| Previous changeset 18:612a2f94522f (2019-06-11) Next changeset 20:f3a219de2d1b (2019-06-13) |
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Commit message:
planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty |
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modified:
rpviz.xml |
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added:
outfile.html rpVisualizer.xml toolRPViz.py |
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| diff -r 612a2f94522f -r dbc40b306014 outfile.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/outfile.html Thu Jun 13 08:56:51 2019 -0400 |
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| b'@@ -0,0 +1,139 @@\n+<!DOCTYPE doctype html>\n+<html>\n+ <head>\n+ <meta charset="utf-8"/>\n+ <title>\n+ Viewer\n+ </title>\n+ <script id="elements">\n+ 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": "[H]Oc1c([H])c([H])c([H])c([H])c1O[H]", "image": "<svg version=\'1.1\' baseProfile=\'full\'\\n xmlns=\'http://www.w3.org/2000/svg\'\\n xmlns:rdkit=\'http://www.rdkit.org/xml\'\\n xmlns:xlink=\'http://www.w3.org/1999/xlink\'\\n xml:space=\'preserve\'\\nwidth=\'200px\' height=\'200px\' >\\n<!-- END OF HEADER -->\\n<rect style=\'opacity:1.0;fill:#FFFFFF;stroke:none\' width=\'200\' height=\'200\' x=\'0\' y=\'0\'> </rect>\\n<path class=\'bond-0\' d=\'M 140.376,147.373 123.965,137.899\' style=\'fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-0\' d=\'M 123.965,137.899 107.555,128.424\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-1\' d=\'M 107.555,128.424 58.3228,156.848\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-1\' d=\'M 94.4851,122.841 60.0228,142.738\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-7\' d=\'M 107.555,128.424 107.555,71.576\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-7\' d=\'M 96.1851,119.897 96.1851,80.1032\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-2\' d=\'M 58.3228,156.848 9.09091,128.424\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-2\' d=\'M 56.6228,142.738 22.1605,122.841\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-3\' d=\'M 9.09091,128.424 9.09091,71.576\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-3\' d=\'M 20.4605,119.897 20.4605,80.1032\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-4\' d=\'M 9.09091,71.576 58.3228,43.1519\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-4\' d=\'M 22.1605,77.1587 56.6228,57.2619\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'b'..b'", "target": "CMPD_0000000049__64__MNXC3"}}, {"data": {"source": "<Reaction RP3>", "target": "CMPD_0000000029__64__MNXC3"}}, {"data": {"source": "<Reaction RP2>", "target": "CMPD_0000000012__64__MNXC3"}}, {"data": {"source": "<Reaction RP1>", "target": "CMPD_0000000003__64__MNXC3"}}, {"data": {"source": "<Reaction RP0>", "target": "TARGET_0000000001__64__MNXC3"}}, {"data": {"source": "MNXM164__64__MNXC3", "target": "<Reaction RP4>"}}, {"data": {"source": "MNXM6__64__MNXC3", "target": "<Reaction RP4>"}}, {"data": {"source": "CMPD_0000000049__64__MNXC3", "target": "<Reaction RP3>"}}, {"data": {"source": "MNXM4__64__MNXC3", "target": "<Reaction RP3>"}}, {"data": {"source": "MNXM4__64__MNXC3", "target": "<Reaction RP0>"}}, {"data": {"source": "CMPD_0000000029__64__MNXC3", "target": "<Reaction RP2>"}}, {"data": {"source": "MNXM2__64__MNXC3", "target": "<Reaction RP2>"}}, {"data": {"source": "CMPD_0000000012__64__MNXC3", "target": "<Reaction RP1>"}}, {"data": {"source": "CMPD_0000000003__64__MNXC3", "target": "<Reaction RP0>"}}, {"data": {"source": "TARGET_0000000001__64__MNXC3", "target": "<Reaction targetSink>"}}]}}\n+ </script>\n+ <script id="svg">\n+ </script>\n+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js">\n+ </script>\n+ <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.0/cytoscape.min.js">\n+ </script>\n+ <script>\n+ function displaynet(network){\n+ var cy = cytoscape({\n+ container: $(\'#cy\'),\n+\n+ elements:network\n+ ,\n+\n+ layout: {\n+ name: \'breadthfirst\',\n+ roots: "node[root = \'root\']"\n+ },\n+\n+ style: [\n+ {\n+ selector: "node",\n+ style: {\n+ "background-color": \'#80D0D0\',\n+ "label": "data(name)",\n+ "font-size": "7px"\n+ }\n+ },\n+ {selector: "node[category=\'reactions\']",\n+ style: {\n+ \'background-color\': \'#FA8072\',\n+ \'shape\': \'roundrectangle\'\n+ }},\n+ {selector: "node[category=\'reactant\']",\n+ style: {\n+ \'background-color\': \'#52be80\',\n+ }},\n+ {\n+ selector: \'edge\',\n+ style: {\n+ \'curve-style\': \'bezier\',\n+ \'width\': \'3px\',\n+ \'target-arrow-shape\': \'triangle\',\n+ }\n+ }]\n+ });\n+\n+ cy.on(\'mouseover\',\'node\',function(e){\n+ var node_select=e.target;\n+ molecule=node_select.data("image");\n+ if(molecule){\n+ $("#molecule").append(molecule)};\n+ });\n+\n+ cy.on(\'mouseout\',\'node\',function(e){\n+ $("#molecule").empty();\n+ });\n+\n+ cy.on(\'tap\',\'node\',function(e){\n+ var node_select=e.target;\n+ console.log(node_select.data("name"));\n+ link=node_select.data("link");\n+ if(link){\n+ window.open(link)\n+ };\n+ });\n+ };\n+\n+ $(function() {\n+ $("#selectbox").change(function(){\n+ value=$("#selectbox :selected").val();\n+ displaynet(obj[value]);\n+ });\n+ });\n+ </script>\n+ </head>\n+ <style>\n+ #cy {\n+ width: 80%;\n+ height: 100%;\n+ position: absolute;\n+ left : 20%;\n+ }\n+\n+.interact{\n+ position:relative;\n+ width: 19%;\n+ height:100%;\n+}\n+#molecule{\n+ position : absolute;\n+ top : 80px;\n+}\n+ </style>\n+ <body>\n+ <div id="cy">\n+ </div>\n+ <div class="interact" id="interaction">\n+ <div id="molecule">\n+ </div>\n+ <form>\n+ Choose a pathway :\n+ <select id="selectbox">\n+ <option value="select">\n+ Select a pathway\n+ </option>\n+ <option value="rp_2">\n+ rp_2\n+ </option>\n+ <option value="rp_3">\n+ rp_3\n+ </option>\n+ <option value="rp_4">\n+ rp_4\n+ </option>\n+ <option value="rp_63">\n+ rp_63\n+ </option>\n+ <option value="rp_64">\n+ rp_64\n+ </option>\n+ <option value="rp_65">\n+ rp_65\n+ </option>\n+ </select>\n+ </form>\n+ </div>\n+ </body>\n+</html>\n' |
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| diff -r 612a2f94522f -r dbc40b306014 rpVisualizer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpVisualizer.xml Thu Jun 13 08:56:51 2019 -0400 |
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| @@ -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> |
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| diff -r 612a2f94522f -r dbc40b306014 rpviz.xml --- a/rpviz.xml Tue Jun 11 12:09:38 2019 -0400 +++ b/rpviz.xml Thu Jun 13 08:56:51 2019 -0400 |
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| @@ -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> |
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| diff -r 612a2f94522f -r dbc40b306014 toolRPViz.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolRPViz.py Thu Jun 13 08:56:51 2019 -0400 |
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| @@ -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 ) |