diff toolfactory/html_dir.py @ 41:f8c1694190f0 draft

Uploaded
author fubar
date Sun, 16 Aug 2020 08:11:10 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/html_dir.py	Sun Aug 16 08:11:10 2020 -0400
@@ -0,0 +1,180 @@
+
+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
+
+