Use_of_temporary_filVOTable00 VOTable with metadata for generation of configurartion and report files 2013-04-22 16:27:06.830 UTC <?xml version='1.0'?> <VOTABLE version="1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.ivoa.net/xml/VOTable/v1.1 http://www.ivoa.net/xml/VOTable/v1.1" xmlns="http://www.ivoa.net/xml/VOTable/v1.1"> <RESOURCE> <TABLE> <FIELD arraysize="12" datatype="char" name="col1"/> <FIELD arraysize="16" datatype="char" name="col2"/> <FIELD arraysize="6" datatype="char" name="col3"/> <FIELD arraysize="3" datatype="char" name="col4"/> <FIELD arraysize="3" datatype="char" name="col5"/> <FIELD arraysize="3" datatype="char" name="col6"/> <FIELD arraysize="3" datatype="char" name="col7"/> <FIELD arraysize="4" datatype="char" name="col8"/> <FIELD arraysize="4" datatype="char" name="col9"/> <DATA> <TABLEDATA> <TR> <TD>/tmp/report1</TD> <TD>/tmp/configfile1</TD> <TD>5</TD> <TD>30</TD> <TD>60</TD> <TD>80</TD> <TD>3</TD> <TD>9</TD> <TD>25</TD> </TR> <TR> <TD>/tmp/report2</TD> <TD>/tmp/configfile2</TD> <TD>4</TD> <TD>45</TD> <TD>90</TD> <TD>60</TD> <TD>4</TD> <TD>8</TD> <TD>36</TD> </TR> <TR> <TD>/tmp/report3</TD> <TD>/tmp/configfile3</TD> <TD>5</TD> <TD>65</TD> <TD>48</TD> <TD>90</TD> <TD>5</TD> <TD>9</TD> <TD>18</TD> </TR> </TABLEDATA> </DATA> </TABLE> </RESOURCE> </VOTABLE> 2013-04-22 16:26:44.217 UTC TemplateConfig00 #CONFIGURATION FILE FOR SCRIPT RANDOM $col3$ SIN $col4$ COS $col5$ LOG $col6$ EXP $col7$ FACT $col8$ SQRT $col9$ # --- # END OF CONFIG 2013-04-15 12:26:48.69 UTC Template for a Configuration File 2013-04-22 16:14:57.572 UTC TemplateReport00 THIS IS A REPORT FOR EXECUTION OF CONFIG FILE: $col1$ #-- END OF REPORT 2013-04-22 16:31:51.140 UTC Template for a Report File 2013-04-22 16:14:27.196 UTC ReportFilesNamesResultContentFill_template_to_CreateConfigFilestemplate0ColumnNameWithResultFileName0voTable0list11org.purl.wf4ever.astrotavernastilts-activity1.07org.purl.wf4ever.astrotaverna.voutils.TemplateFillerActivity String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeColFileConfigvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity col2 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeToolinFile0outFiles00net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local_2_2 <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 28c3ddc7-7a10-454a-bae4-c8fb4cb25f63 python script.py %%inFile%% 1200 1800 inFile script.py true false false MacRoman false import sys import random import math dico = {} result = {} inFile = sys.argv[1] f = open(inFile, 'r') for line in f.readlines(): if line[0] !="#" and line!="\n": key, val = line.split() dico[key] = float(val) f.close() result['RANDOM'] = random.randint(1, int(dico['RANDOM'])) result['SIN'] = math.sin(dico['SIN']) result['COS'] = math.cos(dico['COS']) result['LOG'] = math.log10(dico['LOG']) result['EXP'] = math.exp(dico['EXP']) result['FACT'] = math.factorial(dico['FACT']) result['SQRT'] = math.sqrt(dico['SQRT']) up = result['RANDOM']*((result['LOG']/(result['SIN']+result['COS']))+result['EXP']) down = result['FACT'] - result['SQRT'] result['TOTAL'] = up/down f = open('outFiles', 'w') rowline = str(result['RANDOM'])+"\t" rowline += str(result['SIN'])+"\t" rowline += str(result['COS'])+"\t" rowline += str(result['LOG'])+"\t" rowline += str(result['EXP'])+"\t" rowline += str(result['FACT'])+"\t" rowline += str(result['SQRT'])+"\t" rowline += str(result['TOTAL'])+"\t" f.write(rowline) f.close() inFile inFile false false false MacRoman false false false outFiles outFiles false false true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeColReportFilevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity col1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFill_template_to_CreateReportFilestemplate0ColumnNameWithResultFileName0voTable0list11org.purl.wf4ever.astrotavernastilts-activity1.07org.purl.wf4ever.astrotaverna.voutils.TemplateFillerActivity String net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFill_template_to_CreateConfigFilestemplateTemplateConfigFill_template_to_CreateConfigFilesColumnNameWithResultFileNameColFileConfigvalueFill_template_to_CreateConfigFilesvoTableVOTableToolinFileFill_template_to_CreateConfigFileslistFill_template_to_CreateReportFilestemplateTemplateReportFill_template_to_CreateReportFilesColumnNameWithResultFileNameColReportFilevalueFill_template_to_CreateReportFilesvoTableVOTableReportFilesNamesFill_template_to_CreateReportFileslistResultContentTooloutFiles 03c07a77-f60b-4c11-8b69-50082216a9a3 2013-04-15 12:27:03.5 UTC 30daf1b6-3b07-4b84-8c5a-e861b0934eb5 2013-04-22 16:29:48.537 UTC 19ed3def-66c4-4d4b-9f8c-313ee679b091 2013-04-15 11:34:56.552 UTC 8d494339-2d17-46b4-a657-74152ba6be18 2013-04-15 11:49:10.762 UTC 89e4828f-a661-450b-85a1-642fc22dbd75 2013-04-15 16:57:19.361 UTC 38ba26d6-0cf4-4655-945d-a57a24d5da42 2013-04-15 11:48:25.603 UTC f05fad92-055a-447e-aef0-f538131b2854 2013-04-22 16:23:37.578 UTC ffa3f6df-a9bd-4dcf-8a5f-c877b4f6c62f 2013-04-15 11:28:47.397 UTC 0faa6340-2b83-4087-8dfa-a5b1e153d225 2012-08-16 11:58:09.420 UTC 9d2d0ce0-7cf9-4781-995d-2621b12a0d95 2013-04-15 12:21:18.614 UTC 9c373f46-d9f4-4098-bcf5-eaac15d73421 2013-04-15 10:56:48.441 UTC 5d32909d-6f37-4c04-8485-4ab961fca9d0 2013-04-22 16:36:38.308 UTC 2be74928-599a-4d59-b04e-f3b7b7e93b90 2013-04-15 08:46:03.996 UTC 767ecde7-6e73-4e5d-8798-c63d7c7ef396 2013-04-12 20:01:17.444 UTC 99486b68-62da-4cf3-a83e-089a04a799d0 2013-04-15 10:50:19.916 UTC afd64ca8-4b3a-4998-899c-2bebbf361827 2013-04-15 11:36:06.140 UTC bca7850f-d317-4deb-9cde-22fa28e8f0ac 2012-08-16 11:52:29.26 UTC db1dcfa3-f18c-49e6-a284-891acfe7c27f 2013-04-22 16:27:37.922 UTC dbc6e726-4018-4178-ad38-956ce7122990 2013-04-15 11:01:01.696 UTC Snippet showing how to use AstroTaverna tool "Fill template from VOTable" for creating temporary files filling a template provided by the user. The input is two templates a one VOTable with information on where to store files created from filling the templates. The VOTable also contains data values to fill the templates. This snippet is particularly useful when a local tool needs different configuration files when looping through different executions. 2013-04-22 16:37:12.227 UTC 70105c02-ecad-4158-b08a-0cd3df1682bb 2013-04-15 08:43:19.471 UTC 2eadcd2d-8b84-497c-8ca3-726e9fb490c2 2013-04-12 20:02:25.193 UTC Use of temporary files to execute local tool and/or create report of execution 2013-04-22 16:33:19.891 UTC Jose Enrique Ruiz 2013-04-22 16:13:33.715 UTC f3a91e6b-3934-4b6a-ae3f-74a7f065cfda 2013-04-15 11:33:03.980 UTC efa18218-36fd-448b-9e96-fb77a690736f 2013-04-15 13:41:22.500 UTC b11c6580-6063-453e-bd39-5442ba1d3bb8 2013-04-15 11:38:06.631 UTC 6ebd39f1-fd00-4040-bd94-ef86982811c7 2013-04-15 12:46:19.144 UTC 323a22ad-57eb-43b8-850c-1b400dc9f785 2013-04-12 20:00:39.350 UTC 567b51a5-d1bc-45d0-bef7-a5b80836b6c2 2013-04-15 13:45:17.400 UTC 123c936a-f89a-4bfd-b634-ae80d8e57994 2013-04-15 12:44:11.969 UTC 43f4a0ef-0168-41fc-b70a-d94c10d4a0b8 2013-04-15 11:31:03.722 UTC 0fd9c3a1-86c4-45a4-9355-458fe847ad6a 2013-04-15 11:50:55.978 UTC e8abfaf7-160f-4e88-a9cf-51bec4684356 2013-04-15 10:46:13.911 UTC a32a7b66-40f0-45db-8fd4-5629302282ef 2013-04-15 11:52:36.650 UTC cdf07584-e74c-4ff2-8094-61fdc1f65082 2013-04-22 16:31:52.939 UTC 6bdba170-2559-4c2d-9424-f86d90783c50 2013-04-15 11:43:57.598 UTC f04ff834-3317-465c-add8-a71d0ab5c394 2013-04-15 12:45:22.179 UTC 14aea4a5-0d74-4b0c-865f-fe52aa97f64f 2013-04-22 16:37:12.440 UTC 7508a095-a672-4e87-a71d-8ef8de71dcfd 2012-08-16 11:47:59.417 UTC 912f3f8b-df57-414b-b856-a2951769ca2b 2013-04-22 16:18:46.14 UTC 3a88eda6-ea9f-4017-857e-bbcef0b7ef14 2013-04-22 16:20:30.750 UTC 6f2bbc19-6d63-4714-8122-d044cc36d165 2013-04-15 08:51:23.264 UTC e2e111e2-8869-4220-818d-560db886fe4e 2013-04-15 11:27:24.974 UTC