Merge tag '2024.2.1' into pcheung/2024.2.1-jchem-23.4.0-commons-lang-…

…3.12

.github/workflows/docker-image.yml

@@ -15,11 +15,11 @@ jobs:
     steps:
       -
         name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       -
         name: Docker meta
         id: meta
-        uses: docker/metadata-action@v3
+        uses: docker/metadata-action@v5
         with:
           # list of Docker images to use as base name for tags
           images: |
@@ -31,19 +31,19 @@ jobs:
             type=ref,event=tag,suffix=-${{ matrix.chemistry_package }}
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.meta.outputs.tags }}

.github/workflows/trigger-tag.yml

@@ -11,7 +11,7 @@ jobs:
     steps:
       # Checkout this repo
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       # Get branch name
@@ -24,11 +24,11 @@ jobs:
       # and 2022.1.1-dev9 will become 2022.1.1-dev10
       - name: Get next dev tag name
         run: |
-          LAST_TAG=$(git tag --sort=v:refname --merged ${{ env.BRANCH_NAME }} | grep -e '-dev' | tail -1)
+          LAST_TAG=$(git tag --sort=v:refname --merged ${{ env.BRANCH_NAME }} | grep -E '^[0-9]{4}\.[0-9]+\.[0-9]+-dev[0-9]+$' | tail -1)
           echo "NEXT_TAG=$(echo $LAST_TAG | awk -F-dev -v OFS=-dev '{$NF += 1 ; print}')" >> $GITHUB_ENV
       # Trigger the build
       - name: Trigger the tagger workflow with branch ${{env.BRANCH_NAME}} and tag ${{ env.NEXT_TAG }}
-        uses: actions/github-script@v5
+        uses: actions/github-script@v7
         with:
           github-token: ${{ secrets.ACAS_WORKFLOWS_TOKEN }}
           script: |

Dockerfile-multistage

@@ -27,7 +27,7 @@ RUN apt-get update && \
 
 # Add nodejs for prepare config files
 ENV NPM_CONFIG_LOGLEVEL warn
-ENV NODE_VERSION 18.x
+ENV NODE_VERSION 20.x
 
 # Second Slowest Step 
 RUN curl -fsSL https://deb.nodesource.com/setup_$NODE_VERSION | bash - && \

find-sort-flywaymigration.bash

@@ -0,0 +1,38 @@
+# /bin/bash
+
+# Find all the flyway migration files and sort them in order of version number (semantically)
+# write them out as tab separated values with version\tfile
+
+java_files=$( find src/main/java/com/labsynch/labseer/db/migration -name "V*.java" )
+
+# Loop through the files and get the version from the beginning of the file name
+# e.g. src/main/java/com/labsynch/labseer/db/migration/postgres/V1_0_6_6__copy_author_value_blob_values.java -> 1_0_6_6
+all_versions=""
+for java_file in $java_files
+do
+    file_name=$( basename $java_file )
+    version=$( echo $file_name | sed -e 's/V\([0-9_]*\)__.*/\1/' | sed -e 's/_/./g' )
+    # add java to the end of the version
+    version="$version\t$java_file"
+    all_versions="$all_versions $version"
+done
+
+# Get teh sql files in src/main/resources/db/migration/postgres
+sql_files=$( find src/main/resources/db/migration -name "*.sql" )
+
+# Loop through the files and get the version from the beginning of the file name
+# e.g. src/main/resources/db/migration/postgres/V1_0_6_6__copy_author_value_blob_values.sql -> 1_0_6_6
+for sql_file in $sql_files
+do
+    file_name=$( basename $sql_file )
+    version=$( echo $file_name | sed -e 's/V\([0-9.]*\)__.*/\1/' )
+    version="$version\t$sql_file"
+    all_versions="$all_versions $version"
+done
+
+
+# Do a semantically sorted list of the versions
+# Use printf to get the tabs to work
+printf "version\tfile"
+printf "$all_versions" | tr ' ' '\n' | sort -V
+

src/main/java/com/labsynch/labseer/api/ApiDDictValueController.java

@@ -4,6 +4,8 @@
 import java.util.Collection;
 import java.util.List;
 
+import javax.persistence.TypedQuery;
+
 import com.labsynch.labseer.domain.DDictValue;
 import com.labsynch.labseer.dto.CodeTableDTO;
 import com.labsynch.labseer.exceptions.ErrorMessage;
@@ -322,7 +324,10 @@ public ResponseEntity<String> listJson(
 	public ResponseEntity<java.lang.String> getDDictValuesByTypeKindFormat(
 			@PathVariable("lsType") String lsType,
 			@PathVariable("lsKind") String lsKind,
-			@PathVariable("format") String format) {
+			@PathVariable("format") String format,
+			@RequestParam(value = "maxHits", required = false) Integer maxHits,
+			@RequestParam(value = "shortName", defaultValue = "", required = false) String shortName,
+			@RequestParam(value = "labelTextSearchTerm", defaultValue = "", required = false) String labelTextSearchTerm) {
 
 		HttpHeaders headers = new HttpHeaders();
 		headers.add("Content-Type", "application/json; charset=utf-8");
@@ -331,12 +336,37 @@ public ResponseEntity<java.lang.String> getDDictValuesByTypeKindFormat(
 			return new ResponseEntity<String>(headers, HttpStatus.BAD_REQUEST);
 		}
 
-		List<DDictValue> dDictResults = DDictValue.findDDictValuesByLsTypeEqualsAndLsKindEquals(lsType, lsKind)
-				.getResultList();
+		// throw an error if the user tries to search by codeName and label text
+		if (!shortName.isEmpty() && !labelTextSearchTerm.isEmpty()) {
+			ErrorMessage errorMessage = new ErrorMessage();
+			errorMessage.setErrorLevel("error");
+			errorMessage.setMessage("Cannot search by codeName and labelTextSearchTerm at the same time");
+			return new ResponseEntity<String>(errorMessage.toJson(), headers, HttpStatus.BAD_REQUEST);
+		}
+
+		List<DDictValue> dDictResults;
+		if (labelTextSearchTerm.isEmpty() && shortName.isEmpty()) {
+			TypedQuery<DDictValue> dDictResultsQuery = DDictValue.findDDictValuesByLsTypeEqualsAndLsKindEquals(lsType, lsKind);
+			if (maxHits != null) {
+				dDictResultsQuery = dDictResultsQuery.setMaxResults(maxHits);
+			}
+			dDictResults = dDictResultsQuery.getResultList();
+		} else if (!shortName.isEmpty()) {
+			TypedQuery<DDictValue> dDictResultsQuery = DDictValue.findDDictValuesByLsTypeEqualsAndLsKindEqualsAndShortNameEquals(lsType, lsKind, shortName);
+			if (maxHits != null) {
+				dDictResultsQuery = dDictResultsQuery.setMaxResults(maxHits);
+			}
+			dDictResults = dDictResultsQuery.getResultList();
+		} else {
+			dDictResults = DDictValue.findDDictValuesByLsTypeEqualsAndLsKindEqualsAndLabelTextSearch(lsType, lsKind, labelTextSearchTerm, maxHits);
+		}
 
 		if (format != null && format.equalsIgnoreCase("codeTable")) {
 			List<CodeTableDTO> codeTables = dataDictionaryService.convertToCodeTables(dDictResults);
-			codeTables = CodeTableDTO.sortCodeTables(codeTables);
+			// labelText searches have their own sort order so we don't need to sort them
+			if (labelTextSearchTerm.isEmpty()) {
+				codeTables = CodeTableDTO.sortCodeTables(codeTables);
+			}
 			return new ResponseEntity<String>(CodeTableDTO.toJsonArray(codeTables), headers, HttpStatus.OK);
 		} else if (format != null && format.equalsIgnoreCase("csv")) {
 			String outputString = dataDictionaryService.getCsvList(dDictResults);

src/main/java/com/labsynch/labseer/api/ApiExperimentController.java

@@ -44,6 +44,7 @@
 import com.labsynch.labseer.dto.TsvLoaderResponseDTO;
 import com.labsynch.labseer.exceptions.ErrorMessage;
 import com.labsynch.labseer.exceptions.NotFoundException;
+import com.labsynch.labseer.exceptions.TooManyResultsException;
 import com.labsynch.labseer.exceptions.UniqueNameException;
 import com.labsynch.labseer.service.AnalysisGroupService;
 import com.labsynch.labseer.service.AnalysisGroupValueService;
@@ -1634,20 +1635,19 @@ public ResponseEntity<java.lang.String> jsonFindExperimentByNameGet(@RequestPara
 	@RequestMapping(value = "/protocol/{codeName}", method = RequestMethod.GET, headers = "Accept=application/json")
 	@ResponseBody
 	public ResponseEntity<java.lang.String> jsonFindExperimentsByProtocolCodeName(
-			@PathVariable("codeName") String codeName, @RequestParam(value = "with", required = false) String with) {
+			@PathVariable("codeName") String codeName, @RequestParam(value = "projects", required = false) List<String> projects, @RequestParam(value = "with", required = false) String with) {
 		HttpHeaders headers = new HttpHeaders();
 		headers.add("Content-Type", "application/json; charset=utf-8");
-		List<Protocol> protocols = Protocol.findProtocolsByCodeNameEqualsAndIgnoredNot(codeName, true).getResultList();
-		if (protocols.size() == 1) {
+		try {
+			Collection<Experiment> experiments = experimentService.findExperimentsByProtocolCodeName(codeName, projects);
 			return new ResponseEntity<String>(
-					Experiment.toJsonArrayStub(Experiment.findExperimentsByProtocol(protocols.get(0)).getResultList()),
+					Experiment.toJsonArrayStub(experiments),
 					headers, HttpStatus.OK);
-		} else if (protocols.size() > 1) {
-			logger.error("ERROR: multiple protocols found with the same code name");
-			return new ResponseEntity<String>("[ ]", headers, HttpStatus.CONFLICT);
-		} else {
-			logger.warn("WARN: no protocols found with the query code name");
+		} catch (NoResultException e) {
 			return new ResponseEntity<String>("[ ]", headers, HttpStatus.NOT_FOUND);
+
+		} catch (TooManyResultsException e) {
+			return new ResponseEntity<String>("[ ]", headers, HttpStatus.CONFLICT);
 		}
 	}
 

src/main/java/com/labsynch/labseer/chemclasses/bbchem/BBChemParentStructure.java

@@ -32,7 +32,7 @@ public static List<BBChemParentStructure> findBBChemParentStructuresBySubstructu
         EntityManager em = BBChemParentStructure.entityManager();
         String fingerprintString = SimpleUtil.bitSetToString(substructure);
         Query q = em.createNativeQuery(
-                "SELECT o.* FROM bbchem_parent_structure AS o WHERE (o.substructure \\& CAST(:fingerprintString AS bit(2048))) = CAST(:fingerprintString AS bit(2048))  ",
+                "SELECT o.* FROM bbchem_parent_structure AS o WHERE (o.substructure \\& CAST(:fingerprintString AS bit(2112))) = CAST(:fingerprintString AS bit(2112))  ",
                 BBChemParentStructure.class);
         q.setParameter("fingerprintString", fingerprintString);
         if (maxResults > -1) {

src/main/java/com/labsynch/labseer/chemclasses/bbchem/BBChemSaltFormStructure.java

@@ -32,7 +32,7 @@ public static List<BBChemSaltFormStructure> findBBChemSaltFormStructuresBySubstr
         EntityManager em = BBChemSaltFormStructure.entityManager();
         String fingerprintString = SimpleUtil.bitSetToString(substructure);
         Query q = em.createNativeQuery(
-                "SELECT o.* FROM bbchem_salt_form_structure AS o WHERE (o.substructure \\& CAST(:fingerprintString AS bit(2048))) = CAST(:fingerprintString AS bit(2048)) ",
+                "SELECT o.* FROM bbchem_salt_form_structure AS o WHERE (o.substructure \\& CAST(:fingerprintString AS bit(2112))) = CAST(:fingerprintString AS bit(2112)) ",
                 BBChemSaltFormStructure.class);
         q.setParameter("fingerprintString", fingerprintString);
         if (maxResults > -1) {

src/main/java/com/labsynch/labseer/domain/DDictValue.java

@@ -11,6 +11,7 @@
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.PersistenceContext;
+import javax.persistence.Query;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.TypedQuery;
 import javax.persistence.Version;
@@ -568,6 +569,45 @@ public static TypedQuery<DDictValue> findDDictValuesByLsTypeEqualsAndLsKindEqual
         return q;
     }
 
+    public static List<DDictValue> findDDictValuesByLsTypeEqualsAndLsKindEqualsAndLabelTextSearch(String lsType, String lsKind, String labelText, Integer maxHits) {
+        if (lsType == null || lsType.length() == 0)
+            throw new IllegalArgumentException("The lsType argument is required");
+        if (lsKind == null || lsKind.length() == 0)
+            throw new IllegalArgumentException("The lsKind argument is required");
+        EntityManager em = DDictValue.entityManager();
+
+        // Format the search text to match any word in the label text
+        // e.g. "word1 word2" -> "word1:* & word2:*"
+        String[] parts = labelText.trim().split("\\s+");
+        for (int i = 0; i < parts.length; i++) {
+            parts[i] = parts[i] + ":*";
+        }
+        String formattedLabelText = String.join(" & ", parts);
+
+        // Native query to use full text search
+        String sql = 
+        "SELECT * " +
+        "FROM ddict_value " +
+        "WHERE ls_type = :lsType " +
+        "AND ls_kind = :lsKind " +
+        "AND to_tsvector('english', lower(label_text)) @@ to_tsquery('english', :formattedLabelText) " +
+        "ORDER BY (lower(label_text) = :labelText) DESC, " +
+        "ts_rank(to_tsvector('english', lower(label_text)), to_tsquery('english', :formattedLabelText)) DESC";
+
+        Query q = em.createNativeQuery(sql, DDictValue.class);
+        q.setParameter("lsType", lsType);
+        q.setParameter("lsKind", lsKind);
+        q.setParameter("labelText", labelText.toLowerCase());
+        q.setParameter("formattedLabelText", formattedLabelText);
+        if (maxHits != null) {
+            q = q.setMaxResults(maxHits);
+        }
+
+        @SuppressWarnings("unchecked")
+        List<DDictValue> results = q.getResultList();
+        return results;
+    }
+
     public static TypedQuery<DDictValue> findDDictValuesByLsTypeEqualsAndLsKindEquals(String lsType, String lsKind,
             String sortFieldName, String sortOrder) {
         if (lsType == null || lsType.length() == 0)

src/main/java/com/labsynch/labseer/domain/Lot.java

@@ -148,7 +148,7 @@ public class Lot {
 
     @Size(max = 255)
     @Column(name = "vendorid")
-    private String vendorId;
+    private String vendorID;
 
     @ManyToOne
     @JoinColumn(name = "salt_form")
@@ -618,10 +618,11 @@ public static TypedQuery<LotsByProjectDTO> findLotsByProjectsList(List<String> p
 
         EntityManager em = Lot.entityManager();
         String query = "SELECT new com.labsynch.labseer.dto.LotsByProjectDTO( "
-                + "lt.id as id, lt.corpName as lotCorpName, lt.lotNumber as lotNumber, lt.registrationDate as registrationDate, prnt.corpName as parentCorpName, lt.project as project) "
+                + "lt.id as id, lt.corpName as lotCorpName, lt.lotNumber as lotNumber, lt.registrationDate as registrationDate, prnt.corpName as parentCorpName, lt.project as project, lt.chemist as chemist, vnd.name as vendorName, vnd.code as vendorCode, lt.supplier as supplier) "
                 + "FROM Lot AS lt "
                 + "JOIN lt.saltForm sltfrm "
                 + "JOIN sltfrm.parent prnt "
+                + "LEFT JOIN lt.vendor vnd "
                 + "WHERE lt.project in (:projects) ";
 
         logger.debug("sql query " + query);
@@ -898,12 +899,12 @@ public void setVendor(Vendor vendor) {
         this.vendor = vendor;
     }
 
-    public String getVendorId() {
-        return this.vendorId;
+    public String getVendorID() {
+        return this.vendorID;
     }
 
-    public void setVendorId(String vendorId) {
-        this.vendorId = vendorId;
+    public void setVendorID(String vendorID) {
+        this.vendorID = vendorID;
     }
 
     public Set<FileList> getFileLists() {
@@ -1074,7 +1075,7 @@ public void setLotAliases(Set<LotAlias> lotAliases) {
             "registeredBy", "modifiedDate", "modifiedBy", "barcode", "color", "notebookPage", "amount", "amountUnits",
             "solutionAmount", "solutionAmountUnits", "supplier", "supplierID", "purity", "purityOperator",
             "purityMeasuredBy", "chemist", "percentEE", "comments", "isVirtual", "ignore", "physicalState", "vendor",
-            "vendorId", "saltForm", "fileLists", "retain", "retainUnits", "retainLocation", "meltingPoint",
+            "vendorID", "saltForm", "fileLists", "retain", "retainUnits", "retainLocation", "meltingPoint",
             "boilingPoint", "supplierLot", "project", "parent", "bulkLoadFile", "lambda", "absorbance", "stockSolvent",
             "stockLocation", "observedMassOne", "observedMassTwo", "tareWeight", "tareWeightUnits", "totalAmountStored",
             "totalAmountStoredUnits", "lotAliases", "storageLocation");

src/main/java/com/labsynch/labseer/domain/SaltForm.java

@@ -29,7 +29,9 @@
 import javax.persistence.criteria.JoinType;
 import javax.persistence.criteria.ParameterExpression;
 import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Expression;
 import javax.persistence.criteria.Root;
+import javax.persistence.criteria.Order;
 import javax.validation.constraints.Size;
 
 import com.labsynch.labseer.dto.SearchFormDTO;
@@ -239,6 +241,7 @@ public static TypedQuery<SaltForm> findSaltFormsByMeta(SearchFormDTO searchParam
 
 		Predicate[] predicates = new Predicate[0];
 		List<Predicate> predicateList = new ArrayList<Predicate>();
+		List<Order> orderList = new ArrayList<Order>();
 
 		if (searchParams.getChemist() != null && !searchParams.getChemist().equals("anyone")) {
 			logger.debug("incoming chemist :" + searchParams.getChemist().toString());
@@ -279,9 +282,37 @@ public static TypedQuery<SaltForm> findSaltFormsByMeta(SearchFormDTO searchParam
 			predicateList.add(predicate);
 		}
 		if (searchParams.getFormattedCorpNameList() != null) {
-			logger.debug("incoming corpNameList :" + searchParams.getFormattedCorpNameList().toString());
-			Predicate predicate = saltFormParent.get("corpName").in(searchParams.getFormattedCorpNameList());
+			List<String> corpNames = searchParams.getFormattedCorpNameList();
+			logger.debug("incoming corpNameList :" + corpNames.toString());
+			ArrayList<Predicate> corpNameLikePredicates = new ArrayList<Predicate>();
+			Expression<Double> maxSimilarity = null;
+			for (String corpName : corpNames) {
+				Predicate predicate = criteriaBuilder.like(saltFormParent.get("corpName"), '%' + corpName);
+				corpNameLikePredicates.add(predicate);
+				// Using pg_trgm.similarity to order results based on how similar the value is to
+				// the formatted corporate names.
+				Expression<Double> similarity = criteriaBuilder.function(
+					"similarity",
+					Double.class,
+					saltFormParent.get("corpName"),
+					criteriaBuilder.literal(corpName)
+				);
+				if (maxSimilarity == null) {
+					maxSimilarity = similarity;
+				}
+				else {
+					maxSimilarity = criteriaBuilder.selectCase()
+						.when(criteriaBuilder.greaterThan(similarity, maxSimilarity), similarity)
+						.otherwise(maxSimilarity)
+						.as(Double.class);
+				}
+			}
+			Predicate predicate = criteriaBuilder.or(corpNameLikePredicates.toArray(new Predicate[0]));
 			predicateList.add(predicate);
+			if (maxSimilarity != null) {
+				// Rows with a higher similarity will be ordered first.
+				orderList.add(criteriaBuilder.desc(maxSimilarity));
+			}
 		}
 		if (searchParams.getAlias() != null && !searchParams.getAlias().equals("")) {
 			Predicate predicate = null;
@@ -329,6 +360,7 @@ public static TypedQuery<SaltForm> findSaltFormsByMeta(SearchFormDTO searchParam
 
 		predicates = predicateList.toArray(predicates);
 		criteria.where(criteriaBuilder.and(predicates));
+		criteria.orderBy(orderList);
 		TypedQuery<SaltForm> q = em.createQuery(criteria);
 
 		if (searchParams.getMaxSynthDate() != null) {