# HG changeset patch # User fubar # Date 1339038358 14400 # Node ID 6985104392b90fec81e9f7e0cfd14562c720f734 # Parent ab0148be211130a3bc014a9bbf65973f79633e02 Deleted selected files diff -r ab0148be2111 -r 6985104392b9 inkblotheatmap/inkblotheatmap.Rscript --- a/inkblotheatmap/inkblotheatmap.Rscript Wed Jun 06 23:04:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ - -# note this script takes NO input or output because it generates random data -foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) -bar = as.matrix(foo) -pdf( "heattest.pdf" ) -heatmap(bar,main='Random Heatmap') -dev.off() diff -r ab0148be2111 -r 6985104392b9 inkblotheatmap/inkblotheatmap.py --- a/inkblotheatmap/inkblotheatmap.py Wed Jun 06 23:04:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,428 +0,0 @@ -# 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. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool. -# - -# -# 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 - - - a tabular file - - reverse.py --script_path "$runMe" --interpreter "python" - --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" - - - - - - - - - - - -**What it Does** - -Reverse the columns in a tabular file - - - - - -# reverse order of columns in a tabular file -import sys -inp = sys.argv[1] -outp = sys.argv[2] -i = open(inp,'r') -o = open(outp,'w') -for row in i: - rs = row.rstrip().split('\t') - rs.reverse() - o.write('\t'.join(rs)) - o.write('\n') -i.close() -o.close() - - - - - - - """ - newXML=""" - %(tooldesc)s - %(command)s - - %(inputs)s - - - %(outputs)s - - - %(help)s - - - - %(script)s - - - """ # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto - - newCommand=""" - %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" - --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s - """ # may NOT be an input or htmlout - tooltests = """ - - - - """ - 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'] = '%s' % self.opts.tool_desc - else: - xdict['tooldesc'] = '' - xdict['command_outputs'] = '' - xdict['outputs'] = '' - if self.opts.input_tab <> 'None': - xdict['command_inputs'] = '--input_tab "$input1"' - xdict['inputs'] = '' % self.inputFormats - else: - xdict['command_inputs'] = '' # assume no input - eg a random data generator - xdict['inputs'] = '' - xdict['inputs'] += '\n' % self.toolname - xdict['toolname'] = self.toolname - xdict['toolid'] = self.toolid - xdict['interpreter'] = self.opts.interpreter - xdict['scriptname'] = self.sfile - if self.opts.make_HTML: - xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"' - xdict['outputs'] += '\n' - if self.opts.output_tab <> 'None': - xdict['command_outputs'] += '--output_tab "$tab_file"' - xdict['outputs'] += '\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,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')) - 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 = """ - - - - - - - - -
- """ - galhtmlattr = """
Galaxy Tool Factory Script Wrapper tool output %s run at %s
""" - galhtmlpostfix = """
\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('

Galaxy %s outputs run at %s


\n' % (self.toolname,timenow())) - fhtml = [] - if len(flist) > 0: - html.append('\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= '\n' % (fname,thumb,fname) - html.append(s) - fhtml.append('
  • %s %s
    • ' % (fname,fname,sfsize)) - else: - fhtml.append('
  • %s %s
    • ' % (fname,fname,sfsize)) - html.append('
    \n') - if len(fhtml) > 0: - fhtml.insert(0,'
      ') - fhtml.append('

    ') - html += fhtml # add all non-pdf files to the end of the display - else: - html.append('

    ### Error - %s returned no files - please confirm that parameters are sane

    ' % self.opts.interpreter) - html.append('

    %s log follows below


    \n' % self.opts.interpreter)
-        rlog = open(self.tlog,'r').readlines()
-        html += rlog
-        html.append('
    %s CL = %s
    \n' % (self.toolname,' '.join(sys.argv)))
-        html.append('
    \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: - rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" - - """ - op = optparse.OptionParser() - a = op.add_option - a('--script_path',default=None) - a('--tool_name',default=None) - a('--interpreter',default=None) - a('--output_dir',default=None) - a('--output_html',default=None) - a('--input_tab',default="None") - a('--output_tab',default="None") - a('--user_email',default=None) - a('--bad_user',default=None) - a('--make_Tool',default=None) - a('--make_HTML',default=None) - a('--help_text',default=None) - a('--tool_desc',default=None) - a('--new_tool',default=None) - opts, args = op.parse_args() - assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to admin_users in universe_wsgi.ini' % (opts.bad_user) - assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq' - assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript' - assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R' - if opts.output_dir: - try: - os.makedirs(opts.output_dir) - except: - pass - r = ScriptRunner(opts) - if opts.make_Tool: - retcode = r.makeTooltar() - else: - retcode = r.run() - if retcode: - sys.exit(retcode) # indicate failure to job runner - - -if __name__ == "__main__": - main() - - diff -r ab0148be2111 -r 6985104392b9 inkblotheatmap/inkblotheatmap.xml --- a/inkblotheatmap/inkblotheatmap.xml Wed Jun 06 23:04:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - tool_desc - - inkblotheatmap.py --script_path "$runMe" --interpreter "Rscript" - --tool_name "inkblotheatmap" --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" - - - - - - - - - - - -**What it Does** - - - - - -# note this script takes NO input or output because it generates random data -foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100)) -bar = as.matrix(foo) -pdf( "heattest.pdf" ) -heatmap(bar,main='Random Heatmap') -dev.off() - - - -