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Added comments to 5 classes in the service folder #11310

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97 changes: 88 additions & 9 deletions src/main/java/org/cbioportal/service/CopyNumberSegmentService.java
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Expand Up @@ -9,17 +9,96 @@

public interface CopyNumberSegmentService {

List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String chromosome, String projection,
Integer pageSize, Integer pageNumber, String sortBy,
String direction)
throws SampleNotFoundException, StudyNotFoundException;
/**
* Retrieves sorted list of copy number segments for a specific sample
* within a specific study. This method allows filtering by chromosome and projection.
*
* @param studyId the ID of the study
* @param sampleId the ID of the sample
* @param chromosome the chromosome to filter by
* @param projection the projection type
* @param pageSize the number of records per page
* @param pageNumber the page number to retrieve
* @param sortBy the field to sort the results by
* @param direction the sort direction (e.g., ASC or DESC)
* @return a list of copy number segments
* @throws SampleNotFoundException if the sample is not found
* @throws StudyNotFoundException if the study is not found
*/
List<CopyNumberSeg> getCopyNumberSegmentsInSampleInStudy(
String studyId,
String sampleId,
String chromosome,
String projection,
Integer pageSize,
Integer pageNumber,
String sortBy,
String direction
) throws SampleNotFoundException, StudyNotFoundException;

BaseMeta getMetaCopyNumberSegmentsInSampleInStudy(String studyId, String sampleId, String chromosome)
throws SampleNotFoundException, StudyNotFoundException;
/**
* Retrieves metadata for copy number segments for a specific sample
* within a specific study, filtered by chromosome.
*
* @param studyId the ID of the study
* @param sampleId the ID of the sample
* @param chromosome the chromosome to filter by
* @return the metadata for the copy number segments
* @throws SampleNotFoundException if the sample is not found
* @throws StudyNotFoundException if the study is not found
*/
BaseMeta getMetaCopyNumberSegmentsInSampleInStudy(
String studyId,
String sampleId,
String chromosome
) throws SampleNotFoundException, StudyNotFoundException;

List<CopyNumberSeg> fetchCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome, String projection);
/**
* Fetches copy number segments for multiple studies and samples,
* filtered by chromosome and projection.
*
* @param studyIds a list of study IDs
* @param sampleIds a list of sample IDs
* @param chromosome the chromosome to filter by
* @param projection the projection type
* @return a list of copy number segments
*/
List<CopyNumberSeg> fetchCopyNumberSegments(
List<String> studyIds,
List<String> sampleIds,
String chromosome,
String projection
);

BaseMeta fetchMetaCopyNumberSegments(List<String> studyIds, List<String> sampleIds, String chromosome);
/**
* Fetches metadata for copy number segments for multiple studies and samples,
* filtered by chromosome.
*
* @param studyIds a list of study IDs
* @param sampleIds a list of sample IDs
* @param chromosome the chromosome to filter by
* @return the metadata for the copy number segments
*/
BaseMeta fetchMetaCopyNumberSegments(
List<String> studyIds,
List<String> sampleIds,
String chromosome
);

List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(String studyId, String sampleListId, String chromosome, String projection);
/**
* Retrieves copy number segments for a list of samples within a study,
* filtered by chromosome and projection.
*
* @param studyId the ID of the study
* @param sampleListId the ID of the sample list
* @param chromosome the chromosome to filter by
* @param projection the projection type
* @return a list of copy number segments
*/
List<CopyNumberSeg> getCopyNumberSegmentsBySampleListId(
String studyId,
String sampleListId,
String chromosome,
String projection
);
}
187 changes: 144 additions & 43 deletions src/main/java/org/cbioportal/service/DiscreteCopyNumberService.java
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Expand Up @@ -8,46 +8,147 @@

public interface DiscreteCopyNumberService {

List<DiscreteCopyNumberData> getDiscreteCopyNumbersInMolecularProfileBySampleListId(String molecularProfileId,
String sampleListId,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes,
String projection)
throws MolecularProfileNotFoundException;

BaseMeta getMetaDiscreteCopyNumbersInMolecularProfileBySampleListId(String molecularProfileId, String sampleListId,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes)
throws MolecularProfileNotFoundException;

List<DiscreteCopyNumberData> fetchDiscreteCopyNumbersInMolecularProfile(String molecularProfileId,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes,
String projection)
throws MolecularProfileNotFoundException;

List<DiscreteCopyNumberData> getDiscreteCopyNumbersInMultipleMolecularProfiles(List<String> molecularProfileIds,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes,
String projection);

List<DiscreteCopyNumberData> getDiscreteCopyNumbersInMultipleMolecularProfilesByGeneQueries(List<String> molecularProfileIds,
List<String> sampleIds,
List<GeneFilterQuery> geneQueries,
String projection);

BaseMeta fetchMetaDiscreteCopyNumbersInMolecularProfile(String molecularProfileId, List<String> sampleIds,
List<Integer> entrezGeneIds, List<Integer> alterationTypes)
throws MolecularProfileNotFoundException;

List<CopyNumberCountByGene> getSampleCountByGeneAndAlterationAndSampleIds(String molecularProfileId,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterations)
throws MolecularProfileNotFoundException;

List<CopyNumberCount> fetchCopyNumberCounts(String molecularProfileId, List<Integer> entrezGeneIds,
List<Integer> alterations) throws MolecularProfileNotFoundException;
}
/**
* Retrieves discrete copy number data for a specific molecular profile based on a sample list ID.
* Allows filtering by gene IDs, alteration types, and projection type.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleListId the ID of the sample list
* @param entrezGeneIds a list of Entrez gene IDs to filter by
* @param alterationTypes a list of alteration types to filter by
* @param projection the projection type
* @return a list of discrete copy number data
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
List<DiscreteCopyNumberData> getDiscreteCopyNumbersInMolecularProfileBySampleListId(
String molecularProfileId,
String sampleListId,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes,
String projection
) throws MolecularProfileNotFoundException;

/**
* Retrieves metadata for discrete copy number data in a specific molecular profile
* using a sample list ID and filters by gene IDs and alteration types.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleListId the ID of the sample list
* @param entrezGeneIds a list of Entrez gene IDs to filter by
* @param alterationTypes a list of alteration types to filter by
* @return metadata for the discrete copy number data
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
BaseMeta getMetaDiscreteCopyNumbersInMolecularProfileBySampleListId(
String molecularProfileId,
String sampleListId,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes
) throws MolecularProfileNotFoundException;

/**
* Fetches discrete copy number data for a specific molecular profile based on sample IDs.
* Filters by gene IDs, alteration types, and projection type.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleIds a list of sample IDs
* @param entrezGeneIds a list of Entrez gene IDs to filter by
* @param alterationTypes a list of alteration types to filter by
* @param projection the projection type
* @return a list of discrete copy number data
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
List<DiscreteCopyNumberData> fetchDiscreteCopyNumbersInMolecularProfile(
String molecularProfileId,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes,
String projection
) throws MolecularProfileNotFoundException;

/**
* Retrieves discrete copy number data for multiple molecular profiles based on sample IDs.
* Filters by gene IDs, alteration types, and projection type.
*
* @param molecularProfileIds a list of molecular profile IDs
* @param sampleIds a list of sample IDs
* @param entrezGeneIds a list of Entrez gene IDs to filter by
* @param alterationTypes a list of alteration types to filter by
* @param projection the projection type
* @return a list of discrete copy number data
*/
List<DiscreteCopyNumberData> getDiscreteCopyNumbersInMultipleMolecularProfiles(
List<String> molecularProfileIds,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes,
String projection
);

/**
* Retrieves discrete copy number data for multiple molecular profiles using gene queries.
*
* @param molecularProfileIds a list of molecular profile IDs
* @param sampleIds a list of sample IDs
* @param geneQueries a list of gene filter queries
* @param projection the projection type
* @return a list of discrete copy number data
*/
List<DiscreteCopyNumberData> getDiscreteCopyNumbersInMultipleMolecularProfilesByGeneQueries(
List<String> molecularProfileIds,
List<String> sampleIds,
List<GeneFilterQuery> geneQueries,
String projection
);

/**
* Fetches metadata for discrete copy number data in a specific molecular profile based on sample IDs.
* Filters by gene IDs and alteration types.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleIds a list of sample IDs
* @param entrezGeneIds a list of Entrez gene IDs to filter by
* @param alterationTypes a list of alteration types to filter by
* @return metadata for the discrete copy number data
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
BaseMeta fetchMetaDiscreteCopyNumbersInMolecularProfile(
String molecularProfileId,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterationTypes
) throws MolecularProfileNotFoundException;

/**
* Retrieves sample counts grouped by gene and alteration type for specific sample IDs
* in a molecular profile.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleIds a list of sample IDs
* @param entrezGeneIds a list of Entrez gene IDs
* @param alterations a list of alteration types
* @return a list of copy number counts by gene
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
List<CopyNumberCountByGene> getSampleCountByGeneAndAlterationAndSampleIds(
String molecularProfileId,
List<String> sampleIds,
List<Integer> entrezGeneIds,
List<Integer> alterations
) throws MolecularProfileNotFoundException;

/**
* Fetches copy number counts grouped by gene and alteration type for a specific molecular profile.
*
* @param molecularProfileId the ID of the molecular profile
* @param entrezGeneIds a list of Entrez gene IDs
* @param alterations a list of alteration types
* @return a list of copy number counts
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
List<CopyNumberCount> fetchCopyNumberCounts(
String molecularProfileId,
List<Integer> entrezGeneIds,
List<Integer> alterations
) throws MolecularProfileNotFoundException;
}
77 changes: 66 additions & 11 deletions src/main/java/org/cbioportal/service/GenericAssayService.java
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Expand Up @@ -7,18 +7,73 @@
import org.cbioportal.service.exception.MolecularProfileNotFoundException;

public interface GenericAssayService {

List<GenericAssayMeta> getGenericAssayMetaByStableIdsAndMolecularIds(List<String> stableIds, List<String> molecularProfileIds, String projection);

List<GenericAssayData> getGenericAssayData(String molecularProfileId, String sampleListId,
List<String> genericAssayStableIds, String projection)
throws MolecularProfileNotFoundException;
/**
* Retrieves metadata for generic assay data based on a list of stable IDs and molecular profile IDs.
* Allows filtering by projection type.
*
* @param stableIds a list of stable IDs for the generic assays
* @param molecularProfileIds a list of molecular profile IDs
* @param projection the projection type
* @return a list of generic assay metadata
*/
List<GenericAssayMeta> getGenericAssayMetaByStableIdsAndMolecularIds(
List<String> stableIds,
List<String> molecularProfileIds,
String projection
);

List<GenericAssayData> fetchGenericAssayData(String molecularProfileId, List<String> sampleIds,
List<String> genericAssayStableIds, String projection)
throws MolecularProfileNotFoundException;
/**
* Retrieves generic assay data for a specific molecular profile and sample list.
* Filters by a list of stable IDs and allows specifying a projection type.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleListId the ID of the sample list
* @param genericAssayStableIds a list of stable IDs for the generic assays
* @param projection the projection type
* @return a list of generic assay data
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
List<GenericAssayData> getGenericAssayData(
String molecularProfileId,
String sampleListId,
List<String> genericAssayStableIds,
String projection
) throws MolecularProfileNotFoundException;

List<GenericAssayData> fetchGenericAssayData(List<String> molecularProfileIds, List<String> sampleIds,
List<String> genericAssayStableIds, String projection)
throws MolecularProfileNotFoundException;
/**
* Fetches generic assay data for a specific molecular profile and a list of sample IDs.
* Filters by a list of stable IDs and allows specifying a projection type.
*
* @param molecularProfileId the ID of the molecular profile
* @param sampleIds a list of sample IDs
* @param genericAssayStableIds a list of stable IDs for the generic assays
* @param projection the projection type
* @return a list of generic assay data
* @throws MolecularProfileNotFoundException if the molecular profile is not found
*/
List<GenericAssayData> fetchGenericAssayData(
String molecularProfileId,
List<String> sampleIds,
List<String> genericAssayStableIds,
String projection
) throws MolecularProfileNotFoundException;

/**
* Fetches generic assay data for multiple molecular profiles and sample IDs.
* Filters by a list of stable IDs and allows specifying a projection type.
*
* @param molecularProfileIds a list of molecular profile IDs
* @param sampleIds a list of sample IDs
* @param genericAssayStableIds a list of stable IDs for the generic assays
* @param projection the projection type
* @return a list of generic assay data
* @throws MolecularProfileNotFoundException if any of the molecular profiles are not found
*/
List<GenericAssayData> fetchGenericAssayData(
List<String> molecularProfileIds,
List<String> sampleIds,
List<String> genericAssayStableIds,
String projection
) throws MolecularProfileNotFoundException;
}
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