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changeset 19:dbc40b306014 draft

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planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty
author pablocarb
date Thu, 13 Jun 2019 08:56:51 -0400
parents 612a2f94522f
children f3a219de2d1b
files outfile.html rpVisualizer.xml rpviz.xml toolRPViz.py
diffstat 4 files changed, 220 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/outfile.html	Thu Jun 13 08:56:51 2019 -0400
@@ -0,0 +1,139 @@
+<!DOCTYPE doctype html>
+<html>
+ <head>
+  <meta charset="utf-8"/>
+  <title>
+   Viewer
+  </title>
+  <script id="elements">
+   var obj ={"rp_2": {"nodes": [{"data": {"category": "reactions", "id": "<Reaction RP1>", "value": "<Reaction RP1>", "name": "<Reaction RP1>"}}, {"data": {"category": "reactions", "id": "<Reaction RP0>", "value": "<Reaction RP0>", "name": "<Reaction RP0>"}}, {"data": {"category": "reactions", "id": "<Reaction targetSink>", "value": "<Reaction targetSink>", "name": "<Reaction targetSink>"}}, {"data": {"category": "reactant", "name": "anthranilate", "link": "http://identifiers.org/metanetx.chemical/MNXM188", "root": "root", "id": "MNXM188__64__MNXC3", "value": "MNXM188__64__MNXC3"}}, {"data": {"category": "reactant", "name": "O2", "link": "http://identifiers.org/metanetx.chemical/MNXM4", "root": "root", "id": "MNXM4__64__MNXC3", "value": "MNXM4__64__MNXC3"}}, {"data": {"category": "reactant", "name": "NADPH", "link": "http://identifiers.org/metanetx.chemical/MNXM6", "root": "root", "id": "MNXM6__64__MNXC3", "value": "MNXM6__64__MNXC3"}}, {"data": {"category": "product", "smiles": 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+
+      cy.on('tap','node',function(e){
+        var node_select=e.target;
+        console.log(node_select.data("name"));
+        link=node_select.data("link");
+        if(link){
+          window.open(link)
+        };
+      });
+      };
+
+    $(function() {
+      $("#selectbox").change(function(){
+        value=$("#selectbox :selected").val();
+        displaynet(obj[value]);
+      });
+    });
+  </script>
+ </head>
+ <style>
+  #cy {
+        width: 80%;
+        height: 100%;
+        position: absolute;
+        left : 20%;
+    }
+
+.interact{
+  position:relative;
+  width: 19%;
+  height:100%;
+}
+#molecule{
+  position : absolute;
+  top : 80px;
+}
+ </style>
+ <body>
+  <div id="cy">
+  </div>
+  <div class="interact" id="interaction">
+   <div id="molecule">
+   </div>
+   <form>
+    Choose a pathway :
+    <select id="selectbox">
+     <option value="select">
+      Select a pathway
+     </option>
+     <option value="rp_2">
+      rp_2
+     </option>
+     <option value="rp_3">
+      rp_3
+     </option>
+     <option value="rp_4">
+      rp_4
+     </option>
+     <option value="rp_63">
+      rp_63
+     </option>
+     <option value="rp_64">
+      rp_64
+     </option>
+     <option value="rp_65">
+      rp_65
+     </option>
+    </select>
+   </form>
+  </div>
+ </body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpVisualizer.xml	Thu Jun 13 08:56:51 2019 -0400
@@ -0,0 +1,25 @@
+<tool id="rpviz" name="rpVisualizer" version="0.1.0" python_template_version="3.5">
+    <description>Pathway visualizer</description>
+    <requirements>
+        <requirement type="package">python-libsbml</requirement>
+        <requirement type="package">networkx</requirement>
+        <requirement type="package">beautifulsoup4</requirement>
+        <requirement type="package">rdkit</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+     git clone https://github.com/pablocarb/rpviz.git $__tool_directory__/rpviz;
+     cd $__tool_directory__/rpviz; git pull; cd ..;
+     cd $__tool_directory__;
+     echo `which python` > $__tool_directory__/info.log;
+     PYTHONPATH="$__tool_directory__" python $__tool_directory__/toolVisualizer.py $input1 $output1
+   ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="xml" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="html" from_work_dir="out.html" />
+    </outputs>
+    <help><![CDATA[
+        python3 toolVisualizer.py inputfile outputfile
+    ]]></help>
+</tool>
--- a/rpviz.xml	Tue Jun 11 12:09:38 2019 -0400
+++ b/rpviz.xml	Thu Jun 13 08:56:51 2019 -0400
@@ -1,25 +1,19 @@
-<tool id="rpviz" name="rpVisualizer" version="0.1.0" python_template_version="3.5">
+<tool id="rpviz" name="rpviz" version="0.1.0" python_template_version="3.5">
     <description>Pathway visualizer</description>
     <requirements>
-        <requirement type="package">python-libsbml</requirement>
-        <requirement type="package">networkx</requirement>
-        <requirement type="package">beautifulsoup4</requirement>
-        <requirement type="package">rdkit</requirement>
+        <requirement type="package">requests</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-     git clone https://github.com/pablocarb/rpviz.git $__tool_directory__/rpviz;
-     cd $__tool_directory__/rpviz; git pull; cd ..;
-     cd $__tool_directory__;
-     echo `which python` > $__tool_directory__/info.log;
-     PYTHONPATH="$__tool_directory__" python $__tool_directory__/toolVisualizer.py $input1 $output1
+     python $__tool_directory__/toolRPViz.py $input1 $output1 -server $server
    ]]></command>
     <inputs>
         <param type="data" name="input1" format="xml" />
+    	<param name="server" type="text" label="RPViz RES server" value="http://rpviz.synbiochem.co.uk/REST" help="RPviz REST server" />
     </inputs>
     <outputs>
         <data name="output1" format="html" from_work_dir="out.html" />
     </outputs>
     <help><![CDATA[
-        python3 toolVisualizer.py inputfile outputfile
+        python3 toolRPViz.py [server SERVER] inputfile outputfile
     ]]></help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolRPViz.py	Thu Jun 13 08:56:51 2019 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mar 19
+
+@author: Pablo Carbonell
+@description: Query RPViz: pathway visualizer.
+
+"""
+import requests
+import argparse
+import csv
+import os
+import json
+
+def arguments():
+    parser = argparse.ArgumentParser(description='toolRPViz: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019')
+    parser.add_argument('infile', 
+                        help='Pathways in SBML format.')
+    parser.add_argument('outfile', 
+                        help='HTML visualizer file.')
+    parser.add_argument('-server', default='http://rpviz.synbiochem.co.uk/REST',
+                        help='RPViz server.')
+    return parser
+
+def testApp(url):
+    r = requests.get( url )
+    res = json.loads( r.content.decode('utf-8') )
+    print( res )
+    
+def pathwayUpload(infile, outfile, url):
+    files = { 'file': open(infile, 'rb' ) }
+    r = requests.post( os.path.join(url, 'Query' ), files=files )
+    res = json.loads( r.content.decode('utf-8') )
+    html = res['data']['html']
+    with open(outfile, 'w') as h:
+        h.write(html)
+    print( 'Success!')
+
+def testHTML(f='outfile.html', outfile):
+    content = open(f).read()
+    with open(outfile, 'w') as h:
+        outfile.write(content)
+
+
+if __name__ == "__main__":
+    parser = arguments()
+    arg = parser.parse_args()
+    assert os.path.exists(arg.infile)
+    testHTML( 'outfile.html', arg.outfile )
+#    pathwayUpload( arg.infile, arg.outfile, arg.server )