", hgTracksPathAndSettings(), database, seqName, start+1, end, articleId, pslTrack, dispId); printf("Show these sequence matches individually on genome browser (activates track \"" "Individual matches for article\")
"); } printPositionAndSize(start, end, 1); printf( "\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("This marker is mentioned more than %d times
\n", itemLimit);
printf("The results would take too long to load in your browser and are "
"therefore limited to the %d most recent articles.
\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("%s
", url, title);
// cut author string at 40 chars, like scholar
printf("");
if (strlen(authors)>40)
{
authors[60] = 0;
printf("%s... ", authors);
}
else if (!isEmpty(authors))
printf("%s ", 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("");
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(", PMID%s\n", pmid, pmid);
+ printf(", PMID%s\n", pmid, pmid);
didPrint = TRUE;
}
printf("\n");
if (didPrint)
printf("
\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("already seen");
continue;
}
slPairAdd(&secSnips, section, snippet);
hashAdd(doneSnips, snipHash, 0);
snipCount++;
}
hashFree(&doneSnips);
// now iterate over list and print
struct slPair *pair;
printf("
![](\"../images/add_sm.gif\")
printf("more"); } 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("
%s
\n", authors); // // logo of publisher char *logoUrl = urlToLogoUrl(pubsArticleTable, articleId, url); if (logoUrl) printf("%s", cit); if (strlen(pmid)!=0 && strcmp(pmid, "0")) - printf(", PMID%s\n", pmid, pmid); + printf(", PMID%s\n", pmid, pmid); printf("
\n"); printf("%s
\n", abstract); if (pubsIsElsevier) printf("Copyright 2012 Elsevier B.V. All rights reserved.
"); 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>%s-%d\n", extId, rowId);
else
printf(">seq%d\n", rowId);
writeSeqWithBreaks(stdout, seq, strlen(seq), 80);
printf("\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), "%s", 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("
");
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("");
printf("\nLiterature Sequence vs Genomic \n\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; iblockCount; 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("Genomic Alignment with sequence found in publication fulltext
");
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);
}