Mercurial > repos > fubar > tool_factory_2


class tooloutHTMLifyer(self):

    def compressPDF(self,inpdf=None,thumbformat='png'):
        """need absolute path to pdf
           note that GS gets confoozled if no $TMP or $TEMP
           so we set it
        """
        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
        hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
        sto = open(hlog,'a')
        our_env = os.environ.copy()
        our_tmp = our_env.get('TMP',None)
        if not our_tmp:
            our_tmp = our_env.get('TEMP',None)
        if not (our_tmp and os.path.exists(our_tmp)):
            newtmp = os.path.join(self.opts.output_dir,'tmp')
            try:
                os.mkdir(newtmp)
            except:
                sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
            our_env['TEMP'] = newtmp
            if not self.temp_warned:
               sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
               self.temp_warned = True
        outpdf = '%s_compressed' % inpdf
        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
        retval1 = x.wait()
        sto.close()
        if retval1 == 0:
            os.unlink(inpdf)
            shutil.move(outpdf,inpdf)
            os.unlink(hlog)
        hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
        sto = open(hlog,'w')
        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,env=our_env)
        retval2 = x.wait()
        sto.close()
        if retval2 == 0:
             os.unlink(hlog)
        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))
                    else:
                        pdflist.append((fname,fname))
                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>&nbsp;</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
author	fubar
date	Sun, 16 Aug 2020 08:11:10 -0400
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