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ObservationUnitPropertyDao.kt
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ObservationUnitPropertyDao.kt
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package com.fieldbook.tracker.database.dao
import android.content.Context
import android.database.Cursor
import android.database.MatrixCursor
import android.util.Log
import androidx.preference.PreferenceManager
import com.fieldbook.tracker.database.DataHelper
import com.fieldbook.tracker.database.Migrator.Companion.sObservationUnitPropertyViewName
import com.fieldbook.tracker.database.Migrator.ObservationUnit
import com.fieldbook.tracker.database.Migrator.ObservationUnitAttribute
import com.fieldbook.tracker.database.Migrator.ObservationUnitValue
import com.fieldbook.tracker.database.Migrator.Study
import com.fieldbook.tracker.database.query
import com.fieldbook.tracker.database.toFirst
import com.fieldbook.tracker.database.toTable
import com.fieldbook.tracker.database.withDatabase
import com.fieldbook.tracker.objects.RangeObject
import com.fieldbook.tracker.objects.TraitObject
import com.fieldbook.tracker.preferences.GeneralKeys
import com.fieldbook.tracker.utilities.CategoryJsonUtil
class ObservationUnitPropertyDao {
companion object {
// internal fun selectAllRange(): Array<Map<String, Any?>>? = withDatabase { db ->
// db.query(sObservationUnitPropertyViewName).toTable().toTypedArray()
// }
fun getObservationUnitPropertyByUniqueId(uniqueName: String, column: String, uniqueId: String): String = withDatabase { db ->
db.query(sObservationUnitPropertyViewName, select = arrayOf(column), where = "`${uniqueName}` = ?", whereArgs = arrayOf(uniqueId))
.toFirst()[column].toString()
}?: ""
fun getAllRangeId(context: Context): Array<Int> {
val studyId = PreferenceManager.getDefaultSharedPreferences(context)
.getInt(GeneralKeys.SELECTED_FIELD_ID, 0)
getSortedObservationUnitData(context, studyId)?.use { cursor ->
val ids = mutableListOf<Int>()
while (cursor.moveToNext()) {
val idIndex = cursor.getColumnIndex("id")
if (idIndex != -1) {
ids.add(cursor.getInt(idIndex))
}
}
return ids.toTypedArray()
}
return emptyArray()
}
fun getRangeFromId(firstName: String, secondName: String, uniqueName: String, id: Int): RangeObject = withDatabase { db ->
// data.range = cursor.getString(0);
// data.plot = cursor.getString(1);
// data.plot_id = cursor.getString(2);
RangeObject().apply {
val model = db.query(sObservationUnitPropertyViewName,
select = arrayOf(firstName, secondName, uniqueName, "id"),
where = "id = ?",
whereArgs = arrayOf(id.toString())).toFirst()
range = model[firstName].toString()
plot = model[secondName].toString()
plot_id = model[uniqueName].toString()
}
} ?: RangeObject().apply {
range = ""
plot = ""
plot_id = ""
}
/**
* This function's parameter trait is not always a trait and can be an observation unit property column.
* For example this is used when selecting the top-left drop down in the collect activity.
*/
fun getDropDownRange(uniqueName: String, trait: String, plotId: String): Array<String>? = withDatabase { db ->
//added sanitation to the uniqueName in case it has a space
val unique = if ("`" in uniqueName) uniqueName else "`$uniqueName`"
db.query(sObservationUnitPropertyViewName,
select = arrayOf(trait),
where = "$unique LIKE ?",
whereArgs = arrayOf(plotId)).toTable().map {
it[trait].toString()
}.toTypedArray()
}
fun getRangeColumnNames(): Array<String?> = withDatabase { db ->
val cursor = db.rawQuery("SELECT * FROM $sObservationUnitPropertyViewName limit 1", null)
//Cursor cursor = db.rawQuery("SELECT * from range limit 1", null);
//Cursor cursor = db.rawQuery("SELECT * from range limit 1", null);
var data: Array<String?>? = null
if (cursor.moveToFirst()) {
data = arrayOfNulls(cursor.columnCount - 1)
var k = 0
for (j in 0 until cursor.columnCount) {
if (cursor.getColumnName(j) != "id") {
data[k++] = cursor.getColumnName(j).replace("//", "/")
}
}
}
if (!cursor.isClosed) {
cursor.close()
}
data
} ?: emptyArray()
fun getRangeColumns(): Array<String?> = withDatabase { db ->
val cursor = db.rawQuery("SELECT * from $sObservationUnitPropertyViewName limit 1", null)
var data: Array<String?>? = null
if (cursor.moveToFirst()) {
data = arrayOfNulls(cursor.columnCount - 1)
var k = 0
for (j in 0 until cursor.columnCount) {
if (cursor.getColumnName(j) != "id") {
data[k++] = cursor.getColumnName(j)
}
}
}
if (!cursor.isClosed) {
cursor.close()
}
data
// db.query(sObservationUnitPropertyViewName).toFirst().keys
// .filter { it != "id" }.toTypedArray()
} ?: emptyArray<String?>()
/**
* This function is used when database is checked on export.
* The traits array is used to determine which traits are exported.
* In the case of "all active traits" only the visible traits are given to this query.
* The final AND clause checks if the query's observation_variable_name exists in the list of traits.
* Database format prints off one observation per row s.a
* "plot_id","column","plot","tray_row","tray_id","seed_id","seed_name","pedigree","trait","value","timestamp","person","location","number"
* "13RPN00001","1","1","1","13RPN_TRAY001","12GHT00001B","Kharkof","Kharkof","height","3","2021-08-05 11:52:45.379-05:00"," ","","2"
*/
fun getExportDbData(
context: Context,
studyId: Int,
fieldList: Array<String?>,
traits: ArrayList<TraitObject>
): Cursor? = withDatabase { db ->
val traitRequiredFields =
arrayOf("trait", "userValue", "timeTaken", "person", "location", "rep")
val requiredFields = fieldList + traitRequiredFields
MatrixCursor(requiredFields).also { cursor ->
val placeholders = traits.joinToString(", ") { "?" }
val traitNames = traits.map { DataHelper.replaceIdentifiers(it.name) }.toTypedArray()
val unitSelectAttributes = fieldList.map { attributeName ->
"MAX(CASE WHEN attr.observation_unit_attribute_name = '$attributeName' THEN vals.observation_unit_value_name ELSE NULL END) AS \"$attributeName\""
}.joinToString(", ")
val obsSelectAttributes =
arrayOf("observation_variable_name", "observation_variable_field_book_format", "value", "observation_time_stamp", "collector", "geoCoordinates", "rep")
val sortOrderClause = getSortOrderClause(context, studyId.toString())
val query = """
SELECT $unitSelectAttributes, ${obsSelectAttributes.joinToString { "obs.`$it` AS `$it`" }}
FROM observations AS obs
LEFT JOIN observation_units AS units ON units.observation_unit_db_id = obs.observation_unit_id
LEFT JOIN observation_units_values AS vals ON units.internal_id_observation_unit = vals.observation_unit_id
LEFT JOIN observation_units_attributes AS attr ON vals.observation_unit_attribute_db_id = attr.internal_id_observation_unit_attribute
WHERE obs.study_id = ?
AND obs.observation_variable_name IN ($placeholders)
GROUP BY obs.internal_id_observation
$sortOrderClause
""".trimIndent()
Log.d("getExportDbData", "Final Query: $query")
val table = db.rawQuery(query, arrayOf(studyId.toString()) + traitNames).toTable()
table.forEach { row ->
cursor.addRow(fieldList.map { row[it] } + traitRequiredFields.map {
when (it) {
"trait" -> row["observation_variable_name"]
"userValue" -> CategoryJsonUtil.processValue(row)
"timeTaken" -> row["observation_time_stamp"]
"person" -> row["collector"]
"location" -> row["geoCoordinates"]
"rep" -> row["rep"]
else -> String()
}
})
}
}
}
/**
* Same as database export function above, but filters all all attribute columns other than the unique id
* (The other attributes need to be retrieved for sorting, but can then be discarded)
*/
fun getExportDbDataShort(
context: Context,
studyId: Int,
fieldList: Array<String?>,
uniqueName: String,
traits: ArrayList<TraitObject>
): Cursor? {
// Get the full data set
getExportDbData(context, studyId, fieldList, traits)?.use { fullCursor ->
val traitRequiredFields = arrayOf("trait", "userValue", "timeTaken", "person", "location", "rep")
val requiredColumns = mutableListOf(uniqueName).apply {
addAll(traitRequiredFields)
}.toTypedArray()
// Create and return a cursor that only includes the required columns
val matrixCursor = MatrixCursor(requiredColumns)
while (fullCursor.moveToNext()) {
val rowData = requiredColumns.map { columnName ->
val columnIndex = fullCursor.getColumnIndex(columnName)
if (columnIndex != -1) fullCursor.getString(columnIndex) else null
}.toTypedArray()
matrixCursor.addRow(rowData)
}
// Return a cursor that only includes the required columns
return MatrixCursor(requiredColumns).also { filteredCursor ->
matrixCursor.moveToFirst()
while (!matrixCursor.isAfterLast) {
val rowValues = requiredColumns.map { columnName ->
matrixCursor.getString(matrixCursor.getColumnIndex(columnName))
}.toTypedArray()
filteredCursor.addRow(rowValues)
matrixCursor.moveToNext()
}
}
}
// Return null if the original data retrieval fails
return null
}
/**
* This will print all observation data (if a trait is not observed it is null/empty string) and attributes for all observation units in a study.
* The maxStatements parameter builds aggregate case statements for each variable, this way the output has column names that are one-to-one with variable names.
* Where the column observation_variable_name value will be the observation value.
* All observation_units are captured, even if they did not make an observation.
* Inputs:
* @param expId the field/study id
* @param traits the list of traits to print, either all traits or just the active ones
* @return a cursor that is used in CSVWriter and closed elsewhere
*/
fun getExportTableData(
context: Context,
expId: Int,
traits: ArrayList<TraitObject>
): Cursor? = withDatabase { db ->
val headers = ObservationUnitAttributeDao.getAllNames(expId)
val selectAttributes = headers.map { attributeName ->
"MAX(CASE WHEN attr.observation_unit_attribute_name = '$attributeName' THEN vals.observation_unit_value_name ELSE NULL END) AS \"$attributeName\""
}.joinToString(", ")
val selectObservations = traits.map { trait ->
val traitName = DataHelper.replaceIdentifiers(trait.name)
"MAX(CASE WHEN obs.observation_variable_name='$traitName' THEN obs.value ELSE NULL END) AS \"$traitName\""
}.joinToString(", ")
val combinedSelection = listOf(selectAttributes, selectObservations).filter { it.isNotEmpty() }.joinToString(", ")
val orderByClause = getSortOrderClause(context, expId.toString())
// SELECT units.internal_id_observation_unit AS id, $combinedSelection
val query = """
SELECT $combinedSelection
FROM observation_units AS units
LEFT JOIN observation_units_values AS vals ON units.internal_id_observation_unit = vals.observation_unit_id
LEFT JOIN observation_units_attributes AS attr ON vals.observation_unit_attribute_db_id = attr.internal_id_observation_unit_attribute
LEFT JOIN observations AS obs ON units.observation_unit_db_id = obs.observation_unit_id AND obs.study_id = $expId
WHERE units.study_id = $expId
GROUP BY units.internal_id_observation_unit
$orderByClause
""".trimIndent()
Log.d("getExportTableData", "Executing query: $query")
db.rawQuery(query, null)
}
/**
* Same as table export function above, but filters all all attribute columns other than the unique id
* (The other attributes need to be retrieved for sorting, but can then be discarded)
*/
fun getExportTableDataShort(
context: Context,
expId: Int,
uniqueName: String,
traits: ArrayList<TraitObject>
): Cursor? {
getExportTableData(context, expId, traits)?.use { cursor ->
val requiredColumns = arrayOf(uniqueName) + traits.map { it.name }.toTypedArray()
val matrixCursor = MatrixCursor(requiredColumns)
while (cursor.moveToNext()) {
val rowData = mutableListOf<String?>()
val uniqueNameIndex = cursor.getColumnIndex(uniqueName)
if (uniqueNameIndex != -1) {
rowData.add(cursor.getString(uniqueNameIndex))
} else {
rowData.add(null) // or handle appropriately
}
traits.forEach { trait ->
val traitIndex = cursor.getColumnIndex(trait.name)
if (traitIndex != -1) {
rowData.add(cursor.getString(traitIndex))
} else {
rowData.add(null) // or handle appropriately
}
}
matrixCursor.addRow(rowData.toTypedArray())
}
return matrixCursor
}
return null
}
/**
* Same as above but filters by obs unit and trait format
*/
fun convertDatabaseToTable(
expId: Int,
uniqueName: String,
unit: String,
col: Array<String?>,
traits: Array<TraitObject>
): Cursor? = withDatabase { db ->
val sanitizeTraits = traits.map { DataHelper.replaceIdentifiers(it.name) }
val sanitizeFormats = traits.map { DataHelper.replaceIdentifiers(it.format) }
val select = col.joinToString(",") { "props.'${DataHelper.replaceIdentifiers(it)}'" }
val maxStatements = arrayListOf<String>()
sanitizeTraits.forEachIndexed { index, it ->
maxStatements.add(
"MAX (CASE WHEN o.observation_variable_name='$it' AND o.observation_variable_field_book_format='${sanitizeFormats[index]}' THEN o.value ELSE NULL END) AS '$it'"
)
}
val query = """
SELECT $select,
${maxStatements.joinToString(",\n")}
FROM ObservationUnitProperty as props
LEFT JOIN observations o ON props.`${uniqueName}` = o.observation_unit_id AND o.${Study.FK} = $expId
WHERE props.`${uniqueName}` = "$unit"
GROUP BY props.id
""".trimIndent()
db.rawQuery(query, null)
}
fun getSortedObservationUnitData(context: Context, studyId: Int): Cursor? = withDatabase { db ->
val headers = ObservationUnitAttributeDao.getAllNames(studyId).filter { it != "geo_coordinates" }
val selectStatement = headers.map { col ->
"MAX(CASE WHEN attr.observation_unit_attribute_name = \"$col\" THEN vals.observation_unit_value_name ELSE NULL END) AS \"$col\""
}.joinToString(", ")
val orderByClause = getSortOrderClause(context, studyId.toString())
val query = """
SELECT ${if (selectStatement.isNotEmpty()) "$selectStatement, " else ""} units.internal_id_observation_unit AS id, units.geo_coordinates
FROM ${ObservationUnit.tableName} AS units
LEFT JOIN ${ObservationUnitValue.tableName} AS vals ON units.internal_id_observation_unit = vals.observation_unit_id
LEFT JOIN ${ObservationUnitAttribute.tableName} AS attr ON vals.observation_unit_attribute_db_id = attr.internal_id_observation_unit_attribute
WHERE units.study_id = $studyId
GROUP BY units.internal_id_observation_unit
$orderByClause
""".trimIndent()
Log.d("getSortedObsUnitData", "Executing dynamic query: $query")
db.rawQuery(query, null)
}
// private fun getSortOrderClause(context: Context, studyId: String): String = withDatabase { db ->
// val sortOrder = if (PreferenceManager.getDefaultSharedPreferences(context)
// .getBoolean("${GeneralKeys.SORT_ORDER}.$studyId", true)) "ASC" else "DESC"
//
// var sortCols = "internal_id_observation_unit" // Default sort column
// try {
// val sortName = db.query(
// Study.tableName,
// select = arrayOf("study_sort_name"),
// where = "${Study.PK} = ?",
// whereArgs = arrayOf(studyId)
// ).toFirst()["study_sort_name"]?.toString()
//
// if (!sortName.isNullOrEmpty() && sortName != "null") {
// sortCols = sortName.split(',')
// .joinToString(",") { col -> "cast(`$col` as integer), `$col`" } + ", internal_id_observation_unit"
// }
// } catch (e: Exception) {
// Log.e("ObsUnitPropertyDao", "Error fetching sort order for study: $e")
// }
//
// "$sortCols $sortOrder"
// } ?: "internal_id_observation_unit ASC" // Provide a default non-null value
private fun getSortOrderClause(context: Context, studyId: String): String? = withDatabase { db ->
val sortOrder = if (PreferenceManager.getDefaultSharedPreferences(context)
.getBoolean("${GeneralKeys.SORT_ORDER}.$studyId", true)) "ASC" else "DESC"
var sortCols = "" // Adjusted to start as an empty string
val sortName = db.query(
Study.tableName,
select = arrayOf("study_sort_name"),
where = "${Study.PK} = ?",
whereArgs = arrayOf(studyId)
).toFirst()["study_sort_name"]?.toString()
if (!sortName.isNullOrEmpty() && sortName != "null") {
sortCols = sortName.split(',')
.joinToString(",") { col -> "cast(`$col` as integer), `$col`" } + (if (sortCols.isNotEmpty()) ", " else "")
}
if (sortCols.isNotEmpty()) "ORDER BY $sortCols $sortOrder" else ""
}
}
}