8f07ea1e9137dc164688def8459f6784879ebbeb max Sun Jun 4 08:09:48 2017 -0700 fixes for openbel dataset in hgGeneGraph, refs #13634 diff --git src/hg/hgGeneGraph/hgGeneGraph src/hg/hgGeneGraph/hgGeneGraph index c463d06..94ae679 100755 --- src/hg/hgGeneGraph/hgGeneGraph +++ src/hg/hgGeneGraph/hgGeneGraph @@ -89,31 +89,31 @@ # ==== GLOBALS ===== # CGI parameters as a FieldStorage object # args = None # external DB information dbData = { "kegg" : ("KEGG", "http://www.kegg.jp/kegg-bin/show_pathway?%s"), "wikipathways" : ("WikiPathways", "http://www.wikipathways.org/index.php/Pathway:%s"), "iref" : ("Iref", "http://wodaklab.org/iRefWeb/interaction/show/%s"), #"pid" : ("NCI Pathway Database", "http://pid.nci.nih.gov/search/InteractionPage?atomid=%s"), #PID server is down, linking to NDex now, adapted the IDs, see ggPidToTables "pid" : ("NCI Pathway Database", "http://www.ndexbio.org/#/search?searchType=All&searchString=labels%%253A%s"), "biocarta" : ("BioCarta", "https://cgap.nci.nih.gov/Pathways/BioCarta/%s"), -"belLarge" : ("OpenBEL Large Corpus", "http://www.ndexbio.org/#/newNetwork/%s"), +"belLarge" : ("OpenBEL", "http://www.ndexbio.org/#/newNetwork/%s"), "reactome" : ("Reactome", "http://www.reactome.org/content/detail/%s"), "go" : ("Gene Ontology Complexes", "http://www.ebi.ac.uk/QuickGO/GTerm?id=%s#info=2"), "fastforward" : ("FastForward", "http://fastforward.sys-bio.net/popup.php?name_target=%s"), "argdb" : ("ARGDB", "http://argdb.fudan.edu.cn/geneshow_id.php?gene_id=%s"), "corum" : ("MIPS CORUM", "http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=%s"), "string" : ("STRING", "http://string-db.org/newstring_cgi/show_network_section.pl?multiple_input_items=%s&multi_input=1&multiple_input_type=multi_identifier&limit=0&input_page_type=multiple_identifiers&have_user_input=2&species_text=Homo%%20sapiens&input_query_species=auto_detect&flash=15&required_score=400") } # mime types to send in http header for other downloads mimeTypes = { "svg" : "image/svg+xml", "pdf" : "application/pdf", "json" : "application/json", "sif" : "application/octet-stream" } @@ -701,32 +701,30 @@ d["URL"] = url if g==targetGene: if g not in geneAnnots: d["penwidth"] = "1" d["fontcolor"] = "black" d["fillcolor"] = "yellow" 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" if color: addStr = 'color="%s";' % color if gene2==gene1: addStr += 'len="5"; ' thick = pmidCountToThick(score) @@ -736,39 +734,42 @@ elif "fwd" in tags: arrDir = "forward" elif "rev" in tags: arrDir = "back" else: arrDir = "none" if "text" in tags: style = "solid" else: style = "dashed" thick = 1 tooltipLines = ["<b>%s-%s</b> " % (gene1, gene2)] tooltipLines.append("<ul>") + + dbs = [x.upper().replace("BELLARGE","OpenBEL") for x in dbs if x!=''] if len(dbs)==0: tooltipLines.append("<li>No curated information") else: suffix = "" if len(dbs)>3: suffix = "..." tooltipLines.append("<li>Databases: %s%s" % (", ".join(dbs[:3]), suffix)) if docCount==0: + if minResCount!=0: tooltipLines.append("<li>%d interactions were curated from source document" % minResCount) tooltipLines.append("<li>No text-mining data") thick = minResToThick(minResCount) else: tooltipLines.append("<li>Text-mining: %d abstracts" % docCount) if linkSnips.get( (gene1, gene2), None): snip = linkSnips[(gene1, gene2)].replace(" , ", ", ") tooltipLines.append(" e.g. <i>"+snip+"</i>") tooltipLines.append("</ul>") tooltipLines.append(" <small>Click link to show details</small>") tooltip = "".join(tooltipLines) url = makeSelfUrl({"gene" : None, "lastGene":targetGene, "link":gene2+":"+gene1}) @@ -918,31 +919,31 @@ " print a html dropdown <select> box. " print("<select name='%s'%s>" % (cgiArgName, addStr)) for name, label in options: addStr = "" if name==selectedName: addStr = " selected" print('<option value="%s"%s>%s</option>' % (name, addStr, label)) print("</select>") def printFilterMenu(targetGene, addNeighbors): # form to filter by type print "<small>" print '<form name="filterForm" action="%s" method="GET">' % makeSelfUrl({}, True) print """<b>Gene:</b>""" - print '<input type="text" size="6" name="gene" value="%s" />' % targetGene + print '<input type="text" size="10" name="gene" value="%s" />' % targetGene print " " print '<input type="submit" name="1" value="OK">' print " " supportLevel = getCgiVar("supportLevel", "text") if supportLevel not in ["text", "pwy", "ppi"]: errAbort("Illegal value for the supportLevel argument. Can only be text,pwy or ppi.") onChangeAttr = '''onchange="document.forms['filterForm'].submit();"''' printDropdown("supportLevel", supportLevel, [("text", "Show all interactions, even only text-mining support"), ("ppi", "Show only interactions with some database support"), ("pwy", "Show only interactions with pathway database support")], addStr=onChangeAttr ) #filterTags = getFilterStatus() #printCheckbox("pwy", "pwy" in filterTags, onChangeAttr) @@ -1473,30 +1474,31 @@ url = dbUrlPat % sourceId print "<li>" if sourceDesc=="": if isPpi: sourceDesc = "Interaction" else: sourceDesc = "Reaction" print '%s <a href="%s" target="_BLANK">%s</a>: ' % (dbName, url, sourceDesc) print entToDesc(causeType, causeName, causeGenes) + desc = "" if themeGenes!="": if isPpi: print "—" # unicode long dash else: print "→" # Unicode Arrow desc = entToDesc(themeType, themeName, themeGenes) print desc if relType!="" or relSubtype!="": if relType!="" and relSubtype!="": print "(%s/%s)" % (relType, relSubtype) elif relType!="": print "(%s)" % (relType) elif relSubtype!="":