Mercurial > repos > bernhardlutz > rest_tool
changeset 0:a9793e52a3ef draft
Uploaded
| author | bernhardlutz |
|---|---|
| date | Sun, 23 Mar 2014 09:27:27 -0400 |
| parents | |
| children | 954a489c1606 |
| files | rest_tool.py rest_tool.xml test-data/bsp_graph.gml~ tool_dependencies.xml |
| diffstat | 4 files changed, 128 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rest_tool.py Sun Mar 23 09:27:27 2014 -0400 @@ -0,0 +1,31 @@ +#!/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 )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rest_tool.xml Sun Mar 23 09:27:27 2014 -0400 @@ -0,0 +1,43 @@ +<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 $output_format + </command> + + <inputs> + <param format="txt" name="id" type="text" label="Specify the ID" /> + <param name="input_type" multiple="false" type="select" label="Input Type"> + <option value="bioassay">BioAssay</option> + <option value="compound">Compound</option> + </param> + <param name="output_format" type="select" label="Output Format"> + <option value="tsv">tsv</option> + <option value="csv">csv</option> + <option value="txt">txt</option> + <option value="png">png</option> + <option value="json">json</option> + </param> + </inputs> + <outputs> + <data format="csv" name="output"> + <change_format> + <when input="output_format" value="tsv" format="tsv" /> + <when input="output_format" value="png" format="png" /> + <when input="output_format" value="csv" format="csv" /> + <when input="output_format" value="txt" format="txt" /> + <when input="output_format" value="json" format="json" /> + </change_format> + </data> + </outputs> + <tests> + </tests> + <help> +**What it does** + +This tool fetches data from pubchem + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bsp_graph.gml~ Sun Mar 23 09:27:27 2014 -0400 @@ -0,0 +1,49 @@ + Creator "yFiles" + Version 2.2 + graph + [ hierarchic 1 + directed 1 + node + [ id 0 + graphics + [ x 200.0 + y 0.0 + ] + LabelGraphics + [ text "January" ] + ] + node + [ id 1 + graphics + [ x 425.0 + y 75.0 + ] + LabelGraphics + [ text "December" ] + ] + edge + [ source 1 + target 0 + graphics + [ Line + [ point + [ x 425.0 + y 75.0 + ] + point + [ x 425.0 + y 0.0 + ] + point + [ x 200.0 + y 0.0 + ] + ] + ] + LabelGraphics + [ text "Happy New Year!" + model "six_pos" + position "head" + ] + ] + ]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Mar 23 09:27:27 2014 -0400 @@ -0,0 +1,5 @@ +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="REST_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency>