1b20a1774021cdcb07303801d55b7ca3fa6cff09 braney Wed Jan 8 05:54:20 2025 -0800 fix up chop functions so they don't call ArraySize with NULL diff --git src/hg/encode/hgEncodeVocab/hgEncodeVocab.c src/hg/encode/hgEncodeVocab/hgEncodeVocab.c index 6b23d8b..17761f6 100644 --- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c +++ src/hg/encode/hgEncodeVocab/hgEncodeVocab.c @@ -1,922 +1,922 @@ /* hgEncodeVocab - print table of controlled vocabulary from ENCODE configuration files */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "cheapcgi.h" #include "hCommon.h" #include "htmshell.h" #include "ra.h" #include "hui.h" #include "cv.h" #include "web.h" #include "jsHelper.h" #include "hgConfig.h" /* hgEncodeVocab - A CGI script to display the different types of encode controlled vocabulary. * usage: * hgEncodeVocab type=[Antibody|"Cell Line"|localization|rnaExtract|"Gene Type"] [tier=(1|2|3)] * options:\n" * type=TypeName : Type to display * tier=N : If type="Cell Line" then this is the tier to display * bgcolor=RRGGBB : Change background color (hex digits) * term=a[,b,c] : Display row for a single term [or comma delimited set of terms] * tag=a[,b,c] : Display row for a single term, using tag as identifier [or comma delimited * set of tags] * target=a[,b,c] : Display all antibodies for a single target. If 'a'[,b,c] is a term, * corresponding targets will be looked up and used * label=a[,b,c] : Display row for a single term with the specific label. * Must use with 'type' or terms must have same type. * deprectate=y : Include deprecated terms. Usually these are excluded unles the term * is reqested by name. * Hint: try "hgEncodeVocab type=typeOfTerm" for a complete list of types with links to * each specific type. */ //options that apply to all vocab types #define ORGANISM "organism" #define ORG_HUMAN "human" #define ORG_MOUSE "mouse" #define MAX_TABLE_COLS 11 #define TABLE_COLS_AVAILABLE(colsUsed) (MAX_TABLE_COLS - (colsUsed)) static char *termOpt = NULL; static char *tagOpt = NULL; static char *typeOpt = NULL; static char *targetOpt = NULL; static char *labelOpt = NULL; static char *organismOpt = NULL; // we default to human if nothing else is set static char *organismOptLower = NULL; // version of above used for path names int documentLink(struct hash *ra, char *term, char *docTerm,char *dir, char *title,boolean genericDoc) // Compare controlled vocab based on term value { boolean docsPrinted = 0; char *s; if (title == NULL) title = docTerm; //can use hg.conf to direct links back to main UCSC server if a mirror doesn't //want all the PDFs char *baseUrl = cfgOptionDefault("hgEncodeVocabDocBaseUrl", ""); // add links to protocol doc if it exists char docUrl[PATH_LEN]; char docFile[PATH_LEN]; // parse setting s = hashFindVal(ra,docTerm); if (s != NULL) { if (sameWord(s,"missing")) printf(" <em>missing</em>\n"); else { char *docSetting = cloneString(s); char *settings=docSetting; int count=0; while ((s = nextWord(&settings)) != NULL) { char *docTitle = NULL; char *fileName = NULL; if (strchr(s,':')) // lab Specific setting { docTitle = strSwapChar(s,':',0); fileName = docTitle + strlen(docTitle) + 1; } else { docTitle = title; fileName = s; } if (count>0) printf("<BR>"); count++; docTitle = htmlEncode(strSwapChar(docTitle,'_',' ')); if (sameWord(fileName,"missing")) printf("%s<em>missing</em>\n",docTitle); else { safef(docUrl, sizeof(docUrl), "%s%s%s", baseUrl, dir, fileName); safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl); printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,docTitle); docsPrinted++; } freeMem(docTitle); } freeMem(docSetting); } } else if (genericDoc) { // generate a standard name safef(docUrl, sizeof(docUrl), "%s%s%s_protocol.pdf", baseUrl, dir, term); safef(docFile, sizeof(docFile), "%s%s", hDocumentRoot(), docUrl); if (fileExists(docFile)) { printf(" <A TARGET=_BLANK HREF=%s>%s</A>\n", docUrl,title); docsPrinted++; } } return docsPrinted; } void printDocumentLink(struct hash *ra, char *term, char *docTerm,char *dir, char *title,boolean genericDoc) // prints a document link { printf(" <TD>"); (void)documentLink(ra,term,docTerm,dir,title,genericDoc); printf(" </TD>\n"); } int termCmp(const void *va, const void *vb) /* Compare controlled vocab based on term value */ { const struct hash *a = *((struct hash **)va); const struct hash *b = *((struct hash **)vb); char *typeA = hashMustFindVal((struct hash *)a, CV_TYPE); char *typeB = hashMustFindVal((struct hash *)b, CV_TYPE); int ret = strcasecmp(typeA, typeB); if (ret != 0) return ret; char *targA = hashFindVal((struct hash *)a, CV_TARGET); char *targB = hashFindVal((struct hash *)b, CV_TARGET); if (targA != NULL && targB != NULL) { ret = strcasecmp(targA, targB); if (ret != 0) return ret; } char *termA = hashMustFindVal((struct hash *)a, CV_TERM); char *termB = hashMustFindVal((struct hash *)b, CV_TERM); return (strcasecmp(termA, termB)); } char *getDescription(struct hash *ra,char *alternateSetting) // Returns allocated string that is description. Will include DEPRECATED if appropriate { struct dyString *dyDescription = dyStringNew(256); char *deprecated = hashFindVal(ra, "deprecated"); if (deprecated != NULL) dyStringPrintf(dyDescription,"DEPRECATED - %s",deprecated); char *description = hashFindVal(ra, CV_DESCRIPTION); if (description == NULL && alternateSetting != NULL) description = hashFindVal(ra, alternateSetting); if (description == NULL) description = hashFindVal(ra, CV_TITLE); if (description == NULL) description = hashFindVal(ra, CV_LABEL); if (description != NULL) { if (dyStringLen(dyDescription) > 0) dyStringAppend(dyDescription,"<BR>"); dyStringAppend(dyDescription,description); } if (dyStringLen(dyDescription) > 0) return dyStringCannibalize(&dyDescription); dyStringFree(&dyDescription); return NULL; } void printDescription(struct hash *ra,char *alternateSetting,int colsUsed) { char *description = getDescription(ra,alternateSetting); if (colsUsed >= 0) printf(" <TD colspan=%d>", TABLE_COLS_AVAILABLE(colsUsed) ); else printf(" <TD>"); if (description != NULL) { printf("%s</TD>\n", description ); freeMem(description); } else puts(" </TD>\n"); } void printLabel(struct hash *ra,char *term) { char *label = hashFindVal(ra, CV_LABEL); if (label != NULL) printf(" <TD><I>%s</I></TD>\n", label ); else printf(" <TD>%s</TD>\n", term ); } char *printTerm(struct hash *ra) { char *term = (char *)hashMustFindVal(ra, CV_TERM); printf(" <TD>%s</TD>\n", term); return term; } void printSetting(struct hash *ra,char *setting) { char *val = hashFindVal(ra, setting); printf(" <TD>%s</TD>\n", val ? val : " "); } void printSettingsWithUrls(struct hash *ra,char *urlSetting,char *nameSetting,char *idSetting) // will print one or more urls with name and optional id. Only Name is required! // If more than one, then should add same number of slots to each ("fred;ethyl" & " ;wife") { char *names = hashFindVal(ra, nameSetting); struct slName *nameList = slNameListFromString(names, ';');; char *urls = NULL; struct slName *urlList = NULL; char *ids = NULL; struct slName *idList = NULL; if (idSetting != NULL) ids = hashFindVal(ra, idSetting); if (ids != NULL) { idList = slNameListFromString(ids, ';'); if (slCount(idList) > slCount(nameList)) { if (slCount(nameList) == 1) { while (slCount(nameList) < slCount(idList)) slAddHead(&nameList,slNameNew(nameList->name)); } else errAbort("The number of of items in %s and %s must match for term %s", nameSetting,idSetting,(char *)hashMustFindVal(ra,CV_TERM)); } } if (urlSetting != NULL) urls = hashFindVal(ra, urlSetting); if (urls != NULL) { if (slCount(nameList) == 1) urlList = slNameNew(urls); // It is the case that singleton URLs sometimes have ';'! else { urlList = slNameListFromString(urls, ';'); if (slCount(urlList) > slCount(nameList)) errAbort("The number of of items in %s and %s must match for term %s", nameSetting,urlSetting,(char *)hashMustFindVal(ra,CV_TERM)); } } printf(" <TD>"); // while there are items in the list of vendorNames, print the vendorName // and vendorID together with the url if present struct slName *curName = NULL; struct slName *curId; struct slName *curUrl; for (curName=nameList,curId=idList,curUrl=urlList; curName != NULL; curName=curName->next) { if (curName!=nameList) // Break between links printf("<BR>\n "); // if there is a url, add it as a link char *url = NULL; if (curUrl != NULL) { url = trimSpaces(curUrl->name); if (isNotEmpty(url)) printf("<A TARGET=_BLANK HREF=%s>", url); curUrl=curUrl->next; } printf("%s", curName->name); if (curId != NULL) { char *id = trimSpaces(curId->name); if (isNotEmpty(id)) printf(" %s", id ); curId=curId->next; } if (isNotEmpty(url)) printf("</A>"); } puts("</TD>"); // Free the memory slFreeList(&nameList); slFreeList(&idList); slFreeList(&urlList); } boolean doTypeDefinition(char *type,boolean inTable,boolean showType) // Write out description of the type if it is known { struct hash *typeHash = (struct hash *)cvTermTypeHash(); struct hash *ra = hashFindVal(typeHash,(char *)cvTermNormalized(type)); // Find by term if (ra == NULL) return FALSE; char *label = hashFindVal(ra, CV_LABEL); struct dyString *dyDefinition = dyStringNew(256); if (inTable) dyStringPrintf(dyDefinition,"<tr><td colspan=%d style='background:%s; color:%s;'> ", TABLE_COLS_AVAILABLE(0),COLOR_LTGREEN,COLOR_DARKBLUE); else dyStringPrintf(dyDefinition,"<div style='max-width:900px;'>"); if (label != NULL) { dyStringPrintf(dyDefinition,"<B><em>%s</em></B>",label); if (showType) dyStringPrintf(dyDefinition," [%s]",type); dyStringAppend(dyDefinition,": "); } else if (showType) dyStringPrintf(dyDefinition,"<B>%s</B>: ",type); char *val = getDescription(ra,NULL); dyStringPrintf(dyDefinition,"%s",val); freeMem(val); if (inTable) dyStringAppend(dyDefinition," </td></tr>"); else dyStringPrintf(dyDefinition,"</div>"); printf("%s\n",dyStringContents(dyDefinition)); dyStringFree(&dyDefinition); return TRUE; } void printColHeader(boolean emphasis,char *title,int sortOrder,char *extra,int colSpan) { printf("<TH"); if (sortOrder > 0) printf(" class='sortable sort%d'",sortOrder); if (colSpan > 1) printf(" colspan=%d",colSpan); if (extra) printf(" %s",extra); printf(">"); if (emphasis) printf("<em>"); printf("%s",title); if (emphasis) printf("</em>"); printf("</TH>"); } void doTypeHeader(char *type, char *cellOrg,boolean sortable) { if ((organismOptLower != NULL) && !sameWord(cellOrg, organismOptLower)) errAbort("specified organism %s not consistent with cell type which is org %s\n", organismOpt, cellOrg); // NOTE: All tables must have the same number of columns in order to allow 'control' // to be swapped in Use colSapn= on description column printf("<THEAD><TR valign='bottom' style='background:%s;'>\n",COLOR_BG_HEADER_LTBLUE); int sortOrder = (sortable ? 1: -999); // hint: -999 will keep sortOrtder++ < 0 if (sameWord(type,CV_TERM_CELL)) { printf("<!-- Cell Line table: contains links to protocol file and vendor description page -->"); /* Venkat: To differentiate between the print statments of Mouse and Human Cell Lines */ if (sameWord(cellOrg,ORG_HUMAN)) { printColHeader(FALSE,type, sortOrder++,NULL,1); printColHeader(FALSE,"Tier", sortOrder++,NULL,1); printColHeader(FALSE,"Description",sortOrder++,NULL,1); printColHeader(FALSE,"Lineage", sortOrder++,NULL,1); printColHeader(FALSE,"Tissue", sortOrder++,NULL,1); printColHeader(FALSE,"Karyotype", sortOrder++,NULL,1); printColHeader(FALSE,"Sex", sortOrder++,NULL,1); printColHeader(FALSE,"Documents", sortOrder++,NULL,1); printColHeader(FALSE,"Vendor ID", sortOrder++,NULL,1); printColHeader(FALSE,"Term ID", sortOrder++,NULL,1); printColHeader(TRUE ,"Label", sortOrder++,NULL,1); } else { printColHeader(FALSE,"Source", sortOrder++,NULL,1); printColHeader(FALSE,"Description",sortOrder++,NULL,TABLE_COLS_AVAILABLE(8)); printColHeader(FALSE,"Category", sortOrder++,NULL,1); printColHeader(FALSE,"Tissue", sortOrder++,NULL,1); printColHeader(FALSE,"Sex", sortOrder++,NULL,1); printColHeader(FALSE,"Documents", sortOrder++,NULL,1); printColHeader(FALSE,"Source Lab", sortOrder++,NULL,1); printColHeader(FALSE,"Term ID", sortOrder++,NULL,1); printColHeader(TRUE ,"Label", sortOrder++,NULL,1); } } else if (sameWord(type,CV_TERM_ANTIBODY)) { printColHeader(FALSE,type, sortOrder++,NULL,1); printColHeader(FALSE,"Antibody Description",sortOrder++,NULL,TABLE_COLS_AVAILABLE(9)); printColHeader(FALSE,"Target", sortOrder++,NULL,1); printColHeader(FALSE,"Target Description", sortOrder++,"style='min-width:600px;'",1); printColHeader(FALSE,"Vendor ID", sortOrder++,NULL,1); printColHeader(FALSE,"Lab", sortOrder++,NULL,1); printColHeader(FALSE,"Documents", sortOrder++,NULL,1); printColHeader(FALSE,"Lots", sortOrder++,NULL,1); printColHeader(FALSE,"Target Link", sortOrder++,NULL,1); printColHeader(TRUE ,"Label", sortOrder++,NULL,1); } else { char *caplitalized = NULL; if (sameWord(type,CV_TERM_DATA_TYPE)) caplitalized = cloneString("Data Type"); else { caplitalized = cloneString(type); toUpperN(caplitalized,1); } printColHeader(FALSE,caplitalized,sortOrder++,NULL,1); if (sameWord(type,CV_TERM_LOCALIZATION)) { printColHeader(FALSE,"Description",sortOrder++,NULL,TABLE_COLS_AVAILABLE(3)); printColHeader(FALSE,"GO ID", sortOrder++,NULL,1); } else if (sameWord(type,CV_TERM_LAB)) { printColHeader(FALSE,"Institution",sortOrder++,NULL,TABLE_COLS_AVAILABLE(5)); printColHeader(FALSE,"Lab PI", sortOrder++,NULL,1); printColHeader(FALSE,"Grant PI", sortOrder++,NULL,1); printColHeader(FALSE,"Organism", sortOrder++,NULL,1); } else printColHeader(FALSE,"Description",sortOrder++,NULL,TABLE_COLS_AVAILABLE(2)); printColHeader(TRUE ,"Label",sortOrder++,NULL,1); freeMem(caplitalized); } puts("</TR></THEAD><TBODY>"); } boolean doCellRow(struct hash *ra, char *org) // print one cell row { char *s; s = hashFindVal(ra, ORGANISM); if (s != NULL) { char *cellOrg = cloneString(s); strLower(cellOrg); if (differentString(cellOrg, org)) return FALSE; } // pathBuffer for new protocols not in human char pathBuffer[PATH_LEN]; safef(pathBuffer, sizeof(pathBuffer), "/ENCODE/protocols/cell/%s/",org); if (sameWord(org, ORG_HUMAN)) { if (cgiOptionalInt("tier",0)) { if (hashFindVal(ra,"tier") == NULL) return FALSE; if (atoi(hashFindVal(ra,"tier"))!=cgiOptionalInt("tier",0)) return FALSE; } if (cgiOptionalString("tiers")) { if (hashFindVal(ra,"tier") == NULL) return FALSE; boolean found=FALSE; char *tiers=cloneString(cgiOptionalString("tiers")); char *tier; (void)strSwapChar(tiers,',',' '); while ((tier=nextWord(&tiers))) { if (atoi(hashFindVal(ra,"tier"))==atoi(tier)) { found=TRUE; break; } } if (!found) return FALSE; } puts("<TR>"); char *term = printTerm(ra); printSetting(ra, "tier"); printDescription(ra,NULL,-1); printSetting(ra,"lineage"); printSetting(ra,"tissue"); printSetting(ra,"karyotype"); printSetting(ra,"sex"); printDocumentLink(ra,term,"protocol",pathBuffer,NULL,TRUE); printSettingsWithUrls(ra,"orderUrl","vendorName","vendorId"); printSettingsWithUrls(ra,"termUrl","termId",NULL); printLabel(ra,term); puts("</TR>"); } else // non-human cell type { puts("<TR>"); char *term = printTerm(ra); printDescription(ra,NULL,8); printSetting(ra,"category"); printSetting(ra,"tissue"); printSetting(ra,"sex"); //printSetting(ra,"karyotype"); printDocumentLink(ra,term,"protocol",pathBuffer,NULL,TRUE); printSettingsWithUrls(ra,"orderUrl","vendorName","vendorId"); printSettingsWithUrls(ra,"termUrl","termId",NULL); printLabel(ra,term); puts("</TR>"); } return TRUE; } boolean doAntibodyRow(struct hash *ra, char *org) // print one antibody row { puts("<TR>"); char *term = printTerm(ra); printDescription(ra,"antibodyDescription",9); printSetting(ra,"target"); // target is NOT first but still is major sort order printSetting(ra,"targetDescription"); printSettingsWithUrls(ra,"orderUrl","vendorName","vendorId"); printSetting(ra,"lab"); printDocumentLink(ra,term,"validation","/ENCODE/validation/antibodies/",NULL,FALSE); printSetting(ra,"lots"); printSettingsWithUrls(ra,"targetUrl","targetId",NULL); printLabel(ra,term); puts("</TR>"); return TRUE; } boolean doTypeOfTermRow(struct hash *ra, char *org) // print one typeOfTerm row { char *term = (char *)hashMustFindVal(ra, CV_TERM); if (sameString(term,cvTypeNormalized(CV_TERM_CELL))) term = CV_TERM_CELL; else if (sameString(term,cvTypeNormalized(CV_TERM_ANTIBODY))) term = CV_TERM_ANTIBODY; puts("<TR>"); printf(" <TD><A HREF='hgEncodeVocab?type=%s' title='%s details' " "TARGET=ucscVocabChild>%s</a></TD>\n", term, term, term); printDescription(ra,NULL,2); printLabel(ra,term); puts("</TR>"); if (sameString(term,CV_TERM_CELL)) { puts("<TR>"); printf(" <TD><A HREF='hgEncodeVocab?type=%s&organism=Mouse' title='Mouse %s details' " "TARGET=ucscVocabChild>%s</a> <em>(for mouse)</em></TD>\n", term, term, term); char *s = getDescription(ra,NULL); printf(" <TD colspan=%d>%s <em>(for mouse)</em></TD>\n", TABLE_COLS_AVAILABLE(2), s?s:" "); freeMem(s); printLabel(ra,term); puts("</TR>"); } return TRUE; } boolean doTypeRow(struct hash *ra, char *org) { char *type = (char *)cvTermNormalized(hashMustFindVal(ra, CV_TYPE)); if (sameWord(type,CV_TOT)) return doTypeOfTermRow(ra,org); else if (sameWord(type,CV_TERM_CELL)) return doCellRow(ra,org); else if (sameWord(type,CV_TERM_ANTIBODY)) return doAntibodyRow(ra,org); else if (sameWord(type,CV_TERM_LAB)) { puts("<TR>"); char *term = printTerm(ra); printDescription(ra,"labInst",5); printSetting(ra,"labPiFull"); printSetting(ra,"grantPi"); printSetting(ra,"organism"); printLabel(ra,term); puts("</TR>"); } else if (sameWord(type,CV_TERM_GRANT)) { puts("<TR>"); char *term = printTerm(ra); printDescription(ra,"grantInst",2); printLabel(ra,term); puts("</TR>"); } else if (sameWord(type,CV_TERM_LOCALIZATION)) { puts("<TR>"); char *term = printTerm(ra); printDescription(ra,NULL,3); printSettingsWithUrls(ra,"termUrl","termId",NULL); printLabel(ra,term); puts("</TR>"); } else // generic term: term, description, label { puts("<TR>"); char *term = printTerm(ra); printDescription(ra,NULL,2); printLabel(ra,term); puts("</TR>"); } return TRUE; } static char **convertAntibodiesToTargets(struct hash *cvHash,char **requested,int requestCount) /* Convers requested terms from antibodies to their corresponding targets */ { struct hashCookie hc = hashFirst(cvHash); struct hashEl *hEl; struct hash *ra; char **targets = needMem(sizeof(char *)*requestCount); int ix = 0; assert(requested != NULL); while ((hEl = hashNext(&hc)) != NULL) { ra = (struct hash *)hEl->val; ix = stringArrayIx(hashMustFindVal(ra, CV_TERM),requested,requestCount); if (ix != -1 && targets[ix] == NULL) // but not yet converted to antibody { // Special case for Inputs that do not have targets but are listed as Antibody // It is generalized to cover all cases for missing target targets[ix] = cloneString(hashFindVal(ra, CV_TARGET)); // May have a target if (targets[ix] == NULL) targets[ix] = cloneString(hashMustFindVal(ra, CV_TERM)); // Must have a term } } // At this point every term should have been found for (ix=0;ix<requestCount;ix++) { if (targets[ix] == NULL) errAbort("Failed to find antibody %s=%s\n",CV_TERM,requested[ix]); } return targets; } static char *normalizeType(char *type) /* Strips any quotation marks and converts common synonyms */ { if (type != NULL) { (void)stripChar(type,'\"'); if (sameWord(type,"Factor")) return cloneString(CV_TERM_ANTIBODY); char *cleanType = cloneString(cvTermNormalized(type)); if (differentString(cleanType,type)) return cleanType; freeMem(cleanType); /* if ((sameWord(type,"Cell Line")) || (sameWord(type,"cellLine" )) || (sameWord(type,"Cell Type")) || (sameWord(type,"Cell Type")) || (sameWord(type,"Cell" ))) // sameWord is case insensitive return cloneString(CV_TERM_CELL); else if (sameWord(type,"Factor")) || (sameString(type,"Antibody"))) return cloneString(CV_TERM_ANTIBODY); */ } return type; } static char *findType(struct hash *cvHash,char **requested,int requestCount, char **queryBy, char **org,boolean silent) /* returns the type that was requested or else the type associated with the term requested */ { struct hashCookie hc = hashFirst(cvHash); struct hashEl *hEl; struct hash *ra; char *type = typeOpt; if (requested != NULL) // if no type, find it from requested terms. Will validate terms match type { // NOTE: Enter here even if there is a type, to confirm the type while ((hEl = hashNext(&hc)) != NULL) // FIXME: This should be using mdbCv APIs to get hashes. { // One per "request[]" ra = (struct hash *)hEl->val; if (sameWord(hashMustFindVal(ra, CV_TYPE),CV_TOT)) // TOT = typeOfTerm continue; char *val = hashFindVal(ra, *queryBy); if (val != NULL) { int ix = stringArrayIx(val,requested,requestCount); if (ix != -1) // found { char *thisType = hashMustFindVal(ra, CV_TYPE); char *thisOrg = hashFindVal(ra, ORGANISM); if (type == NULL) { if (thisOrg != NULL) { *org = strLower(cloneString(thisOrg)); } type = thisType; } else if (differentWord(type,thisType)) { if (sameWord(CV_TERM_CONTROL,type)) type = thisType; else if (differentWord(CV_TERM_CONTROL,thisType)) errAbort("Error: Requested %s of type '%s'. But '%s' has type '%s'\n", *queryBy,type,requested[ix],thisType); } } } } } if (type == NULL && sameWord(*queryBy,CV_TERM)) // Special case of term becoming target { char *queryByTarget = CV_TARGET; type = findType(cvHash,requested,requestCount,&queryByTarget,org,TRUE); // silent here if (type != NULL) *queryBy = queryByTarget; } if (type == NULL && !silent) // Still not type? abort errAbort("Error: Required %s=%s ['%s', '%s', '%s', '%s' or '%s'] argument not found\n", *queryBy,(requested != NULL) ? *requested : "?", CV_TYPE, CV_TERM, CV_TAG, CV_TARGET, CV_LABEL); return normalizeType(type); } void doMiddle() { struct hash *cvHash = raReadAll((char *)cvFile(), CV_TERM); struct hashCookie hc = hashFirst(cvHash); struct hashEl *hEl; struct slList *termList = NULL; struct hash *ra; int totalPrinted = 0; boolean excludeDeprecated = (cgiOptionalString("deprecated") == NULL); // Prepare an array of selected terms (if any) int requestCount = 0; char **requested = NULL; char *requestVal = termOpt; char *queryBy = CV_TERM; if (tagOpt) { requestVal = tagOpt; queryBy = CV_TAG; } else if (targetOpt) { requestVal = targetOpt; queryBy = CV_TERM; // request target is special: lookup term, convert to target, display target } else if (labelOpt) { requestVal = labelOpt; queryBy = CV_LABEL; } if (requestVal) { (void)stripChar(requestVal,'\"'); - requestCount = chopCommas(requestVal,NULL); + requestCount = chopCommasLen(requestVal); requested = needMem(requestCount * sizeof(char *)); chopByChar(requestVal,',',requested,requestCount); } char *org = NULL; // if the org is specified in the type (eg. cell line) // then use that for the org, otherwise use the command line option, // otherwise use human. char *type = findType(cvHash,requested,requestCount,&queryBy, &org, FALSE); if (org == NULL) org = organismOptLower; if (org == NULL) org = ORG_HUMAN; // Special logic for requesting antibody by target if (targetOpt && requestCount > 0 && sameWord(queryBy,CV_TERM) && sameWord(type,CV_TERM_ANTIBODY)) { // Several antibodies may have same target. // requested target={antibody} and found antibody // Must now convert each of the requested terms to its target before displaying all targets char **targets = convertAntibodiesToTargets(cvHash,requested,requestCount); if (targets != NULL) { freeMem(requested); requested = targets; queryBy = CV_TARGET; } } //warn("Query by: %s = '%s' type:%s",queryBy,requestVal?requestVal:"all",type); // Get just the terms that match type and requested, then sort them if (differentWord(type,CV_TOT) || typeOpt != NULL ) // If type resolves to typeOfTerm and { // typeOfTerm was not requested, while ((hEl = hashNext(&hc)) != NULL) // then just show definition { ra = (struct hash *)hEl->val; char *thisType = (char *)cvTermNormalized(hashMustFindVal(ra,CV_TYPE)); if (differentWord(thisType,type) && (requested == NULL || differentWord(thisType,CV_TERM_CONTROL))) continue; // Skip all rows that do not match queryBy param if specified if (requested) { char *val = hashFindVal(ra, queryBy); if (val == NULL) { // Special case for input that has no target if (sameString(queryBy, CV_TARGET)) val = hashMustFindVal(ra, CV_TERM); else continue; } if (-1 == stringArrayIx(val,requested,requestCount)) continue; } else if (excludeDeprecated) { if (hashFindVal(ra, "deprecated") != NULL) continue; } slAddTail(&termList, ra); } } slSort(&termList, termCmp); boolean described = doTypeDefinition(type,FALSE,(slCount(termList) == 0)); boolean sortable = (slCount(termList) > 5); if (sortable) { webIncludeResourceFile("HGStyle.css"); jsIncludeFile("jquery.js",NULL); jsIncludeFile("utils.js",NULL); printf("<TABLE class='sortable' border=1 CELLSPACING=0 style='border: 2px outset #006600; " "background-color:%s;'>\n",COLOR_BG_DEFAULT); } else printf("<TABLE BORDER=1 BGCOLOR=%s CELLSPACING=0 CELLPADDING=2>\n",COLOR_BG_DEFAULT); if (slCount(termList) > 0) { doTypeHeader(type, org,sortable); // Print out the terms while ((ra = slPopHead(&termList)) != NULL) { if (doTypeRow( ra, org )) totalPrinted++; } } puts("</TBODY></TABLE><BR>"); if (sortable) jsInline("{$(document).ready(function() " "{sortTable.initialize($('table.sortable')[0],true,true);});}\n"); if (totalPrinted == 0) { if (!described) warn("Error: Unrecognised type (%s)\n", type); } else if (totalPrinted > 1) printf("Total = %d\n", totalPrinted); } int main(int argc, char *argv[]) /* Process command line */ { long enteredMainTime = clock1000(); cgiSpoof(&argc, argv); termOpt = cgiOptionalString(CV_TERM); tagOpt = cgiOptionalString(CV_TAG); typeOpt = cgiOptionalString(CV_TYPE); targetOpt = cgiOptionalString(CV_TARGET); labelOpt = cgiOptionalString(CV_LABEL); organismOpt = cgiUsualString(ORGANISM, organismOpt); if (organismOpt != NULL) { organismOptLower=cloneString(organismOpt); strLower(organismOptLower); } char *bgColor = cgiOptionalString("bgcolor"); if (bgColor) htmlSetBgColor(strtol(bgColor, 0, 16)); htmlSetStyle(htmlStyleUndecoratedLink); htmShell("ENCODE Controlled Vocabulary", doMiddle, "get"); cgiExitTime("hgEncodeVocab", enteredMainTime); return 0; }