static struct slName *setup_labels(char *long_form, struct slName *bw_list, struct slName **labels_from_bw_list)
{
struct slName *lf_labels = NULL;
if (long_form && !sameString(long_form, "on"))
/* first check labels from CL */
{
lf_labels = slNameListFromComma(long_form);
int num_labels = slCount(lf_labels);
if (num_labels != slCount(bw_list))
errAbort("number of labels provided should equal the number of bigWigs given");
}
/* from file */
else
{
if (*labels_from_bw_list)
{
if (slCount(*labels_from_bw_list) == slCount(bw_list))
lf_labels = *labels_from_bw_list;
else
slNameFreeList(labels_from_bw_list);
}
if (!lf_labels)
lf_labels = slNameCloneList(bw_list);
}
return lf_labels;
}
static void getVar(struct cartJson *cj, struct hash *paramHash)
/* Print out the requested cart var(s). varString may be a comma-separated list.
* If a var is a list variable, prints out a list of values for that var. */
{
char *varString = cartJsonRequiredParam(paramHash, "var", cj->jw, "get");
if (! varString)
return;
struct slName *varList = slNameListFromComma(varString), *var;
for (var = varList; var != NULL; var = var->next)
{
if (cartListVarExists(cj->cart, var->name))
{
// Use cartOptionalSlNameList and return a list:
struct slName *valList = cartOptionalSlNameList(cj->cart, var->name);
jsonWriteSlNameList(cj->jw, var->name, valList);
slFreeList(&valList);
}
else
{
// Regular single-value variable (or not in the cart):
char *val = cartOptionalString(cj->cart, var->name);
//#*** TODO: move jsonStringEscape inside jsonWriteString
char *encoded = jsonStringEscape(val);
jsonWriteString(cj->jw, var->name, encoded);
freeMem(encoded);
}
}
slFreeList(&varList);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *database = cgiOptionalString("db");
char *rtdbServer = cfgOption("rtdb.server");
char *rtdbPort = cfgOption("rtdb.port");
char *rtdbChoices = cfgOption("rtdb.databases");
struct slName *dbs = slNameListFromComma(rtdbChoices);
cart = theCart;
cartWebStart(cart, database, "MGC RTDB Update");
if (!rtdbServer)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
if (!rtdbPort)
errAbort("rtdb.update not defined in the hg.conf file. "
"Chances are this CGI isn't meant for this machine.");
/* create HMTL form if button wasn't pressed. Otherwise, run the update */
if (!cgiVarExists("RTDBSubmit"))
makeForm(dbs);
else if ((database == NULL) || (!slNameInList(dbs, database)))
{
makeForm(dbs);
printf("<br>Error: Select one of databases listed.");
}
else
updateServer(rtdbServer, rtdbPort, database);
cartWebEnd();
slNameFreeList(&dbs);
}
int createSubmissionId(struct sqlConnection *conn,
char *contributors, char *publication,
char *pubUrl, char *setUrl, char *itemUrl)
/* Add submission and contributors to database and return submission ID */
{
struct slName *slNameListFromString(char *s, char delimiter);
struct slName *contribList = NULL, *contrib;
int submissionSetId;
char query[1024];
safef(query, sizeof(query),
"insert into submissionSet "
"values(default, \"%s\", \"%s\", '%s', '%s', '%s')",
contributors, publication, pubUrl, setUrl, itemUrl);
sqlUpdate(conn, query);
submissionSetId = sqlLastAutoId(conn);
contribList = slNameListFromComma(contributors);
for (contrib = contribList; contrib != NULL; contrib = contrib->next)
{
int contribId = findOrAddIdTable(conn, "contributor", "name",
skipLeadingSpaces(contrib->name));
safef(query, sizeof(query),
"insert into submissionContributor values(%d, %d)",
submissionSetId, contribId);
sqlUpdate(conn, query);
}
slFreeList(&contribList);
return submissionSetId;
}
void metaBigSetRgList(struct metaBig* mb, char* commaSep, boolean isBlackList)
/* sets the whitelist (or blacklist) */
{
struct slName* commas = slNameListFromComma(commaSep);
struct slName* rgName;
struct hash* rgHash = newHash(10);
for (rgName = commas; rgName != NULL; rgName = rgName->next)
hashAdd(rgHash, rgName->name, rgName->name);
slNameFreeList(&commas);
mb->rgList = rgHash;
mb->rgListIsBlack = isBlackList;
}
void edwMetaManiToTdb(char *metaInput, char *manifestInput, char *varCommaList, char *tdbOutput)
/* edwMetaManiToTdb - Create a trackDb file based on input from meta file and manifest file.. */
{
struct encode2Manifest *manList = encode2ManifestShortLoadAll(manifestInput);
struct meta *metaForest = metaLoadAll(metaInput, "meta", "parent", TRUE, FALSE);
struct slName *varList = slNameListFromComma(varCommaList);
struct hash *hash = metaHash(metaForest);
struct composite *comp, *compList = makeCompositeList(manList, hash);
uglyf("%d elements in manList, %d in metaForest top level, %d total, %d vars, %d composites\n", slCount(manList), slCount(metaForest), hash->elCount, slCount(varList), slCount(compList));
FILE *f = mustOpen(tdbOutput, "w");
for (comp = compList; comp != NULL; comp = comp->next)
{
outputComposite(comp, varList, hash, f);
}
carefulClose(&f);
}
static struct aHubMatch *filterTrixSearchMatches(struct dbDb *dbDbList,
struct trixSearchResult *tsrList)
/* Collect the assembly hub matches (not track hub matches) from a search in hub trix files. */
{
if (tsrList == NULL)
return NULL;
struct aHubMatch *aHubMatchList = NULL;
// Make a hash of local dbs so we can tell which hub dbs must be assembly hubs
// not track hubs.
struct hash *localDbs = hashNew(0);
struct dbDb *dbDb;
for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next)
hashStore(localDbs, dbDb->name);
// tsrList gives hub URLs which we can then look up in hubPublic.
struct dyString *query = sqlDyStringCreate("select shortLabel,hubUrl,dbList from %s "
"where hubUrl in (",
hubPublicTableName());
struct trixSearchResult *tsr;
for (tsr = tsrList; tsr != NULL; tsr = tsr->next)
{
if (tsr != tsrList)
dyStringAppend(query, ", ");
dyStringPrintf(query, "'%s'", tsr->itemId);
}
dyStringAppendC(query, ')');
struct sqlConnection *conn = hConnectCentral();
struct sqlResult *sr = sqlGetResult(conn, query->string);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *shortLabel = row[0];
char *hubUrl = row[1];
struct slName *dbName, *dbList = slNameListFromComma(row[2]);
for (dbName = dbList; dbName != NULL; dbName = dbName->next)
if (! hashLookup(localDbs, dbName->name))
{
slAddHead(&aHubMatchList, aHubMatchNew(shortLabel, hubUrl, dbName->name));
}
}
slReverse(&aHubMatchList);
hDisconnectCentral(&conn);
return aHubMatchList;
}
static struct slName *parseDatabaseList(struct lineFile *lf, char *s)
/* Parse out comma-separated list of databases, with
* possible !db's. */
{
struct slName *list, *el;
struct hash *notHash;
/* Get comma-separated list. */
list = slNameListFromComma(s);
if (list == NULL)
errAbort("Empty database name line %d of %s",
lf->lineIx, lf->fileName);
/* Remove !'s */
notHash = makeNotHash(list);
if (notHash != NULL)
{
struct slName *newList = NULL, *next;
for (el = list; el != NULL; el = next)
{
next = el->next;
if (el->name[0] != '!' && !hashLookup(notHash, el->name))
{
slAddHead(&newList, el);
}
else
{
freeMem(el);
}
}
hashFree(¬Hash);
slReverse(&newList);
list = newList;
}
return list;
}
void bwtool_matrix(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *range_s, char *bigfile, char *tmp_dir, char *outputfile)
/* bwtool_matrix - main for matrix-creation program */
{
boolean do_k = (hashFindVal(options, "cluster") != NULL) ? TRUE : FALSE;
boolean do_tile = (hashFindVal(options, "tiled-averages") != NULL) ? TRUE : FALSE;
boolean do_binary_matrix = (hashFindVal(options, "binary-matrix") != NULL) ? TRUE : FALSE;
boolean keep_bed = (hashFindVal(options, "keep-bed") != NULL) ? TRUE : FALSE;
boolean starts = (hashFindVal(options, "starts") != NULL) ? TRUE : FALSE;
boolean ends = (hashFindVal(options, "ends") != NULL) ? TRUE : FALSE;
boolean lf_header = (hashFindVal(options, "long-form-header") != NULL) ? TRUE : FALSE;
char *centroid_file = (char *)hashFindVal(options, "cluster-centroids");
char *long_form = (char *)hashFindVal(options, "long-form");
boolean do_long_form = (long_form != NULL);
unsigned left = 0, right = 0;
int meta = 0;
int num_parse = parse_left_right(range_s, &left, &right, &meta);
boolean do_meta = (num_parse == 3);
int k = (int)sqlUnsigned((char *)hashOptionalVal(options, "cluster", "0"));
int tile = (int)sqlUnsigned((char *)hashOptionalVal(options, "tiled-averages", "1"));
if ((do_k) && ((k < 2) || (k > 10)))
errAbort("k should be between 2 and 10\n");
if ((do_tile) && (tile < 2))
errAbort("tiling should be done for larger regions");
if ((left % tile != 0) || (right % tile != 0))
errAbort("tiling should be multiple of both up and down values");
if (do_meta && starts && ends)
warn("meta uses -starts and -ends anyway");
else if ((do_meta) && (starts || ends))
warn("-starts and -ends both automatically used with meta");
if (do_meta && do_tile)
errAbort("meta not compatible with -tile... yet");
if (do_binary_matrix && do_long_form)
errAbort("Writing binary matrix is not compatible with -long-form... yet");
struct slName *bw_names = slNameListFromComma(bigfile);
struct slName *bw_name;
struct slName *labels_from_file = NULL;
int num_bigwigs = check_for_list_files(&bw_names, &labels_from_file, 0);
struct slName *labels = setup_labels(long_form, bw_names, &labels_from_file);
struct bed6 *regs = NULL;
struct bed6 *regions_left = NULL, *regions_right = NULL, *regions_meta = NULL;
struct perBaseMatrix *pbm = NULL;
int i;
if (do_meta)
{
if (meta == -1)
{
meta = calculate_meta_file(regions);
fprintf(stderr, "calculated meta = %d bases\n", meta);
}
regions_left = load_and_recalculate_coords(regions, left, 0, FALSE, TRUE, FALSE);
regions_right = load_and_recalculate_coords(regions, 0, right, FALSE, FALSE, TRUE);
regions_meta = (meta > 0) ? readBed6Soft(regions) : NULL;
}
else
regs = load_and_recalculate_coords(regions, left, right, FALSE, starts, ends);
for (bw_name = bw_names; bw_name != NULL; bw_name = bw_name->next)
{
struct metaBig *mb = metaBigOpenWithTmpDir(bw_name->name, tmp_dir, NULL);
if (do_meta)
{
struct perBaseMatrix *one_pbm = load_perBaseMatrix(mb, regions_left, fill);
struct perBaseMatrix *right_pbm = load_perBaseMatrix(mb, regions_right, fill);
if (meta > 0)
{
struct perBaseMatrix *meta_pbm = load_meta_perBaseMatrix(mb, regions_meta, meta, fill);
fuse_pbm(&one_pbm, &meta_pbm, TRUE);
}
fuse_pbm(&one_pbm, &right_pbm, TRUE);
fuse_pbm(&pbm, &one_pbm, FALSE);
}
else
{
struct perBaseMatrix *one_pbm = (do_tile) ? load_ave_perBaseMatrix(mb, regs, tile, fill) :
load_perBaseMatrix(mb, regs, fill);
fuse_pbm(&pbm, &one_pbm, FALSE);
}
metaBigClose(&mb);
}
if (do_k)
{
struct cluster_bed_matrix *cbm = NULL;
/* ordered by cluster with label in first column */
cbm = init_cbm_from_pbm(pbm, k);
do_kmeans_sort(cbm, 0.001, TRUE);
if (do_long_form)
{
output_cluster_matrix_long(cbm, labels, keep_bed, outputfile, lf_header);
}
else
{
if (do_binary_matrix)
{
output_binary_cluster_matrix(cbm, keep_bed, outputfile);
}
else
{
output_cluster_matrix(cbm, decimals, keep_bed, outputfile);
}
}
if (centroid_file)
{
output_centroids(cbm, centroid_file, decimals);
}
free_cbm(&cbm);
}
else
{
if (do_long_form)
{
output_matrix_long(pbm, decimals, labels, keep_bed, left, right, tile, lf_header, outputfile);
}
else
{
if (do_binary_matrix)
{
output_binary_matrix(pbm, keep_bed, outputfile);
}
else
{
output_matrix(pbm, decimals, keep_bed, outputfile);
}
}
/* unordered, no label */
free_perBaseMatrix(&pbm);
}
if (do_meta)
{
bed6FreeList(®ions_left);
bed6FreeList(®ions_right);
if (meta > 0)
bed6FreeList(®ions_meta);
}
else
bed6FreeList(®s);
}
static struct hash *outputPublicTable(struct sqlConnection *conn, char *publicTable)
/* Put up the list of public hubs and other controls for the page. */
{
struct hash *publicHash = NULL;
char query[512];
sqlSafef(query, sizeof(query), "select hubUrl,shortLabel,longLabel,dbList from %s",
publicTable);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
boolean gotAnyRows = FALSE;
while ((row = sqlNextRow(sr)) != NULL)
{
char *url = row[0], *shortLabel = row[1], *longLabel = row[2],
*dbList = row[3];
if (gotAnyRows)
webPrintLinkTableNewRow();
else
{
/* output header */
printf("<div id=\"publicHubs\" class=\"hubList\"> \n");
printf("<table id=\"publicHubsTable\"> "
"<thead><tr> "
"<th>Display</th> "
"<th>Hub Name</th> "
"<th>Description</th> "
"<th>Assemblies</th> "
"<th>URL</th> "
"</tr></thead>\n");
// start first row
printf("<tbody> <tr>");
gotAnyRows = TRUE;
// allocate the hash to store hubUrl's
publicHash = newHash(5);
}
char *errorMessage = NULL;
// get an id for this hub
unsigned id = hubFindOrAddUrlInStatusTable(database, cart,
url, &errorMessage);
if ((id != 0) && isEmpty(errorMessage))
{
ourCellStart();
char hubName[32];
safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
cartMakeCheckBox(cart, hubName, FALSE);
ourCellEnd();
}
else if (!isEmpty(errorMessage))
{
// give user a chance to clear the error
ourCellStart();
printf(
"<input name=\"hubClearButton\""
"onClick=\"document.resetHubForm.elements['hubUrl'].value='%s';"
"document.resetHubForm.submit();return true;\" "
"class=\"hubField\" type=\"button\" value=\"check hub\">"
, url);
ourCellEnd();
}
else
errAbort("cannot get id for hub with url %s\n", url);
ourPrintCell(shortLabel);
if (isEmpty(errorMessage))
ourPrintCell(longLabel);
else
printf("<TD><span class=\"hubError\">ERROR: %s </span>"
"<a href=\"../goldenPath/help/hgTrackHubHelp.html#Debug\">Debug</a></TD>",
errorMessage);
printGenomeList(slNameListFromComma(dbList)); // Leaking a bit of memory
ourPrintCell(url);
hashStore(publicHash, url);
}
sqlFreeResult(&sr);
if (gotAnyRows)
{
printf("</TR></tbody></TABLE>\n");
printf("</div>");
}
return publicHash;
}
