51669978674f8d49a13b96e72d71418633719176 max Tue Mar 20 02:35:48 2012 -0700 creating a authorYear label on the fly for pubBlat tracks diff --git src/hg/hgc/pubs.c src/hg/hgc/pubs.c index a722cbc..cd09f14 100644 --- src/hg/hgc/pubs.c +++ src/hg/hgc/pubs.c @@ -56,31 +56,31 @@ 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 query[4000]; /* Mysql specific setting to make the group_concat function return longer strings */ sqlUpdate(conn, "SET SESSION group_concat_max_len = 100000"); -safef(query, sizeof(query), "SELECT distinct %s.articleId, url, title, authors, citation," +safef(query, sizeof(query), "SELECT distinct %s.articleId, url, title, authors, citation, pmid, " "group_concat(snippet, section SEPARATOR ' (...) ') FROM %s " "JOIN %s USING (articleId) " "WHERE markerId='%s' AND section in (%s) " "GROUP by articleId " "ORDER BY year DESC " "LIMIT %d", markerTable, markerTable, articleTable, item, sectionList, itemLimit); if (pubsDebug) printf("%s", query); struct sqlResult *sr = sqlGetResult(conn, query); return sr; } @@ -152,117 +152,129 @@ printSectionCheckboxes(); char* sectionList = makeSqlMarkerList(); printLimitWarning(conn, markerTable, item, itemLimit, sectionList); printf("

Snippets from Publications:

"); struct sqlResult* sr = queryMarkerRows(conn, markerTable, articleTable, item, itemLimit, sectionList); 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* snippets = row[5]; + char* pmid = row[5]; + char* snippets = row[6]; char* addParam = ""; if (strstrNoCase(url, "sciencedirect.com")) addParam = "?svAppaddApp=298535"; // add the "UCSC matches" sciverse application to article view printf("%s ", url, addParam, title); printf("%s; ", authors); - printf("%s
", citation); + printf("%s ", citation); + if (!isEmpty(pmid) && strcmp(pmid, "0")!=0 ) + printf(", PMID%s\n", pmid, pmid); + printf("
\n"); if (pubsDebug) printf("articleId=%s", articleId); printf("%s

", snippets); printf("

"); } freeMem(sectionList); sqlFreeResult(&sr); } static char* printArticleInfo(struct sqlConnection *conn, char* item) /* Header with information about paper, return documentId */ { char query[512]; - safef(query, sizeof(query), "SELECT articleId, url, title, authors, citation, abstract, pmid FROM %s WHERE displayId='%s'", pubsArticleTable, item); + safef(query, sizeof(query), "SELECT articleId, url, title, authors, citation, abstract, pmid FROM %s WHERE articleId='%s'", pubsArticleTable, item); struct sqlResult *sr = sqlGetResult(conn, query); char **row; char *articleId=NULL; - if ((row = sqlNextRow(sr)) != 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]; - if (strlen(abstract)==0) - { - abstract = "(No abstract found for this article. Please use the link to the fulltext above.)"; - } - articleId = cloneString(row[0]); - printf("

%s

\n", row[3]); - printf("%s\n", row[1], row[2]); + abstract = "(No abstract available for this article. " + "Please follow the link to the fulltext above.)"; + + printf("

%s

\n", authors); + printf("%s\n", url, title); printf("

%s", cit); - if (nullIfAllSpace(pmid)!=NULL) + if (strlen(pmid)!=0 && strcmp(pmid, "0")) printf(", PMID%s\n", pmid, pmid); printf("

\n"); printf("

%s

\n", abstract); - } + 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 */ { char query[512]; /* check first if the column exists (some debugging tables on hgwdev don't have seqIds) */ safef(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*/ safef(query, sizeof(query), "SELECT seqIds,'' FROM %s WHERE name='%s' " - "and chrom='%s' and chromStart=%d", trackTable, item, seqName, start); + "and chrom='%s' and chromStart=%d;", trackTable, item, seqName, start); if (pubsDebug) - puts(query); + printf("%s
", query); // split comma-sep list into parts char* seqIdCoordString = sqlQuickString(conn, query); char* seqIdCoords[1024]; int partCount = chopString(seqIdCoordString, ",", seqIdCoords, ArraySize(seqIdCoords)); int i; // format of part :-, e.g. 12312345:0-23 struct hash *seqIdHash = NULL; seqIdHash = newHash(0); for (i=0; i", annotIdHitCoord[0], annotIdHitCoord[1]); - // put articleId and annotId together to create annotation(=sequence) Id char fullAnnotId[4096]; safef(fullAnnotId, sizeof(fullAnnotId), "%s%s", articleId, annotIdHitCoord[0]); + if (pubsDebug) + printf("%s, %s, %s
", annotIdHitCoord[0], annotIdHitCoord[1], fullAnnotId); + hashAdd(seqIdHash, fullAnnotId, annotIdHitCoord[1]); } freeMem(seqIdCoordString); return seqIdHash; } static void printSeqHeaders(bool showDesc, bool isClickedSection) { printf("\n", HG_COL_BORDER); printf("\n", HG_COL_TABLE_LABEL); if (showDesc) puts(" \n"); puts(" \n"); if (pubsDebug) puts(" \n"); @@ -272,38 +284,38 @@ puts("\n"); } 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=='&') + if ((*c=='&') || (*c=='<')) doNotBreak = TRUE; - if (*c==';') + if (*c==';' || (*c =='>')) doNotBreak = FALSE; + printf("%c", *c); if (i % distance == 0 && ! doNotBreak) printf(""); - printf("%c", *c); c++; i++; } } } static bool printSeqSection(char* articleId, char* title, bool showDesc, struct sqlConnection* conn, struct hash* clickedSeqs, bool isClickedSection, bool fasta) /* print 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 @@ -331,30 +343,32 @@ bool foundSkippedRows = FALSE; while ((row = sqlNextRow(sr)) != NULL) { char* fileDesc = row[0]; char* snippet = row[1]; char* locList = 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; } if (fasta) { printf(">%s
%s
", annotId, seq); } else { printf("\n", HG_COL_LOCAL_TABLE); if (showDesc) @@ -405,31 +419,31 @@ /* 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); else skippedRows=1; if (skippedRows) printSeqSection(articleId, "Other Sequences in this article", \ fileDesc, conn, clickedSeqs, 0, fasta); - printf("

Copyright 2011 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]; @@ -481,31 +495,31 @@ void doPubsDetails(struct trackDb *tdb, char *item) /* publications custom display */ { int start = cgiInt("o"); int end = cgiInt("t"); char* trackTable = cgiString("g"); int fasta = cgiOptionalInt("fasta", 0); pubsDebug = cgiOptionalInt("debug", 0); struct sqlConnection *conn = hAllocConn(database); printTrackVersion(tdb, conn, item); -if (startsWith("pubsMarker", trackTable)) +if (hashFindVal(tdb->settingsHash, "pubsMarkerTable")) { char* markerTable = hashMustFindVal(tdb->settingsHash, "pubsMarkerTable"); char* articleTable = hashMustFindVal(tdb->settingsHash, "pubsArticleTable"); printPositionAndSize(start, end, 0); printMarkerSnippets(conn, articleTable, markerTable, item); } else { printPositionAndSize(start, end, 1); pubsSequenceTable = hashMustFindVal(tdb->settingsHash, "pubsSequenceTable"); pubsArticleTable = hashMustFindVal(tdb->settingsHash, "pubsArticleTable"); char* articleId = printArticleInfo(conn, item); if (articleId!=NULL) {

Article fileOne table row per sequence, with flanking text, sequence in boldIdentifiers