diff --git a/.classpath b/.classpath index f00842b..639c8b2 100755 --- a/.classpath +++ b/.classpath @@ -1,25 +1,638 @@ - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.gitignore b/.gitignore index 7728c0a..e91f6df 100755 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,4 @@ build .settings bin .gradle +.DS_Store diff --git a/.project b/.project index 974292e..b0a8cd9 100755 --- a/.project +++ b/.project @@ -2,29 +2,27 @@ pegasus-data - - + + + org.eclipse.jdt.core.javanature + org.eclipse.buildship.core.gradleprojectnature + org.eclipse.jdt.core.javabuilder - - + org.eclipse.buildship.core.gradleprojectbuilder - - + - - org.eclipse.jdt.core.javanature - org.eclipse.buildship.core.gradleprojectnature - + 1 - 30 + org.eclipse.core.resources.regexFilterMatcher node_modules|.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__ diff --git a/README.md b/README.md index 6931273..821d0e8 100755 --- a/README.md +++ b/README.md @@ -34,3 +34,11 @@ Repository for the Atlas Explorer Tool service layer 2. Update .env ENV_MYSQL_PASSWORD to the password for QA KE 3. Add your IP address to a new security group called sg-0597e054f11d2e31a (Developer to KE Mariadb) 4. Restart your knowledge-environment (don't worry that you have your own copy of mariadb, it'll be ignored) + +If you have already followed these steps and are still having trouble connecting, check to see if your ip address has changed, you may need to update the security group rules + +# Talking to GraphQL + +1. Start up your atlas/knowledge-environment server +2. Open a tool like GraphQLPlayground and connect to "http://localhost:3030/graphql" +3. Write and execute your query diff --git a/src/main/java/org/kpmp/Query.java b/src/main/java/org/kpmp/Query.java index 30c0d1f..be63d44 100755 --- a/src/main/java/org/kpmp/Query.java +++ b/src/main/java/org/kpmp/Query.java @@ -10,8 +10,9 @@ import org.kpmp.cellType.CellTypeService; import org.kpmp.cellTypeSummary.ClusterHierarchy; import org.kpmp.cellTypeSummary.ClusterHierarchyService; +import org.kpmp.dataSummary.AtlasRepoSummaryResult; import org.kpmp.dataSummary.DataSummaryService; -import org.kpmp.datasetSummary.DatasetSummary; +import org.kpmp.dataSummary.DataTypeSummary; import org.kpmp.gene.GeneService; import org.kpmp.gene.MyGeneInfoHit; import org.kpmp.geneExpression.RTExpressionByTissueType; @@ -20,9 +21,9 @@ import org.kpmp.geneExpressionSummary.GeneExpressionSummary; import org.kpmp.geneExpressionSummary.GeneExpressionSummaryService; import org.kpmp.participant.ParticipantDataTypeSummary; -import org.kpmp.participant.ParticipantTissueTypeSummary; import org.kpmp.participant.ParticipantService; import org.kpmp.participant.ParticipantSummaryDataset; +import org.kpmp.participant.ParticipantTissueTypeSummary; import org.kpmp.umap.PlotData; import org.kpmp.umap.UmapDataService; import org.slf4j.Logger; @@ -100,7 +101,7 @@ public PlotData getUmapPlotData(String dataType, String geneSymbol, String tissu } } - public List getGeneDatasetInformation(String geneSymbol) throws Exception { + public List getGeneDatasetInformation(String geneSymbol) throws Exception { try { return geneExpressionSummaryService.getGeneDatasetInformation(geneSymbol); } catch (Exception e) { @@ -109,7 +110,7 @@ public List getGeneDatasetInformation(String geneSymbol) throws } } - public List getSummaryData() throws Exception { + public List getSummaryData() throws Exception { try { return dataSummaryService.getSummaryData(); } catch (Exception e) { @@ -170,9 +171,18 @@ public ParticipantSummaryDataset participantClinicalDataset(String redcap_id) th public List getTissueTypeSummaryData() throws Exception { try { return participantService.getTissueData(); - }catch (Exception e) { + } catch (Exception e) { logger.error(e.getMessage()); throw e; - } + } + } + + public AtlasRepoSummaryResult getAtlasSummaryRows() throws Exception { + try { + return dataSummaryService.getAtlasRepoSummary(); + } catch (Exception e) { + logger.error("Unable to get Atlas Summary data: ", e.getMessage()); + throw e; + } } } \ No newline at end of file diff --git a/src/main/java/org/kpmp/autocomplete/AutocompleteResult.java b/src/main/java/org/kpmp/autocomplete/AutocompleteResult.java index 2c0284f..3d07095 100755 --- a/src/main/java/org/kpmp/autocomplete/AutocompleteResult.java +++ b/src/main/java/org/kpmp/autocomplete/AutocompleteResult.java @@ -5,6 +5,7 @@ public class AutocompleteResult implements Serializable { + private static final long serialVersionUID = 762733408490639258L; private String value; private String name; private String id; diff --git a/src/main/java/org/kpmp/cellType/CellType.java b/src/main/java/org/kpmp/cellType/CellType.java index 2c18d3c..e336d0d 100755 --- a/src/main/java/org/kpmp/cellType/CellType.java +++ b/src/main/java/org/kpmp/cellType/CellType.java @@ -17,6 +17,8 @@ @Table(name = "cell_type") public class CellType implements Serializable { + private static final long serialVersionUID = -7240769211757430938L; + @Id @Column(name = "cell_type_id") private int cellTypeId; diff --git a/src/main/java/org/kpmp/cellType/CellTypeHierarchy.java b/src/main/java/org/kpmp/cellType/CellTypeHierarchy.java index c30e8e3..dfc7470 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeHierarchy.java +++ b/src/main/java/org/kpmp/cellType/CellTypeHierarchy.java @@ -10,7 +10,8 @@ @Component public class CellTypeHierarchy implements Serializable { - + + private static final long serialVersionUID = 4174487460309851924L; private Map cellTypeRegionMap = new HashMap<>(); public List getCellTypeRegions() { @@ -20,7 +21,7 @@ public List getCellTypeRegions() { } public void addCellTypeStructureRegion(CellTypeStructureRegion region) { - + if (cellTypeRegionMap.containsKey(region.getRegionName())) { CellTypeStructureRegion existingRegion = cellTypeRegionMap.get(region.getRegionName()); List subregions = region.getCellTypeSubregions(); @@ -32,7 +33,4 @@ public void addCellTypeStructureRegion(CellTypeStructureRegion region) { } } - - } - diff --git a/src/main/java/org/kpmp/cellType/CellTypeStructureRegion.java b/src/main/java/org/kpmp/cellType/CellTypeStructureRegion.java index d80efeb..185fe66 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeStructureRegion.java +++ b/src/main/java/org/kpmp/cellType/CellTypeStructureRegion.java @@ -8,6 +8,7 @@ public class CellTypeStructureRegion implements Serializable { + private static final long serialVersionUID = 3141535632314917816L; private String regionName; private Map subregionMap = new HashMap<>(); private List subregionOrderdList = new ArrayList<>(); diff --git a/src/main/java/org/kpmp/cellType/CellTypeStructureSubregion.java b/src/main/java/org/kpmp/cellType/CellTypeStructureSubregion.java index d8a9315..b6be2c0 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeStructureSubregion.java +++ b/src/main/java/org/kpmp/cellType/CellTypeStructureSubregion.java @@ -8,6 +8,7 @@ public class CellTypeStructureSubregion implements Serializable { + private static final long serialVersionUID = 1366955014710403152L; private String subregionName; private List cellTypes = new ArrayList<>(); diff --git a/src/main/java/org/kpmp/cellType/CellTypeSynonym.java b/src/main/java/org/kpmp/cellType/CellTypeSynonym.java index 3f0ad7f..f33f904 100755 --- a/src/main/java/org/kpmp/cellType/CellTypeSynonym.java +++ b/src/main/java/org/kpmp/cellType/CellTypeSynonym.java @@ -1,45 +1,48 @@ package org.kpmp.cellType; -import javax.persistence.FetchType; -import javax.persistence.Id; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; +import javax.persistence.FetchType; +import javax.persistence.Id; import javax.persistence.IdClass; import javax.persistence.JoinColumn; import javax.persistence.ManyToOne; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "celltype_synonym") @IdClass(CellTypeSynonymId.class) public class CellTypeSynonym implements Serializable { - @Id - @Column(name="cell_type_id") - private int cellTypeId; + private static final long serialVersionUID = -5650797130903696615L; + + @Id + @Column(name = "cell_type_id") + private int cellTypeId; - @Id - @Column(name="cell_type_synonym") - private String cellTypeSynonym; + @Id + @Column(name = "cell_type_synonym") + private String cellTypeSynonym; - @ManyToOne(fetch = FetchType.EAGER) - @JoinColumn(name="cell_type_id", nullable = false, insertable = false, updatable = false) - private CellType cellType; + @ManyToOne(fetch = FetchType.EAGER) + @JoinColumn(name = "cell_type_id", nullable = false, insertable = false, updatable = false) + private CellType cellType; - public int getCellTypeId() { - return cellTypeId; - } + public int getCellTypeId() { + return cellTypeId; + } - public void setCellTypeId(int cellTypeId) { - this.cellTypeId = cellTypeId; - } + public void setCellTypeId(int cellTypeId) { + this.cellTypeId = cellTypeId; + } - public String getCellTypeSynonym() { - return cellTypeSynonym; - } + public String getCellTypeSynonym() { + return cellTypeSynonym; + } - public void setCellTypeSynonym(String cellTypeSynonym) { - this.cellTypeSynonym = cellTypeSynonym; - } + public void setCellTypeSynonym(String cellTypeSynonym) { + this.cellTypeSynonym = cellTypeSynonym; + } } diff --git a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java index 1d3a777..8313e73 100755 --- a/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java +++ b/src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java @@ -1,19 +1,21 @@ package org.kpmp.cellTypeSummary; -import org.springframework.lang.Nullable; +import java.io.Serializable; import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.IdClass; import javax.persistence.Table; -import java.io.Serializable; + +import org.springframework.lang.Nullable; @Entity @Table(name = "cluster_hierarchy_v") @IdClass(ClusterHierarchyId.class) public class ClusterHierarchy implements Serializable { + private static final long serialVersionUID = -7707637379989017634L; @Id @Column(name = "cell_type_id") private int cellTypeId; @@ -31,11 +33,11 @@ public class ClusterHierarchy implements Serializable { @Column(name = "is_single_nuc") private String isSingleNucCluster; @Column(name = "is_rt") - private String isRegionalTranscriptomics; + private String isRegionalTranscriptomics; @Column(name = "cell_type") private String cellType; @Column(name = "cell_type_order") - private Double cellTypeOrder; + private Double cellTypeOrder; public int getCellTypeId() { return cellTypeId; @@ -45,7 +47,7 @@ public void setCellTypeId(int cellTypeId) { this.cellTypeId = cellTypeId; } - @Nullable + @Nullable public int getClusterId() { return clusterId; } @@ -62,7 +64,7 @@ public void setStructureRegion(String structureRegion) { this.structureRegion = structureRegion; } - @Nullable + @Nullable public String getStructureSubregion() { return structureSubregion; } @@ -71,7 +73,7 @@ public void setStructureSubregion(String structureSubregion) { this.structureSubregion = structureSubregion; } - @Nullable + @Nullable public String getClusterName() { return clusterName; } @@ -96,29 +98,29 @@ public void setIsSingleNucCluster(String isSingleNucCluster) { this.isSingleNucCluster = isSingleNucCluster; } - public String getIsRegionalTranscriptomics() { - return isRegionalTranscriptomics; - } + public String getIsRegionalTranscriptomics() { + return isRegionalTranscriptomics; + } - public void setIsRegionalTranscriptomics(String isRegionalTranscriptomics) { - this.isRegionalTranscriptomics = isRegionalTranscriptomics; - } + public void setIsRegionalTranscriptomics(String isRegionalTranscriptomics) { + this.isRegionalTranscriptomics = isRegionalTranscriptomics; + } - @Nullable - public Double getCellTypeOrder() { - return cellTypeOrder; - } + @Nullable + public Double getCellTypeOrder() { + return cellTypeOrder; + } - public void setCellTypeOrder(Double cellTypeOrder) { - this.cellTypeOrder = cellTypeOrder; - } + public void setCellTypeOrder(Double cellTypeOrder) { + this.cellTypeOrder = cellTypeOrder; + } - @Nullable - public String getCellType() { - return cellType; - } + @Nullable + public String getCellType() { + return cellType; + } - public void setCellType(String cellType) { - this.cellType = cellType; - } + public void setCellType(String cellType) { + this.cellType = cellType; + } } diff --git a/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformation.java b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformation.java new file mode 100644 index 0000000..0c94d87 --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformation.java @@ -0,0 +1,49 @@ +package org.kpmp.dataSummary; + +import org.apache.commons.lang3.builder.EqualsBuilder; +import org.apache.commons.lang3.builder.HashCodeBuilder; + +public class AtlasRepoSummaryLinkInformation { + + private String linkType; + private String linkValue; + + public AtlasRepoSummaryLinkInformation(String linkType, String linkValue) { + this.setLinkType(linkType); + this.setLinkValue(linkValue); + } + + public String getLinkType() { + return linkType; + } + + public void setLinkType(String linkType) { + this.linkType = linkType; + } + + public String getLinkValue() { + return linkValue; + } + + public void setLinkValue(String linkValue) { + this.linkValue = linkValue; + } + + @Override + public int hashCode() { + return new HashCodeBuilder().append(linkType).append(linkValue).toHashCode(); + } + + @Override + public boolean equals(Object obj) { + if (obj instanceof AtlasRepoSummaryLinkInformation) { + final AtlasRepoSummaryLinkInformation other = (AtlasRepoSummaryLinkInformation) obj; + return new EqualsBuilder().append(linkType, other.getLinkType()).append(linkValue, other.getLinkValue()) + .isEquals(); + } else { + return false; + } + + } + +} diff --git a/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRepository.java b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRepository.java new file mode 100644 index 0000000..639679b --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRepository.java @@ -0,0 +1,14 @@ +package org.kpmp.dataSummary; + +import java.util.List; + +import org.springframework.cache.annotation.Cacheable; +import org.springframework.data.repository.CrudRepository; + +interface AtlasRepoSummaryRepository extends CrudRepository { + + @Override + @Cacheable("repoSummaryCounts") + List findAll(); + +} diff --git a/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryResult.java b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryResult.java new file mode 100644 index 0000000..387037d --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryResult.java @@ -0,0 +1,37 @@ +package org.kpmp.dataSummary; + +import java.util.ArrayList; +import java.util.List; + +public class AtlasRepoSummaryResult { + + private List summaryRows; + private int totalFiles; + + public AtlasRepoSummaryResult(List summaryRows, int totalFiles) { + this.summaryRows = summaryRows; + this.totalFiles = totalFiles; + + } + + public AtlasRepoSummaryResult() { + summaryRows = new ArrayList<>(); + } + + public List getSummaryRows() { + return summaryRows; + } + + public void setSummaryRows(List summaryRows) { + this.summaryRows = summaryRows; + } + + public int getTotalFiles() { + return totalFiles; + } + + public void setTotalFiles(int totalFiles) { + this.totalFiles = totalFiles; + } + +} diff --git a/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRow.java b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRow.java new file mode 100644 index 0000000..60e356a --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/AtlasRepoSummaryRow.java @@ -0,0 +1,53 @@ +package org.kpmp.dataSummary; + +public class AtlasRepoSummaryRow { + private int openCount; + private int controlledCount; + private String omicsType; + private AtlasRepoSummaryLinkInformation linkInformation; + + public AtlasRepoSummaryRow(String omicsType, AtlasRepoSummaryLinkInformation linkInformation) { + this.omicsType = omicsType; + this.linkInformation = linkInformation; + } + + public int getOpenCount() { + return openCount; + } + + public void setOpenCount(int openCount) { + this.openCount = openCount; + } + + public int getControlledCount() { + return controlledCount; + } + + public void setControlledCount(int controlledCount) { + this.controlledCount = controlledCount; + } + + public String getOmicsType() { + return omicsType; + } + + public void setOmicsType(String omicsType) { + this.omicsType = omicsType; + } + + public void addToControlledCount(int count) { + this.controlledCount = this.controlledCount + count; + } + + public void addToOpenCount(int count) { + this.openCount = this.openCount + count; + } + + public AtlasRepoSummaryLinkInformation getLinkInformation() { + return linkInformation; + } + + public void setLinkInformation(AtlasRepoSummaryLinkInformation linkInformation) { + this.linkInformation = linkInformation; + } +} diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java index ae4b84a..5d198ec 100755 --- a/src/main/java/org/kpmp/dataSummary/DataSummaryService.java +++ b/src/main/java/org/kpmp/dataSummary/DataSummaryService.java @@ -1,90 +1,186 @@ package org.kpmp.dataSummary; import java.util.ArrayList; +import java.util.Collection; +import java.util.Comparator; +import java.util.HashMap; import java.util.List; +import java.util.Map; import org.kpmp.DataTypeEnum; import org.kpmp.FullDataTypeEnum; import org.kpmp.OmicsTypeEnum; import org.kpmp.TissueTypeEnum; -import org.kpmp.datasetSummary.DatasetSummary; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; @Service public class DataSummaryService { + private static final String EXPERIMENTAL_STRATEGY = "experimental_strategy"; + private static final String DATA_CATEGORY = "data_category"; + private static final String CONTROLLED_ACCESS = "controlled"; + private static final String OPEN_ACCESS = "open"; + private static final String BIOMARKERS = "Biomarkers"; + private static final String BIOMARKER = "Biomarker"; + private static final String CLINICAL_STUDY_DATA = "Clinical Study Data"; + private DataSummaryRepository dataSummaryRepository; + private AtlasRepoSummaryRepository repoSummaryRepository; @Autowired - public DataSummaryService(DataSummaryRepository dataSummaryRepository) { + public DataSummaryService(DataSummaryRepository dataSummaryRepository, + AtlasRepoSummaryRepository repoSummaryRepository) { this.dataSummaryRepository = dataSummaryRepository; + this.repoSummaryRepository = repoSummaryRepository; } - public List getSummaryData() { - List summaryData = new ArrayList<>(); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName(), - DataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getAbbreviation(), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryCount(FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()))); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName(), - DataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D.getAbbreviation(), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryCount(FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()))); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName(), - DataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES.getAbbreviation(), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryCount(FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()))); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.CODEX_FULL.getFullName(), - DataTypeEnum.CODEX.getAbbreviation(), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.CODEX_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.CODEX_FULL.getFullName()), - dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.CODEX_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryCount(FullDataTypeEnum.CODEX_FULL.getFullName()))); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName(), - DataTypeEnum.SPATIAL_LIPIDOMICS.getAbbreviation(), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()))); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName(), - DataTypeEnum.SPATIAL_METABOLOMICS.getAbbreviation(), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()))); - - summaryData.add(new DatasetSummary( - OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), - FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName(), - DataTypeEnum.SPATIAL_NGLYCOMICS.getAbbreviation(), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.AKI.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.CKD.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()), - dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()), - dataSummaryRepository.getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()))); + public AtlasRepoSummaryResult getAtlasRepoSummary() throws Exception { + List experimentalStrategies = repoSummaryRepository.findAll(); + Map summaryMap = new HashMap<>(); + int totalFiles = 0; + for (ExperimentalStrategyValue experimentalStrategyValue : experimentalStrategies) { + String experimentalStrategy = experimentalStrategyValue.getExperimentalStrategy(); + if (experimentalStrategy.isEmpty() + && experimentalStrategyValue.getDataType().equalsIgnoreCase(CLINICAL_STUDY_DATA)) { + experimentalStrategy = CLINICAL_STUDY_DATA; + } else if (experimentalStrategyValue.getDataCategory().equalsIgnoreCase(BIOMARKER)) { + experimentalStrategy = BIOMARKERS; + } + + if (summaryMap.containsKey(experimentalStrategy)) { + AtlasRepoSummaryRow atlasRepoSummaryRow = summaryMap.get(experimentalStrategy); + setCounts(experimentalStrategyValue, atlasRepoSummaryRow); + totalFiles += experimentalStrategyValue.getCount(); + } else { + AtlasRepoSummaryRow row = new AtlasRepoSummaryRow(experimentalStrategy, + getLinkInformation(experimentalStrategyValue)); + setCounts(experimentalStrategyValue, row); + summaryMap.put(experimentalStrategy, row); + totalFiles += experimentalStrategyValue.getCount(); + } + } + + Collection values = summaryMap.values(); + List results = new ArrayList<>(values); + results.sort(new Comparator() { + @Override + public int compare(AtlasRepoSummaryRow one, AtlasRepoSummaryRow two) { + return one.getOmicsType().compareToIgnoreCase(two.getOmicsType()); + } + }); + + return new AtlasRepoSummaryResult(results, totalFiles); + } + + private AtlasRepoSummaryLinkInformation getLinkInformation(ExperimentalStrategyValue experimentalStrategy) { + if (experimentalStrategy.getDataCategory().equalsIgnoreCase(BIOMARKER) + || experimentalStrategy.getDataType().equalsIgnoreCase(CLINICAL_STUDY_DATA)) { + return new AtlasRepoSummaryLinkInformation(DATA_CATEGORY, experimentalStrategy.getDataCategory()); + } else { + return new AtlasRepoSummaryLinkInformation(EXPERIMENTAL_STRATEGY, + experimentalStrategy.getExperimentalStrategy()); + } + } + + private void setCounts(ExperimentalStrategyValue experimentalStrategyValue, AtlasRepoSummaryRow atlasRepoSummaryRow) + throws Exception { + if (experimentalStrategyValue.getAccess().equalsIgnoreCase(OPEN_ACCESS)) { + atlasRepoSummaryRow.addToOpenCount(experimentalStrategyValue.getCount()); + } else if (experimentalStrategyValue.getAccess().equalsIgnoreCase(CONTROLLED_ACCESS)) { + atlasRepoSummaryRow.addToControlledCount(experimentalStrategyValue.getCount()); + } else { + throw new Exception( + "Unexpected access value while getting summary counts: " + experimentalStrategyValue.getAccess()); + } + } + + public List getSummaryData() { + List summaryData = new ArrayList<>(); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName(), + DataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getAbbreviation(), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()), + dataSummaryRepository + .getParticipantSummaryCount(FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName()))); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName(), + DataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D.getAbbreviation(), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()), + dataSummaryRepository.getParticipantSummaryCount( + FullDataTypeEnum.TISSUE_IMAGING_AND_CYTOMETRY_3D_FULL.getFullName()))); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName(), + DataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES.getAbbreviation(), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()), + dataSummaryRepository.getParticipantSummaryCount( + FullDataTypeEnum.LIGHT_MICROSCOPIC_WHOLE_SLIDE_IMAGES_FULL.getFullName()))); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.CODEX_FULL.getFullName(), DataTypeEnum.CODEX.getAbbreviation(), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.CODEX_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.CODEX_FULL.getFullName()), + dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.CODEX_FULL.getFullName()), + dataSummaryRepository.getParticipantSummaryCount(FullDataTypeEnum.CODEX_FULL.getFullName()))); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName(), + DataTypeEnum.SPATIAL_LIPIDOMICS.getAbbreviation(), + dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryLinkCount( + TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()), + dataSummaryRepository + .getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_LIPIDOMICS_FULL.getFullName()))); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName(), + DataTypeEnum.SPATIAL_METABOLOMICS.getAbbreviation(), + dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryLinkCount( + TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()), + dataSummaryRepository + .getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_METABOLOMICS_FULL.getFullName()))); + + summaryData.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName(), + DataTypeEnum.SPATIAL_NGLYCOMICS.getAbbreviation(), + dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.AKI.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryLinkCount(TissueTypeEnum.CKD.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()), + dataSummaryRepository.getDataSummaryLinkCount( + TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType(), + FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()), + dataSummaryRepository + .getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName()))); return summaryData; } } diff --git a/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java b/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java index 624cb14..476517c 100755 --- a/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java +++ b/src/main/java/org/kpmp/dataSummary/DataSummaryValue.java @@ -1,15 +1,18 @@ package org.kpmp.dataSummary; -import org.springframework.lang.Nullable; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; + +import org.springframework.lang.Nullable; @Entity @Table(name = "sv_file_v") public class DataSummaryValue implements Serializable { + private static final long serialVersionUID = -1934662137113288596L; @Id @Column(name = "file_id") private Integer fileId; @@ -25,9 +28,9 @@ public class DataSummaryValue implements Serializable { private String fileName; @Column(name = "package_id") private String packageId; - @Column(name = "file_size") + @Column(name = "file_size") private Long fileSize; - @Column(name = "participant_id") + @Column(name = "participant_id") private Integer participantId; @Column(name = "redcap_id") private String redcapId; @@ -37,130 +40,130 @@ public class DataSummaryValue implements Serializable { private String protocol; @Column(name = "sample_type") private String sampleType; - @Column(name = "sex") + @Column(name = "sex") private String sex; - @Column(name = "tissue_source") + @Column(name = "tissue_source") private String tissueSource; - @Column(name = "tissue_type") + @Column(name = "tissue_type") private String tissueType; - @Column(name = "spectrack_sample_id") + @Column(name = "spectrack_sample_id") private String spectrackSampleId; @Nullable public Integer getFileId() { return fileId; } - + public void setFileId(Integer fileId) { this.fileId = fileId; } - + @Nullable public String getConfigType() { return configType; } - + public void setConfigType(String configType) { this.configType = configType; } - + @Nullable public String getImageType() { return imageType; } - + public void setImageType(String imageType) { this.imageType = imageType; } - + @Nullable public String getDataType() { return dataType; } - + public void setDataType(String dataType) { this.dataType = dataType; } - + public String getDlFileId() { return dlFileId; } - + public void setDlFileIdd(String dlFileId) { this.dlFileId = dlFileId; } - + public String getFileName() { return fileName; } - + public void setFileName(String fileName) { this.fileName = fileName; } - + @Nullable public String getPackageId() { return packageId; } - + public void setPackageId(String packageId) { this.packageId = packageId; } - + @Nullable public Long getFileSize() { return fileSize; } - + public void setFileSize(Long fileSize) { this.fileSize = fileSize; } - + @Nullable public Integer getParticipantId() { return participantId; } - + public void setParticipantId(Integer participantId) { this.participantId = participantId; } - + @Nullable public String getRedcapId() { return redcapId; } - + public void setRedcapId(String redcapId) { this.redcapId = redcapId; } - + @Nullable public String getAge() { return age; } - + public void setAge(String age) { this.age = age; } - + @Nullable public String getProtocol() { return protocol; } - + public void setProtocol(String protocol) { this.protocol = protocol; } - + @Nullable public String getSampleType() { return sampleType; } - + public void setSampleType(String sampleType) { this.sampleType = sampleType; } - + @Nullable public String getSex() { return sex; @@ -174,7 +177,7 @@ public void setSex(String sex) { public String getTissueSource() { return tissueSource; } - + public void setTissueSource(String tissueSource) { this.tissueSource = tissueSource; } @@ -187,7 +190,7 @@ public String getTissueType() { public void setTissueType(String tissueType) { this.tissueType = tissueType; } - + @Nullable public String getSpectrackSampleId() { return spectrackSampleId; diff --git a/src/main/java/org/kpmp/dataSummary/DataTypeSummary.java b/src/main/java/org/kpmp/dataSummary/DataTypeSummary.java new file mode 100755 index 0000000..819a9ca --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/DataTypeSummary.java @@ -0,0 +1,81 @@ +package org.kpmp.dataSummary; + +import java.io.Serializable; + +public class DataTypeSummary implements Serializable { + private static final long serialVersionUID = 114808450473696153L; + private String omicsType; + private String dataType; + private String dataTypeShort; + private Long akiCount; + private Long ckdCount; + private Long hrtCount; + private Long participantCount; + + public DataTypeSummary(String omicsType, String dataType, String dataTypeShort, Long akiCount, Long ckdCount, + Long hrtCount, Long participantCount) { + this.omicsType = omicsType; + this.dataType = dataType; + this.dataTypeShort = dataTypeShort; + this.akiCount = akiCount; + this.ckdCount = ckdCount; + this.hrtCount = hrtCount; + this.participantCount = participantCount; + } + + public String getOmicsType() { + return this.omicsType; + } + + public void setOmicsType(String omicsType) { + this.omicsType = omicsType; + } + + public String getDataType() { + return this.dataType; + } + + public void setDataTypeType(String dataType) { + this.dataType = dataType; + } + + public String getDataTypeShort() { + return this.dataTypeShort; + } + + public void setDataTypeShort(String dataTypeShort) { + this.dataTypeShort = dataTypeShort; + } + + public Long getAkiCount() { + return this.akiCount; + } + + public void setAkiCount(Long akiCount) { + this.akiCount = akiCount; + } + + public Long getCkdCount() { + return this.ckdCount; + } + + public void setCkdCount(Long ckdCount) { + this.ckdCount = ckdCount; + } + + public Long getHrtCount() { + return this.hrtCount; + } + + public void setHrtCount(Long hrtCount) { + this.hrtCount = hrtCount; + } + + public Long getParticipantCount() { + return this.participantCount; + } + + public void setParticipantCount(Long participantCount) { + this.participantCount = participantCount; + } +} \ No newline at end of file diff --git a/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyId.java b/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyId.java new file mode 100644 index 0000000..ddbe8d1 --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyId.java @@ -0,0 +1,28 @@ +package org.kpmp.dataSummary; + +import java.io.Serializable; + +public class ExperimentalStrategyId implements Serializable { + + private static final long serialVersionUID = 938153099192129678L; + + private String experimentalStrategy; + private String access; + + public String getExperimentalStrategy() { + return experimentalStrategy; + } + + public void setExperimentalStrategy(String experimentalStrategy) { + this.experimentalStrategy = experimentalStrategy; + } + + public String getAccess() { + return access; + } + + public void setAccess(String access) { + this.access = access; + } + +} diff --git a/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java b/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java new file mode 100644 index 0000000..99d0887 --- /dev/null +++ b/src/main/java/org/kpmp/dataSummary/ExperimentalStrategyValue.java @@ -0,0 +1,64 @@ +package org.kpmp.dataSummary; + +import java.io.Serializable; + +import javax.persistence.Entity; +import javax.persistence.Id; +import javax.persistence.IdClass; +import javax.persistence.Table; + +@Entity +@Table(name = "repository_summary_v") +@IdClass(ExperimentalStrategyId.class) +public class ExperimentalStrategyValue implements Serializable { + + private static final long serialVersionUID = 8063582327279878125L; + private int count; + @Id + private String experimentalStrategy; + @Id + private String access; + private String dataType; + private String dataCategory; + + public int getCount() { + return count; + } + + public void setCount(int count) { + this.count = count; + } + + public String getExperimentalStrategy() { + return experimentalStrategy; + } + + public void setExperimentalStrategy(String experimentalStrategy) { + this.experimentalStrategy = experimentalStrategy; + } + + public String getAccess() { + return access; + } + + public void setAccess(String access) { + this.access = access; + } + + public String getDataType() { + return dataType; + } + + public void setDataType(String dataType) { + this.dataType = dataType; + } + + public String getDataCategory() { + return dataCategory; + } + + public void setDataCategory(String dataCategory) { + this.dataCategory = dataCategory; + } + +} diff --git a/src/main/java/org/kpmp/datasetSummary/DatasetSummary.java b/src/main/java/org/kpmp/datasetSummary/DatasetSummary.java deleted file mode 100755 index 125485c..0000000 --- a/src/main/java/org/kpmp/datasetSummary/DatasetSummary.java +++ /dev/null @@ -1,76 +0,0 @@ -package org.kpmp.datasetSummary; - -import java.io.Serializable; - -public class DatasetSummary implements Serializable { - private String omicsType; - private String dataType; - private String dataTypeShort; - private Long akiCount; - private Long ckdCount; - private Long hrtCount; - private Long participantCount; - - public DatasetSummary(String omicsType, String dataType, String dataTypeShort, Long akiCount, Long ckdCount, Long hrtCount, Long participantCount) { - this.omicsType = omicsType; - this.dataType = dataType; - this.dataTypeShort = dataTypeShort; - this.akiCount = akiCount; - this.ckdCount = ckdCount; - this.hrtCount = hrtCount; - this.participantCount = participantCount; - } - public String getOmicsType() { - return this.omicsType; - } - public void setOmicsType(String omicsType) { - this.omicsType = omicsType; - } - - public String getDataType() { - return this.dataType; - } - - public void setDataTypeType(String dataType) { - this.dataType = dataType; - } - - public String getDataTypeShort() { - return this.dataTypeShort; - } - public void setDataTypeShort(String dataTypeShort) { - this.dataTypeShort = dataTypeShort; - } - - public Long getAkiCount() { - return this.akiCount; - } - - public void setAkiCount(Long akiCount) { - this.akiCount = akiCount; - } - - public Long getCkdCount() { - return this.ckdCount; - } - - public void setCkdCount(Long ckdCount) { - this.ckdCount = ckdCount; - } - - public Long getHrtCount() { - return this.hrtCount; - } - - public void setHrtCount(Long hrtCount) { - this.hrtCount = hrtCount; - } - - public Long getParticipantCount() { - return this.participantCount; - } - - public void setParticipantCount(Long participantCount) { - this.participantCount = participantCount; - } -} \ No newline at end of file diff --git a/src/main/java/org/kpmp/gene/MyGeneInfoHit.java b/src/main/java/org/kpmp/gene/MyGeneInfoHit.java index ea25152..82cf3bc 100755 --- a/src/main/java/org/kpmp/gene/MyGeneInfoHit.java +++ b/src/main/java/org/kpmp/gene/MyGeneInfoHit.java @@ -7,56 +7,57 @@ import com.fasterxml.jackson.annotation.JsonProperty; public class MyGeneInfoHit implements Comparable, Serializable { - private String id; - private String symbol; - private String name; - private String entrezgene; - @JsonFormat(with = JsonFormat.Feature.ACCEPT_SINGLE_VALUE_AS_ARRAY) - private List alias; - - public String getId() { - return id; - } - - @JsonProperty("_id") - public void setId(String id) { - this.id = id; - } - - public String getName() { - return name; - } - - public void setName(String name) { - this.name = name; - } - - public String getSymbol() { - return symbol; - } - - public void setSymbol(String symbol) { - this.symbol = symbol; - } - - public String getEntrezgene() { - return entrezgene; - } - - public void setEntrezgene(String entrezgene) { - this.entrezgene = entrezgene; - } - - public List getAlias() { - return alias; - } - - public void setAlias(List alias) { - this.alias = alias; - } - - @Override - public int compareTo(MyGeneInfoHit hit) { - return this.getSymbol().compareTo(hit.getSymbol()); - } + private static final long serialVersionUID = 7498017467676968095L; + private String id; + private String symbol; + private String name; + private String entrezgene; + @JsonFormat(with = JsonFormat.Feature.ACCEPT_SINGLE_VALUE_AS_ARRAY) + private List alias; + + public String getId() { + return id; + } + + @JsonProperty("_id") + public void setId(String id) { + this.id = id; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getSymbol() { + return symbol; + } + + public void setSymbol(String symbol) { + this.symbol = symbol; + } + + public String getEntrezgene() { + return entrezgene; + } + + public void setEntrezgene(String entrezgene) { + this.entrezgene = entrezgene; + } + + public List getAlias() { + return alias; + } + + public void setAlias(List alias) { + this.alias = alias; + } + + @Override + public int compareTo(MyGeneInfoHit hit) { + return this.getSymbol().compareTo(hit.getSymbol()); + } } diff --git a/src/main/java/org/kpmp/gene/MyGeneInfoResult.java b/src/main/java/org/kpmp/gene/MyGeneInfoResult.java index b0fa067..2214db2 100755 --- a/src/main/java/org/kpmp/gene/MyGeneInfoResult.java +++ b/src/main/java/org/kpmp/gene/MyGeneInfoResult.java @@ -4,22 +4,23 @@ import java.util.List; public class MyGeneInfoResult implements Serializable { - private int total; - private List hits; + private static final long serialVersionUID = 2296351561705106315L; + private int total; + private List hits; - public int getTotal() { - return total; - } + public int getTotal() { + return total; + } - public void setTotal(int total) { - this.total = total; - } + public void setTotal(int total) { + this.total = total; + } - public List getHits() { - return hits; - } + public List getHits() { + return hits; + } - public void setHits(List hits) { - this.hits = hits; - } + public void setHits(List hits) { + this.hits = hits; + } } diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java index 97235e8..30cb93b 100755 --- a/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataAllSegments.java @@ -1,15 +1,17 @@ package org.kpmp.geneExpression; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "rt_segments") public class RTExpressionDataAllSegments implements RTExpressionData, Serializable { + private static final long serialVersionUID = 9029734049386312455L; @Id @Column(name = "id") private Integer id; @@ -122,10 +124,12 @@ public void setSampleCount(Integer sampleCount) { this.sampleCount = sampleCount; } + @Override public String getSegmentName() { return segmentName; } + @Override public void setSegmentName(String segmentName) { this.segmentName = segmentName; } diff --git a/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java b/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java index 603ea54..0a33cf2 100755 --- a/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java +++ b/src/main/java/org/kpmp/geneExpression/RTExpressionDataGTI.java @@ -1,15 +1,17 @@ package org.kpmp.geneExpression; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "rt_gti") public class RTExpressionDataGTI implements RTExpressionData, Serializable { + private static final long serialVersionUID = 4789000526795024990L; @Id @Column(name = "id") private Integer id; @@ -122,10 +124,12 @@ public void setSampleCount(Integer sampleCount) { this.sampleCount = sampleCount; } + @Override public String getSegmentName() { return segmentName; } + @Override public void setSegmentName(String segmentName) { this.segmentName = segmentName; } diff --git a/src/main/java/org/kpmp/geneExpression/SCExpressionData.java b/src/main/java/org/kpmp/geneExpression/SCExpressionData.java index 020c8ef..7a738ff 100755 --- a/src/main/java/org/kpmp/geneExpression/SCExpressionData.java +++ b/src/main/java/org/kpmp/geneExpression/SCExpressionData.java @@ -1,5 +1,7 @@ package org.kpmp.geneExpression; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; @@ -8,12 +10,11 @@ import org.json.JSONException; import org.json.JSONObject; -import java.io.Serializable; - @Entity @Table(name = "sc_feature_data") class SCExpressionData implements Serializable { + private static final long serialVersionUID = 1079445825708102694L; @Id @Column(name = "gene_symbol") private String geneSymbol; diff --git a/src/main/java/org/kpmp/geneExpression/SNExpressionData.java b/src/main/java/org/kpmp/geneExpression/SNExpressionData.java index 7929651..1e21871 100755 --- a/src/main/java/org/kpmp/geneExpression/SNExpressionData.java +++ b/src/main/java/org/kpmp/geneExpression/SNExpressionData.java @@ -1,5 +1,7 @@ package org.kpmp.geneExpression; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; @@ -8,12 +10,11 @@ import org.json.JSONException; import org.json.JSONObject; -import java.io.Serializable; - @Entity @Table(name = "sn_feature_data") class SNExpressionData implements Serializable { + private static final long serialVersionUID = -3363426907715685587L; @Id @Column(name = "gene_symbol") private String geneSymbol; diff --git a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java index 0e32c16..91e0452 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryService.java @@ -8,7 +8,7 @@ import org.kpmp.FullDataTypeEnum; import org.kpmp.OmicsTypeEnum; import org.kpmp.TissueTypeEnum; -import org.kpmp.datasetSummary.DatasetSummary; +import org.kpmp.dataSummary.DataTypeSummary; import org.kpmp.geneExpression.RTExpressionDataAllSegmentsRepository; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; @@ -110,23 +110,23 @@ public List findDataTypesByGene(String gene) { return dataTypes; } - public List getGeneDatasetInformation(String geneSymbol) { - List geneSummary = new ArrayList<>(); - geneSummary.add(new DatasetSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + public List getGeneDatasetInformation(String geneSymbol) { + List geneSummary = new ArrayList<>(); + geneSummary.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), FullDataTypeEnum.SINGLE_CELL_FULL.getFullName(), DataTypeEnum.SINGLE_CELL.getAbbreviation(), scrnaGeneExpressionRepository.getCountByTissue(TissueTypeEnum.AKI.getParticipantTissueType()), scrnaGeneExpressionRepository.getCountByTissue(TissueTypeEnum.CKD.getParticipantTissueType()), scrnaGeneExpressionRepository .getCountByTissue(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()), scrnaParticipantRepository.getParticipantCount())); - geneSummary.add(new DatasetSummary(OmicsTypeEnum.NONE.getEnum(), FullDataTypeEnum.SINGLE_NUCLEUS_FULL.getFullName(), + geneSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), FullDataTypeEnum.SINGLE_NUCLEUS_FULL.getFullName(), DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(), snrnaGeneExpressionRepository.getCountByTissue(TissueTypeEnum.AKI.getParticipantTissueType()), snrnaGeneExpressionRepository.getCountByTissue(TissueTypeEnum.CKD.getParticipantTissueType()), snrnaGeneExpressionRepository .getCountByTissue(TissueTypeEnum.HEALTHY_REFERENCE.getParticipantTissueType()), snrnaParticipantRepository.getParticipantCount())); - geneSummary.add(new DatasetSummary(OmicsTypeEnum.NONE.getEnum(), + geneSummary.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), FullDataTypeEnum.REGIONAL_TRANSCRIPTOMICS_FULL.getFullName(), DataTypeEnum.REGIONAL_TRANSCRIPTOMICS.getAbbreviation(), rtParticipantRepository.getCountByTissueType(TissueTypeEnum.AKI.getParticipantTissueType()), diff --git a/src/main/java/org/kpmp/geneExpressionSummary/RTParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/RTParticipantValue.java index 4a5639b..62df11f 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/RTParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/RTParticipantValue.java @@ -1,17 +1,20 @@ package org.kpmp.geneExpressionSummary; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.IdClass; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "rt_participant_tissue_v") @IdClass(ParticipantId.class) class RTParticipantValue implements Participant, Serializable { + private static final long serialVersionUID = 5368734102102552073L; + @Column(name = "tissue_type") private String tissueType; diff --git a/src/main/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionExpressionSummaryValue.java b/src/main/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionExpressionSummaryValue.java index 4aa8c40..8cc08ef 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionExpressionSummaryValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/SCRNAGeneExpressionExpressionSummaryValue.java @@ -17,6 +17,7 @@ @IdClass(GeneExpressionId.class) public class SCRNAGeneExpressionExpressionSummaryValue implements GeneExpressionSummary, Serializable { + private static final long serialVersionUID = 7265280085624504185L; @Column(name = "id") private Integer id; @Column(name = "tissue_type") diff --git a/src/main/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValue.java index d52bda7..a758ab5 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/SCRNAParticipantValue.java @@ -1,17 +1,20 @@ package org.kpmp.geneExpressionSummary; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.IdClass; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "sn_participant_tissue_v") @IdClass(ParticipantId.class) public class SCRNAParticipantValue implements Serializable { + private static final long serialVersionUID = 8746341469788157316L; + @Column(name = "tissue_type") private String tissueType; diff --git a/src/main/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionExpressionSummaryValue.java b/src/main/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionExpressionSummaryValue.java index 6f12920..7093151 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionExpressionSummaryValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/SNRNAGeneExpressionExpressionSummaryValue.java @@ -1,7 +1,6 @@ package org.kpmp.geneExpressionSummary; -import org.kpmp.DataTypeEnum; -import org.springframework.lang.Nullable; +import java.io.Serializable; import javax.persistence.Column; import javax.persistence.Entity; @@ -9,13 +8,17 @@ import javax.persistence.IdClass; import javax.persistence.Table; import javax.persistence.Transient; -import java.io.Serializable; + +import org.kpmp.DataTypeEnum; +import org.springframework.lang.Nullable; @Entity @Table(name = "sn_rnaseq") @IdClass(GeneExpressionId.class) public class SNRNAGeneExpressionExpressionSummaryValue implements GeneExpressionSummary, Serializable { + private static final long serialVersionUID = -443713903175981503L; + @Column(name = "id") private Integer id; @@ -96,20 +99,24 @@ public void setGene(String gene) { this.gene = gene; } + @Override @Nullable public Double getPVal() { return pVal; } + @Override public void setPVal(Double pVal) { this.pVal = pVal; } + @Override @Nullable public Double getPValAdj() { return pValAdj; } + @Override public void setPValAdj(Double pValAdj) { this.pValAdj = pValAdj; } @@ -203,6 +210,7 @@ public boolean equals(Object obj) { if (!(obj instanceof SNRNAGeneExpressionExpressionSummaryValue)) return false; SNRNAGeneExpressionExpressionSummaryValue snrnaGeneExpressionExpressionSummaryValue = (SNRNAGeneExpressionExpressionSummaryValue) obj; - return (snrnaGeneExpressionExpressionSummaryValue.getGene().equals(this.getGene()) && snrnaGeneExpressionExpressionSummaryValue.getCluster().equals(this.getCluster())); + return (snrnaGeneExpressionExpressionSummaryValue.getGene().equals(this.getGene()) + && snrnaGeneExpressionExpressionSummaryValue.getCluster().equals(this.getCluster())); } } diff --git a/src/main/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValue.java b/src/main/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValue.java index 2b6eb04..6c9dadc 100755 --- a/src/main/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValue.java +++ b/src/main/java/org/kpmp/geneExpressionSummary/SNRNAParticipantValue.java @@ -1,17 +1,20 @@ package org.kpmp.geneExpressionSummary; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.IdClass; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "sn_participant_tissue_v") @IdClass(ParticipantId.class) public class SNRNAParticipantValue implements Participant, Serializable { + private static final long serialVersionUID = -2404700991479961255L; + @Column(name = "tissue_type") private String tissueType; diff --git a/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java b/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java index 58e5897..c90a5a0 100755 --- a/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java +++ b/src/main/java/org/kpmp/participant/ParticipantSummaryDataset.java @@ -1,112 +1,114 @@ package org.kpmp.participant; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "participant") -public class ParticipantSummaryDataset implements Serializable { - @Id - @Column(name = "participant_id") - private int participantId; - @Column(name = "old_participant_id") - private String oldparticipantId; - @Column(name = "redcap_id") - private String redcapId; - @Column(name = "age_binned") - private String ageBinned; - private String sex; - @Column(name = "tissue_source") - private String tissueSource; - private String protocol; - @Column(name = "sample_type") - private String sampleType; - @Column(name = "tissue_type") - private String tissueType; - @Column(name = "clinical_data") - private String clinicalData; - - public int getParticipantId() { - return participantId; - } - - public void setParticipantId(int participantId) { - this.participantId = participantId; - } - - public String getOldParticipantId() { - return oldparticipantId; - } - - public void setOldParticipantId(String oldparticipantId) { - this.oldparticipantId = oldparticipantId; - } - - public String getRedcapId() { - return redcapId; - } - - public void setRedcapId(String redcapId) { - this.redcapId = redcapId; - } - - public String getAgeBinned() { - return ageBinned; - } - - public void setAgeBinned(String ageBinned) { - this.ageBinned = ageBinned; - } - - public String getSex() { - return sex; - } - - public void setSex(String sex) { - this.sex = sex; - } - - public String getTissueSource() { - return tissueSource; - } - - public void setTissueSource(String tissueSource) { - this.tissueSource = tissueSource; - } - - public String getProtocol() { - return protocol; - } - - public void setProtocol(String protocol) { - this.protocol = protocol; - } - - public String getSampleType() { - return sampleType; - } - - public void setSampleType(String sampleType) { - this.sampleType = sampleType; - } - - public String getTissueType() { - return tissueType; - } - - public void setTissueType(String tissueType) { - this.tissueType = tissueType; - } - - public String getClinicalData() { - return clinicalData; - } - - public void setClinicalData(String clinicalData) { - this.clinicalData = clinicalData; - } +public class ParticipantSummaryDataset implements Serializable { + private static final long serialVersionUID = -6616360991151079273L; + @Id + @Column(name = "participant_id") + private int participantId; + @Column(name = "old_participant_id") + private String oldparticipantId; + @Column(name = "redcap_id") + private String redcapId; + @Column(name = "age_binned") + private String ageBinned; + private String sex; + @Column(name = "tissue_source") + private String tissueSource; + private String protocol; + @Column(name = "sample_type") + private String sampleType; + @Column(name = "tissue_type") + private String tissueType; + @Column(name = "clinical_data") + private String clinicalData; + + public int getParticipantId() { + return participantId; + } + + public void setParticipantId(int participantId) { + this.participantId = participantId; + } + + public String getOldParticipantId() { + return oldparticipantId; + } + + public void setOldParticipantId(String oldparticipantId) { + this.oldparticipantId = oldparticipantId; + } + + public String getRedcapId() { + return redcapId; + } + + public void setRedcapId(String redcapId) { + this.redcapId = redcapId; + } + + public String getAgeBinned() { + return ageBinned; + } + + public void setAgeBinned(String ageBinned) { + this.ageBinned = ageBinned; + } + + public String getSex() { + return sex; + } + + public void setSex(String sex) { + this.sex = sex; + } + + public String getTissueSource() { + return tissueSource; + } + + public void setTissueSource(String tissueSource) { + this.tissueSource = tissueSource; + } + + public String getProtocol() { + return protocol; + } + + public void setProtocol(String protocol) { + this.protocol = protocol; + } + + public String getSampleType() { + return sampleType; + } + + public void setSampleType(String sampleType) { + this.sampleType = sampleType; + } + + public String getTissueType() { + return tissueType; + } + + public void setTissueType(String tissueType) { + this.tissueType = tissueType; + } + + public String getClinicalData() { + return clinicalData; + } + + public void setClinicalData(String clinicalData) { + this.clinicalData = clinicalData; + } } diff --git a/src/main/java/org/kpmp/participant/ParticipantTissueTypeSummary.java b/src/main/java/org/kpmp/participant/ParticipantTissueTypeSummary.java index 7ec6cc0..2c0b70f 100644 --- a/src/main/java/org/kpmp/participant/ParticipantTissueTypeSummary.java +++ b/src/main/java/org/kpmp/participant/ParticipantTissueTypeSummary.java @@ -1,7 +1,9 @@ package org.kpmp.participant; + import java.io.Serializable; -import java.lang.Long; -public class ParticipantTissueTypeSummary implements Serializable{ + +public class ParticipantTissueTypeSummary implements Serializable { + private static final long serialVersionUID = 4596059416539472482L; private Long akiCount; private Long ckdCount; private Long hrtCount; @@ -13,26 +15,26 @@ public ParticipantTissueTypeSummary(Long akiCount, Long ckdCount, Long hrtCount) } public Long getAkiCount() { - return this.akiCount; - } + return this.akiCount; + } - public void setAkiCount(Long akiCount) { - this.akiCount = akiCount; - } + public void setAkiCount(Long akiCount) { + this.akiCount = akiCount; + } - public Long getCkdCount() { - return this.ckdCount; - } + public Long getCkdCount() { + return this.ckdCount; + } - public void setCkdCount(Long ckdCount) { - this.ckdCount = ckdCount; - } + public void setCkdCount(Long ckdCount) { + this.ckdCount = ckdCount; + } - public Long getHrtCount() { - return this.hrtCount; - } + public Long getHrtCount() { + return this.hrtCount; + } - public void setHrtCount(Long hrtCount) { - this.hrtCount = hrtCount; - } + public void setHrtCount(Long hrtCount) { + this.hrtCount = hrtCount; + } } diff --git a/src/main/java/org/kpmp/participant/SingleCellMetadata.java b/src/main/java/org/kpmp/participant/SingleCellMetadata.java index fea984b..6dc4c08 100755 --- a/src/main/java/org/kpmp/participant/SingleCellMetadata.java +++ b/src/main/java/org/kpmp/participant/SingleCellMetadata.java @@ -1,15 +1,17 @@ package org.kpmp.participant; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "sc_metadata") class SingleCellMetadata implements Serializable { + private static final long serialVersionUID = -7074542040879592316L; @Id private String barcode; @Column(name = "specimen_id") diff --git a/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java b/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java index d92341f..417e59c 100755 --- a/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java +++ b/src/main/java/org/kpmp/participant/SingleNucleusMetadata.java @@ -1,15 +1,17 @@ package org.kpmp.participant; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "sn_metadata") class SingleNucleusMetadata implements Serializable { + private static final long serialVersionUID = -504357775835334661L; @Id private String barcode; @Column(name = "specimen_id") diff --git a/src/main/java/org/kpmp/participant/SpatialViewerDataType.java b/src/main/java/org/kpmp/participant/SpatialViewerDataType.java index 738231c..44f2985 100755 --- a/src/main/java/org/kpmp/participant/SpatialViewerDataType.java +++ b/src/main/java/org/kpmp/participant/SpatialViewerDataType.java @@ -1,15 +1,18 @@ package org.kpmp.participant; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; -import java.io.Serializable; @Entity @Table(name = "sv_data_type_v") class SpatialViewerDataType implements Serializable { + private static final long serialVersionUID = 3095549192644880754L; + @Id @Column(name = "data_type") private String dataType; diff --git a/src/main/java/org/kpmp/umap/FeatureData.java b/src/main/java/org/kpmp/umap/FeatureData.java index afa311e..8ebb50f 100755 --- a/src/main/java/org/kpmp/umap/FeatureData.java +++ b/src/main/java/org/kpmp/umap/FeatureData.java @@ -6,13 +6,13 @@ public class FeatureData implements Serializable { + private static final long serialVersionUID = 6332061560137675936L; private List xValues = new ArrayList<>(); private List yValues = new ArrayList<>(); private List expression = new ArrayList<>(); - private List hoverDisplay = new ArrayList<>(); + private List hoverDisplay = new ArrayList<>(); - - public List getXValues() { + public List getXValues() { return xValues; } @@ -48,16 +48,16 @@ public void addExpression(Double expressionValue) { this.expression.add(expressionValue); } - public List getHoverDisplay() { - return hoverDisplay; - } + public List getHoverDisplay() { + return hoverDisplay; + } - public void setHoverDisplay(List hoverDisplay) { - this.hoverDisplay = hoverDisplay; - } + public void setHoverDisplay(List hoverDisplay) { + this.hoverDisplay = hoverDisplay; + } - public void addHoverDisplay(String hoverDisplay) { - this.hoverDisplay.add(hoverDisplay); - } + public void addHoverDisplay(String hoverDisplay) { + this.hoverDisplay.add(hoverDisplay); + } } diff --git a/src/main/java/org/kpmp/umap/PlotData.java b/src/main/java/org/kpmp/umap/PlotData.java index 47b3b3d..24f637f 100755 --- a/src/main/java/org/kpmp/umap/PlotData.java +++ b/src/main/java/org/kpmp/umap/PlotData.java @@ -5,6 +5,7 @@ public class PlotData implements Serializable { + private static final long serialVersionUID = 7957121452487372467L; private List referenceData; private List featureData; diff --git a/src/main/java/org/kpmp/umap/ReferenceCluster.java b/src/main/java/org/kpmp/umap/ReferenceCluster.java index c65eb87..d5a0080 100755 --- a/src/main/java/org/kpmp/umap/ReferenceCluster.java +++ b/src/main/java/org/kpmp/umap/ReferenceCluster.java @@ -6,6 +6,7 @@ public class ReferenceCluster implements Serializable { + private static final long serialVersionUID = -3963666320832242935L; private List xValues = new ArrayList<>(); private List yValues = new ArrayList<>(); private String color; @@ -57,11 +58,11 @@ public void setClusterName(String clusterName) { this.clusterName = clusterName; } - public String getClusterAbbreviation() { - return clusterAbbreviation; - } + public String getClusterAbbreviation() { + return clusterAbbreviation; + } - public void setClusterAbbreviation(String clusterAbbreviation) { - this.clusterAbbreviation = clusterAbbreviation; - } + public void setClusterAbbreviation(String clusterAbbreviation) { + this.clusterAbbreviation = clusterAbbreviation; + } } diff --git a/src/main/java/org/kpmp/umap/SCMetadata.java b/src/main/java/org/kpmp/umap/SCMetadata.java index 96aa658..dff6125 100755 --- a/src/main/java/org/kpmp/umap/SCMetadata.java +++ b/src/main/java/org/kpmp/umap/SCMetadata.java @@ -1,22 +1,24 @@ package org.kpmp.umap; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; import javax.persistence.Transient; -import java.io.Serializable; @Entity @Table(name = "sc_umap_point_v") public class SCMetadata implements UmapPoint, Serializable { + private static final long serialVersionUID = 7947867645080936879L; @Column(name = "umap_x") private double umapX; @Column(name = "umap_y") private double umapY; - @Column(name = "cluster_abbreviation") - private String clusterAbbreviation; + @Column(name = "cluster_abbreviation") + private String clusterAbbreviation; @Column(name = "cluster_name") private String clusterName; @Column(name = "cluster_color") @@ -59,15 +61,15 @@ public void setClusterName(String clusterName) { this.clusterName = clusterName; } - @Override - public String getClusterAbbreviation() { - return clusterAbbreviation; - } + @Override + public String getClusterAbbreviation() { + return clusterAbbreviation; + } - @Override - public void setClusterAbbreviation(String clusterAbbreviation) { - this.clusterAbbreviation = clusterAbbreviation; - } + @Override + public void setClusterAbbreviation(String clusterAbbreviation) { + this.clusterAbbreviation = clusterAbbreviation; + } @Override public String getClusterColor() { diff --git a/src/main/java/org/kpmp/umap/SNMetadata.java b/src/main/java/org/kpmp/umap/SNMetadata.java index 5365c50..7e2a5d4 100755 --- a/src/main/java/org/kpmp/umap/SNMetadata.java +++ b/src/main/java/org/kpmp/umap/SNMetadata.java @@ -1,22 +1,24 @@ package org.kpmp.umap; +import java.io.Serializable; + import javax.persistence.Column; import javax.persistence.Entity; import javax.persistence.Id; import javax.persistence.Table; import javax.persistence.Transient; -import java.io.Serializable; @Entity @Table(name = "sn_umap_point_v") public class SNMetadata implements UmapPoint, Serializable { + private static final long serialVersionUID = -8871186152958713643L; @Column(name = "umap_x") private double umapX; @Column(name = "umap_y") private double umapY; @Column(name = "cluster_abbreviation") - private String clusterAbbreviation; + private String clusterAbbreviation; @Column(name = "cluster_name") private String clusterName; @Column(name = "cluster_color") @@ -59,17 +61,17 @@ public void setClusterName(String clusterName) { this.clusterName = clusterName; } - @Override - public String getClusterAbbreviation() { - return clusterAbbreviation; - } + @Override + public String getClusterAbbreviation() { + return clusterAbbreviation; + } - @Override - public void setClusterAbbreviation(String clusterAbbreviation) { - this.clusterAbbreviation = clusterAbbreviation; - } + @Override + public void setClusterAbbreviation(String clusterAbbreviation) { + this.clusterAbbreviation = clusterAbbreviation; + } - @Override + @Override public String getClusterColor() { return clusterColor; } diff --git a/src/main/resources/knowledge_environment.graphqls b/src/main/resources/knowledge_environment.graphqls index 6d12b12..6d94de6 100755 --- a/src/main/resources/knowledge_environment.graphqls +++ b/src/main/resources/knowledge_environment.graphqls @@ -14,6 +14,24 @@ type Query { participantSummaryDataset(redcapId: String): ParticipantSummaryDataset participantClinicalDataset(redcapId: String): ParticipantSummaryDataset getTissueTypeSummaryData: [ParticipantTissueTypeSummary] + getAtlasSummaryRows: AtlasRepoSummaryResult +} + +type AtlasRepoSummaryResult { + totalFiles: Int + summaryRows: [AtlasRepoSummaryRow] +} + +type AtlasRepoSummaryRow { + openCount: Int + controlledCount: Int + omicsType: String + linkInformation: AtlasRepoSummaryLinkInformation +} + +type AtlasRepoSummaryLinkInformation { + linkType: String + linkValue: String } type ParticipantTissueTypeSummary { diff --git a/src/test/java/org/kpmp/QueryTest.java b/src/test/java/org/kpmp/QueryTest.java index 7f542f9..6be38b3 100755 --- a/src/test/java/org/kpmp/QueryTest.java +++ b/src/test/java/org/kpmp/QueryTest.java @@ -1,6 +1,7 @@ package org.kpmp; import static org.junit.Assert.assertEquals; +import static org.junit.Assert.fail; import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.mock; import static org.mockito.Mockito.times; @@ -20,8 +21,9 @@ import org.kpmp.cellType.CellTypeService; import org.kpmp.cellTypeSummary.ClusterHierarchy; import org.kpmp.cellTypeSummary.ClusterHierarchyService; +import org.kpmp.dataSummary.AtlasRepoSummaryResult; import org.kpmp.dataSummary.DataSummaryService; -import org.kpmp.datasetSummary.DatasetSummary; +import org.kpmp.dataSummary.DataTypeSummary; import org.kpmp.gene.GeneService; import org.kpmp.gene.MyGeneInfoHit; import org.kpmp.geneExpression.RTExpressionByTissueType; @@ -31,9 +33,9 @@ import org.kpmp.geneExpressionSummary.SCRNAGeneExpressionExpressionSummaryValue; import org.kpmp.geneExpressionSummary.SNRNAGeneExpressionExpressionSummaryValue; import org.kpmp.participant.ParticipantDataTypeSummary; -import org.kpmp.participant.ParticipantTissueTypeSummary; import org.kpmp.participant.ParticipantService; import org.kpmp.participant.ParticipantSummaryDataset; +import org.kpmp.participant.ParticipantTissueTypeSummary; import org.kpmp.umap.FeatureData; import org.kpmp.umap.PlotData; import org.kpmp.umap.ReferenceCluster; @@ -78,6 +80,26 @@ public void tearDown() throws Exception { query = null; } + @Test + public void testGetAtlasSummaryRows() throws Exception { + AtlasRepoSummaryResult expectedResult = mock(AtlasRepoSummaryResult.class); + when(dataSummaryService.getAtlasRepoSummary()).thenReturn(expectedResult); + + assertEquals(expectedResult, query.getAtlasSummaryRows()); + } + + @Test + public void testGetAtlasSummaryRows_throwsException() throws Exception { + when(dataSummaryService.getAtlasRepoSummary()).thenThrow(new Exception("ack")); + + try { + query.getAtlasSummaryRows(); + fail("Should have thrown exception"); + } catch (Exception e) { + assertEquals("ack", e.getMessage()); + } + } + @Test public void testGenes() throws Exception { List expectedResult = Arrays.asList(new MyGeneInfoHit()); @@ -192,17 +214,17 @@ public void dataTypesForConceptWhenClusterNameAndBlankGene() throws Exception { @Test public void getGeneDatasetInformation() throws Exception { - List expectedResult = new ArrayList<>(); + List expectedResult = new ArrayList<>(); - expectedResult.add(new DatasetSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + expectedResult.add(new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), FullDataTypeEnum.SINGLE_CELL_FULL.getFullName(), DataTypeEnum.SINGLE_CELL.getAbbreviation(), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0))); - expectedResult.add(new DatasetSummary(OmicsTypeEnum.NONE.getEnum(), + expectedResult.add(new DataTypeSummary(OmicsTypeEnum.NONE.getEnum(), FullDataTypeEnum.SINGLE_NUCLEUS_FULL.getFullName(), DataTypeEnum.SINGLE_NUCLEUS.getAbbreviation(), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0), Long.valueOf(0))); when(geneExpressionService.getGeneDatasetInformation("AAA")).thenReturn(expectedResult); - List datasetSummary = query.getGeneDatasetInformation("AAA"); + List datasetSummary = query.getGeneDatasetInformation("AAA"); assertEquals(expectedResult, datasetSummary); } @@ -251,12 +273,12 @@ public void testParticipantClinicalDataset() throws Exception { assertEquals(expected, query.participantClinicalDataset("participant_id")); } - + public void getParticipantTissueTypeSummary() throws Exception { List expectedResult = new ArrayList<>(); expectedResult.add(new ParticipantTissueTypeSummary(Long.valueOf(4), Long.valueOf(5), Long.valueOf(6))); - + List tissueSummary = query.getTissueTypeSummaryData(); assertEquals(expectedResult, tissueSummary); diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformationTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformationTest.java new file mode 100644 index 0000000..5d12f92 --- /dev/null +++ b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryLinkInformationTest.java @@ -0,0 +1,63 @@ +package org.kpmp.dataSummary; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import org.junit.After; +import org.junit.Before; +import org.junit.Test; + +public class AtlasRepoSummaryLinkInformationTest { + + @Before + public void setUp() throws Exception { + + } + + @After + public void tearDown() throws Exception { + } + + @Test + public void testConstructor() { + AtlasRepoSummaryLinkInformation linkInfo = new AtlasRepoSummaryLinkInformation("type", "value"); + + assertEquals("type", linkInfo.getLinkType()); + assertEquals("value", linkInfo.getLinkValue()); + } + + @Test + public void testSetLinkType() { + AtlasRepoSummaryLinkInformation linkInfo = new AtlasRepoSummaryLinkInformation("type", "value"); + linkInfo.setLinkType("anotherType"); + + assertEquals("anotherType", linkInfo.getLinkType()); + } + + @Test + public void testSetLinkValue() { + AtlasRepoSummaryLinkInformation linkInfo = new AtlasRepoSummaryLinkInformation("type", "value"); + linkInfo.setLinkValue("another value"); + + assertEquals("another value", linkInfo.getLinkValue()); + } + + @Test + public void testEqualsAndHashCode() throws Exception { + AtlasRepoSummaryLinkInformation base = new AtlasRepoSummaryLinkInformation("linkType", "linkValue"); + AtlasRepoSummaryLinkInformation same = new AtlasRepoSummaryLinkInformation("linkType", "linkValue"); + AtlasRepoSummaryLinkInformation differentLinkType = new AtlasRepoSummaryLinkInformation("another type", + "linkValue"); + AtlasRepoSummaryLinkInformation differentLinkValue = new AtlasRepoSummaryLinkInformation("linkType", + "another value"); + String anotherObject = "hey there"; + + assertEquals(base.hashCode(), base.hashCode()); + assertEquals(base.hashCode(), same.hashCode()); + assertEquals(true, base.equals(same)); + assertEquals(true, base.equals(base)); + assertEquals(false, base.equals(differentLinkType)); + assertEquals(false, base.equals(differentLinkValue)); + assertEquals(false, base.equals(anotherObject)); + + } +} diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java new file mode 100644 index 0000000..23f5617 --- /dev/null +++ b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java @@ -0,0 +1,52 @@ +package org.kpmp.dataSummary; + +import static org.junit.Assert.assertEquals; + +import java.util.List; + +import org.junit.After; +import org.junit.Before; +import org.junit.Test; +import org.mockito.Mock; + +public class AtlasRepoSummaryResultTest { + + private AtlasRepoSummaryResult result; + @Mock + private List summaryRows; + + @Before + public void setUp() throws Exception { + result = new AtlasRepoSummaryResult(); + } + + @After + public void tearDown() throws Exception { + result = null; + } + + @Test + public void testConstructor() throws Exception { + int totalFiles = 5; + AtlasRepoSummaryResult constructorTest = new AtlasRepoSummaryResult(summaryRows, totalFiles); + + assertEquals(summaryRows, constructorTest.getSummaryRows()); + assertEquals(5, constructorTest.getTotalFiles()); + + } + + @Test + public void testSetSummaryRows() { + result.setSummaryRows(summaryRows); + + assertEquals(summaryRows, result.getSummaryRows()); + } + + @Test + public void testSetTotalFiles() { + result.setTotalFiles(58); + + assertEquals(58, result.getTotalFiles()); + } + +} diff --git a/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java new file mode 100644 index 0000000..1d12217 --- /dev/null +++ b/src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryRowTest.java @@ -0,0 +1,85 @@ +package org.kpmp.dataSummary; + +import static org.junit.Assert.assertEquals; +import static org.mockito.Mockito.mock; + +import org.junit.After; +import org.junit.Before; +import org.junit.Test; +import org.mockito.Mock; +import org.mockito.MockitoAnnotations; + +public class AtlasRepoSummaryRowTest { + + @Mock + AtlasRepoSummaryLinkInformation linkInformation; + private AtlasRepoSummaryRow row; + + @Before + public void setUp() throws Exception { + MockitoAnnotations.openMocks(this); + row = new AtlasRepoSummaryRow("omicsType", linkInformation); + } + + @After + public void tearDown() throws Exception { + MockitoAnnotations.openMocks(this).close(); + row = null; + } + + @Test + public void testConstructor() throws Exception { + AtlasRepoSummaryLinkInformation expectedLinkInformation = mock(AtlasRepoSummaryLinkInformation.class); + AtlasRepoSummaryRow rowToTest = new AtlasRepoSummaryRow("stuff", expectedLinkInformation); + + assertEquals("stuff", rowToTest.getOmicsType()); + assertEquals(expectedLinkInformation, rowToTest.getLinkInformation()); + assertEquals(0, rowToTest.getOpenCount()); + assertEquals(0, rowToTest.getControlledCount()); + } + + @Test + public void testSetOpenCount() { + row.setOpenCount(43); + + assertEquals(43, row.getOpenCount()); + } + + @Test + public void testSetControlledCount() { + row.setControlledCount(44); + + assertEquals(44, row.getControlledCount()); + } + + @Test + public void testSetOmicsType() { + row.setOmicsType("omicsType 2"); + assertEquals("omicsType 2", row.getOmicsType()); + } + + @Test + public void testAddToControlledCount() { + row.setControlledCount(2); + row.addToControlledCount(30); + + assertEquals(32, row.getControlledCount()); + } + + @Test + public void testAddToOpenCount() { + row.setOpenCount(5); + row.addToOpenCount(5); + + assertEquals(10, row.getOpenCount()); + } + + @Test + public void testSetLinkInformation() { + AtlasRepoSummaryLinkInformation expectedLinkInformation = mock(AtlasRepoSummaryLinkInformation.class); + row.setLinkInformation(expectedLinkInformation); + + assertEquals(expectedLinkInformation, row.getLinkInformation()); + + } +} diff --git a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java index 834bed1..65bb950 100755 --- a/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java +++ b/src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java @@ -3,6 +3,7 @@ import static org.junit.Assert.assertEquals; import static org.mockito.Mockito.when; +import java.util.Arrays; import java.util.List; import org.junit.After; @@ -11,7 +12,6 @@ import org.kpmp.DataTypeEnum; import org.kpmp.FullDataTypeEnum; import org.kpmp.TissueTypeEnum; -import org.kpmp.datasetSummary.DatasetSummary; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -19,11 +19,13 @@ public class DataSummaryServiceTest { private DataSummaryService dataSummaryService; @Mock private DataSummaryRepository dataSummaryRepository; + @Mock + private AtlasRepoSummaryRepository atlasRepoSummaryRepository; @Before public void setUp() throws Exception { MockitoAnnotations.openMocks(this); - dataSummaryService = new DataSummaryService(dataSummaryRepository); + dataSummaryService = new DataSummaryService(dataSummaryRepository, atlasRepoSummaryRepository); } @After @@ -32,6 +34,66 @@ public void tearDown() throws Exception { dataSummaryService = null; } + @Test + public void testGetAtlasRepoSummary() throws Exception { + ExperimentalStrategyValue clinicalData = new ExperimentalStrategyValue(); + clinicalData.setDataCategory("stuff"); + clinicalData.setExperimentalStrategy(""); + clinicalData.setDataType("Clinical Study Data"); + clinicalData.setCount(1); + clinicalData.setAccess("open"); + ExperimentalStrategyValue biomarker1 = new ExperimentalStrategyValue(); + biomarker1.setDataCategory("Biomarker"); + biomarker1.setExperimentalStrategy("something"); + biomarker1.setDataType("stuff"); + biomarker1.setDataCategory("Biomarker"); + biomarker1.setCount(5); + biomarker1.setAccess("open"); + ExperimentalStrategyValue biomarker2 = new ExperimentalStrategyValue(); + biomarker2.setDataCategory("Biomarker"); + biomarker2.setDataType("more stuff"); + biomarker2.setExperimentalStrategy("something else"); + biomarker2.setDataCategory("Biomarker"); + biomarker2.setCount(10); + biomarker2.setAccess("open"); + ExperimentalStrategyValue other1 = new ExperimentalStrategyValue(); + other1.setDataCategory("data category"); + other1.setDataType("different stuff"); + other1.setExperimentalStrategy("strategy1"); + other1.setCount(10); + other1.setAccess("open"); + ExperimentalStrategyValue other2 = new ExperimentalStrategyValue(); + other2.setDataCategory("data category2"); + other2.setDataType("even more different stuff"); + other2.setExperimentalStrategy("strategy1"); + other2.setCount(10); + other2.setAccess("controlled"); + List strategyValues = Arrays.asList(clinicalData, biomarker1, biomarker2, other1, + other2); + when(atlasRepoSummaryRepository.findAll()).thenReturn(strategyValues); + + AtlasRepoSummaryResult result = dataSummaryService.getAtlasRepoSummary(); + List summaryRows = result.getSummaryRows(); + assertEquals(3, summaryRows.size()); + assertEquals("Biomarkers", summaryRows.get(0).getOmicsType()); + assertEquals(0, summaryRows.get(0).getControlledCount()); + assertEquals(15, summaryRows.get(0).getOpenCount()); + assertEquals(new AtlasRepoSummaryLinkInformation("data_category", "Biomarker"), + summaryRows.get(0).getLinkInformation()); + assertEquals("Clinical Study Data", summaryRows.get(1).getOmicsType()); + assertEquals(0, summaryRows.get(1).getControlledCount()); + assertEquals(1, summaryRows.get(1).getOpenCount()); + assertEquals(new AtlasRepoSummaryLinkInformation("data_category", "stuff"), + summaryRows.get(1).getLinkInformation()); + assertEquals("strategy1", summaryRows.get(2).getOmicsType()); + assertEquals(10, summaryRows.get(2).getControlledCount()); + assertEquals(10, summaryRows.get(2).getOpenCount()); + assertEquals(new AtlasRepoSummaryLinkInformation("experimental_strategy", "strategy1"), + summaryRows.get(2).getLinkInformation()); + assertEquals(36, result.getTotalFiles()); + + } + @Test public void testGetGeneDatasetInformation() throws Exception { when(dataSummaryRepository.getDataSummaryCount(TissueTypeEnum.AKI.getParticipantTissueType(), @@ -103,7 +165,7 @@ public void testGetGeneDatasetInformation() throws Exception { .getParticipantSummaryLinkCount(FullDataTypeEnum.SPATIAL_NGLYCOMICS_FULL.getFullName())) .thenReturn(Long.valueOf(22)); - List result = dataSummaryService.getSummaryData(); + List result = dataSummaryService.getSummaryData(); assertEquals(FullDataTypeEnum.SPATIAL_TRANSCRIPTOMICS_FULL.getFullName(), result.get(0).getDataType()); assertEquals(DataTypeEnum.SPATIAL_TRANSCRIPTOMICS.getAbbreviation(), result.get(0).getDataTypeShort()); diff --git a/src/test/java/org/kpmp/datasetSummary/DatasetSummaryTest.java b/src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java similarity index 93% rename from src/test/java/org/kpmp/datasetSummary/DatasetSummaryTest.java rename to src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java index 47cfcad..a85aecd 100755 --- a/src/test/java/org/kpmp/datasetSummary/DatasetSummaryTest.java +++ b/src/test/java/org/kpmp/dataSummary/DataTypeSummaryTest.java @@ -1,4 +1,4 @@ -package org.kpmp.datasetSummary; +package org.kpmp.dataSummary; import static org.junit.Assert.assertEquals; @@ -9,14 +9,14 @@ import org.kpmp.FullDataTypeEnum; import org.kpmp.OmicsTypeEnum; -public class DatasetSummaryTest { +public class DataTypeSummaryTest { - private DatasetSummary datasetSummary; + private DataTypeSummary datasetSummary; @Before public void setUp() { - datasetSummary = new DatasetSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), + datasetSummary = new DataTypeSummary(OmicsTypeEnum.TRANSCRIPTOMICS.getEnum(), FullDataTypeEnum.SINGLE_CELL_FULL.getFullName(), DataTypeEnum.SINGLE_CELL.getAbbreviation(), Long.valueOf(2), Long.valueOf(4), Long.valueOf(6), Long.valueOf(8)); } diff --git a/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java new file mode 100644 index 0000000..d9d80ac --- /dev/null +++ b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyIdTest.java @@ -0,0 +1,35 @@ +package org.kpmp.dataSummary; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import org.junit.After; +import org.junit.Before; +import org.junit.Test; + +public class ExperimentalStrategyIdTest { + + private ExperimentalStrategyId id; + + @Before + public void setUp() throws Exception { + id = new ExperimentalStrategyId(); + } + + @After + public void tearDown() throws Exception { + id = null; + } + + @Test + public void testSetExperimentalStrategy() { + id.setExperimentalStrategy("strategy"); + assertEquals("strategy", id.getExperimentalStrategy()); + } + + @Test + public void testSetAccess() { + id.setAccess("open"); + assertEquals("open", id.getAccess()); + } + +} diff --git a/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java new file mode 100644 index 0000000..b2b3346 --- /dev/null +++ b/src/test/java/org/kpmp/dataSummary/ExperimentalStrategyValueTest.java @@ -0,0 +1,53 @@ +package org.kpmp.dataSummary; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import org.junit.After; +import org.junit.Before; +import org.junit.Test; + +public class ExperimentalStrategyValueTest { + + private ExperimentalStrategyValue value; + + @Before + public void setUp() throws Exception { + value = new ExperimentalStrategyValue(); + } + + @After + public void tearDown() throws Exception { + value = null; + } + + @Test + public void testSetCount() { + value.setCount(23); + assertEquals(23, value.getCount()); + } + + @Test + public void testSetExperimentalStrategy() { + value.setExperimentalStrategy("experimentalStrategy"); + assertEquals("experimentalStrategy", value.getExperimentalStrategy()); + } + + @Test + public void testSetAccess() { + value.setAccess("open"); + assertEquals("open", value.getAccess()); + } + + @Test + public void testSetDataType() { + value.setDataType("dataType"); + assertEquals("dataType", value.getDataType()); + } + + @Test + public void testSetDataCategory() { + value.setDataCategory("dataCategory"); + assertEquals("dataCategory", value.getDataCategory()); + } + +} diff --git a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java index 83c25b8..e7f5054 100755 --- a/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java +++ b/src/test/java/org/kpmp/geneExpressionSummary/GeneExpressionSummaryServiceTest.java @@ -12,7 +12,7 @@ import org.junit.Before; import org.junit.Test; import org.kpmp.DataTypeEnum; -import org.kpmp.datasetSummary.DatasetSummary; +import org.kpmp.dataSummary.DataTypeSummary; import org.kpmp.geneExpression.RTExpressionDataAllSegmentsRepository; import org.mockito.Mock; import org.mockito.MockitoAnnotations; @@ -204,10 +204,10 @@ public void testGetGeneDatasetInformation() throws Exception { when(snrnaGeneExpressionRepository.getCountByTissue("hrt")).thenReturn(Long.valueOf(0)); when(snrnaParticipantRepository.getParticipantCount()).thenReturn(Long.valueOf(0)); - List result = geneExpressionService.getGeneDatasetInformation("AAA"); - DatasetSummary resultDataSC = result.get(0); - DatasetSummary resultDataSN = result.get(1); - DatasetSummary resultDataRt = result.get(2); + List result = geneExpressionService.getGeneDatasetInformation("AAA"); + DataTypeSummary resultDataSC = result.get(0); + DataTypeSummary resultDataSN = result.get(1); + DataTypeSummary resultDataRt = result.get(2); assertEquals(Long.valueOf(0), resultDataSC.getAkiCount()); assertEquals(Long.valueOf(0), resultDataSC.getCkdCount()); diff --git a/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java b/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java index 019b79d..dbea114 100755 --- a/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java +++ b/src/test/java/org/kpmp/participant/SingleCellMetadataTest.java @@ -6,7 +6,7 @@ import org.junit.Before; import org.junit.Test; -public class SingleCellMetadataTest extends SingleCellMetadata { +public class SingleCellMetadataTest { private SingleCellMetadata scMetadata; diff --git a/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java b/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java index 9e95d0d..2c62101 100755 --- a/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java +++ b/src/test/java/org/kpmp/participant/SingleNucleusMetadataTest.java @@ -6,7 +6,7 @@ import org.junit.Before; import org.junit.Test; -public class SingleNucleusMetadataTest extends SingleNucleusMetadata { +public class SingleNucleusMetadataTest { private SingleNucleusMetadata snMetadata;