void doGenePredPal(struct sqlConnection *conn)
/* Output genePred protein alignment. */
{
if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
{
sendParamsToGalaxy(hgtaDoPalOut, "submit");
return;
}
/* get rid of pesky cookies that would bring us back here */
cartRemove(cart, hgtaDoPal);
cartRemove(cart, hgtaDoPalOut);
if (anyIntersection() && intersectionIsBpWise())
errAbort("Can't do CDS FASTA output when bit-wise intersection is on. "
"Please go back and select another output type, or clear the intersection.");
checkNoGenomeDisabled(database, curTable);
struct lm *lm = lmInit(64*1024);
int fieldCount;
struct bed *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
lm, &fieldCount);
//lmCleanup(&lm);
textOpen();
int outCount = palOutPredsInBeds(conn, cart, bedList, curTable);
/* Do some error diagnostics for user. */
if (outCount == 0)
explainWhyNoResults(NULL);
}
boolean userSettingsProcessForm(struct userSettings *us)
/* Handle button press in userSettings form.
* If this returns TRUE then form is finished processing
* and you can call something to make the next page. */
{
struct cart *cart = us->cart;
char *command = cartString(cart, us->formVar);
boolean retVal = TRUE;
char *name = cartNonemptyString(cart, us->nameVar);
command = trimSpaces(command);
if (sameWord(command, "save") && name != NULL)
{
char *varName = settingsVarName(us->savePrefix, name);
saveSettings(us, varName);
freez(&varName);
}
else if (startsWith(command, "load") && name != NULL)
{
userSettingsUseSelected(us);
}
else if (startsWith("delete", command))
{
char *which = cartOptionalString(cart, us->listDisplayVar);
if (which != NULL)
{
char *varName = settingsVarName(us->savePrefix, which);
cartRemove(cart, varName);
userSettingsSaveForm(us);
retVal = FALSE;
}
}
cartRemove(cart, us->formVar);
return retVal;
}
void doGsLogin(struct sqlConnection *conn)
/* Process user password post.
* Log into GS
* if successful save gsToken
* else return to login page or to mainpage */
{
char *user = cloneString(cartUsualString(cart, hgtaGsUser, NULL));
char *password = cloneString(cartUsualString(cart, hgtaGsPassword, NULL));
// do not leave them in the cart
cartRemove(cart, hgtaGsUser);
cartRemove(cart, hgtaGsPassword);
if (!(user && password))
errAbort("expecting GenomeSpace user and password");
char *gsToken = getAuthorizationToken(user, password);
if (gsToken)
{
cartSetString(cart, "gsToken", gsToken);
}
else
{
cartRemove(cart, "gsToken");
}
cartSetString(cart, hgtaDoTopSubmit, "get output");
}
boolean checkGsReady()
/* check that GS requirements are met */
{
// check that the output file has been specified
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
if (sameString(fileName,""))
{
cartRemove(cart, hgtaDoTopSubmit);
showMissingOutputFileForm();
return FALSE;
}
// check login
// is the GS login token in the cart?
char *gsToken = cartUsualString(cart, "gsToken", NULL);
if (!gsToken)
{
cartRemove(cart, hgtaDoTopSubmit);
showGsLoginForm();
return FALSE;
}
else
{
// check if the token still valid
char *temp = getGsPersonalDirectory(gsToken);
if (!temp)
{
cartRemove(cart, hgtaDoTopSubmit);
showGsLoginForm();
return FALSE;
}
freeMem(temp);
}
return TRUE;
}
void doClearSetUserRegionsText(struct sqlConnection *conn)
/* Respond to clear within user regions enter page. */
{
char *fileName = userRegionsFileName();
if (fileName != NULL)
remove(fileName);
cartRemove(cart, hgtaEnteredUserRegions);
cartRemove(cart, hgtaEnteredUserRegionFile);
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaRegionType);
doSetUserRegions(conn);
}
static void doDisconnectHub(struct cart *theCart)
{
char *id = cartOptionalString(cart, "hubId");
if (id != NULL)
{
char buffer[1024];
safef(buffer, sizeof buffer, "hgHubConnect.hub.%s", id);
cartRemove(cart, buffer);
}
cartRemove(theCart, "hubId");
}
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();
}
static void disconnectHubsSamePrefix(struct cart *cart, char *url)
/* disconnect all the hubs with the same prefix */
{
char *prefix = cloneString(url);
char *ptr = strrchr(prefix, '/');
if (ptr == NULL)
return;
*ptr = 0;
char query[2048];
sqlSafef(query, sizeof(query), "select id from %s where hubUrl like \"%s%%\"", getHubStatusTableName(), prefix);
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
int id = sqlUnsigned(row[0]);
char buffer[512];
safef(buffer, sizeof(buffer), "hgHubConnect.hub.%d", id);
cartRemove(cart, buffer);
}
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
}
static void hubConnectRemakeTrackHubVar(struct cart *cart)
/* Remake trackHub cart variable if need be from various check box vars. */
{
if (cartVarExists(cart, hgHubConnectRemakeTrackHub))
{
struct slPair *hubVarList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
int prefixLength = strlen(hgHubConnectHubVarPrefix);
struct dyString *trackHubs = dyStringNew(0);
struct slPair *hubVar;
boolean firstOne = TRUE;
for (hubVar = hubVarList; hubVar != NULL; hubVar = hubVar->next)
{
if (cartBoolean(cart, hubVar->name))
{
if (firstOne)
firstOne = FALSE;
else
dyStringAppendC(trackHubs, ' ');
dyStringAppend(trackHubs, hubVar->name + prefixLength);
}
}
slPairFreeList(&hubVarList);
cartSetString(cart, hubConnectTrackHubsVarName, trackHubs->string);
dyStringFree(&trackHubs);
cartRemove(cart, hgHubConnectRemakeTrackHub);
}
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display and save cart in global. */
{
char *key = NULL;
char *file = NULL;
cart = theCart;
key = cartOptionalString(cart, "key");
if (isValidKey(key))
{
file = cartOptionalString(cart, "file");
if(NULL == file)
{
printIndexFile();
}
else
{
printFile(file);
}
}
else
{
cartWebStart(theCart, database, "SECURE CGI \n");
cartRemove(cart, "key");
printf("INVALID KEY\n");
cartWebEnd();
}
}
void removeCartVars(struct cart *cart, char **vars, int varCount)
/* Remove array of variables from cart. */
{
int i;
for (i=0; i<varCount; ++i)
cartRemove(cart, vars[i]);
}
void doAdvFilterKeyPasted(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle submission in key-paste in form. */
{
char *pasteVarName = colVarName(col, keyWordPastedPrefix);
char *pasteVal = trimSpaces(cartString(cart, pasteVarName));
char *keyVarName = advFilterName(col, "keyFile");
if (pasteVal == NULL || pasteVal[0] == 0)
{
/* If string is empty then clear cart variable. */
cartRemove(cart, keyVarName);
}
else
{
/* Else write variable to temp file and save temp
* file name. */
struct tempName tn;
FILE *f;
makeTempName(&tn, "near", ".key");
f = mustOpen(tn.forCgi, "w");
mustWrite(f, pasteVal, strlen(pasteVal));
carefulClose(&f);
cartSetString(cart, keyVarName, tn.forCgi);
}
cartRemovePrefix(cart, keyWordPastedPrefix);
doAdvFilter(conn, colList);
}
void doGetGreatOutput(void (*dispatch)())
{
struct tempName tn;
int saveStdout;
FILE *f;
trashDirFile(&tn, "great", cartSessionId(cart), ".bed");
f = fopen(tn.forCgi, "w");
/* We want to capture hgTables stdout output to a trash file
* which will later be fetched by Great via URL. */
/* Workaround because stdout stream is not assignable on some operating systems */
fflush(stdout);
saveStdout = dup(STDOUT_FILENO);
dup2(fileno(f),STDOUT_FILENO); /* closes STDOUT before setting it again */
fclose(f);
dispatch(); /* this writes to stdout */
/* restore stdout */
fflush(stdout);
dup2(saveStdout ,STDOUT_FILENO); /* closes STDOUT before setting it back to saved descriptor */
close(saveStdout);
cartRemove(cart, hgtaDoGreatOutput);
htmlOpen("Table Browser integration with GREAT");
doSubmitToGreat(tn.forCgi);
htmlClose();
}
void doAdvFilterKeyClear(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
cartRemovePrefix(cart, keyWordClearPrefix);
cartRemove(cart, advFilterName(col, "keyFile"));
doAdvFilter(conn, colList);
}
void doProbe(struct sqlConnection *conn)
/* Put up probe info page. */
{
int probeId = cartInt(cart, hgpDoProbe);
int submissionSourceId = cartInt(cart, hgpSs);
cartRemove(cart, hgpSs);
probePage(conn, probeId, submissionSourceId);
}
void doId(struct sqlConnection *conn)
/* Set up Gene Pix on given ID. */
{
int id = cartInt(cart, hgpDoId);
struct slName *genes = visiGeneGeneName(conn, id);
if (genes == NULL)
{
cartRemove(cart, hgpListSpec);
cartRemove(cart, hgpId);
}
else
{
cartSetInt(cart, hgpId, id);
cartSetString(cart, hgpListSpec, genes->name);
}
slFreeList(&genes);
doDefault(conn, FALSE);
}
char *userRegionsFileName()
/* File name defined regions are in, or NULL if no such file. */
{
char *fileName = cartOptionalString(cart, hgtaUserRegionsFile);
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(database, db))
return NULL;
if (fileName == NULL)
return NULL;
if (fileExists(fileName))
return fileName;
else
{
cartRemove(cart, hgtaUserRegionsFile);
cartRemove(cart, hgtaRegionType);
return NULL;
}
}
static char *checkForNew( struct cart *cart)
/* see if the user just typed in a new hub url, return id if so */
{
struct hubConnectStatus *hub;
char *url = cartOptionalString(cart, hgHubDataClearText);
if (url != NULL)
disconnectHubsSamePrefix(cart, url);
else
url = cartOptionalString(cart, hgHubDataText);
if (url == NULL)
return NULL;
trimSpaces(url);
gNewHub = hub = getAndSetHubStatus( cart, url, TRUE);
cartRemove(cart, hgHubDataClearText);
cartRemove(cart, hgHubDataText);
char *wantFirstDb = cartOptionalString(cart, hgHubDoFirstDb);
char *newDatabase = NULL;
if ((wantFirstDb != NULL) && (hub->trackHub != NULL))
newDatabase = hub->trackHub->defaultDb;
else
{
// Check to see if the user specified an assembly within
// an assembly hub.
char *assemblyDb = cartOptionalString(cart, hgHubGenome);
if (assemblyDb != NULL)
{
char buffer[512];
safef(buffer, sizeof buffer, "hub_%d_%s", hub->id, assemblyDb);
newDatabase = cloneString(buffer);
}
}
cartRemove(cart, hgHubDoFirstDb);
cartRemove(cart, hgHubGenome);
return newDatabase;
}
boolean checkAndClear(char *cartVar)
/* If cart var exists, clear it and return TRUE */
{
if (cartVarExists(cart, cartVar))
{
cartRemove(cart, cartVar); /* in case of errAbort */
return TRUE;
}
return FALSE;
}
void doDefaultConfigure(struct sqlConnection *conn, struct column *colList)
/* Do configuration starting with defaults. */
{
struct column *col;
for (col=colList; col != NULL; col = col->next)
col->on = col->defaultOn;
cartRemovePrefix(cart, colConfigPrefix);
cartRemove(cart, colOrderVar);
//restoreDefaultOrder(&colList);
doConfigure(conn, colList); //, NULL);
}
void hubDisconnect(struct cart *cart, char *url)
/* drop the information about this url from the hubStatus table, and
* the cart variable the references this hub */
{
/* clear the hubStatus table */
unsigned id = hubClearStatus(url);
/* remove the cart variable */
char buffer[1024];
safef(buffer, sizeof buffer, "hgHubConnect.hub.%d", id);
cartRemove(cart, buffer);
}
void copyCartVars(struct cart *cart, char **source, char **dest, int count)
/* Copy from source to dest. */
{
int i;
for (i=0; i<count; ++i)
{
char *s = cartOptionalString(cart, source[i]);
if (s != NULL)
cartSetString(cart, dest[i], s);
else
cartRemove(cart, dest[i]);
}
}
static char *keyFileName(struct column *col)
/* Return key file name for this column. Return
* NULL if no key file. */
{
char *fileName = advFilterVal(col, "keyFile");
if (fileName == NULL)
return NULL;
if (!fileExists(fileName))
{
cartRemove(cart, advFilterName(col, "keyFile"));
return NULL;
}
return fileName;
}
char *identifierFileName()
/* File name identifiers are in, or NULL if not for curTable or no such file. */
{
char *fileName = cartOptionalString(cart, hgtaIdentifierFile);
if (fileName == NULL)
return NULL;
if (! forCurTable())
return NULL;
if (fileExists(fileName))
return fileName;
else
{
cartRemove(cart, hgtaIdentifierFile);
return NULL;
}
}
void configInitTrackList(
int vis,
char **pGroupTarget,
struct track **pTrackList,
struct track **pIdeoTrack,
struct group **pGroupList
)
{
char *groupTarget = NULL;
struct track *trackList = NULL;
struct track *ideoTrack = NULL;
struct group *groupList = NULL;
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
/* Get track list and group them. */
ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName);
trackList = getTrackList(&groupList, vis);
if (trackHash == NULL)
trackHash = makeGlobalTrackHash(trackList);
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
addDownloadOnlyTracks(database,&groupList,&trackList);
/* The ideogram for some reason is considered a track.
* We don't really want to process it as one though, so
* we see if it's there, and if necessary remove it. */
ideoTrack = chromIdeoTrack(trackList);
if (ideoTrack != NULL)
removeTrackFromGroup(ideoTrack);
/* Fetch group to change on if any from CGI,
* and remove var so it doesn't get used again. */
groupTarget = cloneString(cartUsualString(cart, configGroupTarget, ""));
cartRemove(cart, configGroupTarget);
if (sameString(groupTarget, "none"))
freez(&groupTarget);
*pGroupTarget = groupTarget;
*pTrackList = trackList;
*pIdeoTrack = ideoTrack;
*pGroupList = groupList;
}
void displayData(struct sqlConnection *conn, struct column *colList)
/* Display data in neighborhood of gene. */
{
struct subjInfo *subjList = NULL;
struct column *ordList = colList;
struct column *ord = curOrder(ordList);
if (ord == NULL) /* no columns are visible, go to back to configure page */
{
doConfigure(conn, colList);
return;
}
if (cartVarExists(cart, getTextVarName))
{
subjList = getOrderedList(ord, colList, conn, BIGNUM);
doGetText(conn, colList, subjList);
}
else if (cartVarExists(cart, getSeqVarName))
{
subjList = getOrderedList(ord, colList, conn, BIGNUM);
doGetSeq(conn, subjList, cartString(cart, getSeqHowVarName));
}
else if (cartVarExists(cart, redirectName))
{
subjList = getOrderedList(ord, colList, conn, BIGNUM);
if (subjList)
{
cartRemove(cart, redirectName);
}
else /* if everything has been filtered out, we'll have to go back */
{
hPrintf("No subject(s) found with the filtering conditions specified.<br>");
hPrintf("Click <a href=\"gisaidTable?gisaidTable.do.advFilter=filter+%c28now+on%c29\">here</a> to return to Select Subjects.<br>", '%', '%');
}
}
else
{
subjList = getOrderedList(ord, colList, conn, displayCount);
doMainDisplay(conn, colList, subjList);
}
}
void lookupAdvFilterControls(struct column *col, struct sqlConnection *conn)
/* Print out controls for advanced filter on lookup column. */
{
char *fileName = advFilterVal(col, "keyFile");
hPrintf("%s search (including * and ? wildcards):", col->shortLabel);
advFilterRemakeTextVar(col, "wild", 18);
hPrintf("<BR>\n");
hPrintf("Include if ");
advFilterAnyAllMenu(col, "logic", TRUE);
hPrintf("words in search term match.<BR>");
if (!columnSetting(col, "noKeys", NULL))
{
hPrintf("Limit to items (no wildcards) in list: ");
advFilterKeyPasteButton(col);
hPrintf(" ");
advFilterKeyUploadButton(col);
hPrintf(" ");
if (fileName != NULL)
{
if (fileExists(fileName))
{
int count = countQuotedWordsInFile(fileName);
advFilterKeyClearButton(col);
hPrintf("<BR>\n");
if (count == 1)
hPrintf("(There is currently 1 item in the list.)");
else
hPrintf("(There are currently %d items in the list.)", count);
}
else
{
cartRemove(cart, advFilterName(col, "keyFile"));
}
}
}
if (col->filterDropDown)
showListOfFilterValues(col, conn);
}
void submitUpload(struct sqlConnection *conn)
/* Called when they've submitted from uploads page */
{
char *urlText = cartUsualString(cart, hggUploadUrl, NULL);
char *fileText = cartUsualString(cart, hggUploadFile, NULL);
char *rawText = urlText;
if (isNotEmpty(fileText))
rawText = fileText;
int rawTextSize = strlen(rawText);
struct errCatch *errCatch = errCatchNew();
cartWebStart(cart, database, "Data Upload Complete (%d bytes)", rawTextSize);
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\">");
cartSaveSession(cart);
if (errCatchStart(errCatch))
trySubmitUpload(conn, rawText);
errCatchFinish(&errCatch);
cartRemove(cart, hggUploadFile);
hPrintf("<CENTER>");
cgiMakeButton("submit", "OK");
hPrintf("</CENTER>");
hPrintf("</FORM>");
cartWebEnd();
}
void doOutSelectedFields(char *table, struct sqlConnection *conn)
/* Put up select fields (for tab-separated output) page. */
{
if (anySubtrackMerge(database, curTable))
errAbort("Can't do selected fields output when subtrack merge is on. "
"Please go back and select another output type, or clear the subtrack merge.");
else if (anyIntersection())
errAbort("Can't do selected fields output when intersection is on. "
"Please go back and select another output type, or clear the intersection.");
else
{
char *fsTable = cartOptionalString(cart, hgtaFieldSelectTable);
char *dbTable = NULL;
table = connectingTableForTrack(table);
dbTable = getDbTable(database, table);
/* Remove cart state if table has been changed: */
if (fsTable && ! sameString(fsTable, dbTable))
{
cartRemovePrefix(cart, hgtaFieldSelectPrefix);
cartRemove(cart, hgtaFieldSelectTable);
}
doBigSelectPage(database, table);
}
}