33d37d6a60180fdc11fbdd59641c822579f85995 max Wed May 24 15:04:20 2017 -0700 adding help page for mirrors where graphviz may not work, refs #13634 diff --git src/hg/hgGeneGraph/hgGeneGraph src/hg/hgGeneGraph/hgGeneGraph index f8cb051..56493a6 100755 --- src/hg/hgGeneGraph/hgGeneGraph +++ src/hg/hgGeneGraph/hgGeneGraph @@ -578,65 +578,97 @@ if count > 100: thick = 1 elif count > 50: thick = 2 elif count > 10: thick = 3.5 else: thick = 2 return thick def which(binPath): " find full path of binary " import distutils.spawn return distutils.spawn.find_executable(binPath) -def runDot(fname, alg, format="png"): - " run dot and return tuple outFname, outMapFname " - outFname = splitext(fname)[0]+"."+format - outMap = splitext(fname)[0]+".map" - binPath = cfgOption("graphvizPath", "dot") +def findDot(): + """ this would never be run on the RR but only on mirrors, because we specify it in hg.conf. + It will try to find 'dot' and if it cannot find it, will fall back to cgi-bin/loader/dot_static: - if which(binPath) is None: - print("Could not find the command %s<p>" % binPath) - print("This usually means that on this UCSC Genome Browser, GraphViz is not installed.") - print("To install GraphViz, ask the Administrator of this server to run one of the following commands:<br>") + - if anything is specified in hg.conf, it will use that + - if it can find "dot" in the PATH, it will use that next (dot + installed from the repos will always work) + - if that doesn't work either, we run cgi-bin/loader/dot_static (our + static version may fail due to wrong glibc version) """ + binPath = cfgOption("graphvizPath") + + if binPath is not None and binPath.strip()!="": + return binPath + + installedBin = which("dot") + + if installedBin is None: + staticPath = join("loader", "dot_static") + if not isfile(staticPath): + return None + else: + return staticPath + else: + sys.stderr.write("Using graphviz binary %s\n" % installedBin) + return installedBin + +def printDotErrorHelpAndExit(): + print("This often means that on this UCSC Genome Browser, GraphViz is not installed or is too old and ") + print("that the supplied program dot_static also did not work. It can also mean that the configuration option") + print("graphvizPath in hg.conf specifies a program that does not work.<p>") + print("To resolve any of these problems, you will have to contact the system administrator of this Genome Browser server.<p>") + print("To install GraphViz, ask the administrator of this server to run one of the following commands:<br>") print("<tt>sudo apt-get install graphviz</tt><br>") print("<tt>sudo wget http://www.graphviz.org/graphviz-rhel.repo -o /etc/yum/repos.d/graphviz.rhel.repo; sudo yum install graphviz*</tt><br>") print("<p>") - print("Alternatively, you can compile GraphViz from source and specify the full path to 'dot' with the option 'graphvizPath' in cgi-bin/hg.conf.") + print("If you have graphviz installed but this error message still appears, then the ") + print("graphviz version may be too old.<p>") + print("Also, the Genome Browser ships with a statically compiled version of") + print("dot, cgi-bin/loader/dot_static. This version should work with a") + print("64bit linux, unless the installed glibc is too different from the one compiled into dot_static.<p>") + print("As a last resort, you can compile GraphViz from source and specify the full path to 'dot'") + print("with the option 'graphvizPath' in cgi-bin/hg.conf.<br>") + print("If you see this message on a website managed by UCSC, please contact genome-www@soe.ucsc.edu immediately.<p>") exit(0) +def runDot(fname, alg, format="png"): + """ run dot and return tuple outFname, outMapFname. Makes a real effort to find a working version of dot, + see findDot() + """ + outFname = splitext(fname)[0]+"."+format + outMap = splitext(fname)[0]+".map" + + binPath = findDot() + + if which(binPath) is None: + print("Could not find the command dot or cgi-bin/loader/dot_static<p>") + printDotErrorHelpAndExit() + cmd = [binPath, "-Gdpi=96", "-Gsize=12,5", "-Gratio=fill", "-K"+alg, "-T"+format, fname, "-o",outFname] # create a html map for png format if format=="png": cmd.extend(["-Tcmapx", "-o", outMap]) ret = runCmd(cmd, mustRun=False) if ret!=0: - print("Could not run the command '%s'. <br>" % "".join(cmd)) - print("This means that on this UCSC Genome Browser Installation too old.") - print("To update GraphViz to a more recent version, ask the Administrator of this ") - print("server to try running one of these commands:<br>") - print("<tt>sudo apt-get install graphviz</tt><br>") - print("<tt>sudo wget http://www.graphviz.org/graphviz-rhel.repo -o ") - print("/etc/yum/repos.d/graphviz.rhel.repo;") - print("sudo yum install graphviz*</tt><br>") - print("<p>") - print("If this does not work, you may have to compile GraphViz from source and") - print("specify the 'dot' binary with the option graphvizPath cgi-bin/hg.conf.") - exit(0) + print("Could not run the command '%s'. <p>" % " ".join(cmd)) + printDotErrorHelpAndExit() return outFname, outMap def dictToDot(d): """ reformat a dictionary to a string like [key1="value1"; key2="value2"] """ if len(d)==0: return "" strList = [] for key, val in d.iteritems(): strList.append('%s="%s"' % (key, val.replace('"', ''))) return "[%s]" % (";".join(strList)) def writeDot(allGenes, links, fname, targetGene, geneDescs, annotLabel, geneAnnots, linkSnips): """ write a description of the graph to fname in dot format. @@ -665,35 +697,39 @@ d = {} ttLines = geneDescs[g] if g in geneAnnots: #d["color"]="#3636E2" geneAnnotVal, geneAnnotGrey = geneAnnots[g] transVal = 200 - (geneAnnotGrey*25) # scale to 55-255 transHex = "%0.2X" % transVal # convert to hex d["fillcolor"]="#"+"".join([transHex]*3) # concat three times, creates a grey-value d["fontcolor"] = "white" ttLines.append("<b>%s</b>: %s" % (annotLabel, geneAnnotVal)) d["tooltip"] = " <br> ".join(ttLines) # separate with encoded html linebreaks url = makeSelfUrl({"gene":g}) url = url.replace("&", "&") # otherwise invalid SVG will result d["URL"] = url if g==targetGene: + if g not in geneAnnots: d["penwidth"] = "1" d["fontcolor"] = "black" d["fillcolor"] = "yellow" - #d["style"] = "bold" d["color"] = "blue" + else: + d["penwidth"] = "3" + d["color"] = "yellow" + ofh.write('"%s" %s;\n' % (g, dictToDot(d))) # write the links between genes for gene1, gene2, score, docCount, dbs, tags, minResCount, snippet in links: dbs = [x.upper() for x in dbs if x!=''] addStr = "" # based on http://www.w3schools.com/tags/ref_colorpicker.asp?colorhex=F0F8FF color = None if "pwy" in tags or ("ppi" in tags and minResCount<=LTCUTOFF): color = LTCOLOR+TRANSPARENCY #"#000099A0" elif "ppi" in tags: color = HTCOLOR+TRANSPARENCY # "#8080CCA0" @@ -1260,31 +1296,31 @@ linkStyle = None if color != None: linkStyle = 'color:%s' % color newGeneLink = makeSelfLink("▸", {"gene": g}, title="Center graph on %s" % g, style='text-decoration:none', dataToggle="tooltip") if dbCount == 1 and artCount != 0: detailsText = "interaction %s-%s mentioned by %d articles and %d database" % (gene, g, artCount, dbCount) elif dbCount != 0 and artCount != 0: detailsText = "interaction %s-%s mentioned by %d articles and %d databases" % (gene, g, artCount, dbCount) elif artCount != 0: detailsText = "interaction %s-%s mentioned by %d articles" % (gene, g, artCount) elif dbCount != 0: detailsText = "interaction %s-%s mentioned by %d databases" % (gene, g, dbCount) - detailsLink = makeSelfLink(g, {"gene": None, "link":"%s:%s" % (g, gene)}, + detailsLink = makeSelfLink(g, {"gene": None, "lastGene": gene,"link":"%s:%s" % (g, gene)}, style=linkStyle, title=detailsText, dataToggle="tooltip") print( '<td%s>%s %s</td>' % (cellStyle, detailsLink, newGeneLink)) i += 1 if i % rowSize == 0: print "</tr><tr>" print "</tr>" print "</table>" def listToMysqlList(l): " convert a python list of strings to a mysql list, like ('a', 'b') " newList = [] for s in l: