Merge branch 'master' of github.com:InformaticsMatters/pipelines

Author: tdudgeon

Dockerfile-sdloader

@@ -1,7 +1,7 @@
 FROM busybox
 MAINTAINER Tim Dudgeon <[email protected]>
 
-# An image to populate a Service Descriptor desitination directory
+# An image to populate a Service Descriptor destination directory
 # (SD_DST), which is normally mounted when the image is run,
 # with built-in Service Descriptor files from a source directory (SD_SRC).
 

Dockerfile-sdposter

@@ -0,0 +1,17 @@
+FROM centos
+MAINTAINER Tim Dudgeon <[email protected]>
+
+# An image to populate the Core with the contents of the
+# Service Descriptors located in SD_SRC.
+
+ENV SD_SRC /sd-src
+WORKDIR ${SD_SRC}
+
+# Copy all potential Service Descriptors into the image...
+COPY src/python/ ${SD_SRC}/src/python/
+COPY src/nextflow/ ${SD_SRC}/src/nextflow/
+COPY post-service-descriptors.sh ${SD_SRC}/
+RUN chmod 755 post-service-descriptors.sh
+
+# On execution copy files from source to destination...
+CMD ./post-service-descriptors.sh

build.gradle

@@ -92,10 +92,19 @@ task buildSdLoaderDockerImage(type: DockerBuildImage) {
     tag = "informaticsmatters/rdkit_${pipeline}-sdloader:latest"
 }
 
+task buildSdPosterDockerImage(type: DockerBuildImage) {
+    description 'Builds the pipelines SD-poster Docker image'
+
+    dockerFile = file('Dockerfile-sdposter')
+    inputDir = file('.')
+    tag = "informaticsmatters/rdkit_${pipeline}-sdposter:latest"
+}
+
 task buildDockerImages() {
     dependsOn buildPliImage // that one depends on buildPipelinesImage
     dependsOn buildSmogImage // and so does this one
     dependsOn buildSdLoaderDockerImage
+    dependsOn buildSdPosterDockerImage
 
     group 'Docker'
     description 'Builds all the project Docker images'

post-service-descriptors.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+set -e
+
+POST=${1:-http://coreservices:8080/coreservices/rest/v1/services}
+BASE_D='docker://github.com/InformaticsMatters/pipelines'
+BASE_N='nextflow://github.com/InformaticsMatters/pipelines'
+CT_DJ="application/x-squonk-service-descriptor-docker+json"
+CT_MM="multipart/mixed"
+
+
+for d in 'src/python/pipelines/dmpk' 'src/python/pipelines/docking' 'src/python/pipelines/rdkit'
+do
+    for file in $d/*.dsd.json
+    do
+	    echo $file
+	    curl -X POST \
+         -T $file\
+         -H "Content-Type: $CT_DJ"\
+         -H "Base-URL: $BASE_D"\
+         $POST
+         echo ""
+    done
+done
+
+for d in 'src/nextflow/docking' 'src/nextflow/rdkit'
+do
+    for file in $d/*.nsd.yml
+    do
+	    basename=${file::-4}
+	    echo $basename
+	    curl -X POST \
+         -F "nextflow.nsd.yml=@${basename}.yml;type=application/x-squonk-service-descriptor-nextflow+yaml;filename=nextflow.nsd.yml"\
+         -F "nextflow.nf=@${basename}.nf;type=text/plain;filename=nextflow.nf"\
+         -F "nextflow.config=@${basename}.config;type=text/plain;filename=nextflow.config"\
+         -H "Content-Type: $CT_MM"\
+         -H "Base-URL: $BASE_N"\
+         $POST
+         echo ""
+    done
+done