bb85cad5b5a52f6a5e96f72cbfe681c5c4b863f8 max Wed Aug 21 22:25:39 2013 -0700 fixing a layout bug, adding cgi param for ensembl to linkout to hgc diff --git src/hg/hgc/pubs.c src/hg/hgc/pubs.c index d78f418..dbbeb44 100644 --- src/hg/hgc/pubs.c +++ src/hg/hgc/pubs.c @@ -16,42 +16,43 @@ // cgi var to activate debug output static int pubsDebug = 0; // global var for printArticleInfo to indicate if article has suppl info // Most publishers have supp data. // If they don't have it, we can skip the fileType column in the table bool pubsHasSupp = TRUE; // global var for printArticleInfo to indicate if article is elsevier // If it's elsevier, we print the copyright line bool pubsIsElsevier = FALSE; // the article source is used to modify other parts of the page static char *articleSource; -// we need the external article PMC Id for yif links + +// we need the external article PMC Id for YIF links static char *extId = NULL; // section types in mysql table, for all annotations tables // we note where the hit is located in the document static char *pubsSecNames[] ={ "header", "abstract", "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; /* ------ functions to replace HTML4 tables with HTML5 constructs */ /* Web wrappers incorporating tag, id, and class HTML attributes, to support * styling and test */ @@ -262,47 +263,55 @@ safef(nameBuf, sizeof(nameBuf), "'%s'", secName); slAddHead(&names, slNameNew(nameBuf)); } } if (names==0) errAbort("You need to specify at least one article section."); char *nameListString = slNameListToString(names, ','); slNameFree(names); return nameListString; } static struct sqlResult *queryMarkerRows(struct sqlConnection *conn, char *markerTable, \ - char *articleTable, char *item, int itemLimit, char *sectionList) -/* query marker rows from mysql, based on http parameters */ + char *articleTable, char *item, int itemLimit, char *sectionList, char *artExtIdFilter) +/* query marker rows from mysql, based on http parameters + * optionally filter on sections or just a single article + * */ { char query[4000]; /* Mysql specific setting to make the group_concat function return longer strings */ sqlUpdate(conn, "NOSQLINJ SET SESSION group_concat_max_len = 100000"); +char artFilterSql[4000]; +artFilterSql[0] = 0; +if (isNotEmpty(artExtIdFilter)) + safef(artFilterSql, sizeof(artFilterSql), " AND extId='%s' ", artExtIdFilter); + // no need to check for illegal characters in sectionList sqlSafef(query, sizeof(query), "SELECT distinct %s.articleId, url, title, authors, citation, " "pmid, extId, " "group_concat(snippet, concat(\" (section: \", section, \")\") SEPARATOR ' (...) ') FROM %s " "JOIN %s USING (articleId) " "WHERE markerId='%s' AND section in (%-s) " + "%-s" "GROUP by articleId " "ORDER BY year DESC " "LIMIT %d", - markerTable, markerTable, articleTable, item, sectionList, itemLimit); + markerTable, markerTable, articleTable, item, sectionList, artFilterSql, itemLimit); if (pubsDebug) printf("%s", query); struct sqlResult *sr = sqlGetResult(conn, query); return sr; } static void printSectionCheckboxes() /* show a little form with checkboxes where user can select sections they want to show */ { // labels to show to user, have to correspond to pubsSecNames char *secLabels[] ={ @@ -347,66 +356,100 @@ static void printLimitWarning(struct sqlConnection *conn, char *markerTable, char *item, int itemLimit, char *sectionList) { char query[4000]; // no need to check for illegal characters in sectionList sqlSafef(query, sizeof(query), "SELECT COUNT(*) from %s WHERE markerId='%s' AND section in (%-s) ", markerTable, item, sectionList); if (sqlNeedQuickNum(conn, query) > itemLimit) { printf("<b>This marker is mentioned more than %d times</b><BR>\n", itemLimit); printf("The results would take too long to load in your browser and are " "therefore limited to %d articles.<P>\n", itemLimit); } } +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 <wbr> 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=='<')) + doNotBreak = TRUE; + if (*c==';' || (*c =='>')) + doNotBreak = FALSE; + + printf("%c", *c); + if (i % distance == 0 && ! doNotBreak) + printf("<wbr>"); + c++; + i++; + } +} + static void printMarkerSnippets(struct sqlConnection *conn, char *articleTable, char *markerTable, char *item) { /* do not show more snippets than this limit */ int itemLimit=100; -printSectionCheckboxes(); +char *artExtIdFilter = cgiOptionalString("pubsFilterExtId"); + char *sectionList = makeSqlMarkerList(); +if (artExtIdFilter==NULL) + { + printSectionCheckboxes(); printLimitWarning(conn, markerTable, item, itemLimit, sectionList); - printf("<H3>Snippets from Publications:</H3>"); -struct sqlResult *sr = queryMarkerRows(conn, markerTable, articleTable, item, itemLimit, sectionList); + } +struct sqlResult *sr = queryMarkerRows(conn, markerTable, articleTable, item, itemLimit, sectionList, artExtIdFilter); + +printf("<DIV style=\"width:1024px; font-size:100%%\">\n"); char **row; while ((row = sqlNextRow(sr)) != NULL) { char *articleId = row[0]; char *url = row[1]; char *title = row[2]; char *authors = row[3]; char *citation = row[4]; char *pmid = row[5]; char *snippets = row[7]; url = mangleUrl(url); - printf("<A HREF=\"%s\">%s</A> ", url, title); + printf("<A HREF=\"%s\">%s</A><BR> ", url, title); printf("<SMALL>%s</SMALL>; ", authors); printf("<SMALL>%s ", citation); if (!isEmpty(pmid) && strcmp(pmid, "0")!=0 ) printf(", <A HREF=\"http://www.ncbi.nlm.nih.gov/pubmed/%s\">PMID%s</A>\n", pmid, pmid); printf("</SMALL><BR>\n"); if (pubsDebug) printf("articleId=%s", articleId); - printf("<I>%s</I><P>", snippets); + printf("<I>\n"); + printAddWbr(snippets, 40); + printf("</I><P>"); printf("<HR>"); } +printf("</DIV>\n"); freeMem(sectionList); sqlFreeResult(&sr); } static char *urlToLogoUrl(char *pubsArticleTable, char *articleId, char *urlOrig) /* return a string with relative path of logo for publisher given the url of * fulltext or a table/articleId, has to be freed */ { struct sqlConnection *conn = hAllocConn(database); char *pubCode = NULL; if (hHasField("hgFixed", pubsArticleTable, "publisher")) { char query[4000]; sqlSafef(query, sizeof(query), "SELECT publisher from %s where articleId=%s", @@ -558,55 +601,30 @@ // yif sequences have no flanking text at M. Krauthammer's request if (stringIn("yif", articleSource)) web2PrintHeaderCell("Matching sequences", 60); else web2PrintHeaderCell("One row per sequence, with flanking text, sequence in bold", 60); if (pubsDebug) web2PrintHeaderCell("Identifiers", 30); if (!isClickedSection && !pubsDebug) web2PrintHeaderCell("Link to matching genomic location", 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 <wbr> 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=='<')) - doNotBreak = TRUE; - if (*c==';' || (*c =='>')) - doNotBreak = FALSE; - - printf("%c", *c); - if (i % distance == 0 && ! doNotBreak) - printf("<wbr>"); - c++; - i++; - } -} - void printHgTracksLink(char *db, char *chrom, int start, int end, char *linkText, char *optUrlStr) /* print link to hgTracks for db at pos */ { char buf[1024]; if (linkText==NULL) { char startBuf[64], endBuf[64]; sprintLongWithCommas(startBuf, start + 1); sprintLongWithCommas(endBuf, end); safef(buf, sizeof(buf), "%s:%s-%s (%s)", chrom, startBuf, endBuf, db); linkText = buf; } if (optUrlStr==NULL) optUrlStr = "";