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("<H3>Snippets from Publications:</H3>");
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("<A HREF=\"%s%s\">%s</A> ", url, addParam, title);
printf("<SMALL>%s</SMALL>; ", authors);
- printf("<SMALL>%s</SMALL><BR>", citation);
+ 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("<HR>");
}
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("<P>%s</P>\n", row[3]);
- printf("<A TARGET=\"_blank\" HREF=\"%s\"><B>%s</B></A>\n", row[1], row[2]);
+ abstract = "(No abstract available for this article. "
+ "Please follow the link to the fulltext above.)";
+
+ printf("<P>%s</P>\n", authors);
+ printf("<A TARGET=\"_blank\" HREF=\"%s\"><B>%s</B></A>\n", url, title);
printf("<P style=\"width:800px; font-size:80%%\">%s", cit);
- if (nullIfAllSpace(pmid)!=NULL)
+ 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:800px; font-size:100%%\">%s</P>\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<br>", 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 <fileId:3><annotId:5>:<start>-<end>, e.g. 12312345:0-23
struct hash *seqIdHash = NULL;
seqIdHash = newHash(0);
for (i=0; i<partCount; i++)
{
char* annotIdHitCoord[1024];
chopString(seqIdCoords[i], ":", annotIdHitCoord, ArraySize(annotIdHitCoord));
- if (pubsDebug)
- printf("%s, %s<br>", 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<br>", annotIdHitCoord[0], annotIdHitCoord[1], fullAnnotId);
+
hashAdd(seqIdHash, fullAnnotId, annotIdHitCoord[1]);
}
freeMem(seqIdCoordString);
return seqIdHash;
}
static void printSeqHeaders(bool showDesc, bool isClickedSection)
{
printf("<TABLE style=\"background-color: #%s\" WIDTH=\"100%%\" CELLPADDING=\"2\">\n", HG_COL_BORDER);
printf("<TR style=\"background-color: #%s; color: #FFFFFF\">\n", HG_COL_TABLE_LABEL);
if (showDesc)
puts(" <TH style=\"width: 10%\">Article file</TH>\n");
puts(" <TH style=\"width: 70%\">One table row per sequence, with flanking text, sequence in bold</TH>\n");
if (pubsDebug)
puts(" <TH style=\"width: 30%\">Identifiers</TH>\n");
@@ -272,38 +284,38 @@
puts("</TR>\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 <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=='&')
+ if ((*c=='&') || (*c=='<'))
doNotBreak = TRUE;
- if (*c==';')
+ if (*c==';' || (*c =='>'))
doNotBreak = FALSE;
+ printf("%c", *c);
if (i % distance == 0 && ! doNotBreak)
printf("<wbr>");
- 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("<TT>>%s<BR>%s<BR></TT>", annotId, seq);
}
else
{
printf("<TR style=\"background-color: #%s\">\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("<P><SMALL>Copyright 2011 Elsevier B.V. All rights reserved.</SMALL><P>");
+ printf("<P><SMALL>Copyright 2012 Elsevier B.V. All rights reserved.</SMALL><P>");
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)
{