94c543bda6d443f13e30332161a0e4081afcb52e max Thu Dec 8 11:44:58 2011 -0800 added target=blank to outlinks in t2g diff --git src/hg/hgc/t2g.c src/hg/hgc/t2g.c index 8c7a0c5..aca4595 100644 --- src/hg/hgc/t2g.c +++ src/hg/hgc/t2g.c @@ -1,294 +1,294 @@ /* t2g.c - display details of text2genome literature track (t2gxxx tables) */ #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 "obscure.h" //include "hgTrackUi.h" // cgi var to activate debug output int t2gDebug = 0; char* sequenceTable; char* articleTable; 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 FROM %s WHERE displayId='%s'", articleTable, item); struct sqlResult *sr = sqlGetResult(conn, query); char **row; char *docId=0; if ((row = sqlNextRow(sr)) != NULL) { char* abstract = row[5]; if (strlen(abstract)==0) { abstract = "(No abstract found for this article. Please use the link to the fulltext above.)"; } docId = cloneString(row[0]); printf("

%s

\n", row[3]); - printf("%s\n", row[1], row[2]); + printf("%s\n", row[1], row[2]); printf("

%s

\n", row[4]); printf("

%s

\n", abstract); } sqlFreeResult(&sr); return docId; } struct hash* getSeqIdHash(struct sqlConnection* conn, char* trackTable, char* docId, char *item, char* seqName, int start) { 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); if (t2gDebug) puts(query); char* seqIdCoordString = sqlQuickString(conn, query); char* seqIdCoords[1024]; int partCount = chopString(seqIdCoordString, ",", seqIdCoords, ArraySize(seqIdCoords)); int i; struct hash *seqIdHash = NULL; seqIdHash = newHash(0); for (i=0; i", seqId[0], seqId[1]); hashAdd(seqIdHash, seqId[0], seqId[1]); } freeMem(seqIdCoordString); return seqIdHash; } void printSeqHeaders(bool showDesc, bool isClickedSection) { printf("\n", HG_COL_BORDER); printf("\n", HG_COL_TABLE_LABEL); if (showDesc) puts(" \n"); puts(" \n"); if (t2gDebug) puts(" \n"); if (!isClickedSection && !t2gDebug) puts(" \n"); puts("\n"); } bool printSeqSection(char* docId, char* title, bool showDesc, struct sqlConnection* conn, struct hash* filterIdHash, bool isClickedSection, bool fasta) /* print a table of sequences, show only sequences with IDs in hash, * */ { // get data from mysql char query[4096]; safef(query, sizeof(query), "SELECT fileDesc, snippet, locations, articleId,fileId, seqId, sequence FROM %s WHERE articleId='%s';", sequenceTable, docId); if (t2gDebug) puts(query); struct sqlResult *sr = sqlGetResult(conn, query); // construct title for section char fullTitle[5000]; safef(fullTitle, sizeof(fullTitle), "%s (switch fasta format)", title, cartSidUrlString(cart), cgiString("o"), cgiString("t"), cgiString("g"), cgiString("i"), !fasta); webNewSection(fullTitle); if (!fasta) printSeqHeaders(showDesc, isClickedSection); char **row; 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)); // only display this sequence if we're in the right section if (filterIdHash!=NULL && ((hashLookup(filterIdHash, annotId)==0) ^ !isClickedSection)) { foundSkippedRows = TRUE; continue; } if (fasta) { printf(">%s
%s
", annotId, seq); } else { printf("\n", HG_COL_LOCAL_TABLE); if (showDesc) printf("\n", snippet); printf("\n", snippet); if (t2gDebug) { printf("\n"); } printf("\n"); } } printf("\n"); webEndSectionTables(); sqlFreeResult(&sr); return foundSkippedRows; } void printSeqInfo(struct sqlConnection* conn, char* trackTable, char* docId, char* item, char* seqName, int start, bool fileDesc, bool fasta) /* print sequences, split into two sections * two sections: one for sequences that were clicked, one for all others*/ { struct hash* clickedSeqs = getSeqIdHash(conn, trackTable, docId, item, seqName, start); bool skippedRows; if (clickedSeqs) skippedRows = printSeqSection(docId, "Sequences used to construct this feature", fileDesc, conn, clickedSeqs, 1, fasta); else skippedRows=1; if (skippedRows) printSeqSection(docId, "Other Sequences in this article", fileDesc, conn, clickedSeqs, 0, fasta); //else //printf("

No more sequences

"); if (endsWith(trackTable, "Elsevier")) printf("

Article information and excerpts are Copyright 2011 Elsevier B.V. All rights reserved.

"); freeHash(&clickedSeqs); } 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), "select version,dateReference from hgFixed.trackVersion where db = '%s' AND name = 't2g' 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); } void printPositionAndSize(int start, int end) { printf("Position: " "", hgTracksPathAndSettings(), database, seqName, start+1, end); char startBuf[64], endBuf[64]; sprintLongWithCommas(startBuf, start + 1); sprintLongWithCommas(endBuf, end); printf("%s:%s-%s
\n", seqName, startBuf, endBuf); long size = end - start; sprintLongWithCommas(startBuf, size); printf("Genomic Size: %s
\n", startBuf); } void doT2gDetails(struct trackDb *tdb, char *item) /* text2genome.org custom display */ { int start = cgiInt("o"); int end = cgiInt("t"); char* trackTable = cgiString("g"); int fasta = cgiOptionalInt("fasta", 0); t2gDebug = cgiOptionalInt("debug", 0); struct sqlConnection *conn = hAllocConn(database); printTrackVersion(tdb, conn, item); printPositionAndSize(start, end); sequenceTable = hashMustFindVal(tdb->settingsHash, "sequenceTable"); articleTable = hashMustFindVal(tdb->settingsHash, "articleTable"); char* docId = printArticleInfo(conn, item); if (docId!=0) { bool showDesc; showDesc = (! endsWith(trackTable, "Elsevier")); printSeqInfo(conn, trackTable, docId, item, seqName, start, showDesc, fasta); } printTrackHtml(tdb); hFreeConn(&conn); }

Article fileSequence (in bold) with flanking textIdentifiersMatches
%s\n", fileDesc); //printf("%s%sarticle %s, file %s, seq %s, annotId %s", artId, fileId, seqId, annotId); } // print links to locations if (!isClickedSection && !t2gDebug) { struct slName *locs; // format: hg19/chr1:300-400,mm9/chr1:60006-23234 // split on "," then split on "/" locs = charSepToSlNames(locList, ','); printf(""); if (locs==NULL) printf("No matches"); for ( ; locs!=NULL; locs = locs->next) { char* locString = locs->name; char* parts[2]; int partCount; partCount = chopString(locString, "/", parts, ArraySize(parts)); assert(partCount==2); char* db = parts[0]; char* pos = parts[1]; printf("%s (%s)", cartSidUrlString(cart), db, pos, pos, db); printf("
"); } printf("