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Remove repseqio dependency #207

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Merged
bbimber merged 1 commit into from
Dec 12, 2025
Merged

Remove repseqio dependency #207

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24 changes: 0 additions & 24 deletions tcrdb/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -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}"

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3 changes: 0 additions & 3 deletions tcrdb/gradle.properties
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@@ -1,3 +0,0 @@
repseqVersion=1.7.0
# Related to: https://nvd.nist.gov/vuln/detail/CVE-2025-12183
lz4Version=1.9.0
3 changes: 0 additions & 3 deletions tcrdb/resources/assay/TCRdb/queries/Data.query.xml
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Expand Up @@ -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>
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4 changes: 0 additions & 4 deletions tcrdb/resources/web/tcrdb/window/DownloadCloneWindow.js
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Expand Up @@ -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.');
},
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