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Collaborator lookup #525

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Collaborator lookup #525

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6630751
Merge pull request #509 from wcmc-its/development
paulalbert1 Aug 31, 2023
4fff7c8
Update PubMedQueryType.java
paulalbert1 Nov 17, 2023
9a77f1c
Update KnownRelationshipRetrievalStrategy.java
paulalbert1 Nov 17, 2023
e4c2629
Update SecondInitialRetrievalStrategy.java
paulalbert1 Nov 17, 2023
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68 changes: 34 additions & 34 deletions src/main/java/reciter/xml/retriever/pubmed/KnownRelationshipRetrievalStrategy.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,38 +58,38 @@ protected PubMedQuery buildNameQuery(Set<AuthorName> identitynames, Identity ide
return pubMedQueryBuilder.build();
}

@Override
protected String getStrategySpecificKeyword(Identity identity) {
if (identity.getKnownRelationships() != null && !identity.getKnownRelationships().isEmpty()) {
List<String> nameIgnoredAuthors = Arrays.asList(excludeNames.trim().split("\\s*,\\s*"));
Iterator<KnownRelationship> iter = identity.getKnownRelationships().iterator();
final KnownRelationship firstRelationship = iter.next();
String first = null;
if(!nameIgnoredAuthors.contains(firstRelationship.getName().getLastName() + " " + firstRelationship.getName().getFirstInitial())) {
first = firstRelationship.getName().getLastName() + " " + firstRelationship.getName().getFirstInitial() + "[au]";
}
if (!iter.hasNext()) {
return first;
}
//for more than 1 institutions
final StringBuilder buf = new StringBuilder();
if(first != null) {
buf.append("(" + first);
}
while(iter.hasNext()) {
KnownRelationship knownRelationship = iter.next();
if(!nameIgnoredAuthors.contains(knownRelationship.getName().getLastName() + " " + knownRelationship.getName().getFirstInitial())) {
buf.append(" OR ");
buf.append(knownRelationship.getName().getLastName() + " " + firstRelationship.getName().getFirstInitial() + "[au]");
}
}
buf.append(")");
return buf.toString();
} else {
return null;
}
}

@Override
protected String getStrategySpecificKeyword(Identity identity) {
if (identity.getKnownRelationships() != null && !identity.getKnownRelationships().isEmpty()) {
List<String> nameIgnoredAuthors = Arrays.asList(excludeNames.trim().split("\\s*,\\s*"));
Iterator<KnownRelationship> iter = identity.getKnownRelationships().iterator();
final KnownRelationship firstRelationship = iter.next();
String first = null;
if(!nameIgnoredAuthors.contains(firstRelationship.getName().getLastName() + " " + firstRelationship.getName().getFirstInitial())) {
first = firstRelationship.getName().getLastName() + " " + firstRelationship.getName().getFirstInitial() + "[au] OR "
+ firstRelationship.getName().getLastName() + " " + firstRelationship.getName().getFirstInitial() + "[ir]";
}
if (!iter.hasNext()) {
return first;
}
final StringBuilder buf = new StringBuilder();
if(first != null) {
buf.append("(" + first);
}
while(iter.hasNext()) {
KnownRelationship knownRelationship = iter.next();
if(!nameIgnoredAuthors.contains(knownRelationship.getName().getLastName() + " " + knownRelationship.getName().getFirstInitial())) {
buf.append(" OR ");
buf.append(knownRelationship.getName().getLastName() + " " + knownRelationship.getName().getFirstInitial() + "[au] OR "
+ knownRelationship.getName().getLastName() + " " + knownRelationship.getName().getFirstInitial() + "[ir]");
}
}
buf.append(")");
return buf.toString();
} else {
return null;
}
}
}
77 changes: 40 additions & 37 deletions src/main/java/reciter/xml/retriever/pubmed/PubMedQueryType.java
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Expand Up @@ -150,43 +150,46 @@ public PubMedQuery buildPmids(List<Long> pmids) {
return p;
}

public String contsructAuthorQuery() {
if (this.identityAuthorNames != null && this.identityAuthorNames.size() > 0) {

// Below is code from Apache's StringUtils class, modified to remove null checks.
Iterator<AuthorName> iterator = this.identityAuthorNames.iterator();

final AuthorName first = iterator.next();
String firstName = first.getLastName() + " " + first.getFirstInitial() + "[au]";
if(this.isAuthorFullNameRequired) {
firstName = first.getLastName() + " " + first.getFirstName() + "[au]";
}
if (!iterator.hasNext()) {
return firstName;
}

// two or more elements
final StringBuilder buf = new StringBuilder();
if (first != null) {
buf.append("(" + firstName);
}

while (iterator.hasNext()) {
buf.append(" OR ");
final AuthorName obj = iterator.next();
if(this.isAuthorFullNameRequired) { //For FullName Strict retrieval strategy
buf.append(obj.getLastName() + " " + obj.getFirstName() + "[au]");
} else {
buf.append(obj.getLastName() + " " + obj.getFirstInitial() + "[au]");
}

}
buf.append(")");
return buf.toString();
} else {
return null;
}
}
public String constructAuthorQuery() {
if (this.identityAuthorNames != null && this.identityAuthorNames.size() > 0) {

Iterator<AuthorName> iterator = this.identityAuthorNames.iterator();
final AuthorName first = iterator.next();
String firstName = first.getLastName() + " " + first.getFirstInitial() + "[au] OR "
+ first.getLastName() + " " + first.getFirstInitial() + "[ir]";
if(this.isAuthorFullNameRequired) {
firstName = first.getLastName() + " " + first.getFirstName() + "[au] OR "
+ first.getLastName() + " " + first.getFirstName() + "[ir]";
}
if (!iterator.hasNext()) {
return firstName;
}

final StringBuilder buf = new StringBuilder();
if (first != null) {
buf.append("(" + firstName);
}

while (iterator.hasNext()) {
buf.append(" OR ");
final AuthorName obj = iterator.next();
if(this.isAuthorFullNameRequired) {
buf.append(obj.getLastName() + " " + obj.getFirstName() + "[au] OR "
+ obj.getLastName() + " " + obj.getFirstName() + "[ir]");
} else {
buf.append(obj.getLastName() + " " + obj.getFirstInitial() + "[au] OR "
+ obj.getLastName() + " " + obj.getFirstInitial() + "[ir]");
}
}
buf.append(")");
return buf.toString();
} else {
return null;
}
}




// private static final int THRESHOLD = 25;
//
Expand Down
127 changes: 65 additions & 62 deletions src/main/java/reciter/xml/retriever/pubmed/SecondInitialRetrievalStrategy.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,67 +52,70 @@ protected PubMedQuery buildNameQuery(Set<AuthorName> identitynames, Identity ide
return pubMedQueryBuilder.build();
}

@Override
protected String getStrategySpecificKeyword(Identity identity) {
if (identity.getPrimaryName() != null || (identity.getAlternateNames() != null && !identity.getAlternateNames().isEmpty())) {
String middleName = null;
if(identity.getPrimaryName().getMiddleName() != null) {
middleName = identity.getPrimaryName().getMiddleName();
} else {
middleName = "";
}
String combinedFirstMiddleName = identity.getPrimaryName().getFirstName() + middleName;
String capitalizeFirstMiddle = ReCiterStringUtil.deAccent(combinedFirstMiddleName.chars().filter(Character::isUpperCase)
.mapToObj(c -> Character.toString((char)c))
.collect(Collectors.joining()));
String first = null;
if(capitalizeFirstMiddle.length() >= 2) {
first = identity.getPrimaryName().getLastName() + " " + capitalizeFirstMiddle.substring(0, 2) + "[au]";
}

if(first != null && identity.getAlternateNames() != null && !identity.getAlternateNames().isEmpty()) {
return first;
}

Iterator<AuthorName> iter = identity.getAlternateNames().iterator();

final StringBuilder buf = new StringBuilder();
if(first != null) {
buf.append("(" + first);
} else {
buf.append("(");
}
while(iter.hasNext()) {
AuthorName alternateName = iter.next();
String alternateNameWithInitial = null;
if(alternateName.getMiddleName() != null) {
middleName = alternateName.getMiddleName();
} else {
middleName = "";
}
combinedFirstMiddleName = alternateName.getFirstName() + middleName;
capitalizeFirstMiddle = ReCiterStringUtil.deAccent(combinedFirstMiddleName.chars().filter(Character::isUpperCase)
.mapToObj(c -> Character.toString((char)c))
.collect(Collectors.joining()));
if(capitalizeFirstMiddle.length() >= 2) {
alternateNameWithInitial = alternateName.getLastName() + " " + capitalizeFirstMiddle.substring(0, 2) + "[au]";
}
if(alternateNameWithInitial != null) {
buf.append(alternateNameWithInitial);
buf.append(" OR ");
}
}
buf.append(")");
if(buf.toString().endsWith(" OR )")) {
return buf.toString().substring(0, buf.toString().length() - 5) + ")";
}
else {
return buf.toString();
}
} else {
return null;
}
}

@Override
protected String getStrategySpecificKeyword(Identity identity) {
if (identity.getPrimaryName() != null || (identity.getAlternateNames() != null && !identity.getAlternateNames().isEmpty())) {
String middleName = null;
if(identity.getPrimaryName().getMiddleName() != null) {
middleName = identity.getPrimaryName().getMiddleName();
} else {
middleName = "";
}
String combinedFirstMiddleName = identity.getPrimaryName().getFirstName() + middleName;
String capitalizeFirstMiddle = ReCiterStringUtil.deAccent(combinedFirstMiddleName.chars().filter(Character::isUpperCase)
.mapToObj(c -> Character.toString((char)c))
.collect(Collectors.joining()));
String first = null;
if(capitalizeFirstMiddle.length() >= 2) {
first = identity.getPrimaryName().getLastName() + " " + capitalizeFirstMiddle.substring(0, 2) + "[au] OR "
+ identity.getPrimaryName().getLastName() + " " + capitalizeFirstMiddle.substring(0, 2) + "[ir]";
}

if(first != null && identity.getAlternateNames() != null && !identity.getAlternateNames().isEmpty()) {
return first;
}

Iterator<AuthorName> iter = identity.getAlternateNames().iterator();

final StringBuilder buf = new StringBuilder();
if(first != null) {
buf.append("(" + first);
} else {
buf.append("(");
}
while(iter.hasNext()) {
AuthorName alternateName = iter.next();
String alternateNameWithInitial = null;
if(alternateName.getMiddleName() != null) {
middleName = alternateName.getMiddleName();
} else {
middleName = "";
}
combinedFirstMiddleName = alternateName.getFirstName() + middleName;
capitalizeFirstMiddle = ReCiterStringUtil.deAccent(combinedFirstMiddleName.chars().filter(Character::isUpperCase)
.mapToObj(c -> Character.toString((char)c))
.collect(Collectors.joining()));
if(capitalizeFirstMiddle.length() >= 2) {
alternateNameWithInitial = alternateName.getLastName() + " " + capitalizeFirstMiddle.substring(0, 2) + "[au] OR "
+ alternateName.getLastName() + " " + capitalizeFirstMiddle.substring(0, 2) + "[ir]";
}
if(alternateNameWithInitial != null) {
buf.append(alternateNameWithInitial);
if (iter.hasNext()) {
buf.append(" OR ");
}
}
}
buf.append(")");
if(buf.toString().endsWith(" OR )")) {
return buf.toString().substring(0, buf.toString().length() - 5) + ")";
}
else {
return buf.toString();
}
} else {
return null;
}
}

}