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Polished debug logging.
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@IgorRodchenkov
IgorRodchenkov committed Apr 26, 2024
1 parent 705203e commit f57827d
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Showing 3 changed files with 32 additions and 41 deletions.
4 changes: 2 additions & 2 deletions biopax-validator/src/main/java/org/biopax/validator/CvTermsRule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -239,9 +239,9 @@ private Set<String> 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;
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7 changes: 3 additions & 4 deletions biopax-validator/src/main/java/org/biopax/validator/rules/XrefRule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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;
}
Expand All @@ -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;
}
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62 changes: 27 additions & 35 deletions obo-fetcher/src/main/java/org/biopax/ols/impl/BaseOBO2AbstractLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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");
Expand All @@ -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());
Expand Down Expand Up @@ -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;
}

Expand Down Expand Up @@ -563,10 +563,10 @@ private Collection<Annotation> 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));
}

Expand All @@ -582,10 +582,10 @@ private Collection<Annotation> 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));
}

Expand All @@ -609,9 +609,8 @@ private Collection<Annotation> 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);
Expand Down Expand Up @@ -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;
}

Expand Down Expand Up @@ -806,7 +805,7 @@ private Collection<TermRelationship> 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;
Expand Down Expand Up @@ -920,7 +919,7 @@ private Collection<TermPath> createTermPathBeans(HashMap<String, Integer> 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;
Expand Down Expand Up @@ -952,7 +951,7 @@ private String getSynonymTypeDef(int scope) {
*/
private Collection<TermSynonym> processSynonyms(OBOObject obj, TermBean trm) {

HashSet<TermSynonym> retval = new HashSet<TermSynonym>();
HashSet<TermSynonym> retval = new HashSet<>();

//loop over synonyms
Set<Synonym> syns = obj.getSynonyms();
Expand All @@ -965,32 +964,27 @@ private Collection<TermSynonym> 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:
Expand All @@ -1010,7 +1004,6 @@ private Collection<TermSynonym> processSynonyms(OBOObject obj, TermBean trm) {
tsb.setSynonymType(SYNONYM);
break;
}

}

Collection<Dbxref> oboSynXrefs = aSyn.getXrefs();
Expand All @@ -1033,7 +1026,7 @@ private Collection<TermSynonym> 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());
}

}
Expand Down Expand Up @@ -1098,7 +1091,7 @@ private Collection<TermSynonym> 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;
Expand All @@ -1108,9 +1101,8 @@ private Collection<TermSynonym> 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), "");
}
}
Expand Down Expand Up @@ -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 + " ");
}
Expand Down

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