From 3f793903373767c0b8b1ad654cf44074376d4f96 Mon Sep 17 00:00:00 2001
From: jmz-b <jaymuhz.bee@gmail.com>
Date: Fri, 3 Apr 2020 12:51:02 +0200
Subject: [PATCH] add upload_to_sse step

add a tool to upload edf metadata to the ASCLEPIOS SSE service and
execute it after extracting metadata
---
 README.md                                     |  8 +++++
 .../somnonetz-pipeline/bin/upload_to_sse      | 34 +++++++++++++++++++
 .../resources/upload_to_sse.xml               | 25 ++++++++++++++
 .../somnonetz-pipeline/somnonetz-pipeline.xml | 16 +++++++++
 4 files changed, 83 insertions(+)
 create mode 100755 resources/catalog/somnonetz-pipeline/bin/upload_to_sse
 create mode 100755 resources/catalog/somnonetz-pipeline/resources/upload_to_sse.xml

diff --git a/README.md b/README.md
index bcfdfc2..c37b066 100644
--- a/README.md
+++ b/README.md
@@ -4,10 +4,18 @@ xnat pipelines for use with snet-plugin
 
 # Prerequisites
 
+### extract_edf_header
+
 * python3
 * [edfrd](https://github.com/somnonetz/edfrd)
 * [pyxnat](https://github.com/pyxnat/pyxnat)
 
+### upload_to_sse
+
+* nodejs
+* [asclepios-sse-client](https://github.com/somnonetz/asclepios-sse-client)
+* [argparse](https://github.com/nodeca/argparse)
+
 # Usage
 
 see [Installing Pipelines in XNAT](https://wiki.xnat.org/documentation/xnat-administration/configuring-the-pipeline-engine/installing-pipelines-in-xnat) in the official xnat documentation for installation instructions
diff --git a/resources/catalog/somnonetz-pipeline/bin/upload_to_sse b/resources/catalog/somnonetz-pipeline/bin/upload_to_sse
new file mode 100755
index 0000000..812b14a
--- /dev/null
+++ b/resources/catalog/somnonetz-pipeline/bin/upload_to_sse
@@ -0,0 +1,34 @@
+#!/usr/bin/env node
+'use strict'
+
+const { uploadData } = require('asclepios-sse-client');
+const { ArgumentParser } = require('argparse');
+const { execFile } = require('child_process');
+let parser = new ArgumentParser({});
+
+parser.addArgument('-xnatID', { required: true});
+parser.addArgument('-host', { required: true });
+parser.addArgument('-user', { required: true });
+parser.addArgument('-pwd', { required: true });
+
+const { xnatID, host, user, pwd } = parser.parseArgs();
+const XnatDataClient = '/data/xnat/pipeline/xnat-tools/XnatDataClient'
+const args = ['-u', user, '-p', pwd, '-r', `${host}/REST/experiments/${xnatID}/scans/psg?format=json`];
+
+const { SSE_URL, SSE_KEY_G, SSE_KENC, TA_URL, SALT_VALUE, IV_VALUE } = process.env;
+
+if (!(SSE_URL && SSE_KEY_G && SSE_KENC && TA_URL && SALT_VALUE && IV_VALUE)) {
+    throw 'One or more of the following environment variables are on set: ' +
+        'SSE_URL, SSE_KEY_G, SSE_KENC, TA_URL, SALT_VALUE, IV_VALUE';
+}
+
+execFile(XnatDataClient, args, function callback(error, stdout, stderr) {
+    if (error) {
+        console.error(stderr);
+        throw error;
+    }
+    const session = JSON.parse(stdout);
+    const data = session.items[0].data_fields;
+
+    uploadData(data, data.image_session_ID, SSE_KEY_G, SSE_KENC);
+});
\ No newline at end of file
diff --git a/resources/catalog/somnonetz-pipeline/resources/upload_to_sse.xml b/resources/catalog/somnonetz-pipeline/resources/upload_to_sse.xml
new file mode 100755
index 0000000..1c4ac7e
--- /dev/null
+++ b/resources/catalog/somnonetz-pipeline/resources/upload_to_sse.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pip:Resource xmlns:pip="http://nrg.wustl.edu/pipeline">
+	<pip:name>upload_to_sse</pip:name>
+	<pip:location>somnonetz-pipeline/bin</pip:location>
+	<pip:type>Executable</pip:type>
+	<pip:description>Upload EDF metadata to the ASCLEPIOS symmetric searchable encryption service</pip:description>
+	<pip:input>
+		<pip:argument id="xnatID">
+			<pip:name>xnatID</pip:name>
+			<pip:description>XNAT Session ID</pip:description>
+		</pip:argument>
+		<pip:argument id="host">
+			<pip:name>host</pip:name>
+			<pip:description>XNAT Host</pip:description>
+		</pip:argument>
+		<pip:argument id="user">
+			<pip:name>user</pip:name>
+			<pip:description>XNAT Username</pip:description>
+		</pip:argument>
+		<pip:argument id="pwd" isSensitive="true">
+			<pip:name>pwd</pip:name>
+			<pip:description>XNAT Password</pip:description>
+		</pip:argument>
+	</pip:input>
+</pip:Resource>
diff --git a/resources/catalog/somnonetz-pipeline/somnonetz-pipeline.xml b/resources/catalog/somnonetz-pipeline/somnonetz-pipeline.xml
index cea74cf..408d118 100755
--- a/resources/catalog/somnonetz-pipeline/somnonetz-pipeline.xml
+++ b/resources/catalog/somnonetz-pipeline/somnonetz-pipeline.xml
@@ -69,5 +69,21 @@
 				</argument>
 			</resource>
 		</step>
+		<step id="1" description="Upload EDF metadata to the ASCLEPIOS symmetric searchable encryption service" workdirectory="^/Pipeline/parameters/parameter[name='workdir']/values/unique/text()^">
+			<resource name="upload_to_sse.xml" location="somnonetz-pipeline/resources">
+				<argument id="xnatID">
+					<value>^/Pipeline/parameters/parameter[name='xnatID']/values/unique/text()^</value>
+				</argument>
+				<argument id="host">
+					<value>^if (count(/Pipeline/parameters/parameter[name='aliasHost']/values) > 0) then /Pipeline/parameters/parameter[name='aliasHost']/values/unique/text() else /Pipeline/parameters/parameter[name='host']/values/unique/text()^</value>
+				</argument>
+				<argument id="user">
+					<value>^/Pipeline/parameters/parameter[name='user']/values/unique/text()^</value>
+				</argument>
+				<argument id="pwd">
+					<value>^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^</value>
+				</argument>
+			</resource>
+		</step>
 	</steps>
 </Pipeline>