Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-1948

Investigate AffxFusion jar - can we remove from project?

    Details

    • Type: Improvement
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:

      Description

      We would like to simplify the project and remove legacy maven repositories repo1, repo2, repo3 from 9.1.0 top-level parent POM and all child POMs.
      As per comments below, Prutha Kulkarni learned that this cannot safely be done without removing some dependencies provided by these legacy repositories.

      To test:

      • Ensure that all maven profiles can run
      • Check that default and clean lifecycles can run up to and including "install" phase

        Attachments

          Issue Links

            Activity

            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            [~aloraine], I have tried to build IGB project after removing these legacy maven repos from the POM.
            Build was failing for affymetrix common and was asking for missing dependency jlgfr. I commented it from the POM and it was built successfully.
            After that, it was failing for genometry module because com.affymetrix:fusion dependency. It is being used in the module and its not there in nexus.bioviz.org.
            Please let me know if there is any other repository location which can be referred in the POM?

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - [~aloraine] , I have tried to build IGB project after removing these legacy maven repos from the POM. Build was failing for affymetrix common and was asking for missing dependency jlgfr. I commented it from the POM and it was built successfully. After that, it was failing for genometry module because com.affymetrix:fusion dependency. It is being used in the module and its not there in nexus.bioviz.org. Please let me know if there is any other repository location which can be referred in the POM?
            Hide
            ann.loraine Ann Loraine added a comment -

            For the next steps, can you do this?

            • investigate "affymetrix fusion" - where is the source code? What packages/classes are being used, and where? We may be able to eliminate it. (If the source code is not available, we should write it out of the project.)
            • investigate: what is jlgfr ? Same as above.
            Show
            ann.loraine Ann Loraine added a comment - For the next steps, can you do this? investigate "affymetrix fusion" - where is the source code? What packages/classes are being used, and where? We may be able to eliminate it. (If the source code is not available, we should write it out of the project.) investigate: what is jlgfr ? Same as above.
            Hide
            ann.loraine Ann Loraine added a comment -

            Feel free to make these tasks two new Jira tickets - as you see fit.

            Show
            ann.loraine Ann Loraine added a comment - Feel free to make these tasks two new Jira tickets - as you see fit.
            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            affymetrix fusion -
            1) Its is being used in two files under genometry module.
            comaprator/QuantByIntIdComparator
            comparator/QuantDetectByIntIdComparator
            package used : affymetrix.calvin.data
            2)The source code is present at :
            https://github.com/HenrikBengtsson/Affx-Fusion-SDK/tree/master/affy/sdk/java/AffxFusion

            jlfgr-
            I am not able to locate the source code but it has something to do with the icons in IGB.
            Its a java look and feel Graphics repository dependency.
            Also, in the NOTICES.txt file it is mentioned that " IGB can be used with or without this jar file.".
            So, I am not sure if that is necessary.

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - affymetrix fusion - 1) Its is being used in two files under genometry module. comaprator/QuantByIntIdComparator comparator/QuantDetectByIntIdComparator package used : affymetrix.calvin.data 2)The source code is present at : https://github.com/HenrikBengtsson/Affx-Fusion-SDK/tree/master/affy/sdk/java/AffxFusion jlfgr- I am not able to locate the source code but it has something to do with the icons in IGB. Its a java look and feel Graphics repository dependency. Also, in the NOTICES.txt file it is mentioned that " IGB can be used with or without this jar file.". So, I am not sure if that is necessary.
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Changing scope of this ticket: please remove reference to AffxFusion jar on a topic branch named for this Jira ticket - IGBF-1948.

            We will remove the other dependencies as part of other Jira issues.

            Show
            ann.loraine Ann Loraine added a comment - - edited Changing scope of this ticket: please remove reference to AffxFusion jar on a topic branch named for this Jira ticket - IGBF-1948 . We will remove the other dependencies as part of other Jira issues.
            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            Prof. [~aloraine], I have removed AffxFusion dependency from everywhere except igb module.
            It used in the "ChpParser" file of the Parsers directory of igb module which is used in "getGenome" function of "QuickLoadSymLoaderChp" class. This getGenome function is used almost everywhere in IGB codebase. I am not sure if we can remove this dependency.

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - Prof. [~aloraine] , I have removed AffxFusion dependency from everywhere except igb module. It used in the "ChpParser" file of the Parsers directory of igb module which is used in "getGenome" function of "QuickLoadSymLoaderChp" class. This getGenome function is used almost everywhere in IGB codebase. I am not sure if we can remove this dependency.
            Hide
            ann.loraine Ann Loraine added a comment -

            Thanks Prutha Kulkarni!

            For the next step, can you do this?

            Add a new comment that all functions coming from the AffxFusion artifact that are used in IGB code base?

            Please list:

            • function name - name of function in AffxFusion
            • class name - class where the function is implemented
            • package - package (in AffxFusion) where the class resides

            When done, move this to Needs First Level Review.

            Show
            ann.loraine Ann Loraine added a comment - Thanks Prutha Kulkarni ! For the next step, can you do this? Add a new comment that all functions coming from the AffxFusion artifact that are used in IGB code base? Please list: function name - name of function in AffxFusion class name - class where the function is implemented package - package (in AffxFusion) where the class resides When done, move this to Needs First Level Review.
            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            package is common for all which is "affymetrix.fusion.chp"
            List of classes and function used is given below:
            1) class: FusionCHPData
            function name: getHeader, getExpressionResults
            2) class: FusionCHPDataReg
            function name: read
            3) class: FusionCHPGenericData
            function name: fromBase
            4) class: FusionCHPHeader
            function name: getAlgName, getAlgVersion, getAssayType, getChipType, getRows, getCols, getParentCellFile, getProgID, getNumProbeSets
            5) class: FusionCHPLegacyData
            function name: registerReader
            6) class: FusionCHPQuantificationData
            function name: registerReader
            7) class: FusionCHPQuantificationDetectionData
            function name: registerReader
            8) class: FusionCHPTilingData
            function name: registerReader
            9) class: FusionExpressionProbeSetResults
            function name: getDetectionPValue, getSignal, clear

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - package is common for all which is "affymetrix.fusion.chp" List of classes and function used is given below: 1) class: FusionCHPData function name: getHeader, getExpressionResults 2) class: FusionCHPDataReg function name: read 3) class: FusionCHPGenericData function name: fromBase 4) class: FusionCHPHeader function name: getAlgName, getAlgVersion, getAssayType, getChipType, getRows, getCols, getParentCellFile, getProgID, getNumProbeSets 5) class: FusionCHPLegacyData function name: registerReader 6) class: FusionCHPQuantificationData function name: registerReader 7) class: FusionCHPQuantificationDetectionData function name: registerReader 8) class: FusionCHPTilingData function name: registerReader 9) class: FusionExpressionProbeSetResults function name: getDetectionPValue, getSignal, clear
            Hide
            ann.loraine Ann Loraine added a comment -

            Use of affx jar is documented above. Moving to Closed.

            Show
            ann.loraine Ann Loraine added a comment - Use of affx jar is documented above. Moving to Closed.

              People

              • Assignee:
                prutha Prutha Kulkarni (Inactive)
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                2 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: