void doMainPage(struct sqlConnection *conn)
/* Put up the first page user sees. */
{
htmlOpen("Table Browser");
mainPageAfterOpen(conn);
htmlClose();
}
void doMainPage(struct sqlConnection *conn, boolean webStarted)
/* Put up the first page user sees. */
{
if (!webStarted)
htmlOpen("Table Browser");
mainPageAfterOpen(conn);
htmlClose();
}
void doClearIdentifiers(struct sqlConnection *conn)
/* Respond to clear identifiers button. */
{
char *fileName;
htmlOpen("Table Browser (Cleared Identifiers)");
fileName = identifierFileName();
if (fileName != NULL)
remove(fileName);
cartRemove(cart, hgtaIdentifierFile);
cartRemove(cart, hgtaPastedIdentifiers);
mainPageAfterOpen(conn);
htmlClose();
}
void doClearUserRegions(struct sqlConnection *conn)
/* Respond to clear user regions button. */
{
char *fileName = userRegionsFileName();
htmlOpen("Table Browser (Cleared Region List)");
if (fileName != NULL)
remove(fileName);
cartRemove(cart, hgtaEnteredUserRegions);
cartRemove(cart, hgtaEnteredUserRegionFile);
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaRegionType);
mainPageAfterOpen(conn);
htmlClose();
}
void doPastedIdentifiers(struct sqlConnection *conn)
/* Process submit in paste identifiers page. */
{
char *idText = trimSpaces(cartString(cart, hgtaPastedIdentifiers));
htmlOpen("Table Browser (Input Identifiers)");
if (isNotEmpty(idText))
{
/* Write terms to temp file, checking whether they have matches, and
* save temp file name. */
boolean saveIdText = (strlen(idText) < MAX_IDTEXT);
char *idTextForLf = saveIdText ? cloneString(idText) : idText;
struct lineFile *lf = lineFileOnString("idText", TRUE, idTextForLf);
char *line, *word;
struct tempName tn;
FILE *f;
int totalTerms = 0, foundTerms = 0;
struct slName* missingTerms = NULL;
struct dyString *exampleMissingIds = dyStringNew(256);
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
actualDb = wikiDbName();
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
if (idField == NULL)
{
warn("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
webNewSection("Table Browser");
cartRemove(cart, hgtaIdentifierDb);
cartRemove(cart, hgtaIdentifierTable);
cartRemove(cart, hgtaIdentifierFile);
mainPageAfterOpen(conn);
htmlClose();
return;
}
struct slName *allTerms = NULL, *term;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextWord(&line)) != NULL)
{
term = slNameNew(word);
slAddHead(&allTerms, term);
totalTerms++;
}
}
slReverse(&allTerms);
lineFileClose(&lf);
char *extraWhere = NULL;
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (totalTerms > 0 && totalTerms <= maxIdsInWhere)
extraWhere = slNameToInExpression(idField, allTerms);
struct lm *lm = lmInit(0);
struct hash *matchHash = getAllPossibleIds(conn, lm, idField, extraWhere);
trashDirFile(&tn, "hgtData", "identifiers", ".key");
f = mustOpen(tn.forCgi, "w");
for (term = allTerms; term != NULL; term = term->next)
{
struct slName *matchList = NULL, *match;
if (matchHash == NULL)
{
matchList = slNameNew(term->name);
}
else
{
/* Support multiple alias->id mappings: */
char upcased[1024];
safecpy(upcased, sizeof(upcased), term->name);
touppers(upcased);
struct hashEl *hel = hashLookup(matchHash, upcased);
if (hel != NULL)
{
matchList = slNameNew((char *)hel->val);
while ((hel = hashLookupNext(hel)) != NULL)
{
match = slNameNew((char *)hel->val);
slAddHead(&matchList, match);
}
}
}
if (matchList != NULL)
{
foundTerms++;
for (match = matchList; match != NULL; match = match->next)
{
mustWrite(f, match->name, strlen(match->name));
mustWrite(f, "\n", 1);
}
}
else
{
slAddHead(&missingTerms, slNameNew(term->name));
}
}
slReverse(&missingTerms);
carefulClose(&f);
cartSetString(cart, hgtaIdentifierDb, database);
cartSetString(cart, hgtaIdentifierTable, curTable);
cartSetString(cart, hgtaIdentifierFile, tn.forCgi);
if (saveIdText)
freez(&idTextForLf);
else
cartRemove(cart, hgtaPastedIdentifiers);
int missingCount = totalTerms - foundTerms;
if (missingCount > 0)
{
char *xrefTable, *aliasField;
getXrefInfo(conn, &xrefTable, NULL, &aliasField);
boolean xrefIsSame = xrefTable && sameString(curTable, xrefTable);
struct tempName tn;
trashDirFile(&tn, "hgt/missingIds", cartSessionId(cart), ".tmp");
FILE *f = mustOpen(tn.forCgi, "w");
int exampleCount = 0;
for (term = missingTerms; term != NULL; term = term->next)
{
if (exampleCount < 10)
{
++exampleCount;
dyStringPrintf(exampleMissingIds, "%s\n", term->name);
}
fprintf(f, "%s\n", term->name);
}
carefulClose(&f);
dyStringPrintf(exampleMissingIds, "\n<a href=%s>Complete list of missing identifiers<a>\n", tn.forHtml);
warn("Note: %d of the %d given identifiers have no match in "
"table %s, field %s%s%s%s%s. "
"Try the \"describe table schema\" button for more "
"information about the table and field.\n"
"%d %smissing identifier(s):\n"
"%s\n",
(totalTerms - foundTerms), totalTerms,
curTable, idField,
(xrefTable ? (xrefIsSame ? "" : " or in alias table ") : ""),
(xrefTable ? (xrefIsSame ? "" : xrefTable) : ""),
(xrefTable ? (xrefIsSame ? " or in field " : ", field ") : ""),
(xrefTable ? aliasField : ""),
exampleCount,
exampleCount < missingCount ? "example " : "",
exampleMissingIds->string
);
webNewSection("Table Browser");
}
lmCleanup(&lm);
hashFree(&matchHash);
}
else
{
cartRemove(cart, hgtaIdentifierFile);
}
mainPageAfterOpen(conn);
htmlClose();
}
void doSubmitUserRegions(struct sqlConnection *conn)
/* Process submit in set regions page. */
{
char *idText = trimSpaces(cartString(cart, hgtaEnteredUserRegions));
char *userRegionFile = trimSpaces(cartString(cart, hgtaEnteredUserRegionFile));
boolean hasData = (idText != NULL && idText[0] != 0) ||
(userRegionFile != NULL && userRegionFile[0] != 0);
/* beware, the string pointers from cartString() point to strings in the
* cart hash. If they are manipulated and changed, they will get saved
* back to the cart in their changed form. You don't want to be
* altering them like that. Thus, the idText is duplicated below with
* the cloneString(idText)
*/
htmlOpen("Table Browser (Region definitions)");
/* presence of fileName text overrides previously existing text area
* contents
*/
if (userRegionFile != NULL && userRegionFile[0] != 0)
{
idText = cloneString(userRegionFile);
cartRemove(cart, hgtaEnteredUserRegions);
cartRemove(cart, hgtaUserRegionsFile);
cartSetString(cart, hgtaEnteredUserRegions, idText);
}
else
idText = cloneString(idText);
char *lineLimitText = limitText(idText);
if ( (strlen(lineLimitText) > 0) && (strlen(lineLimitText) != strlen(idText)) )
{
freeMem(idText);
idText = lineLimitText;
cartSetString(cart, hgtaEnteredUserRegions, lineLimitText);
}
else
freeMem(lineLimitText);
if (hasData)
{
struct tempName tn;
FILE *f;
struct bed *bedEl;
struct bed *bedList = parseRegionInput(idText);
if (NULL == bedList)
errAbort("no valid data points found in input");
trashDirFile(&tn, "hgtData", "user", ".region");
f = mustOpen(tn.forCgi, "w");
for (bedEl = bedList; bedEl; bedEl = bedEl->next )
{
if (bedEl->name)
fprintf(f, "%s\t%d\t%d\t%s\n",
bedEl->chrom, bedEl->chromStart, bedEl->chromEnd, bedEl->name);
else
fprintf(f, "%s\t%d\t%d\n",
bedEl->chrom, bedEl->chromStart, bedEl->chromEnd);
}
carefulClose(&f);
cartSetString(cart, hgtaUserRegionsDb, database);
cartSetString(cart, hgtaUserRegionsTable, curTable);
cartSetString(cart, hgtaUserRegionsFile, tn.forCgi);
cartSetString(cart, hgtaRegionType, hgtaRegionTypeUserRegions);
if (strlen(idText) > 64 * 1024)
cartRemove(cart, hgtaEnteredUserRegions);
}
else
{
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaEnteredUserRegionFile);
cartRemove(cart, hgtaRegionType);
}
mainPageAfterOpen(conn);
htmlClose();
}
