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@Copilot Copilot AI commented Oct 1, 2025

Problem

It's currently possible to create a study with a cancer_study_identifier (stableId) that includes special characters like "+". These characters can cause URL encoding issues when the study ID is used in URLs, leading to broken links and navigation problems.

Solution

This PR adds Jakarta Bean Validation annotations to restrict study identifiers to only alphanumeric characters, underscores, and hyphens ([a-zA-Z0-9_-]).

Changes

  1. Added @Pattern validation to CancerStudy.java (legacy model)

    • Enforces the character restriction at the data model level
    • Applies to all code paths using this model
  2. Added @Pattern validation to CancerStudyMetadata.java (application file model)

    • Ensures validation applies to file-based imports via metaImport.py
    • Consistent validation across different import methods
  3. Added comprehensive unit tests

    • Tests for valid identifiers (alphanumeric, underscores, hyphens, mixed)
    • Tests for invalid identifiers (plus signs, spaces, special characters, percent encoding, null)
    • Total: 17 test methods across 2 test classes

Example

// Valid study identifiers
"study_es_0""brca_tcga_2012""study-123""Study_ABC-001"// Invalid study identifiers (will now fail validation)
"study+es+0"      ✗ (plus signs)
"study es 0"      ✗ (spaces)
"study@test"      ✗ (special characters)
"study%20"        ✗ (percent encoding)

When validation fails, a clear error message is returned:

Cancer study identifier can only contain alphanumeric characters, underscores, and hyphens

Backward Compatibility

  • All existing test data uses valid study identifiers
  • No breaking changes to existing valid study IDs
  • Only prevents future creation of studies with problematic characters

Testing

Unit tests verify that:

  • Valid identifiers pass validation
  • Invalid identifiers (including those with "+") fail validation
  • Appropriate error messages are returned

Fixes #[issue-number]

Warning

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    • Triggering command: /usr/lib/jvm/temurin-17-jdk-amd64/bin/java --enable-native-access=ALL-UNNAMED -classpath /usr/share/apache-maven-3.9.11/boot/plexus-classworlds-2.9.0.jar -Dclassworlds.conf=/usr/share/apache-maven-3.9.11/bin/m2.conf -Dmaven.home=/usr/share/apache-maven-3.9.11 -Dlibrary.jansi.path=/usr/share/apache-maven-3.9.11/lib/jansi-native -Dmaven.multiModuleProjectDirectory=/home/REDACTED/work/cbioportal/cbioportal org.codehaus.plexus.classworlds.launcher.Launcher spotless:apply -DskipTests (dns block)

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Original prompt

This section details on the original issue you should resolve

<issue_title>[BUG] Limit allowed characters for studyId in metaImport.py</issue_title>
<issue_description>It's currently possible to create a study with a stableId that includes a "+". These types of characters can mess with the URL, so we should make the validator limit the studyId characters to something like [a-zA-Z0-9_]. The validator is a python script called by metaImport.py
</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes #11727

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Copilot AI and others added 2 commits October 1, 2025 13:46
…o alphanumeric, underscore, and hyphen

Co-authored-by: inodb <1334004+inodb@users.noreply.github.com>
Co-authored-by: inodb <1334004+inodb@users.noreply.github.com>
@Copilot Copilot AI changed the title [WIP] [BUG] Limit allowed characters for studyId in metaImport.py Add validation to restrict study identifiers to alphanumeric characters, underscores, and hyphens Oct 1, 2025
@Copilot Copilot AI requested a review from inodb October 1, 2025 13:51
Copilot finished work on behalf of inodb October 1, 2025 13:51
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[BUG] Limit allowed characters for studyId in metaImport.py

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