Mercurial > repos > fubar > tool_factory_2
changeset 149:ecd1d283b5a7 draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 20 Apr 2021 04:36:02 +0000 |
| parents | 470d3e309508 |
| children | 03b4e5d7ee02 |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| diffstat | 2 files changed, 35 insertions(+), 28 deletions(-) [+] |
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--- a/toolfactory/rgToolFactory2.py Sun Apr 18 08:30:25 2021 +0000 +++ b/toolfactory/rgToolFactory2.py Tue Apr 20 04:36:02 2021 +0000 @@ -1044,13 +1044,21 @@ supplied test outputs are sent to repdir for display """ penv = os.environ - # ourdir = os.getcwd() - # print('########## ourdir=',ourdir,'gr=',self.args.galaxy_root) - # pconfig = os.path.join(ourdir,'planemo', '.planemo.yml') - # penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig - # os.mkdir(os.path.join(ourdir,'planemo')) - # penv["HOME"] = os.path.join(ourdir,'home') - # os.mkdir(os.path.join(ourdir,'home')) + phome = penv['HOME'] + isDocker = os.path.exists('/.dockerenv') + if isDocker: # use the volume if it exists + phome = '/home/planemo' + if os.path.exists(phome): # is mounted + home = phome + else: + home = '/tmp/planemo' # this will be brutal but otherwise /home/galaxy + os.mkdir('/tmp/planemo') + penv["HOME"] = phome + path = penv['PATH'] + penv['PATH'] = '%s:%s' % (phome,path) + print(f"#### set home to {phome} with path={penv['PATH']}") + #pconfig = os.path.join(phome,'.planemo.yml') + #penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig # self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig) xreal = "%s.xml" % self.tool_name tool_test_path = os.path.join( @@ -1069,15 +1077,15 @@ os.path.abspath(self.testdir), "--test_output", os.path.abspath(tool_test_path), - "--galaxy_root", - self.args.galaxy_root, + ## "--galaxy_root", + ## self.args.galaxy_root, "--update_test_data", os.path.abspath(xreal), ] p = subprocess.run( cll, + env = penv, shell=False, - env=penv, cwd=self.tooloutdir, stderr=tout, stdout=tout, @@ -1115,7 +1123,6 @@ f.write(CONFIG_TEMPLATE % galaxyroot) - def main(): """ This is a Galaxy wrapper.
--- a/toolfactory/rgToolFactory2.xml Sun Apr 18 08:30:25 2021 +0000 +++ b/toolfactory/rgToolFactory2.xml Tue Apr 20 04:36:02 2021 +0000 @@ -64,8 +64,8 @@ </xml> <xml name="io"> <section name="io" title="Input and output files" expanded="true"> - <repeat name="history_inputs" title="zero or more input data files to pass on the command line to the executable." - help="USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool"> + <repeat name="history_inputs" title="Inputs" min="0" + help="Input data files to pass on the command line to the executable. USE SMALL SAMPLES for the new tool's test. Prompts will form a history item selector as input for users of this new tool"> <param name="input_files" type="data" format="data" label="Select an input file from your history" multiple="false" help=""/> <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" @@ -83,10 +83,10 @@ </param> <param name="input_repeat" type="boolean" checked="False" truevalue="1" falsevalue="0" label="Allow user to repeat this input as many times as wanted - script/executable must parse these."/> </repeat> - <repeat name="history_outputs" title="one or more new history items output by the executable to appear in the user history after the tool runs" - help="The name will become a history item for users of the new tool you are making containing one of it's outputs"> - <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" - help="No spaces! Argparse will also use this name as --[name]"> + <repeat name="history_outputs" min="1" title="Outputs" + help="New history items output by the executable to appear in the user history after the tool runs. The name will become a history item for users of the new tool you are making containing one of it's outputs"> + <param name="history_name" type="text" label="Output Name" optional="false" + help="Name used for this output in history. No spaces! Argparse will also use this name as --[name]"> <sanitizer invalid_char="_"> <valid initial="string.ascii_letters,string.digits" > <add value="_" /> @@ -99,15 +99,15 @@ <column name="value" index="0"/> </options> </param> - <param name="history_CL" type="text" label="Positional: ordinal integer. Use STDOUT if '>' required. Otherwise ignored if argparse because name is used" - help="If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> - <param name="history_test" type="text" label="Test pass decision criterion for this output compared to test generation" - help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> + <param name="history_CL" type="text" label="Position" + help="Positional: ordinal integer or 'STDOUT' if '>' required. Otherwise ignored if argparse because name is used. If positional parameters, enter the integer ordinal expected for this parameter. If argparse, ignore unless STDOUT needed" value=""/> + <param name="history_test" type="text" label="Output test criteria" + help="Pass/fail decision criterion for this output compared to test generation. Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="diff:0"/> </repeat> - <repeat name="collection_outputs" title="zero or more new history collections to appear in the user history after the tool runs" - help="Hides outputs not needed for downstream tools such as images and intermediate reports." default="0"> - <param name="name" type="text" label="Name for new collection with all outputs not individually passed to history outputs" - help="No spaces! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints"> + <repeat name="collection_outputs" title="Output Collections" min="0" + help="New history collections to appear in the user history after the tool runs. Hides outputs not needed for downstream tools such as images and intermediate reports." default="0"> + <param name="name" type="text" label="Name" + help="for new collection with all outputs not individually passed to history outputs. No spaces! Script MUST create and fill a directory with the same name and the tool test MUST be overwritten - see the plotter example for hints"> <sanitizer invalid_char="_"> <valid initial="string.ascii_letters,string.digits" > <add value="_" /> @@ -127,14 +127,14 @@ </section> </xml> <xml name="additparam"> - <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true"> + <section name="addparam" title="Arguments" help="Executable or script settings passed on the command line other than I/O files" expanded="true"> <param name="edit_params" type="select" display="radio" label="Make these settings on the generated tool form user editable?" help="If no, users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option> <option value="no">No - use the fixed values for all additional parameters - no user editing</option> </param> - <repeat name="additional_parameters" title="zero or more command line settings for the user to pass to the executable" - help="See examples below to see how these can be parsed by scripts in the various languages"> + <repeat name="additional_parameters" title="Command Line Paramters" min="0" + help="Command line settings for the user to pass to the executable. See examples below to see how these can be parsed by scripts in the various languages"> <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!"> <sanitizer invalid_char=""> <valid initial="string.ascii_letters,string.digits"/>