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Fix deleting a Specimen
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@GenieTim
GenieTim committed Sep 28, 2020
1 parent 8e86296 commit 8766ef5
Showing 1 changed file with 31 additions and 31 deletions.
62 changes: 31 additions & 31 deletions src/main/java/edu/harvard/mcz/imagecapture/lifecycle/SpecimenLifeCycle.java
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Original file line number Diff line number Diff line change
Expand Up @@ -60,17 +60,17 @@ public static String[] getMissingBarcodes() {
String sql = "select " +
" (cast(substr(a.barcode,-8) as decimal(8,0)) + 1) " +
" from Specimen a " +
" where " +
" WHERE " +
" not exists " +
" (" +
" select 1 from Specimen b " +
" where " +
" WHERE " +
" cast(substr(b.barcode,-8) as decimal(8,0)) = (cast(substr(a.barcode,-8) as decimal(8,0)) + 1)" +
" ) " +
" and " +
" cast(substr(a.barcode,-8) as decimal(8,0)) not in " +
" ( " +
" select max(cast(substr(c.barcode,-8) as decimal(8,0))) from Specimen c where cast(substr(a.barcode,-8) as decimal(8,0)) > 49999 " +
" select max(cast(substr(c.barcode,-8) as decimal(8,0))) from Specimen c WHERE cast(substr(a.barcode,-8) as decimal(8,0)) > 49999 " +
" ) " +
" order by 1";
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
Expand Down Expand Up @@ -357,8 +357,8 @@ public List<Specimen> findByBarcode(String barcode) {
session.beginTransaction();
List<Specimen> results = null;
try {
Query query = session.createQuery("From Specimen as s where s.barcode = ?1");
query.setParameter(1, barcode);
Query query = session.createQuery("From Specimen s WHERE s.barcode LIKE :barcode");
query.setParameter("barcode", barcode);
results = (List<Specimen>) query.list();
log.debug("find query successful, result size: " + results.size());
session.getTransaction().commit();
Expand Down Expand Up @@ -435,7 +435,7 @@ public List<Specimen> findAllPage(int startAt, int fetchSize) {
}
}

//Select distinct path from ICImage im where im.path is not null order by im.path
//Select distinct path from ICImage im WHERE im.path is not null order by im.path

public List<ICImage> findImagesByPath(String path) {
log.debug("finding images by path " + path);
Expand All @@ -448,12 +448,12 @@ public List<ICImage> findImagesByPath(String path) {
//this works
String sql = "";
if (path.contains("\\")) {
sql = "From ICImage im where im.path='" + path + "\\' order by imageId";
sql = "From ICImage im WHERE im.path='" + path + "\\' order by imageId";
} else {
sql = "From ICImage im where im.path='" + path + "' order by imageId";
sql = "From ICImage im WHERE im.path='" + path + "' order by imageId";
}

//String sql = "From ICImage im where im.path='"+path+"\\\' order by imageId";
//String sql = "From ICImage im WHERE im.path='"+path+"\\\' order by imageId";
Query query = session.createQuery(sql);
results = (List<ICImage>) query.list();
//log.debug("found images, result size: " + results.size());
Expand Down Expand Up @@ -561,7 +561,7 @@ public String findSpecimenCountThrows() throws ConnectionException {
public List<GenusSpeciesCount> countSpecimensForVerbatim() {
ArrayList<GenusSpeciesCount> result = new ArrayList<GenusSpeciesCount>();
try {
String sql = "Select count(S), genus, specificEpithet from Specimen S where S.workFlowStatus = 'Taxon Entered' group by S.genus, S.specificEpithet ";
String sql = "Select count(S), genus, specificEpithet from Specimen S WHERE S.workFlowStatus = 'Taxon Entered' group by S.genus, S.specificEpithet ";
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
try {
session.beginTransaction();
Expand Down Expand Up @@ -640,7 +640,7 @@ public List<Specimen> findForVerbatim(String genus, String specificEpithet, Stri
List<Specimen> results = null;
try {
session.beginTransaction();
Query query = session.createQuery("From Specimen as s where s.genus = ? and s.specificEpithet = ? and s.workFlowStatus = ? ");
Query query = session.createQuery("From Specimen as s WHERE s.genus = ? and s.specificEpithet = ? and s.workFlowStatus = ? ");
query.setParameter(0, genus);
query.setParameter(1, specificEpithet);
query.setParameter(2, workflowStatus);
Expand Down Expand Up @@ -783,7 +783,7 @@ public String[] getDistinctCountries() {
ArrayList<String> collections = new ArrayList<String>();
collections.add(""); // put blank at top of list.
try {
String sql = "Select distinct country from Specimen spe where spe.country is not null order by spe.country ";
String sql = "Select distinct country from Specimen spe WHERE spe.country is not null order by spe.country ";
return loadStringsBySQL(collections, sql);
} catch (RuntimeException re) {
log.error(re);
Expand All @@ -802,37 +802,37 @@ public int deleteSpecimenByBarcode(String barcode) {
//this does not work - need to do it manually as below!!
//this.delete(specimen);

long specimenId = specimen.getSpecimenId();
Long specimenId = specimen.getSpecimenId();
try {
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
session.beginTransaction();
Transaction transaction = session.beginTransaction();
try {
Query query = session.createQuery("delete from Tracking where Tracking.specimen =?");
query.setParameter(0, specimenId);
Query query = session.createQuery("DELETE FROM Tracking WHERE specimen = :specimen");
query.setParameter("specimen", specimen);
query.executeUpdate();

query = session.createQuery("delete from LatLong where LatLong.specimenId =?");
query.setParameter(0, specimenId);
query = session.createQuery("DELETE FROM LatLong WHERE specimenId = :specimen");
query.setParameter("specimen", specimen);
query.executeUpdate();

query = session.createQuery("delete from ICImage where ICImage.specimen =?");
query.setParameter(0, specimenId);
query = session.createQuery("DELETE FROM ICImage WHERE specimen = :specimen");
query.setParameter("specimen", specimen);
query.executeUpdate();

query = session.createQuery("delete from SpecimenPart where SpecimenPart.specimenId =?");
query.setParameter(0, specimenId);
query = session.createQuery("DELETE FROM SpecimenPart WHERE specimenId = :specimen");
query.setParameter("specimen", specimen);
query.executeUpdate();

query = session.createQuery("delete from Specimen where Specimen.id =?");
query.setParameter(0, specimenId);
query = session.createQuery("DELETE FROM Specimen WHERE specimenId = :specimenId");
query.setParameter("specimenId", specimenId);
query.executeUpdate();

session.getTransaction().commit();
transaction.commit();
} catch (HibernateException e) {
session.getTransaction().rollback();
transaction.rollback();
log.error("DeleteByBarcode failed Hibernate Exception", e);
} catch (Exception e) {
session.getTransaction().rollback();
transaction.rollback();
log.error("findByBarcode failed general Exception", e);
}
try {
Expand All @@ -856,7 +856,7 @@ public String[] getDistinctCollections() {
ArrayList<String> collections = new ArrayList<String>();
collections.add(""); // put blank at top of list.
try {
String sql = "Select distinct collection from Specimen spe where spe.collection is not null order by spe.collection ";
String sql = "Select distinct collection from Specimen spe WHERE spe.collection is not null order by spe.collection ";
return loadStringsBySQL(collections, sql);
} catch (RuntimeException re) {
log.error(re);
Expand All @@ -868,7 +868,7 @@ public String[] getDistinctDeterminers() {
ArrayList<String> collections = new ArrayList<String>();
collections.add(""); // put blank at top of list.
try {
String sql = "Select distinct identifiedBy from Specimen spe where spe.identifiedBy is not null order by spe.identifiedBy ";
String sql = "Select distinct identifiedBy from Specimen spe WHERE spe.identifiedBy is not null order by spe.identifiedBy ";
//String sql = "Select distinct identifiedby from Specimen";
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
try {
Expand Down Expand Up @@ -905,7 +905,7 @@ public String[] getDistinctPrimaryDivisions() {
ArrayList<String> collections = new ArrayList<String>();
collections.add(""); // put blank at top of list.
try {
String sql = "Select distinct primaryDivison from Specimen spe where spe.primaryDivison is not null order by spe.primaryDivison ";
String sql = "Select distinct primaryDivison from Specimen spe WHERE spe.primaryDivison is not null order by spe.primaryDivison ";
//String sql = "Select distinct identifiedby from Specimen";
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
try {
Expand Down Expand Up @@ -942,7 +942,7 @@ public String[] getDistinctQuestions() {
ArrayList<String> collections = new ArrayList<String>();
collections.add(""); // put blank at top of list.
try {
String sql = "Select distinct questions from Specimen spe where spe.questions is not null order by spe.questions ";
String sql = "Select distinct questions from Specimen spe WHERE spe.questions is not null order by spe.questions ";
return loadStringsBySQL(collections, sql);
} catch (RuntimeException re) {
log.error(re);
Expand Down

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