static void fillInMissingLabels(struct sqlConnection *conn,
struct column *colList, struct searchResult *srList)
/* Fill in missing columns by looking up name and description
* if possible. */
{
struct column *nameColumn = findNamedColumn("name");
struct column *desColumn = findNamedColumn("description");
struct searchResult *sr;
for (sr = srList; sr != NULL; sr = sr->next)
{
if (sr->shortLabel == NULL)
{
if (nameColumn != NULL)
sr->shortLabel = nameColumn->cellVal(nameColumn, &sr->gp, conn);
if (sr->shortLabel == NULL)
sr->shortLabel = cloneString(sr->gp.name);
}
if (sr->longLabel == NULL)
{
if (desColumn != NULL)
sr->longLabel = desColumn->cellVal(desColumn, &sr->gp, conn);
else
sr->longLabel = cloneString("");
}
}
}
int check_expression()
{
if (! orderByAsc.empty()) {
int colIndex = findNamedColumn(orderByAsc);
if (colIndex == -1) {
std:: cerr << "error: unknown column name '" << orderByAsc << "'" << std:: endl;
return 1;
}
}
else if (! orderByDesc.empty()) {
int colIndex = findNamedColumn(orderByDesc);
if (colIndex == -1) {
std:: cerr << "error: unknown column name '" << orderByDesc << "'" << std:: endl;
return 1;
}
}
else {
conditionsForColumn.resize(columnNames.size());
for (size_t i = 0; i < conditions.size(); ++i) {
const Condition &cond = conditions[i];
int colIndex = findNamedColumn(cond.col);
if (colIndex == -1) {
std:: cerr << "error: unknown column name '" << cond.col << "'" << std:: endl;
return 1;
}
conditionsForColumn[colIndex].push_back(std:: pair<Condition, int>(cond, -1));
}
}
return 0;
}
void doAdvFilterListCol(struct sqlConnection *conn, struct column *colList,
char *colName)
/* List a column for genes matching advanced filter. */
{
struct genePos *gp, *list = NULL, *newList = NULL, *gpNext = NULL;
struct column *col = findNamedColumn(colName);
makeTitle("Current Filters", NULL);
if (col == NULL)
{
warn("No name column");
internalErr();
}
hPrintf("<TT><PRE>");
if (gotAdvFilter())
{
list = advFilterResults(colList, conn);
}
else
{
hPrintf("#No filters activated. List contains all genes.\n");
list = knownPosAll(conn);
}
/* Now lookup names and sort. */
for (gp = list; gp != NULL; gp = gpNext)
{
char *oldName = gp->name;
gp->name = col->cellVal(col, gp, conn);
gpNext = gp->next;
if (gp->name == NULL)
{
warn("Unable to find cellVal for %s -- tables out of sync?",
oldName);
}
else
{
slAddHead(&newList,gp);
}
}
list = newList;
slSort(&list, genePosCmpName);
/* Display. */
for (gp = list; gp != NULL; gp = gp->next)
{
hPrintf("%s\n", gp->name);
}
hPrintf("</PRE></TT>");
}
struct column *colButtonPressed(struct column *colList, char *prefix)
/* See if a button named prefix.column is pressed for some
* column, and if so return the column, else NULL. */
{
static char pattern[64];
char colName[64];
char *match;
safef(pattern, sizeof(pattern), "%s*", prefix);
match = cartFindFirstLike(cart, pattern);
if (match == NULL)
return NULL;
/* Construct column name. If variable is from an file upload
* there __filename suffix attached that we need to remove. */
safef(colName, sizeof(colName), "%s", match + strlen(prefix));
if (endsWith(colName, "__filename"))
{
int newLen = strlen(colName) - strlen("__filename");
colName[newLen] = 0;
}
return findNamedColumn(colName);
}
int main_i(const std::vector<std::string> &argv)
{
int argc = argv.size();
if (argc == 1 || (argc == 2 && argv[1] == "-h")) {
std:: cout << "Picosel ver. 1.5 (C) 2009-2010 AIST" "\n"
"Usage 1: picosel OPTION from inputfile select column where EXPRESSION" "\n"
"Usage 2: picosel OPTION from inputfile select column order by column" "\n"
"Option" "\n"
" -o outputfile: specify output file." "\n";
return 0;
}
if (argc == 3 && argv[1] == "--text") {
return convert_binary_file_to_text(argv[2]);
}
int r = analyze_commandline(argv);
if (r != 0) {
return r;
}
std:: ifstream input;
input.open(fromFile.c_str(), std:: ios::in | std:: ios::binary);
if (! input.is_open()) {
std:: cerr << "error: can not open file '" << fromFile << "'" << std:: endl;
return 1;
}
std:: istream *pInput = &input;
r = get_column_names(pInput);
if (r != 0) {
return r;
}
int selectColIndex = findNamedColumn(selectCol);
if (selectColIndex == -1) {
std:: cerr << "error: unknown column name '" << selectCol << "'" << std:: endl;
return 1;
}
r = check_expression();
if (r != 0) {
return r;
}
std:: ostream *pOutput = &std:: cout;
std:: ofstream output;
if (! outputFile.empty()) {
output.open(outputFile.c_str(), binaryOutputFactor != 0 ? (std:: ios::out | std:: ios::binary) : std:: ios::out);
if (! output.is_open()) {
std:: cerr << "error: can not create file '" << outputFile << "'" << std:: endl;
return 1;
}
pOutput = &output;
}
if (! orderByAsc.empty()) {
int orderColIndex = findNamedColumn(orderByAsc);
if (orderColIndex == -1) {
std:: cerr << "error: unknown column name '" << orderByAsc << "'" << std:: endl;
return 1;
}
r = do_sorting(pInput, pOutput, selectColIndex, orderColIndex, 1/* asc */, outputFile);
}
else if (! orderByDesc.empty()) {
int orderColIndex = findNamedColumn(orderByDesc);
if (orderColIndex == -1) {
std:: cerr << "error: unknown column name '" << orderByDesc << "'" << std:: endl;
return 1;
}
r = do_sorting(pInput, pOutput, selectColIndex, orderColIndex, -1/* desc */, outputFile);
}
else {
r = do_selecting(pInput, pOutput, selectColIndex);
}
output.close();
input.close();
return r;
}
