Merge pull request #207 from bimberlabinternal/25.11_fb_repseqio

Remove repseqio dependency

Author: bbimber

tcrdb/build.gradle

@@ -5,36 +5,12 @@ repositories {
    mavenCentral()
 }
 
-configurations.all {
-    resolutionStrategy {
-        // Related to: https://nvd.nist.gov/vuln/detail/CVE-2025-12183
-        force "at.yawk.lz4:lz4-java:${lz4Version}"
-    }
-}
-
 dependencies {
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:singlecell", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "assay"), depProjectConfig: "apiJarFile")
-   BuildUtils.addExternalDependency(
-           project,
-           new ExternalDependency(
-                   "io.repseq:repseqio:${repseqVersion}",
-                   "repseqio",
-                   "repseqio",
-                   "https://github.com/repseqio/repseqio",
-                   ExternalDependency.APACHE_2_LICENSE_NAME,
-                   ExternalDependency.APACHE_2_LICENSE_URL,
-                   "TCR Analysis"
-           ),
-           {
-              // exclude logback to prevent excessive logging
-              exclude group: "ch.qos.logback", module :"logback-classic"
-              exclude group: "ch.qos.logback", module :"logback-core"
-           }
-   )
    implementation "com.github.samtools:htsjdk:${htsjdkVersion}"
    implementation "net.sf.opencsv:opencsv:${opencsvVersion}"
 

tcrdb/gradle.properties

@@ -1,3 +0,0 @@
-repseqVersion=1.7.0
-# Related to: https://nvd.nist.gov/vuln/detail/CVE-2025-12183
-lz4Version=1.9.0

tcrdb/resources/assay/TCRdb/queries/Data.query.xml

@@ -142,9 +142,6 @@
                         <item text="View Alignments">
                             <onClick>TCRdb.window.ExportDataWindow.viewAlignmentHandler(dataRegionName, arguments[0] ? arguments[0].ownerCt : null);</onClick>
                         </item>
-                        <item text="Download Clone Materials">
-                            <onClick>TCRdb.window.DownloadCloneWindow.buttonHandler(dataRegionName);</onClick>
-                        </item>
                         <item text="Download Clone Sequence">
                             <onClick>TCRdb.window.DownloadCloneWindow.downloadSequenceHandler(dataRegionName);</onClick>
                         </item>

tcrdb/resources/web/tcrdb/window/DownloadCloneWindow.js

@@ -2,10 +2,6 @@ Ext4.define('TCRdb.window.DownloadCloneWindow', {
     extend: 'Ext.window.Window',
 
     statics: {
-        buttonHandler: function(dataRegionName) {
-            TCRdb.window.DownloadCloneWindow.showWindow(dataRegionName, 'downloadCloneMaterials', 'The goal of this is to download a ZIP with any extracted clone/read data for the selected sample(s), along with the reference sequence for the segments used.  These files can be imported into Geneious or a similar program to de novo assemble to construct the FL clone.  Note: per sample, it will export all reads overlapping any TCR segments.  This at minimum will tend to include both chains (i.e. 2 different CDR3s), and might include reads that either match a defunct TCR or other noise.');
-        },
-
         downloadSequenceHandler: function(dataRegionName){
             TCRdb.window.DownloadCloneWindow.showWindow(dataRegionName, 'downloadSequence', 'This will download the full sequence (if available) for the selected rows, along with the reference segments.');
         },