
@@ -41,49 +43,53 @@ public class TriboliumGeneLoader {
     @PostConstruct
     @Transactional
     public void load() {
-        List<TriboliumGene> genes = new ArrayList<>();
-    	
-        Parser.parseGFF(gff, record -> Optional.of(record)
-            .filter(r -> "gene".equals(r.getFeature()))
-            .map(this::getTCNo)
-            .map(tc -> {
-            	TriboliumGene gene = new TriboliumGene();
-            	gene.id = tc;
-            	gene.seqname = record.getSeqname();
-            	gene.start = record.getStart();
-            	gene.end = record.getEnd();
-            	gene.strand = record.getStrand();
-            	return gene;
-            })
-            .ifPresent(genes::add));
-        
-        Map<String, TriboliumGene> geneMap = genes.stream()
-                .collect(toMap(gene -> gene.id, Function.identity()));
-
-        Parser.parseFasta(cdsFasta, record -> {
-            Optional.of(record)
-                .map(FastaRecord::getHeader)
-                .map(this::getTCNo)
-                .map(geneMap::get)
-                .ifPresent(gene -> gene.CDS = record.getSequence());
-        });
-        
-        Parser.parseFasta(mRNAFasta, record -> {
-            Optional.of(record)
-                .map(FastaRecord::getHeader)
-                .map(this::getTCNo)
-                .map(geneMap::get)
-                .ifPresent(gene -> gene.mRNA = record.getSequence());
-        });
-        
-        Parser.parseFasta(proteinFasta, record -> {
-            Optional.of(record)
-                .map(FastaRecord::getHeader)
-                .map(this::getTCNo)
-                .map(geneMap::get)
-                .ifPresent(gene -> gene.protein = record.getSequence());
-        });
-        TriboliumGene.persist(genes);
+    	if (TriboliumGene.count() == 0) {
+	    	LOG.info("Attempting to initialize Tribolium data...");
+	        List<TriboliumGene> genes = new ArrayList<>();
+	    	
+	        Parser.parseGFF(gff, record -> Optional.of(record)
+	            .filter(r -> "gene".equals(r.getFeature()))
+	            .map(this::getTCNo)
+	            .map(tc -> {
+	            	TriboliumGene gene = new TriboliumGene();
+	            	gene.id = tc;
+	            	gene.seqname = record.getSeqname();
+	            	gene.start = record.getStart();
+	            	gene.end = record.getEnd();
+	            	gene.strand = record.getStrand();
+	            	return gene;
+	            })
+	            .ifPresent(genes::add));
+	        
+	        Map<String, TriboliumGene> geneMap = genes.stream()
+	                .collect(toMap(gene -> gene.id, Function.identity()));
+	
+	        Parser.parseFasta(cdsFasta, record -> {
+	            Optional.of(record)
+	                .map(FastaRecord::getHeader)
+	                .map(this::getTCNo)
+	                .map(geneMap::get)
+	                .ifPresent(gene -> gene.CDS = record.getSequence());
+	        });
+	        
+	        Parser.parseFasta(mRNAFasta, record -> {
+	            Optional.of(record)
+	                .map(FastaRecord::getHeader)
+	                .map(this::getTCNo)
+	                .map(geneMap::get)
+	                .ifPresent(gene -> gene.mRNA = record.getSequence());
+	        });
+	        
+	        Parser.parseFasta(proteinFasta, record -> {
+	            Optional.of(record)
+	                .map(FastaRecord::getHeader)
+	                .map(this::getTCNo)
+	                .map(geneMap::get)
+	                .ifPresent(gene -> gene.protein = record.getSequence());
+	        });
+	        TriboliumGene.persist(genes);
+    	}
+        LOG.infov("Tribolium gene count: {0}", TriboliumGene.count());
     }
     
     private String getTCNo(GFFRecord record) {
@@ -94,4 +100,5 @@ public class TriboliumGeneLoader {
         Matcher matcher = TC_PATTERN.matcher(str);
         return matcher.find() ? matcher.group(1) : null;
     }
+    
 }

src/main/resources/application.yaml

@@ -2,50 +2,54 @@ quarkus:
   http:
     cors:
       ~: true
+
   container-image:
     group: ibb/api
     name: geneinfoservice
     tag: latest
     registry: docker.gitlab.gwdg.de
-    build: true
 
   datasource:
     db-kind: h2
     jdbc:
-      url: jdbc:h2:./geneinfoservice
+      url: jdbc:h2:./db/geneinfoservice
+
+  hibernate-orm:
+    database:
+      generation:
+        ~: update
 
 data:
+  dir: ./data
   drosophila:
     gene:
-      tsv: /data/fbgn_fbtr_fbpp_expanded_fb_2020_02.tsv.gz
+      tsv: ${data.dir}/fbgn_fbtr_fbpp_expanded_fb_2020_02.tsv.gz
   tribolium:
     gene:
-      gff: /data/OGS3.gff.gz
+      gff: ${data.dir}/OGS3.gff.gz
     cds:
-      fasta: /data/OGS3_CDS.fasta.gz
+      fasta: ${data.dir}/OGS3_CDS.fasta.gz
     mrna:
-      fasta: /data/OGS3_mRNA.fasta.gz
+      fasta: ${data.dir}/OGS3_mRNA.fasta.gz
     protein:
-      fasta: /data/OGS3_proteins.fasta.gz
+      fasta: ${data.dir}/OGS3_proteins.fasta.gz
 
 "%dev":
   data:
+    dir: ../sample_data
     drosophila:
       gene:
-        tsv: ../sample_data/drosophila.gene.tsv.gz
+        tsv: ${data.dir}/drosophila.gene.tsv.gz
     tribolium:
       gene:
-        gff: ../sample_data/tribolium.gene.gff.gz
+        gff: ${data.dir}/tribolium.gene.gff.gz
       cds:
-        fasta: ../sample_data/tribolium.cds.fasta.gz
+        fasta: ${data.dir}/tribolium.cds.fasta.gz
       mrna:
-        fasta: ../sample_data/tribolium.mrna.fasta.gz
+        fasta: ${data.dir}/tribolium.mrna.fasta.gz
       protein:
-        fasta: ../sample_data/tribolium.protein.fasta.gz
+        fasta: ${data.dir}/tribolium.protein.fasta.gz
   quarkus:
-    datasource:
-      jdbc:
-        url: jdbc:h2:./geneinfoservice
     hibernate-orm:
       database:
         generation: