view rgToolFactory.py @ 20:3f58115c6c5b

Getting ready to implement the test generator. Brainfuck is easier.

# rgToolFactory.py
# https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home

# this is a tool factory for simple scripts in python, R or whatever ails ye.
# 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 binds 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.
# a list in the xml source file is searched for users permitted to run this tool.
# PUT some IDs in the list in the XML before you restart Galaxy to load this new tool please
# otherwise, the tool won't run for anybody.
#

# 
# 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

import sys 
import shutil 
import subprocess 
import os 
import time 
import tempfile 
import optparse
import tarfile
import re
import shutil

progname = os.path.split(sys.argv[0])[1] 
myversion = 'V000.1 May 2012' 
verbose = False 
debug = False


def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
# characters that are allowed but need to be escaped

class ScriptRunner:
    """class is a wrapper for an arbitrary script
    """

    def __init__(self,opts=None):
        """
        cleanup inputs, setup some outputs
        
        """
        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)
        self.toolid = self.toolname
        s = open(self.opts.script_path,'r').read()
        self.script = s
        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
        self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
        if opts.output_dir: # may not want these complexities 
            self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
            artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname) 
            artifact = open(artifactpath,'w')
            artifact.write(self.script)
            artifact.write('\n')
            artifact.close()
        if opts.make_Tool: # need this code and the user script for the tarball 
            localscript = open(self.sfile,'w')
            localscript.write(self.script)
            localscript.close()
            shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user 
        self.cl = []
        self.html = []
        a = self.cl.append
        a(opts.interpreter)
        a('-') # use 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 = 'test1_input.xls'
        self.test1Output = 'test1_output.xls'
        self.test1HTML = 'test1_output.html'

    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="0.01">
            %(tooldesc)s
            %(command)s
            <inputs>
            %(inputs)s
            </inputs>
            <outputs>
            %(outputs)s
            </outputs>
            <help>
            %(help)s
            </help>
            <configfiles>
            <configfile name="runMe">
            %(script)s
            </configfile>
            </configfiles>
            </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 "$runMe" --interpreter "%(interpreter)s" 
            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
            </command>""" # may NOT be an input or htmlout
        tooltests = """<tests><test>
        <param name="input1" value="%s" ftype="%s"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        </test><tests>"""
        xdict = {}
        xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
        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'
        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 "$input1"'
            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
        else:
            xdict['command_inputs'] = '' # assume no input - eg a random data generator          
            xdict['inputs'] = ''
        xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/>\n' % self.toolname
        xdict['toolname'] = self.toolname
        xdict['toolid'] = self.toolid
        xdict['interpreter'] = self.opts.interpreter
        xdict['scriptname'] = self.sfile
        if self.opts.make_HTML:
            xdict['command_outputs'] += '--output_dir "$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': # we may have test data?
            testdir = os.path.join(tdir,'test-data')
            os.mkdir(testdir) # make tests directory
            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,'test1_in.tab'))
            if self.opts.output_tab <> 'None':
                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,'test1_out.tab'))
            if self.opts.make_HTML:
                shutil.copyfile(self.opts.output_html,os.path.join(testdir,'test1_out.html'))
            if self.opts.output_dir:
                shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
        shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
        shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
        shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
        tarpath = "%s.gz" % self.toolname
        tar = tarfile.open(tarpath, "w:gz")
        tar.add(tdir,arcname=self.toolname)
        tar.close()
        shutil.copy(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):
            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 artefacts found in the output_dir
        """

        galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> 
        <!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="document"> 
        """ 
        galhtmlattr = """<hr/><b><a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><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 = [galhtmlprefix % progname,]
        html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow()))
        fhtml = []
        if len(flist) > 0:
            html.append('<table cellpadding="3" cellspacing="3">\n')
            for fname in 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:
                        s= '<tr><td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="10" width="600"></a></td></tr>\n' % (fname,thumb,fname)
                        html.append(s)
                    fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
                else:
                    fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
            html.append('</table>\n')
        if len(fhtml) > 0:
           fhtml.insert(0,'<ul>')
           fhtml.append('</ul><br/>')
           html += fhtml # add all non-pdf files to the end of the display
        else:
            html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
            html.append('<h3>%s log follows below</h3><hr/><pre><br/>\n' % self.opts.interpreter)
        rlog = open(self.tlog,'r').readlines()
        html += rlog
        html.append('<br/>%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
        html.append('</pre>\n')
        html.append(galhtmlattr % (progname,timenow()))
        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):
        """
        """
        if self.opts.output_dir:
            sto = open(self.tlog,'w')
            p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
        else:
            p = subprocess.Popen(' '.join(self.cl),shell=True,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 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=None)
    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)
    opts, args = op.parse_args()
    assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to %s.xml' % (opts.bad_user,os.path.splitext(self.myname)[0])
    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()
    if retcode:
        sys.exit(retcode) # indicate failure to job runner


if __name__ == "__main__":
    main()