a53b9958fa734f73aeffb9ddfe2fbad1ca65f90c galt Mon Jan 30 16:18:41 2017 -0800 Check-in of CSP2 Content-Security-Policy work. All C-language CGIs should now support CSP2 in browser to stop major forms of XSS javascript injection. Javascript on pages is gathered together, and then emitted in a single script block at the end with a nonce that tells the browser, this is js that we generated instead of being injected by a hacker. Both inline script from script blocks and inline js event handlers had to be pulled out and separated. You will not see js sprinkled through-out the page now. Older browsers that support CSP1 or that do not understand CSP at all will still work, just without protection. External js libraries loaded at runtime need to be added to the CSP policy header in src/lib/htmshell.c. diff --git src/hg/hgc/pubs.c src/hg/hgc/pubs.c index 24de7ec..e9f576e 100644 --- src/hg/hgc/pubs.c +++ src/hg/hgc/pubs.c @@ -1,1214 +1,1217 @@ /* pubs.c - display details of publiations literature track (pubsxxx tables) */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "jksql.h" #include "hdb.h" #include "hgc.h" #include "hgColors.h" #include "trackDb.h" #include "web.h" #include "hash.h" #include "net.h" #include "obscure.h" #include "common.h" #include "string.h" #include "dystring.h" #include "dnautil.h" //#include "ctype.h" // 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 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", "supplement", "unknown" }; // labels to show to user, have to correspond to pubsSecNames static char *secLabels[] ={ "Title", "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions", "Acknowledgements", "References", "Supplement", "Undetermined section (e.g. for a brief communication)" }; // whether a checkbox is checked by default, have to correspond to pubsSecNames static int pubsSecChecked[] ={ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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 */ /* Suffix -S for "function accepts style parameter" * Suffix -C for "function accepts class parameter" * Suffix -CI for "function accepts class and id parameter" * * Some functions are commented out because they are not yet used. */ static void web2Start(char *tag) { printf("<%s>\n", tag); } static void web2End(char *tag) { printf("</%s>\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</%s>\n", tag, style, label, tag); } //static void web2PrintC(char *class, char *tag, char *label) //{ //printf("<%s class=\"%s\">%s</%s>\n", tag, class, label, tag); //} //static void web2Print(char *tag, char *label) //{ //printf("<%s>%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("</div> <!-- %s -->\n", comment); } //static void web2Img(char *url, char *alt, int width, int hspace, int vspace) //{ //printf("<img src=\"%s\" alt=\"%s\" width=\"%d\" hspace=\"%d\" vspace=\"%d\">\n", url, alt, width, hspace, vspace); //} static void web2ImgLink(char *url, char *imgUrl, char *alt, int width, int hspace, int vspace) { printf("<a href=\"%s\"><img src=\"%s\" alt=\"%s\" width=\"%d\" hspace=\"%d\" vspace=\"%d\"></a>\n", url, imgUrl, alt, width, hspace, vspace); } static void web2PrintHeaderCell(char *label, int width) /* Print th heading cell with given width in percent */ { printf("<th width=\"%d%%\">", width); printf("%s</th>", 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("<!-- START NEW SECTION -->\n"); web2StartDivCI("section", id); web2StartDivC("subheadingBar windowSize"); vprintf(format, args); web2EndDiv("subheadingBar"); va_end(args); } static void web2EndSection() /* end section */ { web2EndDiv("section"); } /* ------ */ static void printDebug(char *text) { if (pubsDebug) printf("%s<BR>", text); } 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 printPositionAndSize(int start, int end, bool showSize) { printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, seqName, start+1, end); char startBuf[64], endBuf[64]; sprintLongWithCommas(startBuf, start + 1); sprintLongWithCommas(endBuf, end); printf("%s:%s-%s</A><BR>\n", seqName, startBuf, endBuf); long size = end - start; sprintLongWithCommas(startBuf, size); if (showSize) printf("<B>Genomic Size:</B> %s<BR>\n", startBuf); } 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 = cgiOptionalInt("o", -1); if (start==-1) return; int end = cgiInt("t"); char qBuf[1024]; struct sqlConnection *conn = hAllocConn(database); sqlSafef(qBuf, sizeof(qBuf), "SELECT CONCAT(firstAuthor, year) FROM %s WHERE articleId='%s';", articleTable, articleId); char *dispId = sqlQuickString(conn, qBuf); printf(" <div class=\"subsection\">"); if (!containsStringNoCase(pslTrack, "Bing")) { printf( " <P><A HREF=\"%s&db=%s&position=%s%%3A%d-%d&pubsFilterArticleId=%s&%s=pack&hgFind.matches=%s\">", hgTracksPathAndSettings(), database, seqName, start+1, end, articleId, pslTrack, dispId); printf("Show these sequence matches individually on genome browser</A> (activates track \"" "Individual matches for article\")</P>"); } printPositionAndSize(start, end, 1); printf( " </div> <!-- class: subsection --> \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<secCount; i++) { // add ' around name and add to list char *secName = pubsSecNames[i]; if (cgiOptionalInt(secName, pubsSecChecked[i])) { char nameBuf[100]; 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, 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, year, " "pmid FROM %s " //"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, artFilterSql, itemLimit); printDebug(query); struct sqlResult *sr = sqlGetResult(conn, query); return sr; } static struct sqlResult *querySnippets(struct sqlConnection *conn, char *markerTable, \ char *articleId, char *markerId, char *sectionList) /* query marker snippet rows from mysql for an article, markerId combination */ { char query[4000]; sqlSafef(query, sizeof(query), "SELECT section, snippet FROM %s " "WHERE articleId=%s AND markerId='%s' AND section in (%-s) ", markerTable, articleId, markerId, sectionList); 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 */ { int labelCount = sizeof(secLabels)/sizeof(char *); int i; printf("<P>\n"); printf("<B>Sections of article searched:</B><BR>\n"); printf("<FORM ACTION=\"hgc?%s&o=%s&t=%s&g=%s&i=%s\" METHOD=\"get\">\n", cartSidUrlString(cart), cgiString("o"), cgiString("t"), cgiString("g"), cgiString("i")); for (i=0; i<labelCount; i++) { char *name = pubsSecNames[i]; // checkboxes default to 0 unless checked, see // http://stackoverflow.com/questions/2520952/how-come-checkbox-state-is-not-always-passed-along-to-php-script printf("<INPUT TYPE=\"hidden\" name=\"%s\" value=\"0\" />\n", pubsSecNames[i]); printf("<INPUT TYPE=\"checkbox\" name=\"%s\" ", name); int isChecked = cgiOptionalInt(name, pubsSecChecked[i]); if (isChecked) printf("value=\"1\" checked=\"yes\">%s</INPUT>\n", secLabels[i]); else printf("value=\"1\">%s</INPUT>\n", secLabels[i]); } printf("<INPUT TYPE=\"hidden\" name=\"o\" value=\"%s\" />\n", cgiString("o")); printf("<INPUT TYPE=\"hidden\" name=\"g\" value=\"%s\" />\n", cgiString("g")); printf("<INPUT TYPE=\"hidden\" name=\"t\" value=\"%s\" />\n", cgiString("t")); printf("<INPUT TYPE=\"hidden\" name=\"i\" value=\"%s\" />\n", cgiString("i")); printf("<INPUT TYPE=\"hidden\" name=\"hgsid\" value=\"%s\" />\n", cart->sessionId); printf("<BR>"); printf("<INPUT TYPE=\"submit\" VALUE=\"Submit\" />\n"); printf("</FORM><P>\n"); } 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 the %d most recent articles.<P>\n", itemLimit); } } /* keep only uppercase letters in string*/ void eraseAllButUpper(char *s) { char *in, *out; char c; in = out = s; for (;;) { c = *in++; if (c == 0) break; if (isupper(c)) *out++ = c; } *out = 0; } static char* printShortArticleInfo(char **row) { /* print a two-line description of article */ char *articleId = row[0]; char *url = row[1]; char *title = row[2]; char *authors = row[3]; char *citation = row[4]; char *year = row[5]; char *pmid = row[6]; url = mangleUrl(url); printf("<A HREF=\"%s\">%s</A><BR> ", url, title); // cut author string at 40 chars, like scholar printf("<span style=\"color:gray\">"); if (strlen(authors)>40) { authors[60] = 0; printf("<SMALL>%s...</SMALL> ", authors); } else if (!isEmpty(authors)) printf("<SMALL>%s</SMALL> ", authors); // first word of citation is journal name char *words[10]; int wordCount = chopCommas(citation, words); char *journal = NULL; if (wordCount!=0) journal = words[0]; // optional: print the little gray line with author, journal, year info bool didPrint = FALSE; printf("<small>"); if (year!=NULL && differentWord(year, "0")) { printf("%s", year); didPrint = TRUE; } if (!isEmpty(journal)) { printf(" - %s ", journal); didPrint = TRUE; } if (!isEmpty(pmid) && strcmp(pmid, "0")!=0 ) { printf(", <A HREF=\"http://www.ncbi.nlm.nih.gov/pubmed/%s\">PMID%s</A>\n", pmid, pmid); didPrint = TRUE; } printf("</small></span>\n"); if (didPrint) printf("<BR>\n"); if (pubsDebug) printf("articleId=%s", articleId); return articleId; } static void printSnippets(struct sqlResult *srSnip) { char **snipRow; struct hash *doneSnips = newHash(0); // avoid printing a sentence twice int snipCount = 0; struct slPair *secSnips = NULL; // add all pairs to the list, remove duplicated snippets (ignore all lowercase chars) while ((snipRow = sqlNextRow(srSnip)) != NULL) { char *section = cloneString(snipRow[0]); char *snippet = cloneString(snipRow[1]); char *snipHash = cloneString(snippet); eraseAllButUpper(snipHash); if (hashLookup(doneSnips, snipHash)!=NULL) { //printf("<b>already seen</b></br>"); continue; } slPairAdd(&secSnips, section, snippet); hashAdd(doneSnips, snipHash, 0); snipCount++; } hashFree(&doneSnips); // now iterate over list and print struct slPair *pair; printf("<DIV CLASS=\"snips\">\n"); int i = 0; for (pair = secSnips; pair != NULL; pair = pair->next) { char *section = pair->name; char *snippet = pair->val; // print snippet printf("<I>"); printAddWbr(snippet, 40); printf("<style=\"color:gray\">...</style>\n"); if (differentWord(section, "unknown")) printf(" <SPAN style=\"color:gray\">(%s)</SPAN>", section); printf("</I>"); printf("<BR>"); if (snipCount>2) { if (i==0) + { // alternative to "more": <img src=\"../images/add_sm.gif\"> - printf("<A class=\"showSnips\" href=\"#\" onclick=\"$(this).nextUntil('.shownSnips').slideToggle(); return false;\">more</A><BR><DIV class=\"hiddenSnips\" style=\"display:none\">"); + printf("<A id='snowSnips_more' class=\"showSnips\" href=\"#\" >more</A><BR><DIV class=\"hiddenSnips\" style=\"display:none\">"); + jsOnEventById("click", "snowSnips_more", "$(this).nextUntil('.shownSnips').slideToggle(); return false;"); + } if (i==snipCount-2) printf("</DIV><div class=\"shownSnips\"></div>"); } i++; } slPairFreeList(&secSnips); sqlFreeResult(&srSnip); printf("</DIV><P>"); } static void printMarkerSnippets(struct sqlConnection *conn, char *articleTable, char *markerTable, char *item) /* print page with article info and snippets from articles */ { /* do not show more snippets than this limit */ int itemLimit=100; char *artExtIdFilter = cgiOptionalString("pubsFilterExtId"); /* This will have to be activated with the move to new Elsevier identifiers, ~Oct 2013 */ //if (startsWith(artExtIdFilter)) //replaceInStr(artExtIdFilter, "ELS", "PII") 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, artExtIdFilter); // better readable if not across the whole screen printf("<DIV style=\"width:1024px; font-size:100%%\">\n"); char **row; // loop over articles and print out snippets for each while ((row = sqlNextRow(sr)) != NULL) { char *articleId = printShortArticleInfo(row); struct sqlConnection *snipConn = hAllocConn(database); struct sqlResult *srSnip = querySnippets(snipConn, markerTable, articleId, item, sectionList); printSnippets(srSnip); hFreeConn(&snipConn); 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", pubsArticleTable, articleId); pubCode = sqlQuickString(conn, query); // if no publisher is specified, we use the source (e.g. bing, pmc, elsevier, etc) // to find the logo if (isEmpty(pubCode)) { sqlSafef(query, sizeof(query), "SELECT source from %s where articleId=%s", pubsArticleTable, articleId); pubCode = sqlQuickString(conn, query); } } else { // get top-level domain url if not publisher field char url[1024]; memcpy(url, urlOrig, sizeof(url)); char *slashParts[20]; // split http://www.sgi.com/test -> to [http:,www.sgi.com,test] int partCount = chopString(url, "/", slashParts, ArraySize(slashParts)); if (partCount<3) return NULL; // split www.sgi.com to [www,sgi,com] char *dotParts[20]; partCount = chopString(slashParts[1], ".", dotParts, ArraySize(dotParts)); if (partCount<3) return NULL; pubCode = dotParts[partCount-2]; } // construct path to image char *logoUrl = needMem(512); safef(logoUrl, 512, "../images/pubs_%s.png", pubCode); return logoUrl; } static char *printArticleInfo(struct sqlConnection *conn, char *item, char *pubsArticleTable) /* Header with information about paper, return documentId */ { char query[512]; sqlSafef(query, sizeof(query), "SELECT articleId, url, title, authors, citation, abstract, pmid, " "source, extId FROM %s WHERE articleId='%s'", pubsArticleTable, item); struct sqlResult *sr = sqlGetResult(conn, query); char **row; char *articleId=NULL; if ((row = sqlNextRow(sr)) == NULL) { printf("Could not resolve articleId %s, this is an internal error.\n", item); printf("Please send an email to max@soe.ucsc.edu\n"); sqlFreeResult(&sr); return NULL; } articleId = cloneString(row[0]); char *url = row[1]; char *title = row[2]; char *authors = row[3]; char *cit = row[4]; char *abstract = row[5]; char *pmid = row[6]; articleSource = row[7]; extId = row[8]; url = mangleUrl(url); if (strlen(abstract)==0) abstract = "(No abstract available for this article. " "Please follow the link to the fulltext above by clicking on the titel or the fulltext image.)"; if (stringIn("sciencedirect.com", url)) { pubsHasSupp = FALSE; pubsIsElsevier = TRUE; } // authors title printf("<DIV style=\"width:1024px; font-size:100%%\">\n"); printf("<P>%s</P>\n", authors); // // logo of publisher char *logoUrl = urlToLogoUrl(pubsArticleTable, articleId, url); if (logoUrl) printf("<a href=\"%s\"><img align=\"right\" hspace=\"20\" src=\"%s\"></a>\n", url, logoUrl); freeMem(logoUrl); printf("<div style=\"width:800px\">"); printf("<A TARGET=\"_blank\" HREF=\"%s\"><B>%s</B></A></div>\n", url, title); printf("</DIV>\n"); printf("</DIV>\n"); printf("<P style=\"width:1024px; font-size:80%%\">%s", cit); if (strlen(pmid)!=0 && strcmp(pmid, "0")) printf(", <A HREF=\"http://www.ncbi.nlm.nih.gov/pubmed/%s\">PMID%s</A>\n", pmid, pmid); printf("</P>\n"); printf("<P style=\"width:1024px; font-size:100%%\">%s</P>\n", abstract); if (pubsIsElsevier) printf("<P><SMALL>Copyright 2012 Elsevier B.V. All rights reserved.</SMALL></P>"); sqlFreeResult(&sr); return articleId; } static struct hash *getSeqIdHash(struct sqlConnection *conn, char *trackTable, \ char *articleId, char *item, char *seqName, int start) /* return a hash with the sequence IDs for a given chain of BLAT matches */ { if (start==-1) return NULL; char query[512]; /* check first if the column exists (some debugging tables on hgwdev don't have seqIds) */ sqlSafef(query, sizeof(query), "SHOW COLUMNS FROM %s LIKE 'seqIds';", trackTable); char *seqIdPresent = sqlQuickString(conn, query); if (!seqIdPresent) { return NULL; } /* get sequence-Ids for feature that was clicked (item&startPos are unique) and return as hash*/ sqlSafef(query, sizeof(query), "SELECT seqIds,'' FROM %s WHERE name='%s' " "and chrom='%s' and chromStart=%d;", trackTable, item, seqName, start); printDebug(query); // split comma-sep list into parts char *seqIdCoordString = sqlQuickString(conn, query); char *seqIdCoords[1024]; if (isEmpty(seqIdCoordString)) return NULL; int partCount = chopString(seqIdCoordString, ",", seqIdCoords, ArraySize(seqIdCoords)); int i; struct hash *seqIdHash = NULL; seqIdHash = newHash(0); for (i=0; i<partCount; i++) { if (pubsDebug) printf("annotId %s<br>", seqIdCoords[i]); hashAdd(seqIdHash, seqIdCoords[i], NULL); } return seqIdHash; } static void printSeqHeaders(bool showDesc, bool isClickedSection) /* print table and headers */ { //style=\"margin: 10px auto; width: 98%%\"style=\"background-color: #fcecc0\" web2StartTableC("stdTbl centeredStdTbl"); web2StartTheadC("stdTblHead"); if (showDesc) web2PrintHeaderCell("Article file", 10); // 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;"); } 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 = ""; printf("<A HREF=\"%s&db=%s&position=%s:%d-%d&%s\">%s</A>\n", hgTracksPathAndSettings(), db, chrom, start, end, optUrlStr, linkText); } 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("<br>"); freeMem(endStr); //XX why can't I free these? freeMem(chrom); freeMem(startStr); freeMem(db); } } void removeFlank (char *snippet) /* keep only the parts inside <b> to </b> of a string, modifies the string in place */ { char *startPtr = stringIn("<B>", snippet); char *endPtr = stringIn("</B>", snippet); if (startPtr!=0 && endPtr!=0 && startPtr<endPtr) { char *buf = stringBetween("<B>", "</B>", snippet); memcpy(snippet, buf, strlen(buf)+1); freeMem(buf); } } static void printYifSection(char *clickedFileUrl) /* print section with the image on yif and a link to it */ { // parse out yif file Id from yif url to generate link to yif page struct netParsedUrl npu; netParseUrl(clickedFileUrl, &npu); struct hash *params = NULL; struct cgiVar* paramList = NULL; char *paramStr = strchr(npu.file, '?'); cgiParseInput(paramStr, ¶ms, ¶mList); struct cgiVar *var = hashFindVal(params, "file"); char *figId = NULL; if (var!=NULL && var->val!=NULL) figId = var->val; char yifPageUrl[4096]; if (figId) { safef(yifPageUrl, sizeof(yifPageUrl), "http://krauthammerlab.med.yale.edu/imagefinder/Figure.external?sp=S%s%%2F%s", extId, figId); } else return; web2StartSection("section", "<A href=\"%s\">Yale Image Finder</a>: figure where sequences were found", yifPageUrl); web2ImgLink(yifPageUrl, clickedFileUrl, "Image from YIF", 600, 10, 10); web2EndSection(); } 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 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 // I support two different schemas: new and old. On old tables, there is no fileUrl yet on the annotations // that means that oldQuery just uses an empty string for the fileUrl field. char *oldQuery = "SELECT fileDesc, snippet, locations, annotId, sequence, \"\" FROM %s WHERE articleId='%s'"; char *newQuery = "SELECT fileDesc, snippet, locations, annotId, sequence, fileUrl FROM %s WHERE articleId='%s'"; char *queryTemplate = oldQuery; if (hHasField("hgFixed", pubsSequenceTable, "fileUrl")) queryTemplate = newQuery; char query[4096]; sqlSafef(query, sizeof(query), queryTemplate, pubsSequenceTable, articleId); printDebug(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 <A HREF=\"../cgi-bin/hgc?%s&o=%s&t=%s&g=%s&i=%s&fasta=%d\"><SMALL>(%s format)</SMALL></A>\n", title, cartSidUrlString(cart), cgiOptionalString("o"), cgiOptionalString("t"), cgiString("g"), cgiString("i"), !fasta, otherFormat); web2StartSection("pubsSection", "%s", fullTitle); // print filtering link at start of table & table headers if (isClickedSection) { printFilterLink(pslTable, articleId, articleTable); } if (!fasta) printSeqHeaders(showDesc, isClickedSection); // output rows char **row; // the URL of the file from the clicked sequences, for YIF char *clickedFileUrl = NULL; bool foundSkippedRows = FALSE; int rowId = 0; while ((row = sqlNextRow(sr)) != NULL) { rowId++; 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 *annotId = row[3]; char *seq = row[4]; char *fileUrl = row[5]; // annotation (=sequence) ID is a 64 bit int with 10 digits for // article, 3 digits for file, 5 for annotation //char annotId[100]; // some debugging help //safef(annotId, 100, "%10d%03d%05d", atoi(artId), atoi(fileId), atoi(seqId)); //if (pubsDebug) //printf("artId %s, file %s, annot %s -> annotId %s<br>", artId, fileId, seqId, annotId); // only display this sequence if we're in the right section if (clickedSeqs!=NULL && ((hashLookup(clickedSeqs, annotId)!=NULL) != isClickedSection)) { foundSkippedRows = TRUE; continue; } // if we're in the clicked section and the current sequence is one that matched here // then keep the current URL, as we might need it afterwards else clickedFileUrl = cloneString(fileUrl); // suppress non-matches if the sequences come from YIF as figures can // contain tons of non-matching sequences if (stringIn("yif", articleSource) && isEmpty(locString)) { foundSkippedRows = TRUE; continue; } if (fasta) { if (strlen(extId)!=0) printf("<tt><pre>>%s-%d\n", extId, rowId); else printf("<tt><pre>>seq%d\n", rowId); writeSeqWithBreaks(stdout, seq, strlen(seq), 80); printf("</pre></tt>\n"); } else { web2StartRow(); // column 1: type of file (main or supp) if (showDesc) { char linkStr[4096]; if (isEmpty(fileDesc)) fileDesc = "main text"; safef(linkStr, sizeof(linkStr), "<a href=\"%s\">%s</a>", fileUrl, fileDesc); web2PrintCellS("word-break:break-all", linkStr); } // column 2: snippet web2StartCellS("word-break:break-all"); if (stringIn("yif", articleSource)) removeFlank(snippet); printAddWbr(snippet, 40); web2EndCell(); // optional debug info column if (pubsDebug) //web2PrintCellF("article %s, file %s, seq %s, annotId %s", artId, fileId, seqId, annotId); web2PrintCellF("annotId %s", annotId); // 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)); if (partCount==0) printf("No matches"); else { struct slName *locs; locs = slNameListFromStringArray(locArr, partCount); slUniqify(&locs, slNameCmp, slNameFree); printGbLinks(locs); printf("<br>"); slFreeList(&locs); } web2EndCell(); } web2EndRow(); } } if (!fasta) web2EndTable(); web2EndSection(); /* Yale Image finder files contain links to the image itself */ if (pubsDebug) printf("%s %s %d", articleSource, clickedFileUrl, isClickedSection); if (stringIn("yif", articleSource) && (clickedFileUrl!=NULL) && isClickedSection) printYifSection(clickedFileUrl); freeMem(clickedFileUrl); 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 matching here", \ fileDesc, conn, clickedSeqs, 1, fasta, pslTable, articleTable); else skippedRows=1; if (skippedRows) { // the section title should change if the data comes from the yale image finder = a figure char *docType = "article"; if (stringIn("yif", articleSource)) docType = "figure"; char title[1024]; if (clickedSeqs) safef(title, sizeof(title), "Other Sequences in this %s", docType); // NO clicked seqs can happen if the hgc was called with no o or t parameters // from somewhere outside the browser, like elsevier or europmc else safef(title, sizeof(title), "Sequences in this %s", docType); printSeqSection(articleId, title, \ fileDesc, conn, clickedSeqs, 0, fasta, pslTable, articleTable); } 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]; sqlSafef(query, sizeof(query), \ "SELECT version,dateReference FROM hgFixed.trackVersion " "WHERE db = '%s' AND name = 'pubs' ORDER BY updateTime DESC limit 1", database); struct sqlResult *sr = sqlGetResult(conn, query); char **row; /* in case of NULL result from the table */ versionString[0] = 0; while ((row = sqlNextRow(sr)) != NULL) { safef(versionString, sizeof(versionString), "version %s", row[0]); safef(dateReference, sizeof(dateReference), "%s", row[1]); } sqlFreeResult(&sr); } else { versionString[0] = 0; dateReference[0] = 0; } if (versionString[0]) safef(headerTitle, sizeof(headerTitle), "%s - %s", item, versionString); else safef(headerTitle, sizeof(headerTitle), "%s", item); genericHeader(tdb, headerTitle); } static bioSeq *getSeq(struct sqlConnection *conn, char *table, char *id) /* copied from otherOrgs.c */ { char query[512]; struct sqlResult *sr; char **row; bioSeq *seq = NULL; sqlSafef(query, sizeof(query), "select sequence from %s where annotId = '%s'", table, id); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { AllocVar(seq); seq->name = cloneString(id); seq->dna = cloneString(row[0]); seq->size = strlen(seq->dna); } sqlFreeResult(&sr); return seq; } void pubsAli(struct sqlConnection *conn, char *pslTable, char *seqTable, char *item) /* this is just a ripoff from htcCdnaAli, similar to markd's transMapAli */ { bioSeq *oSeq = NULL; writeFramesetType(); puts("<HTML>"); printf("<HEAD>\n<TITLE>Literature Sequence vs Genomic</TITLE>\n</HEAD>\n\n"); struct psl *psl = getAlignments(conn, pslTable, item); if (psl == NULL) errAbort("Couldn't find alignment at %s:%s", pslTable, item); oSeq = getSeq(conn, seqTable, item); if (oSeq == NULL) errAbort("%s is in pslTable but not in sequence table. Internal error.", item); enum gfType qt; if (psl->qSize!=oSeq->size) { qt = gftProt; // trying to correct pslMap's changes to qSize/qStarts and blockSizes psl->strand[1]=psl->strand[0]; psl->strand[0]='+'; psl->strand[2]=0; psl->qSize = psl->qSize/3; psl->match = psl->match/3; // Take care of codons that go over block boundaries: // Convert a block with blockSizes=58,32 and qStarts=0,58, // to blockSizes=19,11 and qStarts=0,19 int i; int remaind = 0; for (i=0; i<psl->blockCount; i++) { psl->qStarts[i] = psl->qStarts[i]/3; int bs = psl->blockSizes[i]; remaind += (bs % 3); if (remaind>=3) { bs += 1; remaind -= 3; } psl->blockSizes[i] = bs/3; } } else qt = gftDna; showSomeAlignment(psl, oSeq, qt, 0, oSeq->size, NULL, 0, 0); } void doPubsDetails(struct trackDb *tdb, char *item) /* publications custom display */ { int start = cgiOptionalInt("o", -1); int end = cgiOptionalInt("t", -1); char *trackTable = cgiString("g"); char *aliTable = cgiOptionalString("aliTable"); int fasta = cgiOptionalInt("fasta", 0); pubsDebug = cgiOptionalInt("debug", 0); struct sqlConnection *conn = hAllocConn(database); char *articleTable = trackDbRequiredSetting(tdb, "pubsArticleTable"); if (stringIn("Psl", trackTable)) { if (aliTable!=NULL) { pubsSequenceTable = trackDbRequiredSetting(tdb, "pubsSequenceTable"); pubsAli(conn, trackTable, pubsSequenceTable, item); return; } else { genericHeader(tdb, item); struct psl *psl = getAlignments(conn, trackTable, item); printf("<H3>Genomic Alignment with sequence found in publication fulltext</H3>"); printAlignmentsSimple(psl, start, trackTable, trackTable, item); } } else { printTrackVersion(tdb, conn, item); if (stringIn("Marker", trackTable)) { char *markerTable = trackDbRequiredSetting(tdb, "pubsMarkerTable"); if (start!=-1) printPositionAndSize(start, end, 0); printMarkerSnippets(conn, articleTable, markerTable, item); } else { pubsSequenceTable = trackDbRequiredSetting(tdb, "pubsSequenceTable"); char *articleId = printArticleInfo(conn, item, articleTable); if (articleId!=NULL) { char *pslTable = trackDbRequiredSetting(tdb, "pubsPslTrack"); printSeqInfo(conn, trackTable, pslTable, articleId, item, \ seqName, start, pubsHasSupp, fasta, articleTable); } } } printTrackHtml(tdb); hFreeConn(&conn); }