Mercurial > repos > fubar > edger_test
diff rgedgeR/rgToolFactory.py @ 54:b1d6dae9c309 draft default tip
Deleted selected files
| author | fubar |
|---|---|
| date | Fri, 26 Jul 2013 23:47:03 -0400 |
| parents | 9cbc5a72fc3f |
| children |
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--- a/rgedgeR/rgToolFactory.py Fri Jul 26 23:46:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,599 +0,0 @@ -# rgToolFactory.py -# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -# -# 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://bitbucket.org/fubar/galaxytoolfactory/wiki/Home -# -# july 2013 -# added ability to combine images and individual log files into html output -# just make sure there's a log file foo.log and it will be output -# together with all images named like "foo_*.pdf -# otherwise old format for html -# -# January 2013 -# problem pointed out by Carlos Borroto -# added escaping for <>$ - thought I did that ages ago... -# -# August 11 2012 -# changed to use shell=False and cl as a sequence - -# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye. -# It also serves as the wrapper for the new tool. -# -# you paste and run your script -# Only works for 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 page. - -# DO NOT install on a public or important site - please. - -# installed generated tools are fine if 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 - -# After you get the script working on some test data, you can -# optionally generate a toolshed compatible gzip file -# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for -# safe and largely automated installation in a production Galaxy. - -# 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 appreciated please. -# -# -# long route to June 2012 product -# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them -# derived from an integrated script model -# called rgBaseScriptWrapper.py -# Note to the unwary: -# This tool allows arbitrary scripting on your Galaxy as the Galaxy user -# There is nothing stopping a malicious user doing whatever they choose -# Extremely dangerous!! -# Totally insecure. So, trusted users only -# -# preferred model is a developer using their throw away workstation instance - ie a private site. -# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. -# - -import sys -import shutil -import subprocess -import os -import time -import tempfile -import optparse -import tarfile -import re -import shutil -import math - -progname = os.path.split(sys.argv[0])[1] -myversion = 'V000.2 June 2012' -verbose = False -debug = False -toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory' - -def timenow(): - """return current time as a string - """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) - -html_escape_table = { - "&": "&", - ">": ">", - "<": "<", - "$": "\$" - } - -def html_escape(text): - """Produce entities within text.""" - return "".join(html_escape_table.get(c,c) for c in text) - -def cmd_exists(cmd): - return subprocess.call("type " + cmd, shell=True, - stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0 - - -class ScriptRunner: - """class is a wrapper for an arbitrary script - """ - - def __init__(self,opts=None,treatbashSpecial=True): - """ - cleanup inputs, setup some outputs - - """ - self.useGM = cmd_exists('gm') - self.useIM = cmd_exists('convert') - self.useGS = cmd_exists('gs') - self.treatbashSpecial = treatbashSpecial - if opts.output_dir: # simplify for the tool tarball - os.chdir(opts.output_dir) - self.thumbformat = 'jpg' - self.opts = opts - self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but.. - self.toolid = self.toolname - self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later - self.pyfile = self.myname # crude but efficient - the cruft won't hurt much - self.xmlfile = '%s.xml' % self.toolname - s = open(self.opts.script_path,'r').readlines() - s = [x.rstrip() for x in s] # remove pesky dos line endings if needed - self.script = '\n'.join(s) - fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter)) - tscript = open(self.sfile,'w') # use self.sfile as script source for Popen - tscript.write(self.script) - tscript.close() - self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help - self.escapedScript = '\n'.join([html_escape(x) for x in s]) - if opts.output_dir: # may not want these complexities - self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname) - art = '%s.%s' % (self.toolname,opts.interpreter) - artpath = os.path.join(self.opts.output_dir,art) # need full path - artifact = open(artpath,'w') # use self.sfile as script source for Popen - artifact.write(self.script) - artifact.close() - self.cl = [] - self.html = [] - a = self.cl.append - a(opts.interpreter) - if self.treatbashSpecial and opts.interpreter in ['bash','sh']: - a(self.sfile) - else: - a('-') # stdin - a(opts.input_tab) - a(opts.output_tab) - self.outFormats = 'tabular' # TODO make this an option at tool generation time - self.inputFormats = 'tabular' # TODO make this an option at tool generation time - self.test1Input = '%s_test1_input.xls' % self.toolname - self.test1Output = '%s_test1_output.xls' % self.toolname - self.test1HTML = '%s_test1_output.html' % self.toolname - - def makeXML(self): - """ - Create a Galaxy xml tool wrapper for the new script as a string to write out - fixme - use templating or something less fugly than this example of what we produce - - <tool id="reverse" name="reverse" version="0.01"> - <description>a tabular file</description> - <command interpreter="python"> - reverse.py --script_path "$runMe" --interpreter "python" - --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" - </command> - <inputs> - <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/> - - </inputs> - <outputs> - <data format="tabular" name="tab_file" label="${job_name}"/> - - </outputs> - <help> - -**What it Does** - -Reverse the columns in a tabular file - - </help> - <configfiles> - <configfile name="runMe"> - -# reverse order of columns in a tabular file -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r') -o = open(outp,'w') -for row in i: - rs = row.rstrip().split('\t') - rs.reverse() - o.write('\t'.join(rs)) - o.write('\n') -i.close() -o.close() - - - </configfile> - </configfiles> - </tool> - - """ - newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s"> - %(tooldesc)s - %(command)s - <inputs> - %(inputs)s - </inputs> - <outputs> - %(outputs)s - </outputs> - <configfiles> - <configfile name="runMe"> - %(script)s - </configfile> - </configfiles> - %(tooltests)s - <help> - %(help)s - </help> - </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto - - newCommand="""<command interpreter="python"> - %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" - --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s - </command>""" # may NOT be an input or htmlout - tooltestsTabOnly = """<tests><test> - <param name="input1" value="%(test1Input)s" ftype="tabular"/> - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="tab_file" file="%(test1Output)s" ftype="tabular"/> - </test></tests>""" - tooltestsHTMLOnly = """<tests><test> - <param name="input1" value="%(test1Input)s" ftype="tabular"/> - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/> - </test></tests>""" - tooltestsBoth = """<tests><test> - <param name="input1" value="%(test1Input)s" ftype="tabular"/> - <param name="job_name" value="test1"/> - <param name="runMe" value="$runMe"/> - <output name="tab_file" file="%(test1Output)s" ftype="tabular" /> - <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/> - </test></tests>""" - xdict = {} - xdict['tool_version'] = self.opts.tool_version - xdict['test1Input'] = self.test1Input - xdict['test1HTML'] = self.test1HTML - xdict['test1Output'] = self.test1Output - if self.opts.make_HTML and self.opts.output_tab <> 'None': - xdict['tooltests'] = tooltestsBoth % xdict - elif self.opts.make_HTML: - xdict['tooltests'] = tooltestsHTMLOnly % xdict - else: - xdict['tooltests'] = tooltestsTabOnly % xdict - xdict['script'] = self.escapedScript - # configfile is least painful way to embed script to avoid external dependencies - # but requires escaping of <, > and $ to avoid Mako parsing - if self.opts.help_text: - xdict['help'] = open(self.opts.help_text,'r').read() - else: - xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation' - coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::'] - coda.append(self.indentedScript) - coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow())) - coda.append('See %s for details of that project' % (toolFactoryURL)) - coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ') - coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573') - xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda)) - if self.opts.tool_desc: - xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc - else: - xdict['tooldesc'] = '' - xdict['command_outputs'] = '' - xdict['outputs'] = '' - if self.opts.input_tab <> 'None': - xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something - xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats - else: - xdict['command_inputs'] = '' # assume no input - eg a random data generator - xdict['inputs'] = '' - xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname - xdict['toolname'] = self.toolname - xdict['toolid'] = self.toolid - xdict['interpreter'] = self.opts.interpreter - xdict['scriptname'] = self.sfile - if self.opts.make_HTML: - xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" ' - xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n' - if self.opts.output_tab <> 'None': - xdict['command_outputs'] += ' --output_tab "$tab_file"' - xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats - xdict['command'] = newCommand % xdict - xmls = newXML % xdict - xf = open(self.xmlfile,'w') - xf.write(xmls) - 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: - print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry' - sys.exit(1) - self.makeXML() - tdir = self.toolname - os.mkdir(tdir) - if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe.. - testdir = os.path.join(tdir,'test-data') - os.mkdir(testdir) # make tests directory - shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input)) - if self.opts.output_tab <> 'None': - shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output)) - if self.opts.make_HTML: - shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML)) - if self.opts.output_dir: - shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log')) - op = '%s.py' % self.toolname # new name - outpiname = os.path.join(tdir,op) # path for the tool tarball - pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM) - notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),] - notes.append('# to make a new Galaxy tool called %s\n' % self.toolname) - notes.append('# User %s at %s\n' % (self.opts.user_email,timenow())) - pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm - notes += pi - outpi = open(outpiname,'w') - outpi.write(''.join(notes)) - outpi.write('\n') - outpi.close() - 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.gz" % self.toolname - tar = tarfile.open(tarpath, "w:gz") - tar.add(tdir,arcname=self.toolname) - tar.close() - shutil.copyfile(tarpath,self.opts.new_tool) - shutil.rmtree(tdir) - ## TODO: replace with optional direct upload to local toolshed? - return retval - - - def compressPDF(self,inpdf=None,thumbformat='png'): - """need absolute path to pdf - """ - assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName) - hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname) - sto = open(hlog,'w') - outpdf = '%s_compressed' % inpdf - cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf] - x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - retval1 = x.wait() - if retval1 == 0: - os.unlink(inpdf) - shutil.move(outpdf,inpdf) - outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat) - if self.useGM: - cl2 = ['gm convert', inpdf, outpng] - else: # assume imagemagick - cl2 = ['convert', inpdf, outpng] - x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - retval2 = x.wait() - sto.close() - retval = retval1 or retval2 - return retval - - - def getfSize(self,fpath,outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath,fpath) - if os.path.isfile(fp): - size = '0 B' - n = float(os.path.getsize(fp)) - if n > 2**20: - size = '%1.1f MB' % (n/2**20) - elif n > 2**10: - size = '%1.1f KB' % (n/2**10) - elif n > 0: - size = '%d B' % (int(n)) - return size - - def makeHtml(self): - """ Create an HTML file content to list all the artifacts found in the output_dir - """ - - galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> - <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> - <title></title> - <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> - </head> - <body> - <div class="toolFormBody"> - """ - galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" - galhtmlpostfix = """</div></body></html>\n""" - - flist = os.listdir(self.opts.output_dir) - flist = [x for x in flist if x <> 'Rplots.pdf'] - flist.sort() - html = [] - html.append(galhtmlprefix % progname) - html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections - logfiles.sort() - logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)] - logfiles.append(os.path.abspath(self.tlog)) # make it the last one - pdflist = [] - npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']) - for rownum,fname in enumerate(flist): - dname,e = os.path.splitext(fname) - sfsize = self.getfSize(fname,self.opts.output_dir) - if e.lower() == '.pdf' : # compress and make a thumbnail - thumb = '%s.%s' % (dname,self.thumbformat) - pdff = os.path.join(self.opts.output_dir,fname) - retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat) - if retval == 0: - pdflist.append((fname,thumb)) - if (rownum+1) % 2 == 0: - fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) - else: - fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize)) - for logfname in logfiles: # expect at least tlog - if more - if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later - sectionname = 'All tool run' - if (len(logfiles) > 1): - sectionname = 'Other' - ourpdfs = pdflist - else: - realname = os.path.basename(logfname) - sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log - ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname] - pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove - nacross = 1 - npdf = len(ourpdfs) - - if npdf > 0: - nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2))) - if int(nacross)**2 != npdf: - nacross += 1 - nacross = int(nacross) - width = min(400,int(1200/nacross)) - html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname) - html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>') - ntogo = nacross # counter for table row padding with empty cells - html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>') - for i,paths in enumerate(ourpdfs): - fname,thumb = paths - s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" - alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname) - if ((i+1) % nacross == 0): - s += '</tr>\n' - ntogo = 0 - if i < (npdf - 1): # more to come - s += '<tr>' - ntogo = nacross - else: - ntogo -= 1 - html.append(s) - if html[-1].strip().endswith('</tr>'): - html.append('</table></div>\n') - else: - if ntogo > 0: # pad - html.append('<td> </td>'*ntogo) - html.append('</tr></table></div>\n') - logt = open(logfname,'r').readlines() - logtext = [x for x in logt if x.strip() > ''] - html.append('<div class="toolFormTitle">%s log output</div>' % sectionname) - if len(logtext) > 1: - html.append('\n<pre>\n') - html += logtext - html.append('\n</pre>\n') - else: - html.append('%s is empty<br/>' % logfname) - if len(fhtml) > 0: - fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n') - fhtml.append('</table></div><br/>') - html.append('<div class="toolFormTitle">All output files available for downloading</div>\n') - html += fhtml # add all non-pdf files to the end of the display - else: - html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter) - html.append(galhtmlpostfix) - htmlf = file(self.opts.output_html,'w') - htmlf.write('\n'.join(html)) - htmlf.write('\n') - htmlf.close() - self.html = html - - - def run(self): - """ - scripts must be small enough not to fill the pipe! - """ - if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']: - retval = self.runBash() - else: - if self.opts.output_dir: - sto = open(self.tlog,'w') - sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) - sto.flush() - p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir) - else: - p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) - p.stdin.write(self.script) - p.stdin.close() - retval = p.wait() - if self.opts.output_dir: - sto.close() - if self.opts.make_HTML: - self.makeHtml() - return retval - - def runBash(self): - """ - cannot use - for bash so use self.sfile - """ - if self.opts.output_dir: - s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl) - sto = open(self.tlog,'w') - sto.write(s) - sto.flush() - p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir) - else: - p = subprocess.Popen(self.cl,shell=False) - retval = p.wait() - if self.opts.output_dir: - sto.close() - if self.opts.make_HTML: - self.makeHtml() - return retval - - -def main(): - u = """ - 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> - """ - op = optparse.OptionParser() - a = op.add_option - a('--script_path',default=None) - a('--tool_name',default=None) - a('--interpreter',default=None) - a('--output_dir',default=None) - a('--output_html',default=None) - a('--input_tab',default="None") - a('--output_tab',default="None") - a('--user_email',default='Unknown') - a('--bad_user',default=None) - a('--make_Tool',default=None) - a('--make_HTML',default=None) - a('--help_text',default=None) - a('--tool_desc',default=None) - a('--new_tool',default=None) - a('--tool_version',default=None) - opts, args = op.parse_args() - assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user) - assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' - assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' - assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' - if opts.output_dir: - try: - os.makedirs(opts.output_dir) - except: - pass - r = ScriptRunner(opts) - if opts.make_Tool: - retcode = r.makeTooltar() - else: - retcode = r.run() - os.unlink(r.sfile) - if retcode: - sys.exit(retcode) # indicate failure to job runner - - -if __name__ == "__main__": - main() - -