Mercurial > repos > fubar > tool_factory_2
changeset 108:e878bfc6b80c draft
Uploaded
| author | fubar |
|---|---|
| date | Sun, 29 Nov 2020 04:32:22 +0000 |
| parents | 18e616939a91 |
| children | 0116bfe0fa5e |
| files | toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
| diffstat | 2 files changed, 58 insertions(+), 40 deletions(-) [+] |
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--- a/toolfactory/rgToolFactory2.py Sat Nov 28 02:52:24 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Sun Nov 29 04:32:22 2020 +0000 @@ -72,7 +72,7 @@ IHELPOS = 4 IOCLPOS = 5 -# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test +# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" ONAMEPOS = 0 OFMTPOS = 1 OCLPOS = 2 @@ -115,13 +115,17 @@ return '"%s"' % s -html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"} - +html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$","#":"#", "$":"$"} +cheetah_escape_table = {"$": "\$","#":"\#"} def html_escape(text): """Produce entities within text.""" return "".join(html_escape_table.get(c, c) for c in text) +def cheetah_escape(text): + """Produce entities within text.""" + return "".join(cheetah_escape_table.get(c, c) for c in text) + def html_unescape(text): """Revert entities within text. Multiple character targets so use replace""" @@ -129,6 +133,8 @@ t = t.replace(">", ">") t = t.replace("<", "<") t = t.replace("\\$", "$") + t = t.replace("$","$") + t = t.replace("#","#") return t @@ -289,11 +295,11 @@ tscript = open(self.sfile, "w") tscript.write(self.script) tscript.close() - self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx]) - self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx]) + self.indentedScript = " %s" % "\n".join([" %s" % cheetah_escape(x) for x in rx]) + self.escapedScript = "%s" % "\n".join([" %s" % cheetah_escape(x) for x in rx]) art = "%s.%s" % (self.tool_name, self.executeme) artifact = open(art, "wb") - artifact.write(bytes(self.script, "utf8")) + artifact.write(bytes(self.escapedScript, "utf8")) artifact.close() def cleanuppar(self): @@ -408,6 +414,7 @@ """flake8 made me do this...""" for p in self.outfiles: newname, newfmt, newcl, test, oldcl = p + test = test.strip() ndash = self.getNdash(newcl) aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) aparm.positional = self.is_positional @@ -419,24 +426,39 @@ aparm.positional = int(oldcl) aparm.command_line_override = "$%s" % newcl self.toutputs.append(aparm) - usetest = None ld = None - if test > "": + if test.strip() > "": if test.startswith("diff"): - usetest = "diff" + c = "diff" + ld = 0 if test.split(":")[1].isdigit: ld = int(test.split(":")[1]) - else: - usetest = test - tp = gxtp.TestOutput( - name=newcl, - value="%s_sample" % newcl, - format=newfmt, - compare=usetest, - lines_diff=ld, - delta=None, - ) - self.testparam.append(tp) + tp = gxtp.TestOutput( + name=newcl, + value="%s_sample" % newcl, + format=newfmt, + compare= c, + lines_diff=ld, + ) + elif test.startswith("sim_size"): + c = "sim_size" + tn = test.split(":")[1].strip() + if tn > '': + if '.' in tn: + delta = None + delta_frac = min(1.0,float(tn)) + else: + delta = int(tn) + delta_frac = None + tp = gxtp.TestOutput( + name=newcl, + value="%s_sample" % newcl, + format=newfmt, + compare= c, + delta = delta, + delta_frac = delta_frac + ) + self.testparam.append(tp) for p in self.infiles: newname = p[ICLPOS] newfmt = p[IFMTPOS] @@ -550,11 +572,12 @@ self.newtool.command_override = self.xmlcl if self.args.help_text: helptext = open(self.args.help_text, "r").readlines() - safertext = [html_escape(x) for x in helptext] - if False and self.args.script_path: - scrp = self.script.split("\n") - scrpt = [" %s" % x for x in scrp] # try to stop templating - scrpt.insert(0, "```\n") + safertext = "\n".join([cheetah_escape(x) for x in helptext]) + if self.args.script_path: + scr = self.script.split("\n") + scrp = [cheetah_escape(x) for x in scr] + scrpt = [' %s' % x for x in scrpt if x.strip() > ''] # indent + scrpt.insert(0,'------\n\nScript::\n') if len(scrpt) > 300: safertext = ( safertext @@ -563,9 +586,8 @@ + scrpt[-100:] ) else: - safertext = safertext + scrpt - safertext.append("\n```") - self.newtool.help = "\n".join([x for x in safertext]) + safertext = safertext + "\n".join(scrpt) + self.newtool.help = safertext else: self.newtool.help = ( "Please ask the tool author (%s) for help \ @@ -593,7 +615,7 @@ self.newtool.inputs = self.tinputs if self.args.script_path: configfiles = gxtp.Configfiles() - configfiles.append(gxtp.Configfile(name="runme", text=self.script)) + configfiles.append(gxtp.Configfile(name="runme", text=self.escapedScript)) self.newtool.configfiles = configfiles tests = gxtp.Tests() test_a = gxtp.Test() @@ -607,8 +629,7 @@ ) self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL)) self.newtool.add_comment( - "Cite: Creating re-usable tools from scripts doi: \ - 10.1093/bioinformatics/bts573" + "Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573" ) exml0 = self.newtool.export() exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted @@ -806,8 +827,6 @@ repos = ts.repositories.get_repositories() rnames = [x.get("name", "?") for x in repos] rids = [x.get("id", "?") for x in repos] - sto.write(f"############names={rnames} rids={rids}\n") - sto.write(f"############names={repos}\n") tfcat = "ToolFactory generated tools" if self.tool_name not in rnames: tscat = ts.categories.get_categories() @@ -827,7 +846,6 @@ category_ids=catID, ) tid = res.get("id", None) - sto.write(f"##########create res={res}\n") else: i = rnames.index(self.tool_name) tid = rids[i]
--- a/toolfactory/rgToolFactory2.xml Sat Nov 28 02:52:24 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Sun Nov 29 04:32:22 2020 +0000 @@ -79,7 +79,7 @@ <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_test" type="text" label="Test pass decision criterion for this output compared to test generation" - help="Available options are diff:lines, sim_size" value="diff:2"/> + help="Available options are diff:[lines], sim_size:[delta (integer) or delta_frac (float)" value="sim_size:0.01"/> </repeat> </xml> <xml name="additparam"> @@ -232,7 +232,7 @@ <param name="tool_name" type="text" value="tool1" label="New tool ID and title for outputs" help="Toolshed repository name. Choose thoughtfully to avoid namespace clashes with other tool writers. Lower case, digits and underscores only"> <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> + <valid initial="string.ascii_lowercase,string.digits"> <add value="_"/> </valid> </sanitizer> @@ -243,8 +243,8 @@ <conditional name="usescript"> <param name="choosescript" type="select" display="radio" label="Supply a script to either a dependency (e.g. python/R/bash) or a system executable such as Bash" help = "For script interpreters like Python or bash. Parameters and i/o specified below must match script's expectations - if you pass parameters, the script must deal with them"> - <option value="no" selected="true">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> - <option value="yes">Yes, a script is ready to be pasted below</option> + <option value="no">No script required for this tool - just pass parameters on the command line to the first dependency listed above</option> + <option value="yes" selected="true">Yes, a script is ready to be pasted below</option> </param> <when value="no"> <param name="dynScript" type="hidden" value="" /> @@ -324,8 +324,8 @@ <param name="make_Tool" type="select" display="radio" label="Choose the steps you want to run. The TF Docker container is recommended for local installation" help="Installation in this Galaxy is optional" > <option value="generate" >Run to generate tests only. Should fail if dependencies needed.</option> - <option value="gentest" selected="true">Test with planemo after generating.</option> - <option value="gentestinstall">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> + <option value="gentest">Test with planemo after generating.</option> + <option value="gentestinstall" selected="true">Install in this Galaxy after generation and testing. Must have local ToolShed as in the TF Docker container</option> </param> <when value="generate"> <param name="galaxy_apikey" value="" type="hidden" ></param>