# HG changeset patch # User fubar # Date 1596801263 14400 # Node ID 6f48315c32c160859f8cacdd8c814e282c24207e # Parent 6db39cbc32427cf7473373f025b26469f116783c Uploaded diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/LICENSE Fri Aug 07 07:54:23 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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Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random + Hacker. + + {signature of Ty Coon}, 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/README.md Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,418 @@ +toolfactory_2 +============= + +This is an upgrade to the tool factory but with added parameters +(optionally editable in the generated tool form - otherwise fixed) and +multiple input files. + +Specify any number of parameters - well at +least up to the limit of your patience with repeat groups. + +Parameter values supplied at tool generation time are defaults and +can be optionally editable by the user - names cannot be changed once +a tool has been generated. + +If not editable, they act as hidden parameters passed to the script +and are not editable on the tool form. + +Note! There will be Galaxy default sanitization for all +user input parameters which your script may need to dance around. + +Any number of input files can be passed to your script, but of course it +has to deal with them. Both path and metadata name are supplied either in the environment +(bash/sh) or as command line parameters (python,perl,rscript) that need to be parsed and +dealt with in the script. This is complicated by the common use case of needing file names +for (eg) column headers, as well as paths. Try the examples are show on the tool factory +form to see how Galaxy file and user supplied parameter values can be recovered in each +of the 4 scripting environments supported. + +Best way to deal with multiple outputs is to let the tool factory generate an HTML +page for your users. It automagically lays out pdf images as thumbnail galleries +and can have separate results sections gathering all similarly prefixed files, such as +a Foo section taking text and results from text (foo_whatever.log) and +artifacts (eg foo_MDS_plot.pdf) file names. All artifacts are linked for download. +A copy of the actual script is provided for provenance - be warned, it exposes +real file paths. + +**WARNING before you start** + +Install this tool on a private Galaxy ONLY +Please NEVER on a public or production instance +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. + +*Differences between TF2 and the original Tool Factory* + +1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined +for the new tool. If these are editable, the user can change them but otherwise, they are passed +as fixed and invisible parameters for each execution. Obviously, there are substantial security +implications with editable parameters, but these are always sanitized by Galaxy's inbuilt +parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__" +into "<" for certain parameters where that is needed. Please practise safe toolshed. + +2. Any number of (the same datatype) of input files may be defined. + +These changes substantially complicate the way your supplied script is supplied with +all the new and variable parameters. Examples in each scripting language are shown +in the tool help + +*Automated outputs in named sections* + +If your script writes to the current directory path, arbitrary mix of (eg) +pdfs, tabular analysis results and run logs,the tool factory can optionally +auto-generate a linked Html page with separate sections showing a thumbnail +grid for all pdfs and the log text, grouping all artifacts sharing a file +name and log name prefix.if "foo.log" is emitted then *all* other outputs matching foo_* will +all be grouped together - eg +- foo_baz.pdf +- foo_bar.pdf and +- foo_zot.xls + +would all be displayed and linked in the same section with foo.log's contents to form the "Foo" section of the Html page. +Sections appear in alphabetic order and there are no limits on the number of files or sections. + +*Automated generation of new Galaxy tools for installation into any Galaxy* + +Once a script is working correctly, this tool optionally generates a +new Galaxy tool, effectively freezing the supplied script into a new, +ordinary Galaxy tool that runs it over one or more input files selected by +the user. Generated tools are installed via a tool shed by an administrator +and work exactly like all other Galaxy tools for your users. + +If you use the Html output option, please ensure that sanitize_all_html is +set to False and uncommented in universe_wsgi.ini - it should show + +By default, all tool output served as 'text/html' will be sanitized +Change ```sanitize_all_html = False``` + +This opens potential security risks and may not be acceptable for public +sites where the lack of stylesheets may make Html pages damage onlookers' +eyeballs but should still be correct. + +*More Detail* + +To use the ToolFactory, you should have prepared a script to paste into a +text box, and a small test input example ready to select from your history +to test your new script. + +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 +``` +
+ +
+``` +If not already there (I just added it to datatypes_conf.xml.sample), +please add: + +``` + +``` +to your local data_types_conf.xml. + + +Of course, R, python, perl etc are needed on your path if you want to test +scripts using those interpreters. Adding new ones to this tool code should +be easy enough. Please make suggestions as bitbucket issues and code. The +HTML file code automatically shrinks R's bloated pdfs, and depends on +ghostscript. The thumbnails require imagemagick . + +* 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 fucking code before you install any tool. Especially this one - +it is really scary. + +If you opt for an HTML output, you get all the script outputs arranged +as a single Html history item - all output files are linked, thumbnails for +all the pdfs. Ugly but really inexpensive. + +Patches and suggestions welcome as bitbucket issues please? + +copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012 + +all rights reserved +Licensed under the LGPL if you want to improve it, feel free +https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home + +Material for our more enthusiastic and voracious readers continues below - +we salute you. + +**Motivation** Simple transformation, filtering or reporting scripts get +written, run and lost every day in most busy labs - even ours where Galaxy is +in use. This 'dark script matter' is pervasive and generally not reproducible. + +**Benefits** For our group, this allows Galaxy to fill that important dark +script gap - all those "small" bioinformatics tasks. Once a user has a working +R (or python or perl) script that does something Galaxy cannot currently do +(eg transpose a tabular file) and takes parameters the way Galaxy supplies +them (see example below), they: + +1. Install the tool factory on a personal private instance + +2. Upload a small test data set + +3. Paste the script into the 'script' text box and iteratively run the +insecure tool on test data until it works right - there is absolutely no +reason to do this anywhere other than on a personal private instance. + +4. Once it works right, set the 'Generate toolshed gzip' option and run +it again. + +5. A toolshed style gzip appears ready to upload and install like any other +Toolshed entry. + +6. Upload the new tool to the toolshed + +7. Ask the local admin to check the new tool to confirm it's not evil and +install it in the local production galaxy + + + +**Parameter passing and file inputs** + +Your script will receive up to 3 named parameters +INPATHS is a comma separated list of input file paths +INNAMES is a comma separated list of input file names in the same order +OUTPATH is optional if a file is being generated, your script should write there +Your script should open and write files in the provided working directory if you are using the Html +automatic presentation option. + +Python script command lines will have --INPATHS and --additional_arguments etc. to make it easy to use argparse + +Rscript will need to use commandArgs(TRUE) - see the example below - additional arguments will +appear as themselves - eg foo="bar" will mean that foo is defined as "bar" for the script. + +Bash and sh will see any additional parameters on their command lines and the 3 named parameters +in their environment magically - well, using env on the CL +``` +***python***:: + + # argparse for 3 possible comma separated lists + # additional parameters need to be parsed ! + # then echo parameters to the output file + import sys + import argparse + argp=argparse.ArgumentParser() + argp.add_argument('--INNAMES',default=None) + argp.add_argument('--INPATHS',default=None) + argp.add_argument('--OUTPATH',default=None) + argp.add_argument('--additional_parameters',default=[],action="append") + argp.add_argument('otherargs', nargs=argparse.REMAINDER) + args = argp.parse_args() + f= open(args.OUTPATH,'w') + s = '### args=%s\n' % str(args) + f.write(s) + s = 'sys.argv=%s\n' % sys.argv + f.write(s) + f.close() + + + +***Rscript***:: + + # tool factory Rscript parser suggested by Forester + # http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/ + # additional parameters will appear in the ls() below - they are available + # to your script + # echo parameters to the output file + ourargs = commandArgs(TRUE) + if(length(ourargs)==0){ + print("No arguments supplied.") + }else{ + for(i in 1:length(ourargs)){ + eval(parse(text=ourargs[[i]])) + } + sink(OUTPATH) + cat('INPATHS=',INPATHS,'\n') + cat('INNAMES=',INNAMES,'\n') + cat('OUTPATH=',OUTPATH,'\n') + x=ls() + cat('all objects=',x,'\n') + sink() + } + sessionInfo() + print.noquote(date()) + + +***bash/sh***:: + + # tool factory sets up these environmental variables + # this example writes those to the output file + # additional params appear on command line + if [ ! -f "$OUTPATH" ] ; then + touch "$OUTPATH" + fi + echo "INPATHS=$INPATHS" >> "$OUTPATH" + echo "INNAMES=$INNAMES" >> "$OUTPATH" + echo "OUTPATH=$OUTPATH" >> "$OUTPATH" + echo "CL=$@" >> "$OUTPATH" + +***perl***:: + + (my $INPATHS,my $INNAMES,my $OUTPATH ) = @ARGV; + open(my $fh, '>', $OUTPATH) or die "Could not open file '$OUTPATH' $!"; + print $fh "INPATHS=$INPATHS\n INNAMES=$INNAMES\n OUTPATH=$OUTPATH\n"; + close $fh; + +``` + +Galaxy as an IDE for developing API scripts +If you need to develop Galaxy API scripts and you like to live dangerously, +please read on. + +Galaxy as an IDE? +Amazingly enough, blend-lib API scripts run perfectly well *inside* +Galaxy when pasted into a Tool Factory form. No need to generate a new +tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, +it is actually quite useable. + +Why bother - what's wrong with Eclipse +Nothing. But, compared with developing API scripts in the usual way outside +Galaxy, you get persistence and other framework benefits plus at absolutely +no extra charge, a ginormous security problem if you share the history or +any outputs because they contain the api script with key so development +servers only please! + +Workflow +Fire up the Tool Factory in Galaxy. + +Leave the input box empty, set the interpreter to python, paste and run an +api script - eg working example (substitute the url and key) below. + +It took me a few iterations to develop the example below because I know +almost nothing about the API. I started with very simple code from one of the +samples and after each run, the (edited..) api script is conveniently recreated +using the redo button on the history output item. So each successive version +of the developing api script you run is persisted - ready to be edited and +rerun easily. It is ''very'' handy to be able to add a line of code to the +script and run it, then view the output to (eg) inspect dicts returned by +API calls to help move progressively deeper iteratively. + +Give the below a whirl on a private clone (install the tool factory from +the main toolshed) and try adding complexity with few rerun/edit/rerun cycles. + +Eg tool factory api script +``` +import sys +from blend.galaxy import GalaxyInstance +ourGal = 'http://x.x.x.x:xxxx' +ourKey = 'xxx' +gi = GalaxyInstance(ourGal, key=ourKey) +libs = gi.libraries.get_libraries() +res = [] +# libs looks like +# u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': +u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data', +for lib in libs: + res.append('%s:\n' % lib['name']) + res.append(str(gi.libraries.show_library(lib['id'],contents=True))) +outf=open(sys.argv[2],'w') +outf.write('\n'.join(res)) +outf.close() +``` + +**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 + +**screenshot** + +![example run](/images/dynamicScriptTool.png) + + +``` + diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/images/dynamicScriptTool.png Binary file toolfactory/images/dynamicScriptTool.png has changed diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/rgToolFactory2.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.py Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,610 @@ +# 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 = '~~~' + +# --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help" +IPATHPOS = 0 +ICLPOS = 1 +IFMTPOS = 2 +ILABPOS = 3 +IHELPOS = 4 +IOCLPOS = 5 +# --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL +ONAMEPOS = 0 +OFMTPOS = 1 +OCLPOS = 2 +OOCLPOS = 3 + +#--additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL" +ANAMEPOS = 0 +AVALPOS = 1 +ALABPOS = 2 +AHELPPOS = 3 +ATYPEPOS = 4 +ACLPOS = 5 +AOCLPOS = 6 + +def timenow(): + """return current time as a string + """ + return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + + +def quote_non_numeric(s): + """return a prequoted string for non-numerics + useful for perl and Rscript parameter passing? + """ + try: + _ = float(s) + return s + except ValueError: + return '"%s"' % s + + +html_escape_table = { + "&": "&", + ">": ">", + "<": "<", + "$": 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 + """ + + self.infiles = [x.split(ourdelim) for x in args.input_files] + self.outfiles = [x.split(ourdelim) for x in args.output_files] + self.addpar = [x.split(ourdelim) for x in args.additional_parameters] + self.args = args + self.cleanuppar() + self.lastclredirect = None + self.lastxclredirect = None + self.cl = [] + self.xmlcl = [] + aCL = self.cl.append + assert args.parampass in ['0','argparse','positional'],'Parameter passing in args.parampass must be "0","positional" or "argparse"' + 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.runmode == "Executable" or self.args.runmode == "system": # binary - no need + aCL(self.args.exe_package) # this little CL will just run + else: + rx = open(self.args.script_path, 'r').readlines() + rx = [x.rstrip() for x in rx ] + rxcheck = [x.strip() for x in rx if x.strip() > ''] + assert len(rxcheck) > 0,"Supplied script is empty. Cannot run" + self.script = '\n'.join(rx) + fhandle, self.sfile = tempfile.mkstemp( + prefix=self.tool_name, suffix=".%s" % (args.interpreter_name)) + 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]) + art = '%s.%s' % (self.tool_name, args.interpreter_name) + artifact = open(art, 'wb') + artifact.write(bytes(self.script, "utf8")) + artifact.close() + aCL(self.args.interpreter_name) + aCL(self.sfile) + self.elog = "%s_error_log.txt" % self.tool_name + self.tlog = "%s_runner_log.txt" % self.tool_name + + if self.args.parampass == '0': + self.clsimple() + else: + clsuffix = [] + xclsuffix = [] + for i, p in enumerate(self.infiles): + appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS]] + clsuffix.append(appendme) + xclsuffix.append([p[IOCLPOS],p[ICLPOS],'$%s' % p[ICLPOS]]) + #print('##infile i=%d, appendme=%s' % (i,appendme)) + for i, p in enumerate(self.outfiles): + if p[OOCLPOS] == "STDOUT": + self.lastclredirect = ['>',p[ONAMEPOS]] + self.lastxclredirect = ['>','$%s' % p[OCLPOS]] + #print('##outfiles i=%d lastclredirect = %s' % (i,self.lastclredirect)) + else: + appendme = [p[OOCLPOS], p[OCLPOS],p[ONAMEPOS]] + clsuffix.append(appendme) + xclsuffix.append([p[OOCLPOS], p[OCLPOS],'$%s' % p[ONAMEPOS]]) + #print('##outfiles i=%d' % i,'appendme',appendme) + for p in self.addpar: + appendme = [p[AOCLPOS], p[ACLPOS], p[AVALPOS]] + clsuffix.append(appendme) + xclsuffix.append([p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS]]) + #print('##adpar %d' % i,'appendme=',appendme) + clsuffix.sort() + xclsuffix.sort() + self.xclsuffix = xclsuffix + self.clsuffix = clsuffix + if self.args.parampass == 'positional': + self.clpositional() + else: + self.clargparse() + + def cleanuppar(self): + """ positional parameters are complicated by their numeric ordinal""" + for i,p in enumerate(self.infiles): + if self.args.parampass == 'positional': + assert p[ICLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[ICLPOS],p[ILABPOS]) + p.append(p[ICLPOS]) + if p[ICLPOS].isdigit() or self.args.parampass == "0": + scl = 'input%d' % (i+1) + p[ICLPOS] = scl + self.infiles[i] = p + for i,p in enumerate(self.outfiles): # trying to automagically gather using extensions + if self.args.parampass == 'positional' and p[OCLPOS] != "STDOUT": + assert p[OCLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[OCLPOS],p[ONAMEPOS]) + p.append(p[OCLPOS]) + if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": + scl = p[ONAMEPOS] + p[OCLPOS] = scl + self.outfiles[i] = p + for i,p in enumerate(self.addpar): + if self.args.parampass == 'positional': + assert p[ACLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[ACLPOS],p[ANAMEPOS]) + p.append(p[ACLPOS]) + if p[ACLPOS].isdigit(): + scl = 'input%s' % p[ACLPOS] + p[ACLPOS] = scl + self.addpar[i] = p + + + + def clsimple(self): + """ no parameters - uses < and > for i/o + """ + aCL = self.cl.append + aCL('<') + aCL(self.infiles[0][IPATHPOS]) + aCL('>') + aCL(self.outfiles[0][OCLPOS]) + aXCL = self.xmlcl.append + aXCL('<') + aXCL('$%s' % self.infiles[0][ICLPOS]) + aXCL('>') + aXCL('$%s' % self.outfiles[0][ONAMEPOS]) + + + def clpositional(self): + # inputs in order then params + aCL = self.cl.append + for (o_v,k, v) in self.clsuffix: + if " " in v: + aCL("%s" % v) + else: + aCL(v) + aXCL = self.xmlcl.append + for (o_v,k, v) in self.xclsuffix: + aXCL(v) + if self.lastxclredirect: + aXCL(self.lastxclredirect[0]) + aXCL(self.lastxclredirect[1]) + + + + def clargparse(self): + """ argparse style + """ + aCL = self.cl.append + aXCL = self.xmlcl.append + # inputs then params in argparse named form + for (o_v,k, v) in self.xclsuffix: + aXCL(k) + aXCL(v) + for (o_v,k, v) in self.clsuffix: + if len(k.strip()) == 1: + k = '-%s' % k + else: + k = '--%s' % k + aCL(k) + aCL(v) + + + + + def makeXML(self): + """ + Create a Galaxy xml tool wrapper for the new script + Uses galaxyhtml + Hmmm. How to get the command line into correct order... + """ + + if self.args.interpreter_name: + exe = "$runMe" + 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) + tool.command_line_override = self.xmlcl + print('#### tool cl override=',self.xmlcl) + if interp: + tool.interpreter = interp + if self.args.help_text: + helptext = open(self.args.help_text, 'r').readlines() + 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 + tinputs = gxtp.Inputs() + toutputs = gxtp.Outputs() + requirements = gxtp.Requirements() + testparam = [] + is_positional = (self.args.parampass == 'positional') + if self.args.interpreter_name: + if self.args.interpreter_name == 'python': + 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 and self.args.parampass != "system": + requirements.append(gxtp.Requirement( + 'package', self.args.exe_package, self.args.exe_package_version)) + tool.requirements = requirements + if self.args.parampass == '0': + alab = self.infiles[0][ILABPOS] + if len(alab) == 0: + alab = self.infiles[0][ICLPOS] + max1s = 'Maximum one input if parampass is 0 - more than one input files supplied - %s' % str(self.infiles) + assert len(self.infiles) == 1,max1s + newname = self.infiles[0][ICLPOS] + aninput = gxtp.DataParam(newname, optional=False, label=alab, help=self.infiles[0][IHELPOS], + format=self.infiles[0][IFMTPOS], multiple=False, num_dashes=0) + aninput.command_line_override = '< $%s' % newname + aninput.positional = is_positional + tinputs.append(aninput) + tp = gxtp.TestParam(name=newname, value='%s_sample' % newname) + testparam.append(tp) + newname = self.outfiles[0][OCLPOS] + newfmt = self.outfiles[0][OFMTPOS] + anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) + anout.command_line_override = '> $%s' % newname + anout.positional = is_positional + toutputs.append(anout) + tp = gxtp.TestOutput(name=newname, value='%s_sample' % newname,format=newfmt) + testparam.append(tp) + else: + for p in self.outfiles: + newname,newfmt,newcl,oldcl = p + if is_positional: + ndash = 0 + else: + ndash = 2 + if len(newcl) < 2: + ndash = 1 + aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) + aparm.positional = is_positional + if is_positional: + if oldcl == "STDOUT": + aparm.positional = 9999999 + aparm.command_line_override = "> $%s" % newcl + else: + aparm.positional = int(oldcl) + aparm.command_line_override = '$%s' % newcl + toutputs.append(aparm) + tp = gxtp.TestOutput(name=newcl, value='%s_sample' % newcl ,format=newfmt) + testparam.append(tp) + for p in self.infiles: + newname = p[ICLPOS] + newfmt = p[IFMTPOS] + if is_positional: + ndash = 0 + else: + if len(newname) > 1: + ndash = 2 + else: + ndash = 1 + if not len(p[ILABPOS]) > 0: + alab = p[ICLPOS] + else: + alab = p[ILABPOS] + aninput = gxtp.DataParam(newname, optional=False, label=alab, help=p[IHELPOS], + format=newfmt, multiple=False, num_dashes=ndash) + aninput.positional = is_positional + if is_positional: + aninput.positional = is_positional + tinputs.append(aninput) + tparm = gxtp.TestParam(name=newname, value='%s_sample' % newname ) + testparam.append(tparm) + for p in self.addpar: + newname, newval, newlabel, newhelp, newtype, newcl, oldcl = p + if not len(newlabel) > 0: + newlabel = newname + if is_positional: + ndash = 0 + else: + 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 + if is_positional: + aninput.positional = int(oldcl) + tinputs.append(aparm) + tparm = gxtp.TestParam(newname, value=newval) + testparam.append(tparm) + tool.outputs = toutputs + tool.inputs = tinputs + if not self.args.runmode in ['Executable','system']: + configfiles = gxtp.Configfiles() + configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) + tool.configfiles = configfiles + tests = gxtp.Tests() + test_a = gxtp.Test() + for tp in testparam: + test_a.append(tp) + 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 ... + NOTE names for test inputs and outputs are munged here so must + correspond to actual input and output names used on the generated cl + """ + retval = self.run() + if retval: + sys.stderr.write( + '## Run failed. Cannot build yet. Please fix and retry') + sys.exit(1) + tdir = 'tfout' + 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 p in self.infiles: + pth = p[IPATHPOS] + dest = os.path.join(testdir, '%s_sample' % + p[ICLPOS]) + shutil.copyfile(pth, dest) + for p in self.outfiles: + pth = p[OCLPOS] + if p[OOCLPOS] == 'STDOUT' or self.args.parampass == "0": + pth = p[ONAMEPOS] + dest = os.path.join(testdir,'%s_sample' % p[ONAMEPOS]) + shutil.copyfile(pth, dest) + dest = os.path.join(tdir, p[ONAMEPOS]) + shutil.copyfile(pth, dest) + else: + pth = p[OCLPOS] + dest = os.path.join(testdir,'%s_sample' % p[OCLPOS]) + shutil.copyfile(pth, dest) + dest = os.path.join(tdir, p[OCLPOS]) + shutil.copyfile(pth, dest) + + if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0: + shutil.copyfile(self.tlog, os.path.join( + testdir, 'test1_log.txt')) + if not self.args.runmode in ['Executable','system']: + stname = os.path.join(tdir, '%s' % (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 = 'toolfactory_%s.tgz' % self.tool_name + tf = tarfile.open(tarpath,"w:gz") + tf.add(name=tdir,arcname=self.tool_name) + tf.close() + shutil.copyfile(tarpath, self.args.new_tool) + return retval + + def run(self): + """ + Some devteam tools have this defensive stderr read so I'm keeping with the faith + Feel free to update. + """ + s = 'run cl=%s' % str(self.cl) + + logging.debug(s) + scl = ' '.join(self.cl) + err = None + if self.args.parampass != '0': + ste = open(self.elog, 'wb') + if self.lastclredirect: + sto = open(self.lastclredirect[1],'wb') # is name of an output file + else: + 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) + 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.infiles[0][IPATHPOS], 'rb') + sto = open(self.outfiles[0][ONAMEPOS], '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 os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0: + os.unlink(self.tlog) + if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0: + os.unlink(self.elog) + 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: + rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" + + """ + 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('--input_files', default=[], action="append") + a('--output_files', default=[], action="append") + 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('--tool_version', default=None) + a('--citations', default=None) + a('--additional_parameters', action='append', default=[]) + a('--edit_additional_parameters', action="store_true", default=False) + a('--parampass', default="positional") + a('--tfout', default="./tfout") + a('--new_tool',default="new_tool") + a('--runmode',default=None) + 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' + 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() diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/rgToolFactory2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/rgToolFactory2.xml Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,460 @@ + + Scripts into tools + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + python + + + + + +#if $interexe.interpreter != "Executable" and $interexe.interpreter != "system" : +${interexe.dynScript} +#else: +$tool_name +#end if + + + #if $makeMode.make_Tool == "yes": +${makeMode.help_text} + #else +$tool_name help goes here + #end if + + +#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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + makeMode['make_Tool'] == "yes" + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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, or even better, submit a pull request fixing it, on the github repository GTF_ + +**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://github.com/fubar2/toolfactory +.. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573 + + + + + 10.1093/bioinformatics/bts573 + + + + diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/test-data/infile.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/infile.tabular Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,7 @@ +0.1 +0.00001 +0.2 +0.3 +0.004 +0.5 +0.000000002 diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/test-data/reverseargp2.toolshed.gz Binary file toolfactory/test-data/reverseargp2.toolshed.gz has changed diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/test-data/reverseargp2_test1_output.xls diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/test-data/runme.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/runme.py Fri Aug 07 07:54:23 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() diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/test-data/test1_out.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/test1_out.log Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,1 @@ +## Executing Toolfactory generated command line = python3 /home/ross/galaxy/database/tmp/reverseargp2tzq9wpni.python --infile /home/ross/galaxy/database/objects/3/5/2/dataset_352183fc-9148-44e6-a703-0c1b06d0a365.dat --outfile /home/ross/galaxy/database/objects/6/1/3/dataset_613ab089-f4d1-493c-baf5-0a0bbaebaff8.dat --prefix "hello world" diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/test-data/toolfactory.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/test-data/toolfactory.log Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,39 @@ +### cl=python3 /tmp/reverseargp2_test1veulkauo.python -- /tmp/tmpzal0_664/files/c/8/4/dataset_c84573ea-e358-4a99-bac6-3dfe1b030c65.dat -- /tmp/tmpzal0_664/files/e/b/2/dataset_eb270919-0c8c-4b52-9e58-d351de848508.dat +xml= + + + + testing_tf2 + + python + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 6db39cbc3242 -r 6f48315c32c1 toolfactory/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/tool_dependencies.xml Fri Aug 07 07:54:23 2020 -0400 @@ -0,0 +1,12 @@ + + + + + + + + + + Only Admins can use this tool generator but please do NOT install on a public facing Galaxy as it exposes unrestricted scripting as your Galaxy user + +