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Merged
amattu2 merged 15 commits into from
Apr 3, 2026
Merged

3.3.0 Release #163

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5b7c1e2
Added new datasets property to dataset details
JoonLeeNIH Mar 12, 2026
e1ee0e4
Merge pull request #159 from CBIIT/INS-1561
JoonLeeNIH Mar 12, 2026
23f56a2
Fixes jackson vulnerability by copying C3DC
JoonLeeNIH Mar 13, 2026
dc5356c
Removed unused dependency
JoonLeeNIH Mar 13, 2026
ceabb0b
Merge pull request #160 from CBIIT/vuln-fix
JoonLeeNIH Mar 13, 2026
652bf18
Replaced dataset_source_id with dataset_uuid for dataset details and …
JoonLeeNIH Mar 19, 2026
af59c37
dataset_uuid no longer filtered by .search
JoonLeeNIH Mar 19, 2026
eff4a2e
Merge pull request #161 from CBIIT/INS-1581
amattu2 Mar 19, 2026
63acdea
Attempt at fixing jackson vulnerability
JoonLeeNIH Mar 23, 2026
65d693d
Updated Tomcat base image, which has Java 17.0.18, which fixes Java v…
JoonLeeNIH Mar 23, 2026
d15c3e0
Updated Tomcat version in POM
JoonLeeNIH Mar 23, 2026
d9166d6
Updated log4j dependencies to fix vulnerabilities
JoonLeeNIH Mar 23, 2026
af1b92c
Updated Spring dependencies to fix vulnerabilities
JoonLeeNIH Mar 23, 2026
2915e44
Trying not to upgrade Spring Framework to a new major version
JoonLeeNIH Mar 23, 2026
15d483b
Merge pull request #162 from CBIIT/INS-1584
amattu2 Mar 23, 2026
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ COPY . .
RUN mvn package -DskipTests

# Production stage
FROM tomcat:11.0.13-jdk17 AS fnl_base_image
FROM tomcat:11.0.20-jdk17 AS fnl_base_image

RUN apt-get update && apt-get -y upgrade

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24 changes: 11 additions & 13 deletions pom.xml
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Expand Up @@ -24,7 +24,7 @@
<properties>
<java.version>17</java.version>
<!-- Override Spring Framework version globally for Boot -->
<spring-framework.version>6.2.11</spring-framework.version>
<spring-framework.version>6.2.17</spring-framework.version>

<spring.restdocs.version>3.0.3</spring.restdocs.version>
<snakeyaml.version>2.3</snakeyaml.version>
Expand All @@ -33,6 +33,13 @@

<dependencyManagement>
<dependencies>
<dependency>
<groupId>com.fasterxml.jackson</groupId>
<artifactId>jackson-bom</artifactId>
<version>2.18.6</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-codec</artifactId>
Expand All @@ -46,12 +53,12 @@
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>2.24.3</version>
<version>2.25.3</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>2.24.3</version>
<version>2.25.3</version>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
Expand Down Expand Up @@ -189,7 +196,7 @@
<dependency>
<groupId>org.apache.tomcat.embed</groupId>
<artifactId>tomcat-embed-core</artifactId>
<version>11.0.13</version>
<version>11.0.20</version>
</dependency>
<!-- JUnit -->
<dependency>
Expand Down Expand Up @@ -217,11 +224,6 @@
<version>1.5.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
<version>2.15.2</version>
</dependency>
<!-- Neo4j Graphql -->
<dependency>
<groupId>org.neo4j</groupId>
Expand Down Expand Up @@ -314,10 +316,6 @@
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
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26 changes: 15 additions & 11 deletions src/main/java/gov/nih/nci/bento_ri/model/PrivateESDataFetcher.java
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Expand Up @@ -751,18 +751,20 @@ private Integer numberOfPublications() throws Exception {
/**
* Gets the details for a single Dataset record
*
* @param dataset_source_id The ID of the Dataset
* @param params The filters applied
* @return A map of the Dataset record's properties
* @throws IOException
*/
private Map<String, Object> datasetDetails(Map<String, Object> params) throws IOException {
Map<String, Object> dataset;
String datasetId = (String) params.get("dataset_source_id");
String datasetId = (String) params.get("dataset_uuid");
List<Map<String, Object>> datasets;

final String[][] PROPERTIES = new String[][]{
new String[]{"dataset_uuid", "dataset_uuid"},
new String[]{"dataset_maximum_age_at_baseline", "dataset_maximum_age_at_baseline"},
new String[]{"dataset_minimum_age_at_baseline", "dataset_minimum_age_at_baseline"},
new String[]{"dataset_storage_distribution", "dataset_storage_distribution"},
new String[]{"dataset_title", "dataset_title"},
new String[]{"description", "description"},
new String[]{"experimental_approaches", "experimental_approaches"},
Expand Down Expand Up @@ -790,8 +792,10 @@ private Map<String, Object> datasetDetails(Map<String, Object> params) throws IO
};

Map<String, String> mapping = Map.ofEntries(
Map.entry("dataset_uuid", "dataset_uuid"),
Map.entry("dataset_maximum_age_at_baseline", "dataset_maximum_age_at_baseline"),
Map.entry("dataset_minimum_age_at_baseline", "dataset_minimum_age_at_baseline"),
Map.entry("dataset_storage_distribution", "dataset_storage_distribution"),
Map.entry("dataset_title", "dataset_title"),
Map.entry("description", "description"),
Map.entry("experimental_approaches", "experimental_approaches"),
Expand Down Expand Up @@ -819,14 +823,14 @@ private Map<String, Object> datasetDetails(Map<String, Object> params) throws IO
);

Map<String, Object> dataset_params = Map.ofEntries(
Map.entry("dataset_source_id", List.of(datasetId)),
Map.entry(ORDER_BY, "dataset_source_id"),
Map.entry("dataset_uuid", List.of(datasetId)),
Map.entry(ORDER_BY, "dataset_uuid"),
Map.entry(SORT_DIRECTION, "ASC"),
Map.entry(PAGE_SIZE, 1),
Map.entry(OFFSET, 0)
);

datasets = overview(DATASETS_END_POINT, dataset_params, PROPERTIES, "dataset_source_id", mapping, REGULAR_PARAMS, "nested_filters", "datasets");
datasets = overview(DATASETS_END_POINT, dataset_params, PROPERTIES, "dataset_uuid", mapping, REGULAR_PARAMS, "nested_filters", "datasets");

try {
dataset = datasets.get(0);
Expand All @@ -848,7 +852,7 @@ private List<Map<String, Object>> getDatasetFiles(Map<String, Object> params) th
List<Map<String, Object>> files;

final String[][] PROPERTIES = new String[][]{
new String[]{"dataset_source_id", "dataset_source_id"},
new String[]{"dataset_uuid", "dataset_uuid"},
new String[]{"file_url_repo_prefix", "file_url_repo_prefix"},
new String[]{"file_id", "file_id"},
new String[]{"file_name", "file_name"},
Expand All @@ -858,7 +862,7 @@ private List<Map<String, Object>> getDatasetFiles(Map<String, Object> params) th
};

Map<String, String> mapping = Map.ofEntries(
Map.entry("dataset_source_id", "dataset_source_id.sort"),
Map.entry("dataset_uuid", "dataset_uuid.sort"),
Map.entry("file_url_repo_prefix", "file_url_repo_prefix.sort"),
Map.entry("file_id", "file_id.sort"),
Map.entry("file_name", "file_name.sort"),
Expand All @@ -873,8 +877,8 @@ private List<Map<String, Object>> getDatasetFiles(Map<String, Object> params) th
// Rename 'accessTypes' to 'access_level'
queryParams.put("access_level.search", queryParams.remove("accessTypes"));

// Turn dataset_source_id into a list
queryParams.put("dataset_source_id.search", List.of(queryParams.remove("dataset_source_id")));
// Turn dataset_uuid into a list
queryParams.put("dataset_uuid", List.of(queryParams.remove("dataset_uuid")));

// Turn filters into lowercase
for (String key : queryParams.keySet()) {
Expand Down Expand Up @@ -917,7 +921,7 @@ private List<Map<String, Object>> getDatasetFiles(Map<String, Object> params) th
/**
* Gets the details for a single Program record
*
* @param programId The ID of the Program
* @param params The filters applied
* @return A map of the Program record's properties
* @throws IOException
*/
Expand Down Expand Up @@ -972,7 +976,7 @@ private Map<String, Object> programDetails(Map<String, Object> params) throws IO
/**
* Gets the details for a single Project record
*
* @param projectId The ID of the Project
* @param params The filters applied
* @return A map of the Project record's properties
* @throws IOException
*/
Expand Down
6 changes: 4 additions & 2 deletions src/main/resources/graphql/ins-private-es.graphql
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Expand Up @@ -161,8 +161,10 @@ type DatasetFile {
}

type DatasetDetails {
dataset_uuid: String
dataset_maximum_age_at_baseline: Int
dataset_minimum_age_at_baseline: Int
dataset_storage_distribution: String
dataset_title: String
description: String
experimental_approaches: String
Expand Down Expand Up @@ -387,8 +389,8 @@ type QueryType {
): [PublicationsOverview]

programInfo: [ProgramInfo]
datasetDetails(dataset_source_id: String): DatasetDetails
getDatasetFiles(dataset_source_id: String!, accessTypes: [String!]!): [DatasetFile]
datasetDetails(dataset_uuid: String!): DatasetDetails
getDatasetFiles(dataset_uuid: String!, accessTypes: [String!]!): [DatasetFile]
programDetails(program_id: String): ProgramDetails
projectDetails(project_id: String): ProjectDetails
subjectDetail(subject_id: String): SubjectDetail
Expand Down
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