Update code according to OpenCB packages changes

opencb · Oct 13, 2020 · 01fb249 · 01fb249
1 parent a8b9975
commit 01fb249
Show file tree

Hide file tree

Showing 23 changed files with 582 additions and 608 deletions.
diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CommandExecutor.java
@@ -75,7 +75,7 @@ public String getLogLevel() {
     public void setLogLevel(String logLevel) {
         // This small hack allow to configure the appropriate Logger level from the command line, this is done
         // by setting the DEFAULT_LOG_LEVEL_KEY before the logger object is created.
-        System.setProperty(org.slf4j.impl.SimpleLogger.DEFAULT_LOG_LEVEL_KEY, logLevel);
+        //System.setProperty(org.slf4j.impl.SimpleLogger.DEFAULT_LOG_LEVEL_KEY, logLevel);
         logger = LoggerFactory.getLogger(this.getClass().toString());
         this.logLevel = logLevel;
     }

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java
@@ -27,10 +27,7 @@
 import org.opencb.bionetdb.core.neo4j.Neo4JVariantLoader;
 import org.opencb.cellbase.client.config.ClientConfiguration;
 import org.opencb.cellbase.client.config.RestConfig;
-import org.opencb.cellbase.client.rest.CellBaseClient;
-import org.opencb.cellbase.client.rest.GeneClient;
-import org.opencb.cellbase.client.rest.ProteinClient;
-import org.opencb.cellbase.client.rest.VariationClient;
+import org.opencb.cellbase.client.rest.*;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.core.QueryResult;
@@ -190,12 +187,12 @@ public void annotateGenes(List<String> geneIds) throws IOException, BioNetDBExce
     }
 
     public void annotateVariants(NodeQuery query, QueryOptions options) throws IOException, BioNetDBException {
-        VariationClient variationClient = cellBaseClient.getVariationClient();
+        VariantClient variationClient = cellBaseClient.getVariantClient();
         networkDBAdaptor.annotateVariants(query, options, variationClient);
     }
 
     public void annotateVariants(List<String> variantIds) throws IOException, BioNetDBException {
-        VariationClient variationClient = cellBaseClient.getVariationClient();
+        VariantClient variationClient = cellBaseClient.getVariantClient();
         networkDBAdaptor.annotateVariants(variantIds, variationClient);
     }
 

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/InterpretationAnalysis.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/InterpretationAnalysis.java
@@ -1,8 +1,8 @@
 package org.opencb.bionetdb.core.analysis;
 
-import org.opencb.biodata.models.clinical.interpretation.ClinicalProperty;
+import org.opencb.biodata.models.clinical.ClinicalProperty;
+import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
-import org.opencb.biodata.models.commons.Disorder;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.bionetdb.core.analysis.interpretation.ProteinNetworkInterpretationAnalysis;
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/VariantAnalysis.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/VariantAnalysis.java
@@ -2,8 +2,8 @@
 
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang.StringUtils;
+import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
-import org.opencb.biodata.models.commons.Disorder;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.tools.pedigree.ModeOfInheritance;
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
@@ -18,7 +18,7 @@
 import java.io.IOException;
 import java.util.*;
 
-import static org.opencb.biodata.models.clinical.interpretation.ClinicalProperty.Penetrance.COMPLETE;
+import static org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance.COMPLETE;
 
 public class VariantAnalysis extends BioNetDBAnalysis {
 

diff --git a/...rg/opencb/bionetdb/core/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java b/...rg/opencb/bionetdb/core/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java
@@ -1,9 +1,9 @@
 package org.opencb.bionetdb.core.analysis.interpretation;
 
 import org.apache.commons.collections.CollectionUtils;
-import org.opencb.biodata.models.clinical.interpretation.ClinicalProperty;
+import org.opencb.biodata.models.clinical.ClinicalProperty;
+import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
-import org.opencb.biodata.models.commons.Disorder;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.tools.pedigree.ModeOfInheritance;
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
@@ -14,7 +14,7 @@
 
 import java.util.*;
 
-import static org.opencb.biodata.models.clinical.interpretation.ClinicalProperty.Penetrance.COMPLETE;
+import static org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance.COMPLETE;
 
 public class ProteinNetworkInterpretationAnalysis {
 
@@ -29,19 +29,19 @@ public QueryResult<Variant> execute(Pedigree pedigree, Disorder disorder, Clinic
         // Check moi
         Map<String, List<String>> genotypes;
         switch (moi) {
-            case MONOALLELIC:
+            case AUTOSOMAL_DOMINANT:
                 genotypes = org.opencb.biodata.tools.pedigree.ModeOfInheritance.dominant(pedigree, disorder, COMPLETE);
                 break;
-            case BIALLELIC:
+            case AUTOSOMAL_RECESSIVE:
                 genotypes = org.opencb.biodata.tools.pedigree.ModeOfInheritance.recessive(pedigree, disorder, COMPLETE);
                 break;
-            case XLINKED_MONOALLELIC:
+            case X_LINKED_DOMINANT:
                 genotypes = org.opencb.biodata.tools.pedigree.ModeOfInheritance.xLinked(pedigree, disorder, true, COMPLETE);
                 break;
-            case XLINKED_BIALLELIC:
+            case X_LINKED_RECESSIVE:
                 genotypes = org.opencb.biodata.tools.pedigree.ModeOfInheritance.xLinked(pedigree, disorder, false, COMPLETE);
                 break;
-            case YLINKED:
+            case Y_LINKED:
                 genotypes = ModeOfInheritance.yLinked(pedigree, disorder, COMPLETE);
                 break;
             default:

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java
@@ -13,7 +13,7 @@
 import org.opencb.bionetdb.core.models.network.Node;
 import org.opencb.cellbase.client.rest.GeneClient;
 import org.opencb.cellbase.client.rest.ProteinClient;
-import org.opencb.cellbase.client.rest.VariationClient;
+import org.opencb.cellbase.client.rest.VariantClient;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.core.QueryParam;
@@ -85,8 +85,8 @@ enum NetworkQueryParams implements QueryParam {
     // A N N O T A T I O N     M E T H O D s
     //-------------------------------------------------------------------------
 
-    void annotateVariants(NodeQuery query, QueryOptions options, VariationClient variationClient) throws BioNetDBException, IOException;
-    void annotateVariants(List<String> variantIds, VariationClient variationClient) throws BioNetDBException, IOException;
+    void annotateVariants(NodeQuery query, QueryOptions options, VariantClient variantClient) throws BioNetDBException, IOException;
+    void annotateVariants(List<String> variantIds, VariantClient variantClient) throws BioNetDBException, IOException;
 
     void annotateGenes(NodeQuery query, QueryOptions options, GeneClient geneClient) throws BioNetDBException, IOException;
     void annotateGenes(List<String> geneIds, GeneClient geneClient) throws BioNetDBException, IOException;

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/io/BioPaxParser.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/io/BioPaxParser.java
@@ -1,12 +1,12 @@
 package org.opencb.bionetdb.core.io;
 
+import org.apache.commons.lang3.StringUtils;
 import org.biopax.paxtools.model.BioPAXElement;
 import org.biopax.paxtools.model.level3.*;
 import org.biopax.paxtools.model.level3.Process;
 import org.opencb.bionetdb.core.models.network.Network;
 import org.opencb.bionetdb.core.models.network.Node;
 import org.opencb.bionetdb.core.models.network.Relation;
-import org.sqlite.util.StringUtils;
 
 import java.io.IOException;
 import java.nio.file.Path;

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/models/network/Relation.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/models/network/Relation.java
@@ -142,7 +142,7 @@ public enum Type {
         PANEL__PANEL_VARIANT("PANEL__PANEL_VARIANT"),
         PANEL__PANEL_STR("PANEL__PANEL_STR"),
         PANEL__PANEL_REGION("PANEL__PANEL_REGION"),
-        PANEL__PHENOTYPE("PANEL__PHENOTYPE"),
+        PANEL__DISORDER("PANEL__DISORDER"),
         PHENOTYPE__ONTOLOGY_TERM("PHENOTYPE__ONTOLOGY_TERM"),
         PANEL_GENE__GENE("PANEL_GENE__GENE"),
         PANEL_GENE__ONTOLOGY_TERM("PANEL_GENE__ONTOLOGY_TERM"),