/* pubs.c - display details of publiations literature track (pubsxxx 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 "common.h"
#include "string.h"
//include "hgTrackUi.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
bool pubsHasSupp = TRUE; 
// global var for printArticleInfo to indicate if article is elsevier
bool pubsIsElsevier = FALSE; 

// internal section types in mysql table
static char *pubsSecNames[] ={
      "header", "abstract",
      "intro", "methods",
      "results", "discussion",
      "conclusions", "ack",
      "refs", "unknown" };
//
// whether a checkbox is checked by default, have to correspond to pubsSecNames
static int pubsSecChecked[] ={
      1, 1,
      1, 1,
      1, 1,
      1, 0,
      0, 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 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 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 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 = cgiInt("o");
    int end = cgiInt("t");
    char qBuf[1024];
    struct sqlConnection *conn = hAllocConn(database);
    safef(qBuf, sizeof(qBuf), "SELECT CONCAT(firstAuthor, year) FROM %s WHERE articleId='%s';", articleTable, articleId);
    char *dispId = sqlQuickString(conn, qBuf);

    printf(
        "      <div class=\"subsection\">");
    printf(
        "      <P><A HREF=\"%s&amp;db=%s&amp;position=%s%%3A%d-%d&amp;pubsFilterArticleId=%s&amp;%s=pack&amp;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>");
    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)
/* 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, pmid, "  
    "group_concat(snippet, concat(\" (section: \", 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;
}


static void printSectionCheckboxes()
/* show a little form with checkboxes where user can select sections they want to show */
{
// labels to show to user, have to correspond to pubsSecNames
char *secLabels[] ={
      "Title", "Abstract",
      "Introduction", "Methods",
      "Results", "Discussion",
      "Conclusions", "Acknowledgements",
      "References", "Not determined" };

int labelCount = sizeof(secLabels)/sizeof(char *);

int i;
printf("<P>\n");
printf("<B>Sections of article shown:</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=\"%d\" />\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];
safef(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 %d articles.<P>\n", itemLimit);
}
}

static void printMarkerSnippets(struct sqlConnection *conn, char *articleTable, char *markerTable, char *item)
{

/* do not show more snippets than this limit */
int itemLimit=100;

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 *pmid      = row[5];
    char *snippets  = row[6];
    url = mangleUrl(url);
    printf("<A HREF=\"%s\">%s</A> ", url, title);
    printf("<SMALL>%s</SMALL>; ", authors);
    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 *urlToLogoUrl(char *urlOrig)
/* return a string with relative path of logo for publisher given the url of fulltext, has to be freed */
{
// get top-level domain
char url[1024];
memcpy(url, urlOrig, sizeof(url));
char *urlParts[20];
int partCount = chopString(url, ".", urlParts, ArraySize(urlParts));
// construct path
char *logoUrl = needMem(sizeof(url));
safef(logoUrl, sizeof(url), "../images/pubs_%s.png", urlParts[partCount-2]);
return logoUrl;
}

static char *printArticleInfo(struct sqlConnection *conn, char *item, char *pubsArticleTable)
/* 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 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];

url = mangleUrl(url);
if (strlen(abstract)==0) 
        abstract = "(No abstract available for this article. "
            "Please follow the link to the fulltext above.)";

if (stringIn("sciencedirect.com", url)) 
    {
    pubsHasSupp = FALSE;
    pubsIsElsevier = TRUE;
    }

// logo of publisher
char *logoUrl = urlToLogoUrl(url);
printf("<a href=\"%s\"><img align=\"right\" hspace=\"20\" src=\"%s\"></a>\n", url, logoUrl);
freeMem(logoUrl);

printf("<P>%s</P>\n", authors);
printf("<A TARGET=\"_blank\" HREF=\"%s\"><B>%s</B>\n", url, title);
printf("</A>\n");


printf("<P style=\"width:800px; 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:800px; 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 */
{
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 (pubsDebug)
    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;

struct hash *seqIdHash = NULL;
seqIdHash = newHash(0);
for (i=0; i<partCount; 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);
web2PrintHeaderCell("One row per sequence, with flanking text, sequence in bold", 60);
if (pubsDebug)
    web2PrintHeaderCell("Identifiers", 30);

if (!isClickedSection && !pubsDebug)
    web2PrintHeaderCell("Chained matches with this sequence", 20);
web2EndThead();
web2StartTbodyS("font-family: Arial, Helvetica, sans-serif; line-height: 1.5em; font-size: 0.9em;");
}

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=='&') || (*c=='<'))
       doNotBreak = TRUE;
    if (*c==';' || (*c =='>'))
       doNotBreak = FALSE;

    printf("%c", *c);
    if (i % distance == 0 && ! doNotBreak) 
        printf("<wbr>");
    c++;
    i++;
    }
}

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&amp;db=%s&amp;position=%s:%d-%d&amp;%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);
    }
}




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
char query[4096];
safef(query, sizeof(query), 
"SELECT fileDesc, snippet, locations, articleId, fileId, seqId, sequence "
"FROM %s WHERE articleId='%s';", pubsSequenceTable, articleId);
if (pubsDebug)
    puts(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&nbsp;<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), cgiString("o"), cgiString("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;
bool foundSkippedRows = FALSE;
while ((row = sqlNextRow(sr)) != NULL)
    {
    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 *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<br>%s<br>", annotId, seq);
    else
        {
        web2StartRow();

        // column 1: type of file (main or supp)
        if (showDesc)
            web2PrintCellS("word-break:break-all", fileDesc);
        
        // column 2: snippet
        web2StartCellS("word-break:break-all");
        printAddWbr(snippet, 40);
        web2EndCell();

        // optional debug info column
        if (pubsDebug) 
            web2PrintCellF("article %s, file %s, seq %s, annotId %s", artId, fileId, seqId, 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();
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 used to construct this feature", \
        fileDesc, conn, clickedSeqs, 1, fasta, pslTable, articleTable);
else 
    skippedRows=1;

if (skippedRows)
    printSeqSection(articleId, "Other Sequences in this article", \
        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];
    safef(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 void printPositionAndSize(int start, int end, bool showSize)
{
printf("<B>Position:</B>&nbsp;"
           "<A HREF=\"%s&amp;db=%s&amp;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>&nbsp;%s<BR>\n", startBuf);
}

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;
safef(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        = cgiInt("o");
int end          = cgiOptionalInt("t", 0);
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");
        printPositionAndSize(start, end, 0);
        printMarkerSnippets(conn, articleTable, markerTable, item);
        }
    else
        {
        printPositionAndSize(start, end, 1);
        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);
}