Mercurial > repos > fubar > tool_factory_2
changeset 111:223b78754735 draft
Uploaded
| author | fubar |
|---|---|
| date | Sun, 29 Nov 2020 07:51:53 +0000 |
| parents | ab2474035f81 |
| children | 5509dc4c1cf2 |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| diffstat | 2 files changed, 26 insertions(+), 23 deletions(-) [+] |
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--- a/toolfactory/rgToolFactory2.py Sun Nov 29 06:16:34 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Nov 29 07:51:53 2020 +0000 @@ -63,8 +63,8 @@ <exit_code range="100:" level="debug" description="shite happens" /> </stdio>""" -# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label -# ~~~$input_help" +# --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats\ +#~~~$intab.input_label~~~$intab.input_help" IPATHPOS = 0 ICLPOS = 1 IFMTPOS = 2 @@ -263,7 +263,7 @@ clsuffix.append(appendme) xclsuffix.append(xappendme) for i, p in enumerate(self.outfiles): - if p[OOCLPOS] == "STDOUT": + if p[OCLPOS] == "STDOUT": self.lastclredirect = [">", p[ONAMEPOS]] self.lastxclredirect = [">", "$%s" % p[OCLPOS]] else: @@ -296,7 +296,7 @@ tscript.write(self.script) tscript.close() self.escapedScript = [cheetah_escape(x) for x in rx] - self.spacedScript = [f" {x}" for x in self.escapedScript] + self.spacedScript = [f" {x}" for x in rx] art = "%s.%s" % (self.tool_name, self.executeme) artifact = open(art, "wb") artifact.write(bytes('\n'.join(self.escapedScript),'utf8')) @@ -305,21 +305,23 @@ def cleanuppar(self): """ positional parameters are complicated by their numeric ordinal""" for i, p in enumerate(self.infiles): + infp = copy.copy(p) if self.args.parampass == "positional": - assert p[ + assert infp[ ICLPOS ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % ( - p[ICLPOS], - p[ILABPOS], + infp[ICLPOS], + infp[ILABPOS], ) - p.append(p[ICLPOS]) - if p[ICLPOS].isdigit() or self.args.parampass == "0": + icl = infp[ICLPOS] + infp.append(icl) + if infp[ICLPOS].isdigit() or self.args.parampass == "0": scl = "input%d" % (i + 1) - p[ICLPOS] = scl - self.infiles[i] = p + infp[ICLPOS] = scl + self.infiles[i] = infp for i, p in enumerate( self.outfiles - ): # trying to automagically gather using extensions + ): if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT": assert p[ OCLPOS @@ -327,7 +329,7 @@ p[OCLPOS], p[ONAMEPOS], ) - p.append(p[OCLPOS]) + p.append(p[OCLPOS]) # keep copy if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": scl = p[ONAMEPOS] p[OCLPOS] = scl @@ -412,19 +414,19 @@ def doXMLparam(self): """flake8 made me do this...""" - for p in self.outfiles: + for p in self.outfiles: # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" newname, newfmt, newcl, test, oldcl = p test = test.strip() ndash = self.getNdash(newcl) - aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) + aparm = gxtp.OutputData(name=newname, format=newfmt, num_dashes=ndash, label=newcl) aparm.positional = self.is_positional if self.is_positional: if oldcl == "STDOUT": aparm.positional = 9999999 - aparm.command_line_override = "> $%s" % newcl + aparm.command_line_override = "> $%s" % newname else: aparm.positional = int(oldcl) - aparm.command_line_override = "$%s" % newcl + aparm.command_line_override = "$%s" % newname self.toutputs.append(aparm) ld = None if test.strip() > "": @@ -582,7 +584,7 @@ + [">300 lines - stuff deleted", "......"] + scr[-100:] ) - scr.append('\n------\n') + scr.append('\n') safertext = safertext + "\n".join(scr) self.newtool.help = safertext else: @@ -843,6 +845,7 @@ category_ids=catID, ) tid = res.get("id", None) + sto.write(f"#####create_repository {self.args.tool_name} tid={tid} res={res}\n") else: i = rnames.index(self.tool_name) tid = rids[i] @@ -850,10 +853,10 @@ res = ts.repositories.update_repository( id=tid, tar_ball_path=self.newtarpath, commit_message=None ) - sto.write(f"#####update res={res}\n") + sto.write(f"#####update res id {id} ={res}\n") except ConnectionError: sto.write( - "Probably no change to repository - bioblend shed upload failed\n" + "Is the toolshed running and the API key correct? Bioblend shed upload failed\n" ) sto.close()
--- a/toolfactory/rgToolFactory2.xml Sun Nov 29 06:16:34 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Sun Nov 29 07:51:53 2020 +0000 @@ -69,15 +69,15 @@ </repeat> <repeat name="history_outputs" title="Add a tool run output file to the user's history from your tool - Use the '+' button to add as many as needed" 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=""/> + <param name="history_name" type="text" label="Name for this output to appear in new history" optional="false" help="Argparse will also use this name as --[name]"/> <param name="history_format" type="select" multiple="false" label="Select the datatype for this output" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml" value="tabular"> <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> <column name="value" index="0"/> </options> </param> - <param name="history_CL" type="text" label="Positional: ordinal integer. Argparse: argument name expected for this output parameter. Use STDOUT if '>' required." - help="If positional parameters, enter the integer ordinal expected for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""/> + <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="sim_size:0.01"/> </repeat>