Mercurial > repos > fubar > tool_factory_2
changeset 28:ad564ab3cf7b draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 31 Jul 2020 23:00:31 -0400 |
| parents | c4e3cf28545f |
| children | 6db39cbc3242 |
| files | toolfactory/LICENSE toolfactory/README.md toolfactory/images/dynamicScriptTool.png toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml toolfactory/test-data/infile.tabular toolfactory/test-data/reverseargp2.toolshed.gz toolfactory/test-data/reverseargp2_test1_output.xls toolfactory/test-data/runme.py |
| diffstat | 8 files changed, 1647 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/LICENSE Fri Jul 31 23:00:31 2020 -0400 @@ -0,0 +1,504 @@ +GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 + + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +(This is the first released version of the Lesser GPL. It also counts + as the successor of the GNU Library Public License, version 2, hence + the version number 2.1.) + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/README.md Fri Jul 31 23:00:31 2020 -0400 @@ -0,0 +1,166 @@ +*WARNING before you start* + + Install this tool on a private Galaxy ONLY + Please NEVER on a public or production instance + +Updated august 2014 by John Chilton adding citation support + +Updated august 8 2014 to fix bugs reported by Marius van den Beek + +Please cite the resource at +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +if you use this tool in your published work. + +**Short Story** + +This is an unusual Galaxy tool capable of generating new Galaxy tools. +It works by exposing *unrestricted* and therefore extremely dangerous scripting +to all designated administrators of the host Galaxy server, allowing them to +run scripts in R, python, sh and perl over multiple selected input data sets, +writing a single new data set as output. + +*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* + +It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. + + +**Automated generation of new Galaxy tools for installation into any Galaxy** + +A test is generated using small sample test data inputs and parameter settings you supply. +Once the test case outputs have been produced, they can be used to build a +new Galaxy tool. The supplied script or executable is baked as a requirement +into a new, ordinary Galaxy tool, fully workflow compatible out of the box. +Generated tools are installed via a tool shed by an administrator +and work exactly like all other Galaxy tools for your users. + +**More Detail** + +To use the ToolFactory, you should have prepared a script to paste into a +text box, or have a package in mind and a small test input example ready to select from your history +to test your new script. + +```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me + +There is an example in each scripting language on the Tool Factory form. You +can just cut and paste these to try it out - remember to select the right +interpreter please. You'll also need to create a small test data set using +the Galaxy history add new data tool. + +If the script fails somehow, use the "redo" button on the tool output in +your history to recreate the form complete with broken script. Fix the bug +and execute again. Rinse, wash, repeat. + +Once the script runs sucessfully, a new Galaxy tool that runs your script +can be generated. Select the "generate" option and supply some help text and +names. The new tool will be generated in the form of a new Galaxy datatype +*toolshed.gz* - as the name suggests, it's an archive ready to upload to a +Galaxy ToolShed as a new tool repository. + +Once it's in a ToolShed, it can be installed into any local Galaxy server +from the server administrative interface. + +Once the new tool is installed, local users can run it - each time, the script +that was supplied when it was built will be executed with the input chosen +from the user's history. In other words, the tools you generate with the +ToolFactory run just like any other Galaxy tool,but run your script every time. + +Tool factory tools are perfect for workflow components. One input, one output, +no variables. + +*To fully and safely exploit the awesome power* of this tool, +Galaxy and the ToolShed, you should be a developer installing this +tool on a private/personal/scratch local instance where you are an +admin_user. Then, if you break it, you get to keep all the pieces see +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +**Installation** +This is a Galaxy tool. You can install it most conveniently using the +administrative "Search and browse tool sheds" link. Find the Galaxy Main +toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory +repository. Open it and review the code and select the option to install it. + +If you can't get the tool that way, the xml and py files here need to be +copied into a new tools +subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry +pointing to the xml +file - something like:: + + <section name="Tool building tools" id="toolbuilders"> + <tool file="toolfactory/rgToolFactory.xml"/> + </section> + +If not already there, +please add: +<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" +mimetype="multipart/x-gzip" subclass="True" /> +to your local data_types_conf.xml. + + +**Restricted execution** + +The tool factory tool itself will then be usable ONLY by admin users - +people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY +admin_users can run this tool** Think about it for a moment. If allowed to +run any arbitrary script on your Galaxy server, the only thing that would +impede a miscreant bent on destroying all your Galaxy data would probably +be lack of appropriate technical skills. + +**What it does** + +This is a tool factory for simple scripts in python, R and +perl currently. Functional tests are automatically generated. How cool is that. + +LIMITED to simple scripts that read one input from the history. Optionally can +write one new history dataset, and optionally collect any number of outputs +into links on an autogenerated HTML index page for the user to navigate - +useful if the script writes images and output files - pdf outputs are shown +as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and +imagemagik need to be available. + +Generated tools can be edited and enhanced like any Galaxy tool, so start +small and build up since a generated script gets you a serious leg up to a +more complex one. + +**What you do** + +You paste and run your script, you fix the syntax errors and +eventually it runs. You can use the redo button and edit the script before +trying to rerun it as you debug - it works pretty well. + +Once the script works on some test data, you can generate a toolshed compatible +gzip file containing your script ready to run as an ordinary Galaxy tool in +a repository on your local toolshed. That means safe and largely automated +installation in any production Galaxy configured to use your toolshed. + +**Generated tool Security** + +Once you install a generated tool, it's just +another tool - assuming the script is safe. They just run normally and their +user cannot do anything unusually insecure but please, practice safe toolshed. +Read the code before you install any tool. Especially this one - it is really scary. + +**Send Code** + +Patches and suggestions welcome as bitbucket issues please? + +**Attribution** + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref + +**Licensing** + +Copyright Ross Lazarus 2010 +ross lazarus at g mail period com + +All rights reserved. + +Licensed under the LGPL + +**Obligatory screenshot** + +http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.py Fri Jul 31 23:00:31 2020 -0400 @@ -0,0 +1,502 @@ +# rgToolFactory.py +# see https://github.com/fubar2/toolfactory +# +# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 +# +# all rights reserved +# Licensed under the LGPL +# suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory +# +# July 2020: BCC was fun and I feel like rip van winkle after 5 years. +# Decided to +# 1. Fix the toolfactory so it works - done for simplest case +# 2. Fix planemo so the toolfactory function works +# 3. Rewrite bits using galaxyxml functions where that makes sense - done +# +# removed all the old complications including making the new tool use this same script +# galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml +# No support for automatic HTML file creation from arbitrary outputs +# TODO: add option to run that code as a post execution hook +# TODO: add additional history input parameters - currently only one + +import sys +import subprocess +import shutil +import os +import time +import tempfile +import argparse +import tarfile +import re +import galaxyxml.tool as gxt +import galaxyxml.tool.parameters as gxtp +import logging + + +progname = os.path.split(sys.argv[0])[1] +myversion = 'V2.1 July 2020' +verbose = True +debug = True +toolFactoryURL = 'https://github.com/fubar2/toolfactory' +ourdelim = '~~~' + + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + + +def quote_non_numeric(s): + """return a prequoted string for non-numerics + useful for perl and Rscript parameter passing? + """ + try: + _ = float(s) + return s + except ValueError: + return '"%s"' % s + + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "$": r"\$" +} + + +def html_escape(text): + """Produce entities within text.""" + return "".join(html_escape_table.get(c, c) for c in text) + + +def html_unescape(text): + """Revert entities within text. Multiple character targets so use replace""" + t = text.replace('&', '&') + t = t.replace('>', '>') + t = t.replace('<', '<') + t = t.replace('\\$', '$') + return t + + +def parse_citations(citations_text): + """ + """ + citations = [c for c in citations_text.split("**ENTRY**") if c.strip()] + citation_tuples = [] + for citation in citations: + if citation.startswith("doi"): + citation_tuples.append(("doi", citation[len("doi"):].strip())) + else: + citation_tuples.append( + ("bibtex", citation[len("bibtex"):].strip())) + return citation_tuples + + +class ScriptRunner: + """Wrapper for an arbitrary script + uses galaxyxml + + """ + + def __init__(self, args=None): + """ + prepare command line cl for running the tool here + and prepare elements needed for galaxyxml tool generation + """ + lastclredirect = None + self.cl = [] + aCL = self.cl.append + if args.output_dir: # simplify for the tool tarball + os.chdir(args.output_dir) + self.args = args + # a sanitizer now does this but.. + self.tool_name = re.sub('[^a-zA-Z0-9_]+', '', args.tool_name) + self.tool_id = self.tool_name + self.xmlfile = '%s.xml' % self.tool_name + if self.args.interpreter_name == "Executable": # binary - no need + aCL(self.args.exe_package) # this little CL will just run + else: # a script has been provided + rx = open(self.args.script_path, 'r').readlines() + # remove pesky dos line endings if needed + rx = [x.rstrip() for x in rx] + self.script = '\n'.join(rx) + fhandle, self.sfile = tempfile.mkstemp( + prefix=self.tool_name, suffix=".%s" % (args.interpreter_name)) + # use self.sfile as script source for Popen + tscript = open(self.sfile, 'w') + tscript.write(self.script) + tscript.close() + self.indentedScript = " %s" % '\n'.join( + [' %s' % html_escape(x) for x in rx]) # for restructured text in help + self.escapedScript = "%s" % '\n'.join( + [' %s' % html_escape(x) for x in rx]) + aCL(self.args.interpreter_name) + aCL(self.sfile) + self.elog = os.path.join(self.args.output_dir, + "%s_error.log" % self.tool_name) + if args.output_dir: # may not want these complexities + self.tlog = os.path.join( + self.args.output_dir, "%s_runner.log" % self.tool_name) + art = '%s.%s' % (self.tool_name, args.interpreter_name) + artpath = os.path.join( + self.args.output_dir, + art) # need full path + # use self.sfile as script source for Popen + artifact = open(artpath, 'w') + artifact.write(self.script) + artifact.close() + self.infile_paths = [] + self.infile_format = [] + self.infile_cl = [] + self.infile_label = [] + self.infile_help = [] + if self.args.input_files: + aif = [x.split(ourdelim) for x in self.args.input_files] + # transpose the input_files array passed as + # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help" + laif = list(map(list, zip(*aif))) + self.infile_paths, self.infile_cl, self.infile_format, self.infile_label, self.infile_help = laif + self.infile_name = [] + # positionals have integers indicating order - need valid internal + # names + for i, scl in enumerate(self.infile_cl): + if scl.isdigit(): + scl = 'input%s' % scl + if scl.upper() in ['STDOUT', 'STDIN']: + scl = 'input%d' % (i + 1) + # make a list of internal names for each input file + self.infile_name.append(scl) + # list all (cl param) pairs - positional needs sorting by cl index so decorate + clsuffix = [] + clsuffix.append([self.args.output_cl, self.args.output_tab]) + if self.args.parampass == '0': # only need two + aCL('<') + aCL('%s' % self.infile_paths[0]) + aCL('>') + aCL('%s' % self.args.output_tab) + else: + for i, p in enumerate(self.infile_paths): + # decorator is cl - sort for positional + clsuffix.append([self.infile_cl[i], p]) + for p in self.args.additional_parameters: + psplit = p.split(ourdelim) + pform = psplit[5] + if pform == 'STDOUT': + lastclredirect = ['>', psplit[1]] + else: + clsuffix.append([pform, psplit[1]]) # cl,value + clsuffix.sort() + if self.args.parampass == "positional": + # inputs in order then params in order TODO fix ordering using + # self.infile_cl + for (k, v) in clsuffix: + if ' ' in v: + aCL("v") + else: + aCL(v) + elif self.args.parampass == "argparse": + # inputs then params in argparse named form + for (k, v) in clsuffix: + if ' ' in v: + aCL('--%s' % k) + aCL('"%s"' % v) + else: + aCL('--%s' % k) + aCL('%s' % v) + if lastclredirect: + for v in lastclredirect: + aCL(v) # add the stdout parameter last + self.test1Output = '%s_test1_output.xls' % self.tool_name + self.test1HTML = '%s_test1_output.html' % self.tool_name + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script + Uses galaxyhtml + """ + # need interp and executable (?script) or else executable only + if self.args.interpreter_name: + exe = "$runMe" # our dynamic script from the tool builder + interp = self.args.interpreter_name + else: + interp = None + exe = self.args.exe_package + assert exe is not None, 'No interpeter or executable passed in to makeXML' + tool = gxt.Tool(self.args.tool_name, self.tool_id, + self.args.tool_version, self.args.tool_desc, exe) + if interp: + tool.interpreter = interp + if self.args.help_text: + helptext = open(self.args.help_text, 'r').readlines() + # must html escape here too - thanks to Marius van den Beek + helptext = [html_escape(x) for x in helptext] + tool.help = ''.join([x for x in helptext]) + else: + tool.help = 'Please ask the tool author (%s) for help \ + as none was supplied at tool generation\n' % (self.args.user_email) + tool.version_command = None # do not want + inputs = gxtp.Inputs() + outputs = gxtp.Outputs() + requirements = gxtp.Requirements() + testparam = [] + is_positional = (self.args.parampass == 'positional') + if self.args.include_dependencies == "yes": + requirements.append(gxtp.Requirement('package', 'ghostscript')) + requirements.append(gxtp.Requirement('package', 'graphicsmagick')) + if self.args.interpreter_name: + if self.args.interpreter_name == 'python': # always needed for this runner script + requirements.append(gxtp.Requirement( + 'package', 'python', self.args.interpreter_version)) + elif self.args.interpreter_name not in ['bash', 'sh']: + requirements.append(gxtp.Requirement( + 'package', self.args.interpreter_name, self.args.interpreter_version)) + else: + if self.args.exe_package: # uses exe not interpreter + requirements.append(gxtp.Requirement( + 'package', self.args.exe_package, self.args.exe_package_version)) + tool.requirements = requirements + for i, infpath in enumerate(self.infile_paths): + if self.args.parampass == 0: + assert len( + self.infile_name) == 1, 'Maximum one "<" if parampass is 0 - more than one input files supplied' + newname = self.infile_name[i] + if len(newname) > 1: + ndash = 2 + else: + ndash = 1 + if not len(self.infile_label[i]) > 0: + alab = self.infile_name[i] + else: + alab = self.infile_label[i] + aninput = gxtp.DataParam(self.infile_name[i], optional=False, label=alab, help=self.infile_help[i], + format=self.infile_format[i], multiple=False, num_dashes=ndash) + if self.args.parampass == '0': + aninput.command_line_override = '< $%s' % self.infile_name[i] + aninput.positional = is_positional + inputs.append(aninput) + for parm in self.args.additional_parameters: + newname, newval, newlabel, newhelp, newtype, newcl = parm.split( + ourdelim) + if not len(newlabel) > 0: + newlabel = newname + if len(newname) > 1: + ndash = 2 + else: + ndash = 1 + if newtype == "text": + aparm = gxtp.TextParam( + newname, label=newlabel, help=newhelp, value=newval, num_dashes=ndash) + elif newtype == "integer": + aparm = gxtp.IntegerParam( + newname, label=newname, help=newhelp, value=newval, num_dashes=ndash) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, label=newname, help=newhelp, value=newval, num_dashes=ndash) + else: + raise ValueError('Unrecognised parameter type "%s" for\ + additional parameter %s in makeXML' % (newtype, newname)) + aparm.positional = is_positional + inputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + testparam.append(tparm) + tool.inputs = inputs + configfiles = gxtp.Configfiles() + configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) + tool.configfiles = configfiles + if self.args.output_tab: + ext = self.args.output_format + aparm = gxtp.OutputData( + self.args.output_cl, format=ext, num_dashes=ndash) + if is_positional: + aparm.command_line_override = '> $output1' + aparm.positional = is_positional + outputs.append(aparm) + tool.outputs = outputs + tests = gxtp.Tests() + test_a = gxtp.Test() + ext = self.infile_format[0].split(',')[0] + if is_positional: + param = gxtp.TestParam( + 'input1', value='input1.%s' % ext, ftype=ext) + else: + param = gxtp.TestParam(self.infile_name[0], value='%s.%s' % ( + self.infile_name[0], ext), ftype=ext) + test_a.append(param) + param = gxtp.TestParam('job_name', value='test_a') + test_a.append(param) + param = gxtp.TestParam('runMe', value="$runMe") + test_a.append(param) + for aparam in testparam: + test_a.append(aparam) + test_out = gxtp.TestOutput( + name=self.args.output_cl, value=self.test1Output) + test_a.append(test_out) + tests.append(test_a) + tool.tests = tests + tool.add_comment('Created by %s at %s using the Galaxy Tool Factory.' % ( + self.args.user_email, timenow())) + tool.add_comment('Source in git at: %s' % (toolFactoryURL)) + tool.add_comment( + 'Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573') + exml = tool.export() + xf = open(self.xmlfile, 'w') + xf.write(exml) + xf.write('\n') + xf.close() + # ready for the tarball + + def makeTooltar(self): + """ + a tool is a gz tarball with eg + /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ... + """ + retval = self.run() + if retval: + sys.stderr.write( + '## Run failed. Cannot build yet. Please fix and retry') + sys.exit(1) + tdir = 'tdir_%s' % self.tool_name + if not os.path.exists(tdir): + os.mkdir(tdir) + self.makeXML() + testdir = os.path.join(tdir, 'test-data') + if not os.path.exists(testdir): + os.mkdir(testdir) # make tests directory + for i, infile in enumerate(self.infile_paths): + dest = os.path.join(testdir, '%s.%s' % + (self.infile_name[i], self.infile_format[i])) + if infile != dest: + shutil.copyfile(infile, dest) + if self.args.output_tab and os.path.exists(self.args.output_tab): + shutil.copyfile(self.args.output_tab, + os.path.join(testdir, self.test1Output)) + else: + print('#### no output_tab %s exists' % self.args.output_tab) + if self.args.output_dir: + if os.path.exists(self.tlog): + shutil.copyfile(self.tlog, os.path.join( + testdir, 'test1_out.log')) + stname = os.path.join(tdir, self.sfile) + if not os.path.exists(stname): + shutil.copyfile(self.sfile, stname) + xtname = os.path.join(tdir, self.xmlfile) + if not os.path.exists(xtname): + shutil.copyfile(self.xmlfile, xtname) + tarpath = "%s.tar.gz" % self.tool_name + tar = tarfile.open(tarpath, "w:gz") + tar.add(tdir, recursive=True, arcname='%s' % self.tool_name) + tar.close() + shutil.copyfile(tarpath, self.args.new_tool) + shutil.rmtree(tdir) + # TODO: replace with optional direct upload to local toolshed? + return retval + + def run(self): + """ + Some devteam tools have this defensive stderr read so I'm keeping with the faith + Feel free to update. + """ + logging.debug('run cl=%s' % str(self.cl)) + scl = ' '.join(self.cl) + err = None + if self.args.parampass != '0': + ste = open(self.elog, 'wb') + sto = open(self.tlog, 'wb') + sto.write( + bytes('## Executing Toolfactory generated command line = %s\n' % scl, "utf8")) + sto.flush() + p = subprocess.run(self.cl, shell=False, stdout=sto, + stderr=ste, cwd=self.args.output_dir) + sto.close() + ste.close() + tmp_stderr = open(self.elog, 'rb') + err = '' + buffsize = 1048576 + try: + while True: + err += str(tmp_stderr.read(buffsize)) + if not err or len(err) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + retval = p.returncode + else: # work around special case of simple scripts that take stdin and write to stdout + sti = open(self.infile_paths[0], 'rb') + sto = open(self.args.output_tab, 'wb') + # must use shell to redirect + p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti) + retval = p.returncode + sto.close() + sti.close() + if self.args.output_dir: + if p.returncode != 0 and err: # problem + sys.stderr.write(err) + logging.debug('run done') + return retval + + +def main(): + """ + This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: + <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + </command> + """ + parser = argparse.ArgumentParser() + a = parser.add_argument + a('--script_path', default='') + a('--tool_name', default=None) + a('--interpreter_name', default=None) + a('--interpreter_version', default=None) + a('--exe_package', default=None) + a('--exe_package_version', default=None) + a('--output_dir', default='./') + a('--input_files', default=[], action="append") + a("--input_formats", default="tabular") + a('--output_tab', default=None) + a('--output_format', default='tabular') + a('--output_cl', default=None) + a('--user_email', default='Unknown') + a('--bad_user', default=None) + a('--make_Tool', default=None) + a('--help_text', default=None) + a('--tool_desc', default=None) + a('--new_tool', default=None) + a('--tool_version', default=None) + a('--include_dependencies', default=None) + a('--citations', default=None) + a('--additional_parameters', dest='additional_parameters', + action='append', default=[]) + a('--edit_additional_parameters', action="store_true", default=False) + a('--parampass', default="positional") + args = parser.parse_args() + assert not args.bad_user, 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' % ( + args.bad_user, args.bad_user) + assert args.tool_name, '## Tool Factory expects a tool name - eg --tool_name=DESeq' + assert (args.interpreter_name or args.exe_package), '## Tool Factory wrapper expects an interpreter - eg --interpreter_name=Rscript or an executable package findable by the dependency management package' + assert args.exe_package or (len(args.script_path) > 0 and os.path.isfile( + args.script_path)), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable' + if args.output_dir: + try: + os.makedirs(args.output_dir) + except BaseException: + pass + args.input_files = [x.replace('"', '').replace("'", '') + for x in args.input_files] + # remove quotes we need to deal with spaces in CL params + for i, x in enumerate(args.additional_parameters): + args.additional_parameters[i] = args.additional_parameters[i].replace( + '"', '') + r = ScriptRunner(args) + if args.make_Tool: + retcode = r.makeTooltar() + else: + retcode = r.run() + if retcode: + sys.exit(retcode) # indicate failure to job runner + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.xml Fri Jul 31 23:00:31 2020 -0400 @@ -0,0 +1,449 @@ +<tool id="rgTF2" name="toolfactory" version="2.00"> + <description>Scripts into tools</description> + <macros> + <xml name="addpar"> + <param name="edit_params" type="select" display="radio" label="Add all additional parameters to the generated tool form so they are user editable?" + help="If no (default), 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">Yes, allow user to edit all additional parameters on the generated tool form</option> + <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option> + </param> + <repeat name="additional_history_inputs" title="Additional Current history data files to pass in to the script - Use the '+' button to add as many as needed" + help="Each of these will become a history item selector as input for users of the new tool you are making"> + <param name="input_files" type="data" format="data" label="Select an input file from your history" optional="true" size="120" multiple="false" + help=""/> + <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input" + 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="param_label" type="text" value="" label="This will become the user prompt for the form so please make it informative" size="60" + help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_help" type="text" value="parameter_help" label="This will become help text on the form." + help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" size="60"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="CL" type="text" size="60" label="Positional: ordinal integer. Argparse: argument name." + help="If you will pass positional parameters, enter the integer ordinal for this parameter. If Argparse style, '--' will be prepended or '-' if single character" value=""> + </param> + </repeat> + <repeat name="additional_parameters" title="Pass additional parameters to the script" + help="See examples below to see how these can be parsed by scripts in the various languages"> + <param name="param_name" type="text" value="parameter_name" label="Choose the name for this parameter" size="60"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"/> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_type" type="select" label="Select the type for this parameter"> + <option value="text" selected="true">text</option> + <option value="integer">integer</option> + <option value="float">float</option> + </param> + <param name="param_value" type="text" value="parameter_value" label="Enter this parameter's default value" size="60" + help="Note that '~~~' is an internal delimiter must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_label" type="text" value="parameter_label" label="Enter this parameter's label for the form" size="60" + help="Note that '~~~' is an internal delimiter so must not appear in this text field - please work around this technical limitation" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="param_help" type="text" value="parameter_help" label="Help for this parameter" + help="Note that three consecutive ~ cannot be used in this text field - please work around this technical limitation" size="60"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="CL" type="text" size="60" label="Positional order (must be integer > 1) or Argument name to be prefixed with '--' or '-' if single letter" + help="Using positional parameters, enter the integer ordinal for this parameter on the command line. Using Argparse style, '--' will be prepended on the CL" value=""> + </param> + </repeat> + </xml> + <xml name="builtin_dynpar"> + <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="20x120" + help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </xml> + <xml name="dynpar"> + <param name="interpreter_version" type="text" value="" label="Specific script interpreter version to match dependency (Conda) repositories - e.g. for python '3.8.5' Latest if empty" size="60"/> + <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="20x120" + help="If there are parameters, either positional or argparse style, the script must parse and use them appropriately"> + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </xml> + </macros> + <requirements> + <requirement type="package">python</requirement> + <requirement type="package">galaxyxml</requirement> + </requirements> + <command interpreter="python"><![CDATA[ +#import os +#set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' +#if not $dev_env and ( $__user_email__ not in $__admin_users__ ): +$__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ + #else: +$__tool_directory__/rgToolFactory2.py --script_path "$runme" + #if str($interexe.interpreter)=="Executable": +--exe_package="$interexe.exe_package" --exe_package_version="$interexe.exe_package_version" + #else: +--interpreter_name="$interexe.interpreter" + #if not str($interexe.interpreter) in ['bash','sh']: +--interpreter_version="$interexe.interpreter_version" + #end if + #end if +--tool_name="$tool_name" --user_email="$__user_email__" --citations="$citeme" --parampass="$ppass.parampass" +--output_tab="$output1" --output_format="$output_format" --output_cl="$output_CL" + #if str($makeMode.make_Tool)=="yes": +--make_Tool="$makeMode.make_Tool" +--tool_desc="$makeMode.tool_desc" +--tool_version="$makeMode.tool_version" +--new_tool="$new_tool" +--help_text="$helpme" + #end if + #if $ppass.parampass != '0': + #if str($ppass.edit_params) == "yes": +--edit_additional_parameters + #end if + #for i in $ppass.additional_parameters: +--additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL" + #end for + #end if +--output_dir="." + #if str($input_files) != '': +--input_files="$input_files~~~$input_CL~~~$input_formats~~~$input_label~~~$input_help" + #end if + #if $ppass.parampass != '0' and $ppass.additional_history_inputs: + #for $intab in $ppass.additional_history_inputs: +--input_files="$intab.input_files~~~$intab.CL~~~$intab.input_formats~~~$intab.param_label~~~$intab.param_help" + #end for + #end if +#end if +]]></command> + <configfiles> + <configfile name="runme"> + #if $interexe.interpreter != "Executable": +${interexe.dynScript} + #else +"Not used" + #end if + </configfile> + <configfile name="helpme"> + #if $makeMode.make_Tool == "yes": + ${makeMode.help_text} + #end if + </configfile> + <configfile name="citeme"> + #if $makeMode.make_Tool == "yes": + #for $citation in $makeMode.citations: + #if $citation.citation_type.type == "bibtex": + **ENTRY**bibtex + ${citation.citation_type.bibtex} + #else + **ENTRY**doi + ${citation.citation_type.doi} + #end if + #end for + #end if + </configfile> + </configfiles> + <inputs> + + <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60" + help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_"/> + </valid> + </sanitizer> + </param> + <param name="input_files" format="data" type="data" label="Select a small test input file" optional="true" size="120" multiple="false" + help="This will be used to test the new tool to generate a built in test for the generated tool"/> + <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts for this input" + help="If not listed here, datatypes can 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="input_label" type="text" value="parameter_label" label="Data input user prompt on the generated tool form" size="60" + help="Describe the input file so the user can understand how it will be used" > + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="input_help" type="text" value="parameter_help" label="Data input user help on the generated tool form" + help="Enter text to appear as help for the user on the generated tool form" size="60"> + <sanitizer invalid_char=""> + <valid initial="string.printable"> <remove value='~~~'/> </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="input_CL" type="text" size="60" label="Positional order (must be integer > 1) or Argument name to be prefixed with '--'. Use 'STDIN' if your script reads from STDIN" + help="If you will pass positional parameters, enter the integer index for this parameter on the command line. If Argparse style, '--' will be prepended on the CL" value=""> + </param> + <param name="output_format" type="select" multiple="false" label="Select the Galaxy datatype that your tool/script emits as output for the new history item" + 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="output_CL" type="text" size="60" label="Positional order (must be integer > 1) or Argument name to be prefixed with '--'. Use 'STDOUT' if your script writes to stdout" + help="If you will pass positional parameters, enter the integer index for this parameter on the command line. If Argparse style, '--' will be prepended on the CL" value=""> + </param> + <conditional name="interexe"> + <param name="interpreter" type="select" label="For binaries, choose 'Executable'. Otherwise choose the interpreter for your code" + help = "If executable, the supplied package will become a requirement so must match the tool dependency resolver package name - conda is the default."> + <option value="Executable" selected="true">An executable binary to be provided and managed by the Conda dependency management subsystem</option> + <option value="python">python</option> + <option value="r-base">Rscript</option> + <option value="perl">perl</option> + <option value="bash">bash</option> + <option value="sh">sh</option> + </param> + <when value="Executable"> + <param name="exe_package" type="text" value="" label="Executable package name in dependency (Conda) repositories - e.g. 'bwa'" size="60" optional="false"/> + <param name="exe_package_version" type="text" value="" label="Executable package version to match dependency (Conda) repositories - e.g. for bwa='0.7.17'. Latest if empty" size="60"/> + </when> + <when value = "python"> + <expand macro="dynpar" /> + </when> + <when value = "r-base"> + <expand macro="dynpar" /> + </when> + <when value = "perl"> + <expand macro="dynpar" /> + </when> + <when value = "bash"> + <expand macro="builtin_dynpar" /> + </when> + <when value = "sh"> + <expand macro="builtin_dynpar" /> + </when> + </conditional> + <conditional name="ppass"> + <param name="parampass" type="select" display="radio" label="Command line parameter passing method to use"> + <option value="argparse" selected="true">Argparse style: on CL in the form of --inputbam="foo.bam" if label below is "inputbam"</option> + <option value="positional">Positional: on CL in the order defined on this screen -> "... foo.bam bar.idx zot.xls"</option> + <option value="0">No parameters needed because tool reads selected history file from STDIN and writes to STDOUT for history"</option> + </param> + <when value="0"> + </when> + <when value = "argparse"> + <expand macro="addpar" /> + </when> + <when value = "positional"> + <expand macro="addpar" /> + </when> + </conditional> + <conditional name="makeMode"> + <param name="make_Tool" type="select" display="radio" label="Generate new tool as a tar.gz file ready to upload to a toolshed repository" + help="Generate a toolshed archive - upload to a toolshed from where it can be auto-installed via the Galaxy admin functions" + size="60"> + <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option> + <option value="" selected="true">No. Just run the script please</option> + </param> + <when value = "yes"> + <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" + help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> + <param name="tool_desc" label="Tool Description" type="text" value="" size="40" + help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" /> + <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" + size="8x120" value="**What it Does**" + help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <repeat name="citations" title="Citation"> + <conditional name="citation_type"> + <param name="type" type="select" display="radio" label="Citation Type"> + <option value="doi">DOI</option> + <option value="bibtex">BibTeX</option> + </param> + <when value="doi"> + <param name="doi" label="DOI" type="text" value="" + help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." /> + </when> + <when value="bibtex"> + <param name="bibtex" label="BibTex" type="text" area="true" size="8x120" + help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > + <sanitizer> + <valid initial="string.printable"> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </when> + <when value = ""> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" label="${tool_name}.${output_format}" format="tabular" metadata_source="input_file"> + <actions> + <action type="format"> + <option type="from_param" name="output_format" /> + </action> + </actions> + </data> + <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz"> + <filter>makeMode['make_Tool'] == "yes"</filter> + </data> + </outputs> + +<tests> +<test> + <param name='input_files' value='infile.tabular' ftype='tabular' /> + <param name='script_path' value='runme.py' /> + <param name='tool_name' value='reverseargp2_test1' /> + <param name='make_Tool' value='yes' /> + <param name='tool_version' value='0.01' /> + <param name="tool_desc" value='testing_tf2' /> + <param name="help_text" value='help text goes here' /> + <param name="output_format" value="tabular" /> + <param name="input_formats" value="tabular" /> + <param name="interpreter" value='python' /> + <output name='output1' file='reverseargp2_test1_output.xls' compare='diff' lines_diff = '10'/> + <output name='new_tool' file="reverseargp2.toolshed.gz" compare="sim_size" delta="600" /> +</test> +</tests> +<help> + +.. class:: warningmark + +**Details and attribution** +(see GTF_) + +**Local Admins ONLY** +Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool. + +**If you find a bug** +Please raise an issue at the bitbucket repository GTFI_ + +**What it does** +This tool optionally generates normal workflow compatible first class Galaxy tools + +Generated tools can run existing binary packages that become requirements, existing scripts, or new scripts pasted into this tool form. +Pasted scripts are written so they are part of the new tool and cannot be adjusted by the downstream user. +Binary packages are managed by the dependency subsystem - conda usually, so anything in bioconda or conda_forge is available for example. + +Any number of parameters can be built into the new tool form for passing in to the script or executable at runtime. +These can be editable by the downstream user or baked in. + +When you run this tool, your executable or script and supplied parameter values will be run to produce a canonical +set of outputs - these are used to construct a test for the new tool. + +If tool generation is required, a new tarball compatible with any Galaxy toolshed is created. +It can be unpacked in your galaxy/tools directory and manually added to tool_conf.xml, or +installed into any toolshed from where it can be installed into your Galaxy. + + +.. class:: warningmark + +**Note to system administrators** +This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances. +Admin_users will have the power to do anything they want as the Galaxy user if you install this tool. + +.. class:: warningmark + +**Use on public servers** is STRONGLY discouraged for obvious reasons + +The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. +We recommend that you follow the good code hygiene practices associated with safe toolshed practices. + +Here's a sample python script that can be cut and pasted into the tool form, suitable for positional parameter passing: + +:: + + # reverse order of text by row + import sys + inp = sys.argv[1] + outp = sys.argv[2] + i = open(inp,'r').readlines() + o = open(outp,'w') + for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) + o.write('\n') + o.close() + +With argparse style parameters: + +:: + + # reverse order of text by row + import argparse + parser = argparse.ArgumentParser() + a = parser.add_argument + a('--infile',default='') + a('--outfile',default=None) + args = parser.parse_args() + inp = args.infile + outp = args.outfile + i = open(inp,'r').readlines() + o = open(outp,'w') + for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write(''.join(rs)) + o.write('\n') + o.close() + + +Paper_ : + +Creating re-usable tools from scripts: The Galaxy Tool Factory +Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team +Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 + +**Licensing** + +Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012 +All rights reserved. +Licensed under the LGPL_ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html +.. _GTF: https://bitbucket.org/fubar/galaxytoolfactory +.. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues +.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 + + +</help> +<citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> +</citations> +</tool> + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/infile.tabular Fri Jul 31 23:00:31 2020 -0400 @@ -0,0 +1,7 @@ +0.1 +0.00001 +0.2 +0.3 +0.004 +0.5 +0.000000002
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/runme.py Fri Jul 31 23:00:31 2020 -0400 @@ -0,0 +1,19 @@ +# reverse order of columns in a tabular file +import argparse +parser = argparse.ArgumentParser() +a = parser.add_argument +a('--infile',default='') +a('--outfile',default=None) +a('--prefix',default=None) +args = parser.parse_args() +inp = args.infile +outp = args.outfile +i = open(inp,'r').readlines() +o = open(outp,'w') +for row in i: + rs = row.rstrip() + rs = list(rs) + rs.reverse() + o.write('%s:%s' % (args.prefix,''.join(rs))) + o.write('\n') +o.close()