Merge 79423d6 into 3c90a08

Jenkinsfile

@@ -0,0 +1,72 @@
+pipeline {
+    agent any
+    triggers {
+	// Every two days at 11 pm
+	cron('0 23 */2 * *')
+    }
+    options{
+	timestamps()
+    }
+    stages {
+	// Very first: pause for a minute to give a chance to
+	// cancel and clean the workspace before use.
+	stage('Ready and clean') {
+	    steps {
+		// Give us a minute to cancel if we want.
+		// sleep time: 1, unit: 'MINUTES'
+		cleanWs()
+	    }
+	}
+	stage('Initialize') {
+	    steps {
+		// Start preparing environment.
+		parallel(
+		    "Report": {
+			sh 'env > env.txt'
+			sh 'echo $BRANCH_NAME > branch.txt'
+			sh 'echo "$BRANCH_NAME"'
+			sh 'cat env.txt'
+			sh 'cat branch.txt'
+			sh 'echo $START_DAY > dow.txt'
+			sh 'echo "$START_DAY"'
+		    })
+	    }
+	}
+
+        stage('Build kg_covid_19') {
+            steps {
+                dir('./config') {
+                    git(
+                        url: 'https://github.com/Knowledge-Graph-Hub/kg-covid-19',
+                        branch: 'master'
+                    )
+		    sh '/usr/bin/python3.7 -m venv venv'
+		    sh '. venv/bin/activate'
+		    sh './venv/bin/pip install bmt'
+		    sh './venv/bin/pip install -r requirements.txt'
+		    sh './venv/bin/python setup.py install'
+                }
+            }
+        }
+        stage('Download') {
+            steps {
+                  sh 'cd config;. venv/bin/activate; python3.7 run.py download'
+            }
+        }
+        stage('Transform') {
+            steps {
+                  sh 'cd config;. venv/bin/activate; python3.7 run.py transform'
+            }
+        }
+        stage('Load') {
+            steps {
+		  sh 'cd config;. venv/bin/activate; python3.7 run.py load'
+            }
+        }
+        stage('Push to s3 bucket') {
+            steps {
+                echo "???? # Need some details for this item"
+            }
+	}
+    }
+}

download.yaml

@@ -74,7 +74,7 @@
 # SciBite CORD-19 annotations v1.2
 #
 -
-  url: https://github.com/SciBiteLabs/CORD19/raw/d2fb4998a504bcb06f5d0fd407f58feda2f140b1/annotated-CORD-19/1.2/CORD-19_1_2.zip
+  url: http://idg.berkeleybop.io/CORD-19_1_2.zip
   local_name: CORD-19_1_2.zip
 
 # SciBite CORD-19 entity co-occurrences v1.0

requirements.txt

@@ -1 +1 @@
-git+git://github.com/LucaCappelletti94/kgx.git
+git+git://github.com/NCATS-Tangerine/kgx.git