a2e996babf1ad91f08f6a1a3ceca8ec9af0fe2cf max Thu Apr 19 16:16:58 2012 -0700 changed almost all html in pubs hgc page to get rid of unnecessary tables (this part does not conform to kent style but really looks better) diff --git src/hg/hgc/pubs.c src/hg/hgc/pubs.c index b2a0cf1..3616e83 100644 --- src/hg/hgc/pubs.c +++ src/hg/hgc/pubs.c @@ -28,57 +28,190 @@ "intro", "methods", "results", "discussion", "conclusions", "ack", "refs", "unknown" }; // // whether a checkbox is checked by default, have to correspond to pubsSecNames static int pubsSecChecked[] ={ 1, 1, 1, 1, 1, 1, 1, 0, 0, 1 }; static char* pubsSequenceTable; + +/* ------ START based on QA's suggestions, functions to replace old HTML tables */ + + +/* Suffix -S for "function accepts style parameter" + * Suffix -C for "function accepts class parameter" + * Suffix -CI for "function accepts class and id parameter" + */ + +static void web2Start(char* tag) +{ +printf("<%s>\n", tag); +} + +static void web2End(char* tag) +{ +printf("\n", tag); +} + +static void web2StartS(char* style, char* tag) +{ +printf("<%s style=\"%s\">\n", tag, style); +} + +static void web2StartC(char* class, char* tag) +{ +printf("<%s class=\"%s\">\n", tag, class); +} + +static void web2StartCI(char* class, char* id, char* tag) +{ +if ((id==NULL) && (class==NULL)) + web2Start(tag); +else if (id==NULL) + web2StartC(class, tag); +else + printf("<%s class=\"%s\" id=\"%s\">\n", tag, class, id); +} + +static void web2PrintS(char* style, char* tag, char* label) +{ +printf("<%s style=\"%s\">%s\n", tag, style, label, tag); +} + +//static void web2PrintC(char* class, char* tag, char* label) +//{ +//printf("<%s class=\"%s\">%s\n", tag, class, label, tag); +//} + +//static void web2Print(char* tag, char* label) +//{ +//printf("<%s>%s\n", tag, label, tag); +//} + +static void web2StartTableC(char* class) { web2StartC(class, "table"); } + +static void web2StartTheadC(char* class) { web2StartC(class, "thead"); } +static void web2EndThead() { web2End("thead"); } + +static void web2StartTbodyS(char* style) { web2StartS(style, "tbody"); } + +static void web2StartCell() { web2Start("td"); } +static void web2EndCell() { web2End("td"); } +static void web2StartCellS(char* style) { web2StartS(style, "td"); } +//static void web2PrintCell(char* label) { web2Print("td", label); } +static void web2PrintCellS(char* style, char *label) { web2PrintS(style, "td", label); } + +static void web2StartRow() { web2Start("tr"); } +static void web2EndRow() { web2End("tr"); } + +//static void web2StartTbody() { web2Start("tbody"); } +static void web2EndTbody() { web2End("tbody"); } + +//static void web2StartTable() { web2Start("table"); } +static void web2EndTable() { web2EndTbody(); web2End("table"); } + +static void web2StartDivCI(char* class, char* id) { web2StartCI(class, id, "div"); } +static void web2StartDivC(char* class) { web2StartC(class, "div"); } + +static void web2EndDiv(char* comment) +{ +printf(" \n", comment); +} + +static void web2PrintHeaderCell(char *label, int width) +/* Print th heading cell with given width in percent */ +{ +printf("", width); +printf("%s", label); +} + +static void web2PrintCellF(char* format, ...) +/* print a td with format */ +{ +va_list args; +va_start(args, format); + +web2StartCell(); +vprintf(format, args); +web2EndCell(); +va_end(args); +} + + + +static void web2StartSection(char* id, char* format, ...) +/* create a new section on the web page */ +{ +va_list args; +va_start(args, format); + +puts("\n"); +web2StartDivCI("section", id); +web2StartDivC("subheadingBar windowSize"); +vprintf(format, args); +web2EndDiv("subheadingBar"); +va_end(args); +} + +static void web2EndSection() +/* end section */ +{ +web2EndDiv("section"); +} + +/* ------ END based on QA's suggestions, functions to replace old HTML tables */ + static char* mangleUrl(char* url) /* add publisher specific parameters to url and return new url*/ { if (!stringIn("sciencedirect.com", url)) return url; // cgi param to add the "UCSC matches" sciverse application to elsevier's sciencedirect char* sdAddParam = "?svAppaddApp=298535"; char* longUrl = catTwoStrings(url, sdAddParam); char* newUrl = replaceChars(longUrl, "article", "svapps"); return newUrl; } static void printFilterLink(char* pslTrack, char* articleId, char* articleTable) /* print a link to hgTracks with an additional cgi param to activate the single article filter */ { int start = cgiInt("o"); int end = cgiInt("t"); char qBuf[1024]; struct sqlConnection *conn = hAllocConn(database); safef(qBuf, sizeof(qBuf), "SELECT CONCAT(firstAuthor, year) FROM %s WHERE articleId='%s';", articleTable, articleId); char* dispId = sqlQuickString(conn, qBuf); - printf("

", + printf( + "

"); + printf( + "

", hgTracksPathAndSettings(), database, seqName, start+1, end, articleId, pslTrack, dispId); + printf("Show these sequence matches individually on genome browser (activates track \"" "Individual matches for article\")

"); + printf( + "
\n"); hFreeConn(&conn); } static char* makeSqlMarkerList(void) /* return list of sections from cgi vars, format like "'abstract','header'" */ { int secCount = sizeof(pubsSecNames)/sizeof(char *); struct slName* names = NULL; int i; for (i=0; i\n"); -printf("\n"); +//style=\"margin: 10px auto; width: 98%%\"style=\"background-color: #fcecc0\" +web2StartTableC("stdTbl centeredStdTbl"); +web2StartTheadC("stdTblHead"); if (showDesc) - puts(" Article file\n"); -puts(" One row per sequence, with flanking text, sequence in bold\n"); + web2PrintHeaderCell("Article file", 10); +web2PrintHeaderCell("One row per sequence, with flanking text, sequence in bold", 60); if (pubsDebug) - puts(" Identifiers\n"); + web2PrintHeaderCell("Identifiers", 30); if (!isClickedSection && !pubsDebug) - puts(" Chained matches with this sequence\n"); -puts("\n"); + web2PrintHeaderCell("Chained matches with this sequence", 20); +web2EndThead(); +web2StartTbodyS("font-family: Arial, Helvetica, sans-serif; line-height: 1.5em; font-size: 0.9em;"); } static 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. */ { int i; i = 0; char* c; c = text; bool doNotBreak = FALSE; while (*c != 0) { if ((*c=='&') || (*c=='<')) @@ -367,176 +502,180 @@ void printGbLinks(struct slName* locs) /* print hash keys in format hg19/chr1:1-1000 as links */ { struct slName *el; for (el = locs; el != NULL; el = el->next) { char* locString = el->name; char* db = cloneNextWordByDelimiter(&locString, '/'); char* chrom = cloneNextWordByDelimiter(&locString, ':'); char* startStr = cloneNextWordByDelimiter(&locString, '-'); char* endStr = cloneString(locString); int start = atoi(startStr); int end = atoi(endStr); printHgTracksLink(db, chrom, start, end, NULL, NULL); - printf("
"); + printf("
"); freeMem(endStr); //XX why can't I free these? freeMem(chrom); freeMem(startStr); freeMem(db); } } + + + static bool printSeqSection(char* articleId, char* title, bool showDesc, struct sqlConnection* conn, struct hash* clickedSeqs, bool isClickedSection, bool fasta, char* pslTable, char* articleTable) -/* print a table of sequences, show only sequences with IDs in hash, +/* print a section with a table of sequences, show only sequences with IDs in hash, * There are two sections, respective sequences are shown depending on isClickedSection and clickedSeqs * - seqs that were clicked on (isClickedSection=True) -> show only seqs in clickedSeqs * - other seqs (isClickedSection=False) -> show all other seqs * * */ { // get data from mysql char query[4096]; safef(query, sizeof(query), "SELECT fileDesc, snippet, locations, articleId, fileId, seqId, sequence " "FROM %s WHERE articleId='%s';", pubsSequenceTable, articleId); if (pubsDebug) puts(query); struct sqlResult *sr = sqlGetResult(conn, query); // construct title for section char* otherFormat = NULL; if (fasta) otherFormat = "table"; else otherFormat = "fasta"; char fullTitle[5000]; safef(fullTitle, sizeof(fullTitle), -"%s (%s format)", +"%s (%s format)\n", title, cartSidUrlString(cart), cgiString("o"), cgiString("t"), cgiString("g"), cgiString("i"), !fasta, otherFormat); -webNewSection("%s", fullTitle); +web2StartSection("pubsSection", "%s", fullTitle); +// print filtering link at start of table & table headers if (isClickedSection) - { printFilterLink(pslTable, articleId, articleTable); - printf(""); - } -else - printf(""); if (!fasta) printSeqHeaders(showDesc, isClickedSection); +// output rows char **row; bool foundSkippedRows = FALSE; while ((row = sqlNextRow(sr)) != NULL) { char* fileDesc = row[0]; char* snippet = row[1]; char* locString= row[2]; char* artId = row[3]; char* fileId = row[4]; char* seqId = row[5]; char* seq = row[6]; // annotation (=sequence) ID is a 64 bit int with 10 digits for // article, 3 digits for file, 5 for annotation char annotId[100]; safef(annotId, 100, "%010d%03d%05d", atoi(artId), atoi(fileId), atoi(seqId)); if (pubsDebug) printf("%s", annotId); // only display this sequence if we're in the right section if (clickedSeqs!=NULL && ((hashLookup(clickedSeqs, annotId)!=NULL) != isClickedSection)) { foundSkippedRows = TRUE; continue; } - printf(""); - if (fasta) - printf(">%s
%s
", annotId, seq); + printf(">%s
%s
", annotId, seq); else { - printf("\n"); + web2StartRow(); + + // column 1: type of file (main or supp) if (showDesc) - printf("%s\n", fileDesc); - //printf("%s\n", snippet); - printf(""); + web2PrintCellS(fileDesc, "word-break:break-all"); + + // column 2: snippet + web2StartCellS("word-break:break-all"); printAddWbr(snippet, 40); - printf("\n"); + web2EndCell(); + + // optional debug info column if (pubsDebug) - printf("article %s, file %s, seq %s, annotId %s", artId, fileId, seqId, annotId); + web2PrintCellF("article %s, file %s, seq %s, annotId %s", artId, fileId, seqId, annotId); - // print links to locations + // column 3: print links to locations, only print this in the 2nd section if (!isClickedSection && !pubsDebug) { // format: hg19/chr1:300-400,mm9/chr1:60006-23234 // split on "," then split on "/" //locs = charSepToSlNames(locString, ','); + web2StartCell(); char* locArr[1024]; int partCount = chopString(locString, ",", locArr, ArraySize(locArr)); - printf(""); if (partCount==0) printf("No matches"); else { struct slName *locs; locs = slNameListFromStringArray(locArr, partCount); slUniqify(&locs, slNameCmp, slNameFree); printGbLinks(locs); - printf("
"); - printf("\n"); + printf("
"); slFreeList(&locs); } - + web2EndCell(); } - printf("\n"); + web2EndRow(); } } -printf("\n"); // finish section -webEndSectionTables(); +if (!fasta) + web2EndTable(); + +web2EndSection(); sqlFreeResult(&sr); return foundSkippedRows; } static void printSeqInfo(struct sqlConnection* conn, char* trackTable, char* pslTable, char* articleId, char* item, char* seqName, int start, bool fileDesc, bool fasta, char* articleTable) /* print sequences, split into two sections * two sections: one for sequences that were clicked, one for all others*/ { struct hash* clickedSeqs = getSeqIdHash(conn, trackTable, articleId, item, seqName, start); bool skippedRows; if (clickedSeqs) skippedRows = printSeqSection(articleId, "Sequences used to construct this feature", \ fileDesc, conn, clickedSeqs, 1, fasta, pslTable, articleTable); else skippedRows=1; if (skippedRows) printSeqSection(articleId, "Other Sequences in this article", \ fileDesc, conn, clickedSeqs, 0, fasta, pslTable, articleTable); if (pubsIsElsevier) - printf("

Copyright 2012 Elsevier B.V. All rights reserved.

"); + printf("

Copyright 2012 Elsevier B.V. All rights reserved.

"); freeHash(&clickedSeqs); } static void printTrackVersion(struct trackDb *tdb, struct sqlConnection* conn, char* item) { char versionString[256]; char dateReference[256]; char headerTitle[512]; /* see if hgFixed.trackVersion exists */ boolean trackVersionExists = hTableExists("hgFixed", "trackVersion"); if (trackVersionExists) { char query[256]; safef(query, sizeof(query), \