a55caf35864fc8a67c3c2e84919e75e78143c99f tdreszer Tue Nov 2 14:52:26 2010 -0700 Added support for getting cv typeOfTerms hash and made the cv whitelist ise cv.ra diff --git src/hg/lib/mdb.c src/hg/lib/mdb.c index 158746e..713b01e 100644 --- src/hg/lib/mdb.c +++ src/hg/lib/mdb.c @@ -2135,105 +2135,78 @@ if (label != NULL) { freeMem(pair->name); // Allocated when pair was created pair->name = strSwapChar(cloneString(label),'_',' '); // vestigial _ meaning space if (limit > 0 && strlen(pair->name) > limit) pair->name[limit] = '\0'; } } slAddHead(&pairs, pair); } sqlFreeResult(&sr); slPairSortCase(&pairs); return pairs; } -struct slPair *mdbCvWhiteList(boolean searchTracks, boolean cvLinks) +struct hash *mdbCvTermTypeHash() +// returns a hash of hashes of mdb and controlled vocabulary (cv) term types +// Those terms should contain label,descrition,searchable,cvDefined,hidden +{ +static struct hash *cvHashOfTermTypes = NULL; + +// Establish cv hash of Term Types if it doesn't already exist +if (cvHashOfTermTypes == NULL) + { + cvHashOfTermTypes = raReadWithFilter(cv_file(), "term","type","typeOfTerm"); + // Patch up an ugly inconsistency with 'cell' + struct hash *cellHash = hashRemove(cvHashOfTermTypes,"cellType"); + if (cellHash) + hashAdd(cvHashOfTermTypes,"cell",cellHash); + } + + +return cvHashOfTermTypes; +} + +struct slPair *mdbCvWhiteList(boolean searchTracks, boolean cvDefined) // returns the official mdb/controlled vocabulary terms that have been whitelisted for certain uses. { -#define WHITE_LIST_COUNT 35 - -struct cvTerms - { - char *term; // The actual term as it appears in the mdb or cv.ra - void *title; // The title that should appear in Track Search - boolean searchable; // Can this term be searched for in Track Search? - boolean cvTerm; // Can this term be linked to cv.ra content? - }; - -// TODO: move this list into cv.ra as type=term -// TODO: If hgEncodeVocab was changed to give a description of a term not found in cv.ra, then many more of these could be linked. -struct cvTerms whiteList[] = { - // term Title search cvTerm - {"accession" ,"Lab provided accession" ,FALSE,FALSE}, // Superceded by geoSample? - {"age" ,"Age of experimental organism" ,TRUE ,TRUE }, - {"annotation" ,"Gencode annotation" ,FALSE,FALSE}, - {"antibody" ,"Antibody or target protein" ,TRUE ,TRUE }, - {"bioRep" ,"UNKNOWN" ,FALSE,FALSE}, - {"cell" ,"Cell, tissue or DNA sample" ,TRUE ,TRUE }, - {"composite" ,"UCSC Composite Track" ,FALSE,FALSE}, // Could be in cv.ra - {"control" ,"Control or Input for ChIPseq" ,TRUE ,TRUE }, - {"controlId" ,"ControlId - explicit relationship",FALSE,FALSE}, - {"dataType" ,"Experiment type" ,TRUE ,TRUE }, - {"dataVersion" ,"ENCODE release" ,TRUE ,FALSE}, - {"dateResubmitted" ,"Date resubmitted to UCSC" ,FALSE,FALSE}, - {"dateSubmitted" ,"Date submitted to UCSC" ,FALSE,FALSE}, - {"dateUnrestricted" ,"Date restrictions are lifted" ,FALSE,FALSE}, - {"expVars" ,"Experimental variables" ,FALSE,FALSE}, // Only defined for one obj: wgEncodeCaltechRnaSeq - {"fileIndex" ,"BAM Index file" ,FALSE,FALSE}, - {"fileName" ,"File Name for downloading" ,FALSE,FALSE}, - {"fragLength" ,"Mean Length of DNA fragments" ,FALSE,FALSE}, - {"fragSize" ,"Length of GIS PET fragments" ,FALSE,FALSE}, // WHAT IS THIS? - {"freezeDate" ,"Gencode freeze date" ,FALSE,FALSE}, - {"geoSample" ,"GEO accession" ,TRUE ,FALSE}, - //{"geoSampleAccession" ,"GEO sample accession" ,TRUE ,FALSE}, // Should be replaced by geoSample - {"geoSeries" ,"GEO series accession" ,TRUE ,FALSE}, - //{"geoSeriesAccession" ,"GEO series" ,TRUE ,FALSE}, // Should be replaced by geoSeries - {"grant" ,"Principal Investigator" ,TRUE ,TRUE }, - {"insertLength" ,"Insertion length" ,FALSE,FALSE}, // WHAT IS THIS? - {"lab" ,"Lab producing data" ,TRUE ,TRUE }, - {"labExpId" ,"Lab specific identifier" ,TRUE ,FALSE}, - {"labProtocolId" ,"Lab specific protocol ID" ,FALSE,FALSE}, - {"labVersion" ,"Lab specific details" ,TRUE ,FALSE}, - {"level" ,"Gencode level" ,FALSE,FALSE}, - {"localization" ,"Cell compartment" ,TRUE ,TRUE }, - {"mapAlgorithm" ,"Mapping algorithm" ,TRUE ,TRUE }, - {"origAssembly" ,"Assembly originally mapped to" ,TRUE ,FALSE}, // Could be cv.ra term - //{"parentTable" ,"Closest related table" ,FALSE,FALSE}, // On its way out - {"phase" ,"Cell phase" ,FALSE,FALSE}, // Only one exp in hg18: wgEncodeUwDnaseSeqPeaksRep1JurkatG1 - //{"project" ,"Project funded by" ,FALSE,FALSE}, // Only one: all encode is under single project='wgEncode' - {"protocol" ,"Library Protocol" ,TRUE ,TRUE }, - {"rank" ,"Rank of replicate" ,FALSE,FALSE}, // UW used rank in hg18 only - {"readType" ,"Paired/Single reads lengths" ,TRUE ,TRUE }, - {"replicate" ,"Replicate number" ,TRUE ,FALSE}, - {"restrictionEnzyme" ,"Restriction Enzyme used" ,FALSE,TRUE }, - {"rnaExtract" ,"RNA Extract" ,TRUE ,TRUE }, - {"seqPlatform" ,"Sequencing Platform" ,TRUE ,TRUE }, - {"setType" ,"Experiment or Input" ,TRUE ,FALSE}, - {"sex" ,"Sex of organism" ,TRUE ,TRUE }, // really want to link to this? - //{"size" ,"Mapability windowing size" ,FALSE,FALSE}, // Used in hg19 mapability only - {"softwareVersion" ,"Lab specific informatics" ,TRUE ,FALSE}, - {"strain" ,"Strain of organism" ,TRUE ,TRUE }, - {"subId" ,"Submission Id" ,TRUE ,FALSE}, - {"submittedDataVersion","Version of data if resubmitted" ,FALSE,FALSE}, - {"tableName" ,"Name of msql table at UCSC" ,FALSE,FALSE}, - {"treatment" ,"Treatment" ,TRUE ,TRUE }, - //{"type" ,"Data Format type" ,FALSE,FALSE}, // Used rarely in hg18 to distinguish wig and bedGraph - //{"uniqueness" ,"Number of mismatches tolerated" ,FALSE,FALSE}, // Used in hg19 mapability only - {"view" ,"View - Peaks or Signals" ,TRUE ,FALSE}, -}; -int ix,size = sizeof(whiteList)/sizeof(struct cvTerms); struct slPair *whitePairs = NULL; -for(ix=0;ix<size;ix++) + +// Get the list of term types from thew cv +struct hash *termTypeHash = mdbCvTermTypeHash(); +struct hashCookie hc = hashFirst(termTypeHash); +struct hashEl *hEl; +while ((hEl = hashNext(&hc)) != NULL) + { + char *setting = NULL; + struct hash *typeHash = (struct hash *)hEl->val; + //if (!includeHidden) + { + setting = hashFindVal(typeHash,"hidden"); + if(SETTING_IS_ON(setting)) + continue; + } + if (searchTracks) { - if (searchTracks && !whiteList[ix].searchable) + setting = hashFindVal(typeHash,"searchable"); + if (setting == NULL || differentWord(setting,"select")) // TODO: Currently only 'select's are supported continue; - if (cvLinks && !whiteList[ix].cvTerm) + } + if (cvDefined) + { + setting = hashFindVal(typeHash,"cvDefined"); + if(SETTING_NOT_ON(setting)) continue; + } + char *term = hashMustFindVal(typeHash,"term"); + char *label = hashFindVal(typeHash,"label"); + if (label == NULL) + label = term; - slPairAdd(&whitePairs, whiteList[ix].term, cloneString(whiteList[ix].title)); + slPairAdd(&whitePairs, term, cloneString(label)); // Term gets cloned in slPairAdd } if (whitePairs != NULL) slPairValSortCase(&whitePairs); return whitePairs; }