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add document for inter-repository dependencies (#10621)
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| # Inter-Repository Dependencies | ||
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| ## cbioportal-core Repository | ||
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| [cbioportal-core](https://github.com/cBioPortal/cbioportal-core) is dependent on | ||
| [cbioportal](https://github.com/cBioPortal/cbioportal). | ||
| This can be seen in its [pom.xml](https://github.com/cBioPortal/cbioportal-core/blob/main/pom.xml). | ||
| By removing the dependency and attempting to build cbioportal-core, errors are reported. This | ||
| document captures a summary of the reported errors. This analysis was done at the time of release | ||
| v6.0.0. | ||
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| cbioportal-core now primarily provides import functionality, which is mainly located | ||
| in the packages: | ||
| - [org.mskcc.cbio.portal.dao](https://github.com/cBioPortal/cbioportal-core/tree/main/src/main/java/org/mskcc/cbio/portal/dao) | ||
| - [org.mskcc.cbio.portal.model](https://github.com/cBioPortal/cbioportal-core/tree/main/src/main/java/org/mskcc/cbio/portal/model) | ||
| - [org.mskcc.cbio.portal.scripts](https://github.com/cBioPortal/cbioportal-core/tree/main/src/main/java/org/mskcc/cbio/portal/scripts) | ||
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| ### Dependencies in cbioportal-core import functionality | ||
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| Code in cbioportal which is referenced directly by code in cbioportal-core consists of three | ||
| enum class definitions. | ||
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| - cbioportal class [ResourceType](https://github.com/cBioPortal/cbioportal/blob/master/src/main/java/org/cbioportal/model/ResourceType.java) is imported by cbioportal-core class [ResourceDefinition](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/model/ResourceDefinition.java). This provides enum constants {STUDY, SAMPLE, PATIENT}. | ||
| - cbioportal class [EntityType](https://github.com/cBioPortal/cbioportal/blob/master/src/main/java/org/cbioportal/model/EntityType.java) is imported by cbioportal-core class [ImportTabDelimData](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java). This provides enum constants {GENE, GENESET, PHOSPHOPROTEIN, GENERIC_ASSAY}. | ||
| - cbioportal class [CNA](https://github.com/cBioPortal/cbioportal/blob/master/src/main/java/org/cbioportal/model/CNA.java) is imported by cbioportal-core class [CnaEvent](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/model/CnaEvent.java). This provides enum constants {AMP, GAIN, DIPLOID, HETLOSS, HOMDEL}. | ||
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| The cbioportal-core import functionality code also relies on several packaged libraries in cbioportal. | ||
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| cbioportal packaged library org.apache.commons.commons-collections4 (version 4.4) is used by these cbioportal-core classes: | ||
| - [DaoPatient](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/dao/DaoPatient.java) | ||
| - [ImportClinicalData](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/scripts/ImportClinicalData.java) | ||
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| cbioportal packaged library org.slf4j.slf4j-api (latest version) is used by these cbioportal-core classes: | ||
| - [JdbcUtil](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/dao/JdbcUtil.java) | ||
| - [ProgressMonitor](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/ProgressMonitor.java) | ||
| - [Patient](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/model/Patient.java) | ||
| - [AccessControlImpl](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/internal/AccessControlImpl.java) | ||
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| cbioportal packaged library org.springframework.security.spring-security.core (latest compatible version) | ||
| and other related such as org.springframework.security.spring-security.web are used in these cbioportal-core classes: | ||
| - [AccessControl](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/AccessControl.java) | ||
| - [DaoCancerStudy](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/dao/DaoCancerStudy.java) (transitive dependency through AccessControl) | ||
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| ### Other dependencies in cbioportal-core | ||
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| There are other (non-import) cbioportal-core uses of libraries packaged in cbioportal. | ||
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| cbioportal packaged libraries jakarta.servlet jakarta.servlet.http (ServletConfig, HttpServlet, ServletException, HttpServletRequest, HttpServletResponse} are used by these cbioportal-core classes: | ||
| - [GetSurvivalDataJSON](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/GetSurvivalDataJSON.java) | ||
| - [XDebug](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/XDebug.java) | ||
| - [CalcCoExp](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/CalcCoExp.java) | ||
| - [BioGeneServlet](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/BioGeneServlet.java) | ||
| - [IGVLinkingJSON](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/IGVLinkingJSON.java) | ||
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| cbioportal packaged library org.json.simple / com.googlecode.json-simple.json-simple (version 1.1.1) is used by these cbioportal-core classes: | ||
| - [CalcCoExp](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/CalcCoExp.java) | ||
| - [GetSurvivalDataJSON](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/GetSurvivalDataJSON.java) | ||
| - [IGVLinkingJSON](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/IGVLinkingJSON.java) | ||
| - [GetClinicalData](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/web_api/GetClinicalData.java) | ||
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| cbioportal packaged library org.apache.commonsorg.apache.commons.commons-math3 (version 3.6.1) is used by this cbioportal-core class: | ||
| - [CalcCoExp](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/servlet/CalcCoExp.java) | ||
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| cbioportal packaged library org.slf4j.slf4j-api (latest version) is used by this cbioportal-core class: | ||
| - [AccessControlImpl](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/internal/AccessControlImpl.java) (transitive dependency through many servlets) | ||
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| cbioportal packaged library org.springframework.security.spring-security.core (latest compatible version) | ||
| and other related such as org.springframework.security.spring-security.web are used in these cbioportal-core classes: | ||
| - [AccessControl](https://github.com/cBioPortal/cbioportal-core/blob/main/src/main/java/org/mskcc/cbio/portal/util/AccessControl.java) (transitive dependency through many servlets) | ||
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| ### Consequences | ||
| When any of these dependencies are updated in cbioportal (or in the case of libraries, updated in a non-backwards-compatible way), the cbioportal-core repository should be built and tested using the updated dependencies and proper behavior of the import functionality should be tested. cbioportal-core should also be brought up to date by packaging the current version of cbioportal into cbioportal-core (in pom.xml). |