aca9143822a9c12b16b33d479a5abb6495b6b4f0 braney Wed Aug 19 06:59:39 2026 -0700 lib, hgc, hgTables, hgHubConnect: share hubEncode, refs #38123 hgc.c and hgTables.c each had their own copy of hubEncode(). The two bodies were identical, so move the function to hubConnect.c next to isHubTrack() and let both CGIs call the one definition. Also use cgiEncode() rather than htmlEncode() for the db= value in the hgHubConnect assembly list. That value goes in a query string, so cgiEncode() is the right function there. Genome names are already limited to a safe character set, so this changes no output today. diff --git src/hg/hgc/hgc.h src/hg/hgc/hgc.h index a4c0bd16077..abda4b2f4a1 100644 --- src/hg/hgc/hgc.h +++ src/hg/hgc/hgc.h @@ -1,629 +1,626 @@ /* hgc - Human Genome Click processor - gets called when user clicks * on something in human tracks display. This file contains stuff * shared with other modules in hgc, but not in other programs. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HGC_H #define HGC_H #ifndef CART_H #include "cart.h" #endif #ifndef TRACKDB_H #include "trackDb.h" #endif #ifndef BED_H #include "bed.h" #endif #ifndef HDB_H #include "hdb.h" #endif #ifndef HPRINT_H #include "hPrint.h" #endif #ifndef CUSTOMTRACK_H #include "customTrack.h" #endif #ifndef WIKITRACK_H #include "wikiTrack.h" #endif #ifndef VARIOME_H #include "variome.h" #endif #ifndef BEDDETAIL_H #include "bedDetail.h" #endif #include "hgdpGeo.h" #include "dnaMotif.h" #include "togaClick.h" #include "featureBits.h" #include "snp125.h" extern struct cart *cart; /* User's settings. */ extern char *seqName; /* Name of sequence we're working on. */ extern int winStart, winEnd; /* Bounds of sequence. */ extern char *database; /* Name of mySQL database. */ extern char *organism; /* Colloquial name of organism. */ extern char *genome; /* common name, e.g. Mouse, Human */ extern char *scientificName; /* Scientific name of organism. */ extern struct hash *trackHash; /* A hash of all tracks - trackDb valued */ // A helper struct for allowing variable sized user defined tables. Each table // is encoded in one field of the bigBed with '|' as column separators and ';' as // field separators. struct embeddedTbl { struct embeddedTbl *next; // the next custom table char *field; // field name from bigBed, used as title when title is NULL char *title; // title of the table from trackDb, may be NULL char *encodedTbl; // contents of field in bigBed }; void hgcStart(char *title); /* Print out header of web page with title. Set * error handler to normal html error handler. */ char *hgcPath(); /* Return path of this CGI script. */ char *hgcPathAndSettings(); /* Return path with this CGI script and session state variable. */ void hgcAnchorSomewhere(char *group, char *item, char *other, char *chrom); /* Generate an anchor that calls click processing program with item * and other parameters. */ void hgcAnchorWindow(char *group, char *item, int thisWinStart, int thisWinEnd, char *other, char *chrom); /* Generate an anchor that calls click processing program with item * and other parameters, INCLUDING the ability to specify left and * right window positions different from the current window*/ void hgcAnchor(char *group, char *item, char *other); /* Generate an anchor that calls click processing program with item * and other parameters. */ struct trackDb *tdbForTableArg(); /* get trackDb for track passed in table arg */ void writeFramesetType(); /* Write document type that shows a frame set, rather than regular HTML. */ void htmlFramesetStart(char *title); /* Write DOCTYPE HTML and HEAD sections for framesets. */ void alnModernStart(char *classicTitle); /* Begin an alignment page: modern single-page chrome when the modernAlignPage hg.conf flag is set * (showSomeAlignment then renders the modern body), else the classic . */ struct psl *getAlignments(struct sqlConnection *conn, char *table, char *acc); /* get the list of alignments for the specified acc */ void printAlignmentsSimple(struct psl *pslList, int startFirst, char *hgcCommand, char *typeName, char *itemIn); /* Print list of mRNA alignments, don't add extra textual link when * doesn't honor hgcCommand. */ void printAlignments(struct psl *pslList, int startFirst, char *hgcCommand, char *typeName, char *itemIn); /* Print list of mRNA alignments. */ void printAlignmentsExtra(struct psl *pslList, int startFirst, char *hgcCommand, char *hgcCommandInWindow, char *typeName, char *itemIn); /* Print list of mRNA alignments with special "in window" alignment function. */ void showSomeAlignment(struct psl *psl, bioSeq *oSeq, enum gfType qType, int qStart, int qEnd, char *qName, int cdsS, int cdsE); /* Display protein or DNA alignment in a frame. */ void linkToOtherBrowserTitle(char *otherDb, char *chrom, int start, int end, char *title); /* Make anchor tag to open another browser window with a title. */ void linkToOtherBrowser(char *otherDb, char *chrom, int start, int end); /* Make anchor tag to open another browser window. */ void printEntrezGeneUrl(FILE *f, int geneid); /* Print URL for Entrez browser on a gene details page. */ void printEntrezPubMedUidUrl(FILE *f, int pmid); /* Print URL for Entrez browser on a PubMed search. */ void printSwissProtAccUrl(FILE *f, char *accession); /* Print URL for Swiss-Prot protein accession. */ boolean clipToChrom(int *pStart, int *pEnd); /* Clip start/end coordinates to fit in chromosome. */ void printCappedSequence(int start, int end, int extra); /* Print DNA from start to end including extra at either end. * Capitalize bits from start to end. */ void printPos(char *chrom, int start, int end, char *strand, boolean featDna, char *item); /* Print position lines. 'strand' argument may be null. */ void bedPrintPos(struct bed *bed, int bedSize, struct trackDb *tdb); /* Print first three fields of a bed type structure in * standard format. */ void savePosInTextBox(char *chrom, int start, int end); /* Save basic position/database info in text box and hidden var. Positions becomes chrom:start-end*/ void genericHeader(struct trackDb *tdb, char *item); /* Put up generic track info. */ void genericBedClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int bedSize); /* Handle click in generic BED track. */ void printPosOnChrom(char *chrom, int start, int end, char *strand, boolean featDna, char *item); /* Print position lines referenced to chromosome. Strand argument may be NULL */ void printTrackHtml(struct trackDb *tdb); /* If there's some html associated with track print it out. */ void abbr(char *s, char *fluff); /* Cut out fluff from s. */ void printTableHeaderName(char *name, char *clickName, char *url); /* creates a table to display a name vertically, * basically creates a column of letters */ void printBacStsXRef(char *clone); /* Print out associated STS XRef information for BAC clone on BAC ends */ /* tracks details pages. */ /* ----Routines in other modules in the same directory---- */ void genericWiggleClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start); /* Display details for WIGGLE tracks. */ void genericBigWigClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start); /* Display details for BigWig tracks. */ void bigWigCustomClick(struct trackDb *tdb); /* Display details for BigWig custom tracks. */ void genericBigBedClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end, int bedSize); void doPubsDetails(struct trackDb *tdb, char *item); /* Handle text2Genome track clicks in pubs.c */ /* Handle click in generic bigBed track. */ void bigBedCustomClick(struct trackDb *tdb); /* Display details for BigWig custom tracks. */ void genericMafClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start); /* Display details for MAF tracks. */ void genericAxtClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *otherDb); /* Display details for AXT tracks. */ void genericExpRatio(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start); /* Display details for expRatio tracks. */ void rosettaDetails(struct trackDb *tdb, char *item); /* Set up details for rosetta. */ void affyDetails(struct trackDb *tdb, char *item); /* Set up details for affy. */ void gnfExpRatioDetails(struct trackDb *tdb, char *item); /* Put up details on some gnf track. */ void loweExpRatioDetails(struct trackDb *tdb, char *item); /* Put up details on some lowe track. */ void affyUclaDetails(struct trackDb *tdb, char *item); /* Set up details for affyUcla. */ void cghNci60Details(struct trackDb *tdb, char *item); /* Set up details for cghNci60. */ void nci60Details(struct trackDb *tdb, char *item); /* Set up details for nci60. */ void doAffyHumanExon(struct trackDb *tdb, char *item); /* Details for affyHumanExon all exon arrays. */ void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct); /* Generic expression ratio deatils using microarrayGroups.ra file */ /* and not the expRecord tables. */ void getMsBedExpDetails(struct trackDb *tdb, char *expName, boolean all); /* Create tab-delimited output to download */ void printPslFormat(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, char *subType); /*Handles click in Affy tracks and prints out alignment details with link*/ /* to sequences if available in the database */ void doAffy(struct trackDb *tdb, char *item, char *itemForUrl); /* Display alignment information for Affy tracks */ void doScaffoldEcores(struct trackDb *tdb, char *item); /* Creates details page and gets the scaffold co-ordinates for unmapped */ /* genomes for display and to use to create the correct outside link URL */ struct customTrack *lookupCt(char *name); /* Return custom track for name, or NULL. */ void doRnaSecStr(struct trackDb *tdb, char *itemName); /* Handle click on rnaSecStr type elements. */ void motifHitSection(struct dnaSeq *seq, struct dnaMotif *motif); /* Print out section about motif. */ void motifMultipleHitsSection(struct dnaSeq **seqs, int count, struct dnaMotif *motif, char *title); /* Print out section about motif, possibly with mutliple occurrences. */ void motifLogoAndMatrix(struct dnaSeq **seqs, int count, struct dnaMotif *motif); /* Print out motif sequence logo and text (possibly with multiple occurences) */ struct dnaMotif *loadDnaMotif(char *motifName, char *motifTable); /* Load dnaMotif from table. */ void doTriangle(struct trackDb *tdb, char *item, char *motifTable); /* Display detailed info on a regulatory triangle item. */ void doTransRegCode(struct trackDb *tdb, char *item, char *motifTable); /* Display detailed info on a transcriptional regulatory code item. */ void doTransRegCodeProbe(struct trackDb *tdb, char *item, char *codeTable, char *motifTable, char *tfToConditionTable, char *conditionTable); /* Display detailed info on a CHIP/CHIP probe from transRegCode experiments. */ void doPeakClusters(struct trackDb *tdb, char *item); /* Display detailed info about a cluster of peaks from other tracks. */ void doPeakClusterListItemsAssayed(); /* Put up a page that shows all experiments associated with a cluster track. */ void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end); /* Display detailed info about a cluster of peaks from other tracks. */ void doFlyreg(struct trackDb *tdb, char *item); /* flyreg.org: Drosophila DNase I Footprint db. */ void dbRIP(struct trackDb *tdb, char *item, char *itemForUrl); /* Put up dbRIP track info */ void doCgapSage(struct trackDb *tdb, char *itemName); /* CGAP SAGE details. */ char* getEntrezNucleotideUrl(char *accession); /* get URL for Entrez browser on a nucleotide. free resulting string */ void printEntrezNucleotideUrl(FILE *f, char *accession); /* Print URL for Entrez browser on a nucleotide. */ void printEntrezProteinUrl(FILE *f, char *accession); /* Print URL for Entrez browser on a protein. */ void printCcdsForMappedGene(struct sqlConnection *conn, char *acc, char *mapTable); /* Print out CCDS links a gene mapped via a cddsGeneMap table */ int getImageId(struct sqlConnection *conn, char *acc); /* get the image id for a clone, or 0 if none */ char *getRefSeqSummary(struct sqlConnection *conn, char *acc); /* RefSeq summary or NULL if not available; free result */ char *getRefSeqCdsCompleteness(struct sqlConnection *conn, char *acc); /* get description of RefSeq CDS completeness or NULL if not available */ char *kgIdToSpId(struct sqlConnection *conn, char* kgId); /* get the swissprot id for a known genes id; resulting string should be * freed */ char *hgTracksPathAndSettings(); /* Return path with hgTracks CGI path and session state variable. */ void medlineLinkedTermLine(char *title, char *text, char *search, char *keyword); /* Produce something that shows up on the browser as * TITLE: value * with the value hyperlinked to medline using a specified search term. */ void medlineLinkedLine(char *title, char *text, char *search); /* Produce something that shows up on the browser as * TITLE: value * with the value hyperlinked to medline. */ void hgcAnchorPosition(char *group, char *item); /* Generate an anchor that calls click processing program with item * and group parameters. */ void geneShowPosAndLinks(char *geneName, char *pepName, struct trackDb *tdb, char *pepTable, char *pepClick, char *mrnaClick, char *genomicClick, char *mrnaDescription); /* Show parts of gene common to everything. If pepTable is not null, * it's the old table name, but will check gbSeq first. */ bool loweLabClick(char *track, char *item, struct trackDb *tdb); /* check if we have one of the lowelab tracks */ void showTxInfo(char *geneName, struct trackDb *tdb, char *txInfoTable); /* Print out stuff from txInfo table. */ void showCdsEvidence(char *geneName, struct trackDb *tdb, char *evTable); /* Print out stuff from cdsEvidence table. */ void doWikiTrack(char *itemName, char *chrom, int winStart, int winEnd); /* handle item clicks on wikiTrack - may create new items */ void doCreateWikiItem(char *itemName, char *chrom, int winStart, int winEnd); /* handle create item clicks for wikiTrack */ void doAddWikiComments(char *itemName, char *chrom, int winStart, int winEnd); /* handle add comment item clicks for wikiTrack */ void doDeleteWikiItem(char *itemName, char *chrom, int winStart, int winEnd); /* handle delete item clicks for wikiTrack */ void offerLogin(int id, char *loginType, char *table); /* display login prompts to the wiki when user isn't already logged in */ void outputJavaScript(); /* java script functions used in the create item form */ void doVariome (char *wikiItemId, char *chrom, int winStart, int winEnd); /* handle item clicks on variome - may create new items */ void displayVariomeItem (struct variome *item, char *userName); /* given an already fetched item, get the item description from * the wiki. Put up edit form(s) if userName is not NULL * separate from wikiTrack for form field differences and help */ void doCreateVariomeItem (char *itemName, char *chrom, int winStart, int winEnd); /* handle create item clicks for variome */ void doAddVariomeComments(char *wikiItemId, char *chrom, int winStart, int winEnd); /* handle add comment item clicks for Variome Track */ void doDeleteVariomeItem(char *wikiItemId, char *chrom, int winStart, int winEnd); /* handle delete item clicks for Variome Track */ void printWikiVariomeForm (struct bedDetail *item); /* print the wiki annotation form for the variome track */ void customMafClick(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb); /* handle clicks on a custom maf */ void doBigEncodePeak(struct trackDb *tdb, struct customTrack *cti, char *item); /* details for encodePeak type tracks. */ void doEncodePeak(struct trackDb *tdb, struct customTrack *cti, char *item); /* details for encodePeak type tracks. */ void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb); /* Print details for 5C track */ void doPeptideMapping(struct sqlConnection *conn, struct trackDb *tdb, char *item); /* Print details for a peptideMapping track. */ void doHgdpGeo(struct trackDb *tdb, char *item); /* Show details page for HGDP SNP with population allele frequencies * plotted on a world map. */ void hgdpGeoImg(struct hgdpGeo *geo); /* Generate image as PNG, PDF, EPS: world map with pie charts for population allele frequencies. */ char *hgdpPngFilePath(char *rsId); /* Return the stable PNG trash-cached image path for rsId. */ void hgdpGeoFreqTable(struct hgdpGeo *geo); /* Print an HTML table of populations and allele frequencies. */ void printOtherSnpMappings(char *table, char *name, int start, struct sqlConnection *conn, int rowOffset, struct trackDb *tdb); /* If this SNP (from any bed4+ table) is not uniquely mapped, print the other mappings. */ void printCustomUrl(struct trackDb *tdb, char *itemName, boolean encode); /* Wrapper to call printCustomUrlWithLabel using the url setting in trackDb */ void printCustomUrlWithFields(struct trackDb *tdb, char *itemName, char *itemLabel, boolean encode, struct slPair *fields); /* Wrapper to call printCustomUrlWithLabel with additional fields to substitute */ void printOtherCustomUrl(struct trackDb *tdb, char *itemName, char* urlSetting, boolean encode); /* Wrapper to call printCustomUrlWithLabel to use another url setting other than url in trackDb e.g. url2, this allows the use of multiple urls for a track * to be set in trackDb. */ void printIdOrLinks(struct asColumn *col, struct hash *fieldToUrl, struct trackDb *tdb, char *idList); /* if trackDb does not contain a "urls" entry for current column name, just print idList as it is. * * Otherwise treat idList as a comma-sep list of IDs and print one row per id, with a link to url, * * ($$ in url is OK, wildcards like $P, $p, are also OK) * * */ void printDbSnpRsUrl(char *rsId, char *labelFormat, ...) /* Print a link to dbSNP's report page for an rs[0-9]+ ID. */ #ifdef __GNUC__ __attribute__((format(printf, 2, 3))) #endif ; void doBamDetails(struct trackDb *tdb, char *item); /* Show details of an alignment from a BAM file. */ void doVcfTabixDetails(struct trackDb *tdb, char *item); /* Show details of an alignment from a VCF file compressed and indexed by tabix. */ void doVcfTabixDetailsExt(struct trackDb *tdb, char *item, struct featureBits **pFbList, int start, int end); /* Show details of an alignment from a VCF file compressed and indexed by tabix. */ void doVcfDetails(struct trackDb *tdb, char *item); /* Show details of an alignment from an uncompressed VCF file. */ void doVcfDetailsExt(struct trackDb *tdb, char *item, struct featureBits **pFbList, int start, int end); /* Show details of an alignment from an uncompressed VCF file. */ void doBarChartDetails(struct trackDb *tdb, char *item); /* Details of barChart item */ void doMyVariantsDetails(struct customTrack *ct, char *itemIdString); /* Show details of a myVariants item. */ void doBedDetail(struct trackDb *tdb, struct customTrack *ct, char *itemName); /* generate the detail page for a custom track of bedDetail type */ void doPgSnp(struct trackDb *tdb, char *itemName, struct customTrack *ct); /* print detail page for personal genome track (pgSnp) */ void doGvf(struct trackDb *tdb, char *item); /* Show details for variants represented as GVF, stored in a bed8Attrs table */ void doGeneReviews(struct trackDb *tdb, char *itemName); /* generate the detail page for geneReviews */ void prGeneReviews(struct sqlConnection *conn, char *itemName); /* print GeneReviews associated to this item */ void prGRShortRefGene(struct sqlConnection *conn, char *itemName); /* print GeneReviews short label associated to this refGene item */ void doLrg(struct trackDb *tdb, char *item); /* Locus Reference Genomic (LRG) info. */ void doLrgTranscriptPsl(struct trackDb *tdb, char *item); /* Locus Reference Genomic (LRG) transcript mapping and sequences. */ void htcLrgCdna(char *item); /* Serve up LRG transcript cdna seq */ void doPeptideAtlas(struct trackDb *tdb, char *item); /* Details for PeptideAtlas peptide mapping */ void doGtexGeneExpr(struct trackDb *tdb, char *item); /* Details of GTEX gene expression item */ void doGtexEqtlDetails(struct trackDb *tdb, char *item); /* Details of GTEx eQTL item */ void printSnp125Function(struct trackDb *tdb, struct snp125 *snp); /* If the user has selected a gene track for functional annotation, * report how this SNP relates to any nearby genes. */ void printSnp153Function(struct trackDb *tdb, struct snp125 *snp); /* If the user has selected a gene track for functional annotation, * report how this SNP relates to any nearby genes. */ void doBigDbSnp(struct trackDb *tdb, char *rsId); /* Show details for bigDbSnp item. */ void printAddWbr(char *text, int distance); /* a crazy hack for firefox/mozilla that is unable to break long words in tables * We need to add a tag every x characters in the text to make text breakable. */ void printIframe(struct trackDb *tdb, char *itemName); /* print an iframe with the URL specified in trackDb (iframeUrl), can have * the standard codes in it (like $$ for itemName, etc) */ char *getIdInUrl(struct trackDb *tdb, char *itemName); /* If we have an idInUrlSql tag, look up itemName in that, else just * return itemName. */ // trackDb setting prefix for JS visualization scripts on details pages. // Format: detailsScript.. // Parsed in both bigBedClick.c (to build JSON + load JS) and hgc.c (to skip fields from table). #define DETAILS_SCRIPT_PREFIX "detailsScript.*" -char *hubEncode(struct trackDb *tdb, char *text); -/* Return text escaped for HTML if it belongs to a track hub, otherwise return it unchanged. */ - void printFieldLabel(char *entry); /* print the field label, the first column in the table, as a . Allow a * longer description after a |-char, as some fields are not easy to * understand. */ void printFieldLabelWithId(char *entry, char *fieldName); /* Like printFieldLabel but adds id="bfld_" to the element, * so JavaScript can find the row by field name. */ struct slPair* getExtraFields(struct trackDb *tdb, char **fields, int fieldCount); /* return the extra field names and their values as a list of slPairs */ struct slPair *getFields(struct trackDb *tdb, char **fields); /* return field names and their values as a list of slPairs. */ void printEmbeddedTable(struct trackDb *tdb, struct embeddedTbl *embeddedTblList, struct dyString *tableLabelsDy); /* Pretty print a '|' and ';' encoded table or a JSON encoded table from a bigBed field. * The JSON encoded tables get passed through as json so hgc.js can build them instead, * which preserves the table order */ void getExtraTableFields(struct trackDb *tdb, struct slName **retFieldNames, struct embeddedTbl **retEmbeddedTblList, struct hash *fieldsToEmbeddedTbl); /* Parse the trackDb field "extraTableFields" into the field names and titles specified, * and fill out a hash keyed on the bigBed field name (which may be in an external file * and not in the bigBed itself) to a helper struct for storing user defined tables. */ int extraFieldsPrintAs(struct trackDb *tdb,struct sqlResult *sr,char **fields,int fieldCount, struct asObject *as); // Any extra bed or bigBed fields (defined in as and occurring after N in bed N + types. // sr may be null for bigBeds. // Returns number of extra fields actually printed. int extraFieldsPrint(struct trackDb *tdb,struct sqlResult *sr,char **fields,int fieldCount); // Any extra bed or bigBed fields (defined in as and occurring after N in bed N + types. // sr may be null for bigBeds. // Returns number of extra fields actually printed. struct slPair *parseDetailsTablUrls(struct trackDb *tdb); /* Parse detailsUrls setting string into an slPair list of {offset column name, fileOrUrl} */ char *readOneLineMaybeBgzip(char *fileOrUrl, bits64 offset, bits64 len); /* If fileOrUrl is bgzip-compressed and indexed, then use htslib's bgzf functions to * retrieve uncompressed data from offset; otherwise (plain text) use udc. If len is 0, * read up to next '\n' delimiter. */ #define NUCCORE_SEARCH "https://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&cmd=search&term=" void doJRepeat (struct trackDb *tdb, char *repeat); void doBigRmskRepeat (struct trackDb *tdb, char *repeat); /* New RepeatMasker Visualization defined in joinedRmskClick.c */ INLINE char* strOrNbsp(char* val) /* return val if not empty otherwise HTML entity   */ { return isEmpty(val) ? " " : val; } void doInteractDetails(struct trackDb *tdb, char *item); /* Details of interaction item */ void doParDetails(struct trackDb *tdb, char *name); /* show details of a PAR item. */ void doLorax(struct trackDb *tdb, char *item); /* Display the Lorax multi-tree viewer. */ void doQuickLiftChain(struct trackDb *tdb, char *item); /* Deal with click on quickLift chain track.*/ struct psl *getPslAndSeq(struct trackDb *tdb, char *chromName, struct bigBedInterval *bb, unsigned seqTypeField, DNA **retSeq, char **retCdsStr); /* Read in psl and query sequence out of a bbiInverval on a give chromosome */ #endif