differential_count_models: rgToolFactory.py comparison

comparison rgToolFactory.py @ 32:8051d14cf819 draft

update with better filtering

author	fubar
date	Sun, 22 Dec 2013 01:32:29 -0500
parents
children

comparison

equal deleted inserted replaced

-:5b6af671d985
+:8051d14cf819
+# 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
+#
+# 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()))
+cheetah_escape_table = {
+"$": "\$"
+}
+cheetah_unescape_table = {
+"\$": "$"
+}
+def html_escape(t):
+"""Unescape \$ first in case already done
+cheetah barfs if any $ without \
+xml parsing is controlled with <![CDATA[...]]>
+"""
+text = t
+for k in cheetah_unescape_table.keys():
+text = text.replace(k,cheetah_unescape_table[k])
+for k in cheetah_escape_table.keys():
+text = text.replace(k,cheetah_escape_table[k])
+return text
+class ScriptRunner:
+"""class is a wrapper for an arbitrary script
+"""
+def __init__(self,opts=None,treatbashSpecial=True):
+"""
+cleanup inputs, setup some outputs
+"""
+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.escapedS = [html_escape(x) for x in s] # for restructured text in help
+self.escapedScript = '\n'.join(self.escapedS)
+self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
+if opts.output_dir: # may not want these complexities
+self.tlog = os.path.join(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">
+<![CDATA[
+%(script)s
+]]>
+</configfile>
+</configfiles>
+%(tooltests)s
+<help>
+<![CDATA[
+%(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::\n']
+coda.append(self.indentedScript)
+coda.append('\n\n')
+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", "-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)
+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:
+pdflist = []
+npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
+nacross = 1
+if npdf > 0:
+nacross = int(round(math.log(npdf,2)))
+nacross = max(1,nacross)
+width = min(400,int(1200/nacross))
+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))
+ntogo = nacross # counter for table row padding with empty cells
+if len(pdflist) > 0:
+html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
+for i,paths in enumerate(pdflist):
+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>&nbsp;</td>'*ntogo)
+html.append('</tr></table></div>\n')
+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 += 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)
+rlog = open(self.tlog,'r').readlines()
+rlog = [x for x in rlog if x.strip() > '']
+if len(rlog) > 1:
+html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
+html += rlog
+html.append('</pre>\n')
+html.append(galhtmlattr % (self.toolname))
+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()

Mercurial > repos > fubar > differential_count_models

comparison rgToolFactory.py @ 32:8051d14cf819 draft