diff fubar-galaxytoolfactory-cfcf6c9df5b7/rgToolFactory.py @ 1:87613ace5113 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fubar-galaxytoolfactory-cfcf6c9df5b7/rgToolFactory.py	Sat Aug 11 02:41:28 2012 -0400
@@ -0,0 +1,508 @@
+# 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
+
+# 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 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. 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()))
+
+
+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) # a sanitizer now does this but..
+        self.toolid = self.toolname
+        s = open(self.opts.script_path,'r').readlines()
+        self.script = ''.join(s)
+        self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
+        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()
+        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 = '%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.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'
+        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))
+        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()
+        shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
+        shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
+        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 artefacts 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.opts.output_dir:
+            sto = open(self.tlog,'w')
+            sto.write('## FastQC 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 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()
+    if retcode:
+        sys.exit(retcode) # indicate failure to job runner
+
+
+if __name__ == "__main__":
+    main()
+
+