void doFilterPage(struct sqlConnection *conn)
/* Respond to filter create/edit button */
{
char *table = connectingTableForTrack(curTable);
char *db = database;
if (sameWord(table, WIKI_TRACK_TABLE))
db = wikiDbName();
doBigFilterPage(conn, db, table);
}
static void showTableFields(char *db, char *rootTable, boolean withGetButton)
/* Put up a little html table with a check box, name, and hopefully
* a description for each field in SQL rootTable. */
{
if (isCustomTrack(rootTable))
showTableFieldsCt(db, rootTable, withGetButton);
else if (sameWord(rootTable, WIKI_TRACK_TABLE))
showTableFieldsDb(wikiDbName(), rootTable, withGetButton);
else
showTableFieldsDb(db, rootTable, withGetButton);
}
static void wikiTrackFilteredBedOnRegion(
struct region *region, /* Region to get data from. */
struct hash *idHash, /* Hash of identifiers or NULL */
struct bedFilter *bf, /* Filter or NULL */
struct lm *lm, /* Local memory pool. */
struct bed **pBedList /* Output get's appended to this list */
)
/* Get the wikiTrack items passing filter on a single region. */
{
struct bed *bed;
int fieldCount = 6;
char query[512];
int rowOffset;
char **row;
struct sqlConnection *wikiConn = wikiConnect();
struct sqlResult *sr = NULL;
char where[512];
char *filter = filterClause(wikiDbName(), WIKI_TRACK_TABLE, region->chrom, NULL);
if (filter)
sqlSafefFrag(where, sizeof(where), "db='%s' AND %-s", database, filter);
else
sqlSafefFrag(where, sizeof(where), "db='%s'", database);
sqlSafef(query, sizeof(query), "select * from %s", WIKI_TRACK_TABLE);
sr = hRangeQuery(wikiConn, WIKI_TRACK_TABLE, region->chrom,
region->start, region->end, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
if ((idHash == NULL || hashLookup(idHash, bed->name)) &&
(bf == NULL || bedFilterOne(bf, bed)))
{
struct bed *copy = lmCloneBed(bed, lm);
slAddHead(pBedList, copy);
}
}
sqlFreeResult(&sr);
wikiDisconnect(&wikiConn);
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
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();
}
