From f57827d1fd465d1afdfcd694b3cd2adf742d90dd Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Fri, 26 Apr 2024 00:31:55 -0400 Subject: [PATCH] Polished debug logging. --- .../org/biopax/validator/CvTermsRule.java | 4 +- .../org/biopax/validator/rules/XrefRule.java | 7 +-- .../ols/impl/BaseOBO2AbstractLoader.java | 62 ++++++++----------- 3 files changed, 32 insertions(+), 41 deletions(-) diff --git a/biopax-validator/src/main/java/org/biopax/validator/CvTermsRule.java b/biopax-validator/src/main/java/org/biopax/validator/CvTermsRule.java index 38150fa6..ec1a4892 100644 --- a/biopax-validator/src/main/java/org/biopax/validator/CvTermsRule.java +++ b/biopax-validator/src/main/java/org/biopax/validator/CvTermsRule.java @@ -239,9 +239,9 @@ private Set createTermsFromUnificationXrefs( inferred.add(ot.getPreferredName()); } else if(ot == null) - logger.warn("No term found by the xref.id: " + x.getId()); + logger.warn("No term found by the xref.id: {}", x.getId()); else - logger.debug("Invalid (for this CV context) term: " + x.getId()); + logger.debug("Invalid (for this CV context) term: {}", x.getId()); } return inferred; diff --git a/biopax-validator/src/main/java/org/biopax/validator/rules/XrefRule.java b/biopax-validator/src/main/java/org/biopax/validator/rules/XrefRule.java index 76c00340..9318dc9c 100644 --- a/biopax-validator/src/main/java/org/biopax/validator/rules/XrefRule.java +++ b/biopax-validator/src/main/java/org/biopax/validator/rules/XrefRule.java @@ -40,7 +40,7 @@ public void check(final Validation validation, Xref x) { String id = x.getId(); if (id != null) { if (!xrefUtils.canCheckIdFormatIn(prefix)) { - logger.info("Can't check IDs (no regexp) for " + db + " (" + prefix + ")"); + logger.info("Can't check ID (no regexp) for {} ({})", db, prefix); } else if (!xrefUtils.checkIdFormat(prefix, id)) { String regxp = xrefUtils.getRegexpString(prefix); // report error with fixed=false @@ -101,8 +101,7 @@ else if (prefix.equalsIgnoreCase("mi")) { x.setId(newId); error(validation, x, "invalid.id.format", true); if (logger.isDebugEnabled()) { - logger.debug(x.getModelInterface().getSimpleName() + " " + x - + " 'id' auto-fixed! (was: " + id + ")"); + logger.debug("{} {} 'id' auto-fixed! (was: {})", x.getModelInterface().getSimpleName(), x, id); } break; } @@ -119,7 +118,7 @@ else if (prefix.equalsIgnoreCase("mi")) { x.setId(newId); error(validation, x, "invalid.id.format", true); if (logger.isDebugEnabled()) { - logger.debug(x.getModelInterface().getSimpleName() + " " + x + " 'id' auto-fixed! (was: " + id + ")"); + logger.debug("{} {} 'id' auto-fixed! (was: {})", x.getModelInterface().getSimpleName(), x, id); } break; } diff --git a/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java b/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java index e0c560a8..4ab56541 100644 --- a/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java +++ b/obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java @@ -132,10 +132,10 @@ protected void process() { if (obj instanceof OBOObject) { processTerm((OBOObject) obj); if (count % 1000 == 0) { - logger.debug("Terms Processed: " + count); + logger.debug("Terms Processed: {}", count); } } else { - logger.info("Ignored object: " + obj.toString()); + logger.info("Ignored object: {}", obj.toString()); } } logger.info("Term processing done"); @@ -148,7 +148,7 @@ protected void process() { if (obj instanceof OBOObject) { processTermRelationships((OBOObject) obj); if (count % 1000 == 0) { - logger.debug("Relationships Processed: " + count); + logger.debug("Relationships Processed: {}", count); } } else { logger.info("Ignored object: " + obj.toString()); @@ -379,7 +379,7 @@ protected void processTerm(OBOObject obj) { obo:property obo:class */ - logger.debug("bogus term: " + obj.getID()); + logger.debug("bogus term: {}", obj.getID()); return; } @@ -563,10 +563,10 @@ private Collection processAnnotations(OBOObject obj, TermBean trm) { if (tmpStr.endsWith(":")) { tmpStr = tmpStr.substring(0, tmpStr.length() - 1); } - logger.debug("Setting property type: " + tmpStr); + logger.debug("Setting property type: {}", tmpStr); annot.setAnnotationType(tmpStr.trim()); if (annot.getAnnotationType() != null && annot.getAnnotationType().length() > 2000) { - logger.warn("annotation type longer than allowed database column length - truncating " + trm.getIdentifier()); + logger.warn("annotation type longer than allowed database column length - truncating {}", trm.getIdentifier()); annot.setAnnotationType(annot.getAnnotationType().substring(0, 2000)); } @@ -582,10 +582,10 @@ private Collection processAnnotations(OBOObject obj, TermBean trm) { if (tmpStr.startsWith("\"") && tmpStr.endsWith("\"")) { tmpStr = tmpStr.substring(1, tmpStr.length() - 1); } - logger.debug("Setting property value: " + tmpStr.trim()); + logger.debug("Setting property value: {}", tmpStr.trim()); annot.setAnnotationStringValue(tmpStr.trim()); if (tmpStr != null && tmpStr.length() > 2000) { - logger.warn("annotation value longer than allowed database column length - truncating " + trm.getIdentifier()); + logger.warn("annotation value longer than allowed database column length - truncating {}", trm.getIdentifier()); annot.setAnnotationStringValue(annot.getAnnotationStringValue().substring(0, 2000)); } @@ -609,9 +609,8 @@ private Collection processAnnotations(OBOObject obj, TermBean trm) { annot.setParentTerm(trm); } catch (RuntimeException re) { - logger.warn("Error parsing property_value - Ignoring : " + pv.toString()); - logger.debug("pv.getProperty() = " + pv.getProperty()); - logger.debug("pv.getValue() = " + pv.getValue()); + logger.warn("Error parsing property_value - Ignoring: {}", pv.toString()); + logger.debug("pv.property: {}, pv.value: {}", pv.getProperty(), pv.getValue()); continue; } retval.add(annot); @@ -739,7 +738,7 @@ private void processTermRelationships(OBOObject obj) { obo:property obo:class */ - logger.debug("bogus term: " + obj.getID()); + logger.debug("bogus term: {}", obj.getID()); return; } @@ -806,7 +805,7 @@ private Collection processRelationships(OBOObject obj, TermBea //add to retval retval.add(trb); } else { - logger.debug("No object term found for link: " + lnk.toString()); + logger.debug("No object term found for link: {}", lnk); } } return retval; @@ -920,7 +919,7 @@ private Collection createTermPathBeans(HashMap paths, //add to retval retval.add(tpb); } else { - logger.debug("No object term found for term path: " + trm.getIdentifier() + "->" + termId); + logger.debug("No object term found for term path: {} -> {}", trm.getIdentifier(), termId); } } return retval; @@ -952,7 +951,7 @@ private String getSynonymTypeDef(int scope) { */ private Collection processSynonyms(OBOObject obj, TermBean trm) { - HashSet retval = new HashSet(); + HashSet retval = new HashSet<>(); //loop over synonyms Set syns = obj.getSynonyms(); @@ -965,32 +964,27 @@ private Collection processSynonyms(OBOObject obj, TermBean trm) { String synVal = safeTrim(aSyn.getText()); if (synVal != null) { - //set value tsb.setSynonym(synVal); if (synVal.length() > 2000) { - logger.warn("synonym value longer than allowed database column length - truncating " + trm.getIdentifier()); + logger.warn("synonym value longer than allowed database column length - truncating {}", trm.getIdentifier()); tsb.setSynonym(tsb.getSynonym().substring(0, 2000)); } //check to see if there's a defined synonymType for it if (aSyn.getSynonymType() != null) { - - logger.debug("using user-defined synonym type: " + aSyn.getSynonymType().getName()); + logger.debug("using user-defined synonym type: {}", aSyn.getSynonymType().getName()); Term synTrm = ontologyTerms.get(aSyn.getSynonymType().getID()); if (synTrm != null) { tsb.setSynonymType(synTrm); } else { throw new IllegalStateException( - "Attempting to use user-defined synonym type that has not been initialized in common objects: " - + aSyn.getSynonymType().getID() + "Attempting to use user-defined synonym type that has not been initialized in common objects: " + + aSyn.getSynonymType().getID() ); } - } else { - - //logger.debug("using old-style synonym types"); //link synonymType Term switch (aSyn.getScope()) { case Synonym.EXACT_SYNONYM: @@ -1010,7 +1004,6 @@ private Collection processSynonyms(OBOObject obj, TermBean trm) { tsb.setSynonymType(SYNONYM); break; } - } Collection oboSynXrefs = aSyn.getXrefs(); @@ -1033,7 +1026,7 @@ private Collection processSynonyms(OBOObject obj, TermBean trm) { retval.add(tsb); } else { - logger.debug("Null Synonym value encountered for " + trm.getIdentifier()); + logger.debug("Null Synonym value encountered for {}", trm.getIdentifier()); } } @@ -1098,7 +1091,7 @@ private Collection processSynonyms(OBOObject obj, TermBean trm) { } } catch (IndexOutOfBoundsException e) { - logger.debug("Could not create alt_id from URL from term: " + trm.getIdentifier()); + logger.debug("Could not create alt_id from URL from term: {}", trm.getIdentifier()); } return retval; @@ -1108,9 +1101,8 @@ private Collection processSynonyms(OBOObject obj, TermBean trm) { * for debugging */ protected void dumpOntology() { - for (String id : getRootTerms()) { - logger.debug("Root term: " + id); + logger.debug("Root term: {}", id); dumpTerm(ontologyTerms.get(id), ""); } } @@ -1153,20 +1145,20 @@ protected void dumpOntologyStats() { * @param indent - spaces to indent */ protected void dumpTerm(Term term, String indent) { - if (indent.length() > 15) { return; } if (term != null) { - logger.debug(indent + "id: " + term.getIdentifier()); - logger.debug(indent + "name: " + term.getName()); + logger.debug("{}id: {}", indent, term.getIdentifier()); + logger.debug("{}name: {}", indent, term.getName()); if (term.getSynonyms() != null) - logger.debug(indent + "nb syn: " + term.getSynonyms().size()); + logger.debug("{}nb syn: {}", indent, term.getSynonyms().size()); if (term.getAnnotations() != null) - logger.debug(indent + "nb annot: " + term.getAnnotations().size()); + logger.debug("{}nb annot: {}", indent, term.getAnnotations().size()); if (term.getRelationships() != null) { for (TermRelationship tr : term.getRelationships()) { - String relationStr = indent + tr.getSubjectTerm().getName() + " " + tr.getPredicateTerm().getName() + " " + tr.getObjectTerm().getName(); + String relationStr = indent + tr.getSubjectTerm().getName() + " " + tr.getPredicateTerm().getName() + + " " + tr.getObjectTerm().getName(); logger.debug(relationStr); dumpTerm(tr.getSubjectTerm(), indent + " "); }