Mercurial > repos > bernhardlutz > rest_tool
changeset 1:954a489c1606 draft
Deleted selected files
| author | bernhardlutz |
|---|---|
| date | Mon, 24 Mar 2014 13:59:57 -0400 |
| parents | a9793e52a3ef |
| children | d3f9c70919dc |
| files | rest_tool.py rest_tool.xml test-data/bsp_graph.gml~ tool_dependencies.xml |
| diffstat | 4 files changed, 0 insertions(+), 128 deletions(-) [+] |
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--- a/rest_tool.py Sun Mar 23 09:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -#!/usr/bin/env python -# Aufruf convert_graph.py --type type --id id --outformat format - -import sys, os -import networkx as nx -import argparse -import json - -from xgmml_networkx import XGMMLParserHelper, XGMMLWriter -from networkx.readwrite import json_graph - -#supported graph_types -output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"] - -def main(args): - -if __name__ == "__main__": - - parser = argparse.ArgumentParser() - parser.add_argument('--type', type=str, - help="That you want BioAssay Compund ...") - parser.add_argument('--id', type=str, - help="Specify the format of the input graph") - parser.add_argument('--outformat', type=str, - help="Specify the format of the output", choices = output_types) - if len(sys.argv) < 6: - print "Too few arguments..." - parser.print_help() - exit(1) - args = parser.parse_args() - main( args )
--- a/rest_tool.xml Sun Mar 23 09:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -<tool id="rest_tool" name="Fetch Data from pubchem" version="0.1.0"> - <description>Fetch pubchem data</description> - <version_command>echo "0.1.0"</version_command> - <requirements> - <requirement type="set_environment">REST_TOOL_SCRIPT_PATH</requirement> - </requirements> - <command> - python \$GRAPHCONVERTER_SCRIPT_PATH/rest_tool.py --id $id --type $input_type --outformat $output_format - </command> - - <inputs> - <param format="txt" name="id" type="text" label="Specify the ID" /> - <param name="input_type" multiple="false" type="select" label="Input Type"> - <option value="bioassay">BioAssay</option> - <option value="compound">Compound</option> - </param> - <param name="output_format" type="select" label="Output Format"> - <option value="tsv">tsv</option> - <option value="csv">csv</option> - <option value="txt">txt</option> - <option value="png">png</option> - <option value="json">json</option> - </param> - </inputs> - <outputs> - <data format="csv" name="output"> - <change_format> - <when input="output_format" value="tsv" format="tsv" /> - <when input="output_format" value="png" format="png" /> - <when input="output_format" value="csv" format="csv" /> - <when input="output_format" value="txt" format="txt" /> - <when input="output_format" value="json" format="json" /> - </change_format> - </data> - </outputs> - <tests> - </tests> - <help> -**What it does** - -This tool fetches data from pubchem - </help> -</tool>
--- a/test-data/bsp_graph.gml~ Sun Mar 23 09:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ - Creator "yFiles" - Version 2.2 - graph - [ hierarchic 1 - directed 1 - node - [ id 0 - graphics - [ x 200.0 - y 0.0 - ] - LabelGraphics - [ text "January" ] - ] - node - [ id 1 - graphics - [ x 425.0 - y 75.0 - ] - LabelGraphics - [ text "December" ] - ] - edge - [ source 1 - target 0 - graphics - [ Line - [ point - [ x 425.0 - y 75.0 - ] - point - [ x 425.0 - y 0.0 - ] - point - [ x 200.0 - y 0.0 - ] - ] - ] - LabelGraphics - [ text "Happy New Year!" - model "six_pos" - position "head" - ] - ] - ]
--- a/tool_dependencies.xml Sun Mar 23 09:27:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -<tool_dependency> - <set_environment version="1.0"> - <environment_variable name="REST_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> -</tool_dependency>