From d4aed6584f870682e2a45dab0a65bbe50e0d7906 Mon Sep 17 00:00:00 2001 From: Susan Hert Date: Mon, 18 Apr 2022 17:12:21 -0700 Subject: [PATCH 1/3] Update maven repositories in preparation for Artifactory configuration change (#105) --- primeseq/build.gradle | 8 ++++++++ tcrdb/build.gradle | 8 ++++++++ variantdb/build.gradle | 8 ++++++++ 3 files changed, 24 insertions(+) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 0d7767f20..1a8b44122 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -1,5 +1,13 @@ import org.labkey.gradle.util.BuildUtils; +repositories { + mavenCentral() + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + maven { + url "https://clojars.org/repo" + } +} + dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" implementation "net.sf.opencsv:opencsv:${opencsvVersion}" diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index de1b8d419..44b61bd11 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -1,5 +1,13 @@ import org.labkey.gradle.util.BuildUtils; +repositories { + mavenCentral() + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + maven { + url "https://clojars.org/repo" + } +} + 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") diff --git a/variantdb/build.gradle b/variantdb/build.gradle index 3752d3158..d260381fe 100644 --- a/variantdb/build.gradle +++ b/variantdb/build.gradle @@ -1,5 +1,13 @@ import org.labkey.gradle.util.BuildUtils; +repositories { + mavenCentral() + // Added for org.clojars.chapmanb:sam dependency required by com.github.samtools:htsjdk + maven { + url "https://clojars.org/repo" + } +} + dependencies { implementation "com.github.samtools:htsjdk:${htsjdkVersion}" external "commons-net:commons-net:${commonsNetVersion}" From 076931831be55c0c41ef2cfd18cd269db85c92c2 Mon Sep 17 00:00:00 2001 From: Susan Hert Date: Mon, 23 May 2022 09:11:57 -0700 Subject: [PATCH 2/3] Add scijava repository back to pick up clojars dependency (#115) --- primeseq/build.gradle | 4 ++++ tcrdb/build.gradle | 4 ++++ variantdb/build.gradle | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/primeseq/build.gradle b/primeseq/build.gradle index 1a8b44122..94625804e 100644 --- a/primeseq/build.gradle +++ b/primeseq/build.gradle @@ -6,6 +6,10 @@ repositories { maven { url "https://clojars.org/repo" } + // Added for org.clojars.chapmanb:sam (required by SequenceAnalysis) + maven { + url "https://maven.scijava.org/content/groups/public" + } } dependencies { diff --git a/tcrdb/build.gradle b/tcrdb/build.gradle index 44b61bd11..37cf85b99 100644 --- a/tcrdb/build.gradle +++ b/tcrdb/build.gradle @@ -6,6 +6,10 @@ repositories { maven { url "https://clojars.org/repo" } + // Added for org.clojars.chapmanb:sam (required by SequenceAnalysis) + maven { + url "https://maven.scijava.org/content/groups/public" + } } dependencies { diff --git a/variantdb/build.gradle b/variantdb/build.gradle index d260381fe..71217928c 100644 --- a/variantdb/build.gradle +++ b/variantdb/build.gradle @@ -6,6 +6,10 @@ repositories { maven { url "https://clojars.org/repo" } + // Added for org.clojars.chapmanb:sam (required by SequenceAnalysis) + maven { + url "https://maven.scijava.org/content/groups/public" + } } dependencies { From 8d032fd4a72b7a611063ef6137dbd0c7937ba1d9 Mon Sep 17 00:00:00 2001 From: Ian Sigmon Date: Fri, 22 Jul 2022 12:44:17 -0700 Subject: [PATCH 3/3] Update artifactory URL for 21.11 (#128) --- mcc/.npmrc | 2 +- mcc/package-lock.json | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/mcc/.npmrc b/mcc/.npmrc index b478682b9..2f03279e8 100644 --- a/mcc/.npmrc +++ b/mcc/.npmrc @@ -1 +1 @@ -@labkey:registry=https://artifactory.labkey.com/artifactory/api/npm/libs-client +@labkey:registry=https://labkey.jfrog.io/artifactory/api/npm/libs-client diff --git a/mcc/package-lock.json b/mcc/package-lock.json index c482a1779..8ea9067b5 100644 --- a/mcc/package-lock.json +++ b/mcc/package-lock.json @@ -2500,13 +2500,13 @@ }, "node_modules/@labkey/api": { "version": "1.6.6", - "resolved": "https://artifactory.labkey.com/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.6.6.tgz", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.6.6.tgz", "integrity": "sha1-zRznNQwtNmBOxnijAhf/fRDWQic=", "license": "Apache-2.0" }, "node_modules/@labkey/build": { "version": "3.1.0", - "resolved": "https://artifactory.labkey.com/artifactory/api/npm/libs-client/@labkey/build/-/@labkey/build-3.1.0.tgz", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/build/-/@labkey/build-3.1.0.tgz", "integrity": "sha1-UqOkQe73d2a5ZsxtlMmYNSxG1GA=", "dev": true, "license": "Apache-2.0", @@ -17786,12 +17786,12 @@ }, "@labkey/api": { "version": "1.6.6", - "resolved": "https://artifactory.labkey.com/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.6.6.tgz", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.6.6.tgz", "integrity": "sha1-zRznNQwtNmBOxnijAhf/fRDWQic=" }, "@labkey/build": { "version": "3.1.0", - "resolved": "https://artifactory.labkey.com/artifactory/api/npm/libs-client/@labkey/build/-/@labkey/build-3.1.0.tgz", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/build/-/@labkey/build-3.1.0.tgz", "integrity": "sha1-UqOkQe73d2a5ZsxtlMmYNSxG1GA=", "dev": true, "requires": {