update tests and fixes for #27 and #1133

geneontology · Oct 24, 2019 · 0c1b8f8 · 0c1b8f8
1 parent 1ae45d4
commit 0c1b8f8
Showing 1 changed file with 31 additions and 31 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -360,34 +360,34 @@ pipeline {
 	    }
 	}
 	// Download GAFs from datasets yaml in go-site, and then upload to Skyhook
-	// stage("Download Data") {
-	//     steps {
-	// 	dir("./go-site") {
-	// 	    git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'
-	//
-	// 	    script {
-	// 		def excluded_datasets_args = ""
-	// 		if ( env.DATASET_EXCLUDES ) {
-	// 		    excluded_datasets_args = DATASET_EXCLUDES.split(" ").collect { "-x ${it}" }.join(" ")
-	// 		}
-	// 		def included_resources = ""
-	// 		if (env.RESOURCE_GROUPS) {
-	// 		    included_resources = RESOURCE_GROUPS.split(" ").collect { "-g ${it}" }.join(" ")
-	// 		}
-	// 		def goa_mapping_url = ""
-	// 		if (env.GOA_UNIPROT_ALL_URL) {
-	// 		    goa_mapping_url = "-m goa_uniprot_all gaf ${GOA_UNIPROT_ALL_URL}"
-	// 		}
-	// 		sh "python3 ./scripts/download_source_gafs.py all --datasets ./metadata/datasets --target ./target/ --type gaf ${excluded_datasets_args} ${included_resources} ${goa_mapping_url}"
-	// 	    }
-	//
-	// 	    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
-	// 		// upload to skyhook to the expected location
-	// 		sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" ./target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/annotations/'
-	// 	    }
-	// 	}
-	//     }
-	// }
+	stage("Download Data") {
+	    steps {
+		dir("./go-site") {
+		    git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'
+
+		    script {
+			def excluded_datasets_args = ""
+			if ( env.DATASET_EXCLUDES ) {
+			    excluded_datasets_args = DATASET_EXCLUDES.split(" ").collect { "-x ${it}" }.join(" ")
+			}
+			def included_resources = ""
+			if (env.RESOURCE_GROUPS) {
+			    included_resources = RESOURCE_GROUPS.split(" ").collect { "-g ${it}" }.join(" ")
+			}
+			def goa_mapping_url = ""
+			if (env.GOA_UNIPROT_ALL_URL) {
+			    goa_mapping_url = "-m goa_uniprot_all gaf ${GOA_UNIPROT_ALL_URL}"
+			}
+			sh "python3 ./scripts/download_source_gafs.py all --datasets ./metadata/datasets --target ./target/ --type gaf ${excluded_datasets_args} ${included_resources} ${goa_mapping_url}"
+		    }
+
+		    withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
+			// upload to skyhook to the expected location
+			sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" ./target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/annotations/'
+		    }
+		}
+	    }
+	}
 	// See https://github.com/geneontology/go-ontology for details
 	// on the ontology release pipeline. This ticket runs
 	// daily(TODO?) and creates all the files normally included in
@@ -508,12 +508,12 @@ pipeline {
 		    // to run at this point.
 		    sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/lib/* /opt/lib/'
 		    // Copy the sources we downloaded earlier to local.
-		    // sh "rsync -avz -e \"ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY\" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/annotations/*  /opt/go-site/sources/"
+		    sh "rsync -avz -e \"ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY\" skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/annotations/*  /opt/go-site/sources/"
 		}
 		sh "chmod +x /opt/bin/*"
 
-		//sh "python3 /opt/go-site/scripts/download_source_gafs.py organize --datasets /opt/go-site/metadata/datasets --source /opt/go-site/sources --target /opt/go-site/pipeline/target/groups/"
-		//sh "rm /opt/go-site/sources/*"
+		sh "python3 /opt/go-site/scripts/download_source_gafs.py organize --datasets /opt/go-site/metadata/datasets --source /opt/go-site/sources --target /opt/go-site/pipeline/target/groups/"
+		sh "rm /opt/go-site/sources/*"
 
 		// Make minimal GAF products.
 		// sh "cd /opt/go-site/pipeline"