Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.py @ 95:6d122fd54cd0 draft

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author fubar
date Fri, 20 Nov 2020 06:38:14 +0000
parents 7176af503cdd
children d54976fc996a
comparison
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94:e8f35fec0f2f 95:6d122fd54cd0
18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml 18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
19 # No support for automatic HTML file creation from arbitrary outputs 19 # No support for automatic HTML file creation from arbitrary outputs
20 # essential problem is to create two command lines - one for the tool xml and a different 20 # essential problem is to create two command lines - one for the tool xml and a different
21 # one to run the executable with the supplied test data and settings 21 # one to run the executable with the supplied test data and settings
22 # Be simpler to write the tool, then run it with planemo and soak up the test outputs. 22 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
23 23 # well well. sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
24 # does the needful. Use GALAXY_TEST_SAVE /foo to save outputs - only the tar.gz - not the rest sadly
25 # GALAXY_TEST_NO_CLEANUP GALAXY_TEST_TMP_DIR=wherever
24 26
25 import argparse 27 import argparse
26 import datetime 28 import datetime
27 import json 29 import json
28 import logging 30 import logging
896 else: 898 else:
897 tout = open(self.tlog, "w") 899 tout = open(self.tlog, "w")
898 if genoutputs: 900 if genoutputs:
899 dummy, tfile = tempfile.mkstemp() 901 dummy, tfile = tempfile.mkstemp()
900 cll = [ 902 cll = [
903 ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
901 "planemo", 904 "planemo",
902 "test", 905 "test",
903 "--test_data", os.path.abspath(self.testdir), 906 "--test_data", os.path.abspath(self.testdir),
904 "--test_output", os.path.abspath(tool_test_path), 907 "--test_output", os.path.abspath(tool_test_path),
905 "--skip_venv", 908 "--skip_venv",
916 stdout=dummy, 919 stdout=dummy,
917 ) 920 )
918 921
919 else: 922 else:
920 cll = [ 923 cll = [
924 ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
921 "planemo", 925 "planemo",
922 "test", 926 "test",
923 "--test_data", os.path.abspath(self.testdir), 927 "--test_data", os.path.abspath(self.testdir),
924 "--test_output", os.path.abspath(tool_test_path), 928 "--test_output", os.path.abspath(tool_test_path),
925 "--skip_venv", 929 "--skip_venv",