void doUploadIdentifiers(struct sqlConnection *conn)
/* Respond to upload identifiers button. */
{
struct hTableInfo *hti = maybeGetHti(database, curTable, conn);
char *idField = getIdField(database, curTrack, curTable, hti);
htmlOpen("Upload 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=POST ENCTYPE=\"multipart/form-data\">\n",
getScriptName());
cartSaveSession(cart);
hPrintf("Please enter the name of a file from your computer that contains a ");
hPrintf("space, tab, or ");
hPrintf("line separated list of the items you want to include.\n");
explainIdentifiers(database, conn, idField);
hPrintf("<BR>\n");
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", hgtaPastedIdentifiers);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
}
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);
}
boolean isWiggle(char *db, char *table)
/* Return TRUE if db.table is a wiggle. */
{
boolean typeWiggle = FALSE;
if (db != NULL && table != NULL)
{
if (isCustomTrack(table))
{
struct customTrack *ct = lookupCt(table);
if (ct->wiggle)
typeWiggle = TRUE;
}
else
{
struct hTableInfo *hti = maybeGetHti(db, table);
typeWiggle = (hti != NULL && HTI_IS_WIGGLE);
}
}
return(typeWiggle);
}
void doIntersectMore(struct sqlConnection *conn)
/* Continue working in intersect page. */
{
struct trackDb *iTrack;
char *name = curTableLabel();
char *iName, *iTable;
char *onChange = onChangeEither();
char *op, *setting;
boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable));
// Note - bigWig is purposely left out of wigOptions. It supports more intersection options
// than wig does.
struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL;
htmlOpen("Intersect with %s", name);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE BORDER=0>\n");
/* Print group and track line. */
hPrintf("Select a group, track and table to intersect with:\n");
iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange,
hgtaNextIntersectTrack, onChange, conn);
iName = iTrack->shortLabel;
hPrintf("<TR><TD>\n");
iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE);
hti2 = maybeGetHti(database, iTable, conn);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
if (!wigOptions)
{
if (hti1 && hti1->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the exons/blocks will be considered.\n", name);
if (hti2 && hti2->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the bases covered by its exons/blocks will be "
"considered.\n", iName);
hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n",
name, iName);
hPrintf("These combinations will maintain the names and "
"gene/alignment structure (if any) of %s: <P>\n",
name);
}
else
hPrintf("<P>\n");
op = cartUsualString(cart, hgtaNextIntersectOp, "any");
jsTrackingVar("op", op);
makeOpButton("any", op);
printf("All %s records that have any overlap with %s <BR>\n",
name, iName);
makeOpButton("none", op);
printf("All %s records that have no overlap with %s <BR>\n",
name, iName);
if (!wigOptions)
{
makeOpButton("more", op);
printf("All %s records that have at least ",
name);
setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80");
cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3);
printf(" %% overlap with %s <BR>\n", iName);
makeOpButton("less", op);
printf("All %s records that have at most ",
name);
setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80");
cgiMakeTextVar(hgtaNextLessThreshold, setting, 3);
printf(" %% overlap with %s <P>\n", iName);
}
else
{
/* keep javaScript onClick happy */
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n");
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n");
hPrintf(" <P>\n");
}
if (!wigOptions)
{
boolean bigWig = isBigWigTable(curTable);
hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n",
name, iName);
if (!bigWig)
hPrintf("These combinations will discard the names and "
"gene/alignment structure (if any) of %s and produce a simple "
"list of position ranges.<P>\n",
name);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n",
name, iName);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and %s <P>\n",
name, iName);
hPrintf("Check the following boxes to complement one or both tables. "
"To complement a table means to include a base pair in the "
"intersection/union if it is <I>not</I> included in the table."
"<P>\n");
if (!bigWig)
{
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE);
printf("Complement %s before base-pair-wise intersection/union <BR>\n",
name);
}
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE);
printf("Complement %s before base-pair-wise intersection/union <P>\n",
iName);
}
else
{
/* keep javaScript onClick happy */
jsTrackingVar("op", op);
hPrintf("<SCRIPT>\n");
hPrintf("var invertTable=0;\n");
hPrintf("var invertTable2=0;\n");
hPrintf("</SCRIPT>\n");
hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name);
}
cgiMakeButton(hgtaDoIntersectSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(nextVars);
memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
saveVars[varCount] = hgtaDoIntersectMore;
jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
}
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();
}
