Will describe an experiment in softSOFTtext format
"Experiment.Name",
"!Series_title" => "Publication.Title",
"!Series_type" => "Experiment.Design Type.*",
"!Series_overall_design" => array ("Experiment.Number Of Conditions", "Experiment.Number Of Hybridisations", "Experiment.Quality Control.Description", "Experiment.Replicates.Description"),
"!Series_summary" => "Experiment.Description",
"!Series_contributor" => "Submitter.Name",
"!Series_sample_id" => "Measurement.Name"
);
$cardinality = array (
"^SERIES" => "1",
"!Series_title" => "1",
"!Series_type" => "1",
"!Series_overall_design" => "1",
"!Series_summary" => "1",
"!Series_contributor" => "1*",
"!Series_sample_id" => "1*"
);
foreach ($cardinality as $thing => $card)
{
if ( ($card == "1") || ($card == "1*") )
{
$required[] = $thing;
}
}
// assuming there is only one entry linked to...
// shoddy!
foreach ($input as $linkKey => $linked)
{
$newInput = $linked;
}
//print_r($input);die();
foreach ($newInput as $table => $columns)
{
//print "\n" . $table;
foreach ($columns as $colName => $col)
{
// i don't think you need to strip the -> because
// only Names and Attributes needed...
//$colNameStripped = str_replace ("<-","",$colName);
//$colNameStripped = str_replace ("->","",$colNameStripped);
//print "\n\t" . $colNameStripped;
//$string .= "\n$colName";
$mapKeys = array();
$mappedName = "";
if (in_array ($colName, $map) )
{
$mapKeys = array_keys ( $map, $colName);
$mappedName = $colName;
//print "\n$mapKey\t" . $colName;
} elseif (in_array ($table . "." . $colName, $map) )
{
$mapKeys = array_keys ($map, $table . "." . $colName);
$mappedName = $table . "." . $colName;
//print "\n$mapKey\t" . $table . "." . $colName;
}
if (count($mapKeys) > 0)
{
foreach ($mapKeys as $mapKey)
{
$mappedValues[$mapKey][$mappedName] = $col;
}
} else { // if nothing found chech to see if there's a wildcard
foreach ($map as $mk => $mv)
{
if (preg_match("/$mv/", $colName) )
{
//$string .= "\n$mv ...";
$mappedValues[$mk][$colName] = $col;
} elseif (is_array($mv) )
{
if (in_array($colName, $mv) )
{
$mapKeys = array_keys ($mv, $colName);
$mappedName = $colName;
foreach ($mapKeys as $mapKey)
{
$mappedValues[$mk][$mappedName] = $col;
}
}
}
}
}
}
}
//print_r($mappedValues);
foreach ($mappedValues as $mapKey => $cols)
{
foreach ($cols as $colName => $col)
{
foreach ($col as $rowKey => $rowValue)
{
$strings[$mapKey][] = "$rowValue";
}
}
}
$found = array();
foreach ($strings as $mapKey => $stringSet)
{
if ($cardinality[$mapKey] == "1" ) {
$separator ="";
$string .= "\n$mapKey = ";
foreach ($stringSet as $stringSetString)
{
$string .= $separator . $stringSetString;
$separator = ". ";
}
}
else {
foreach ($stringSet as $stringSetString)
{
$string .= "\n$mapKey = $stringSetString";
}
}
$found[$mapKey] = true;
}
foreach ($required as $req)
{
if (! isset ($found[$req] ) )
{
throw new exception ("sorry, but the value '" . $map[$req] . "' is required for GEO's '$req' so you must add this to the database entry.");
}
}
$string .= "\n";
$output = $string;
]]>
link
Submitter,Measurement
yes
array
02