/**
* Retrieves the metadata for all the supported spatial reference systems.
*
* @param boolean $refresh Set to true to force a full refresh, otherwise the result is cached.
*/
public static function system_metadata($refresh = false)
{
$cacheId = 'spatial-ref-systems';
if ($refresh) {
$cache = Cache::instance();
$cache->delete($cacheId);
self::$system_metadata = false;
}
if (self::$system_metadata === false) {
$latlong_systems = Kohana::config('sref_notations.lat_long_systems');
$cache = Cache::instance();
if ($cached = $cache->get($cacheId)) {
self::$system_metadata = $cached;
} else {
self::$system_metadata = array();
// fetch any systems that are just declared as srids, with no notation module required
foreach (Kohana::config('sref_notations.sref_notations') as $code => $title) {
self::$system_metadata["EPSG:{$code}"] = array('title' => $title, 'srid' => $code, 'treat_srid_as_x_y_metres' => !isset($latlong_systems[$code]));
}
// Now look for any modules which extend the sref systems available
foreach (Kohana::config('config.modules') as $path) {
$plugin = basename($path);
if (file_exists("{$path}/plugins/{$plugin}.php")) {
require_once "{$path}/plugins/{$plugin}.php";
if (function_exists($plugin . '_sref_systems')) {
$metadata = call_user_func($plugin . '_sref_systems');
self::$system_metadata = array_merge(self::$system_metadata, $metadata);
}
}
}
$cache->set($cacheId, self::$system_metadata);
}
}
return self::$system_metadata;
}
/**
* Postprocessing for building a geom from the list of grid squares to make an SQL based check easy
*/
function data_cleaner_without_polygon_data_cleaner_postprocess($id, $db)
{
$db->query('create temporary table geoms_without_polygon (geom geometry)');
try {
$r = $db->select('key, header_name')->from('verification_rule_data')->where('verification_rule_id', $id)->in('header_name', array('10km_GB', '10km_Ireland', '1km_GB', '1km_Ireland', '10km_CI', '1km_CI'))->get()->result();
$wktList = array();
foreach ($r as $gridSquare) {
switch ($gridSquare->header_name) {
case '10km_GB':
case '1km_GB':
$system = 'osgb';
break;
case '10km_Ireland':
case '1km_Ireland':
$system = 'osie';
break;
case '10km_CI':
case '1km_CI':
$system = 'utm30ed50';
break;
default:
continue;
// we don't know this grid square type - should not have come back from the query
}
$srid = kohana::config('sref_notations.internal_srid');
try {
$wktList[] = "(st_geomfromtext('" . spatial_ref::sref_to_internal_wkt($gridSquare->key, $system) . "', {$srid}))";
} catch (Exception $e) {
kohana::debug('alert', 'Did not import grid square ' . $gridSquare->key . " for rule {$id}");
error::log_error('Importing without polygon rules', $e);
}
}
if (!empty($wktList)) {
$db->query("insert into geoms_without_polygon values " . implode(',', $wktList));
}
$date = date("Ymd H:i:s");
$uid = $_SESSION['auth_user']->id;
$db->query("delete from verification_rule_data where verification_rule_id={$id} and header_name='geom'");
$db->query('insert into verification_rule_data (verification_rule_id, header_name, data_group, key, value, value_geom, created_on, created_by_id, updated_on, updated_by_id) ' . "select {$id}, 'geom', 1, 'geom', '-', st_union(geom), '{$date}', {$uid}, '{$date}', {$uid} from geoms_without_polygon");
$db->query('drop table geoms_without_polygon');
} catch (Exception $e) {
$db->query('drop table geoms_without_polygon');
throw $e;
}
}
/**
* Fills the temporary table called occdelta, which contains details of each proposed record to
* verify. This is only done when calling verify directly, since occdelta is prepared by the
* scheduled_tasks process when auto-checks are being run on the schedule.
*/
private function prepareOccdelta($db, $sample, $occurrences)
{
$website_id = $this->website_id;
$srid = kohana::config('sref_notations.internal_srid');
$last_sref = '';
$last_sref_system = '';
foreach ($occurrences as $occurrence) {
$record = array_merge($sample, $occurrence);
$survey_id = $record['sample:survey_id'];
$sref = $record['sample:entered_sref'];
$sref_system = $record['sample:entered_sref_system'];
$taxa_taxon_list_id = $record['occurrence:taxa_taxon_list_id'];
if (isset($record['sample:geom'])) {
$geom = $record['sample:geom'];
} else {
// avoid recalculating the geom if we don't have to as this is relatively expensive
if ($sref !== $last_sref || $sref_system !== $last_sref_system) {
$geom = spatial_ref::sref_to_internal_wkt($sref, $sref_system);
}
$last_sref = $sref;
$last_sref_system = $sref_system;
}
$date = $record['sample:date'];
$vd = vague_date::string_to_vague_date($date);
$date_start = $vd[0];
$date_end = $vd[1];
$date_type = $vd[2];
$db->query("insert into occdelta (website_id, survey_id, date_start, date_end, date_type, public_entered_sref, entered_sref_system, public_geom, taxa_taxon_list_id)\n values ({$website_id}, {$survey_id}, '{$date_start}', '{$date_end}', '{$date_type}', '{$sref}', '{$sref_system}', st_geomfromtext('{$geom}', {$srid}), {$taxa_taxon_list_id});");
}
// patch in some extra details about the taxon required for each cache entry
$db->query("update occdelta o set taxon_meaning_id=ttl.taxon_meaning_id, taxon=ttl.taxon, taxa_taxon_list_external_key=ttl.external_key " . "from list_taxa_taxon_lists ttl where ttl.id=o.taxa_taxon_list_id");
}
/**
* Define a form that is used to capture a set of predetermined values that apply to every record during an import.
*/
public function fixed_values_form()
{
$srefs = array();
$systems = spatial_ref::system_metadata();
foreach ($systems as $code => $metadata) {
$srefs[] = "{$code}:" . $metadata['title'];
}
return array('website_id' => array('display' => 'Website', 'description' => 'Select the website to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:website:id:title'), 'location:centroid_sref_system' => array('display' => 'Spatial Ref. System', 'description' => 'Select the spatial reference system used in this import file. Note, if you have a file with a mix of spatial reference systems then you need a ' . 'column in the import file which is mapped to the Location Spatial Reference System field containing the spatial reference system code.', 'datatype' => 'lookup', 'lookup_values' => implode(',', $srefs)));
}
/**
* The upgrade might involve a change to spatial system support in plugins, so now is a good
* time to refresh the spatial_systems metadata table.
*/
private function populate_spatial_systems_table()
{
$system_metadata = spatial_ref::system_metadata(true);
$existing = $this->db->select('id', 'code')->from('spatial_systems')->get()->result_array(false);
foreach ($system_metadata as $system => $metadata) {
$id = false;
foreach ($existing as $idx => $record) {
if ($record['code'] === $system) {
// record already exists
$id = $record['id'];
unset($existing[$idx]);
break;
}
}
$metadata['treat_srid_as_x_y_metres'] = isset($metadata['treat_srid_as_x_y_metres']) && $metadata['treat_srid_as_x_y_metres'] ? 't' : 'f';
if ($id) {
$this->db->update('spatial_systems', array_merge($metadata, array('code' => $system)), array('id' => $id));
} else {
$this->db->insert('spatial_systems', array_merge($metadata, array('code' => $system)));
}
}
// delete any that remain in $existing, since they are no longer supported
foreach ($existing as $idx => $record) {
$this->db->delete('spatial_systems', array('id' => $record['id']));
}
}
/**
* Define a form that is used to capture a set of predetermined values that apply to every record during an import.
*/
public function fixed_values_form()
{
$srefs = array();
$systems = spatial_ref::system_metadata();
foreach ($systems as $code => $metadata) {
$srefs[] = "{$code}:" . $metadata['title'];
}
return array('website_id' => array('display' => 'Website', 'description' => 'Select the website to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:website:id:title'), 'survey_id' => array('display' => 'Survey', 'description' => 'Select the survey to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:survey:id:title', 'linked_to' => 'website_id', 'linked_filter_field' => 'website_id'), 'sample:entered_sref_system' => array('display' => 'Spatial Ref. System', 'description' => 'Select the spatial reference system used in this import file. Note, if you have a file with a mix of spatial reference systems then you need a ' . 'column in the import file which is mapped to the Sample Spatial Reference System field containing the spatial reference system code.', 'datatype' => 'lookup', 'lookup_values' => implode(',', $srefs)), 'fkFilter:taxa_taxon_list:taxon_list_id' => array('display' => 'Species list', 'description' => 'Select the species checklist which will be used when attempting to match species names.', 'datatype' => 'lookup', 'population_call' => 'direct:taxon_list:id:title', 'linked_to' => 'website_id', 'linked_filter_field' => 'website_id'), 'occurrence:record_status' => array('display' => 'Record Status', 'description' => 'Select the initial status for imported records', 'datatype' => 'lookup', 'lookup_values' => 'C:Data entry complete/unverified,V:Verified,I:Data entry still in progress', 'default' => 'C'));
}
/**
* Define a form that is used to capture a set of predetermined values that apply to every record during an import.
*/
public function fixed_values_form()
{
$srefs = array();
$systems = spatial_ref::system_list();
foreach ($systems as $code => $title) {
$srefs[] = "{$code}:{$title}";
}
$retVal = array('website_id' => array('display' => 'Website', 'description' => 'Select the website to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:website:id:title', 'filterIncludesNulls' => true), 'survey_id' => array('display' => 'Survey', 'description' => 'Select the survey to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:survey:id:title', 'linked_to' => 'website_id', 'linked_filter_field' => 'website_id'), 'sample:entered_sref_system' => array('display' => 'Spatial Ref. System', 'description' => 'Select the spatial reference system used in this import file. Note, if you have a file with a mix of spatial reference systems then you need a ' . 'column in the import file which is mapped to the Sample Spatial Reference System field containing the spatial reference system code.', 'datatype' => 'lookup', 'lookup_values' => implode(',', $srefs)), 'occurrence:fkFilter:taxa_taxon_list:taxon_list_id' => array('display' => 'Species list', 'description' => 'Select the species checklist which will be used when attempting to match species names.', 'datatype' => 'lookup', 'population_call' => 'direct:taxon_list:id:title', 'linked_to' => 'website_id', 'linked_filter_field' => 'website_id', 'filterIncludesNulls' => true), 'occurrence:record_status' => array('display' => 'Record Status', 'description' => 'Select the initial status for imported species records', 'datatype' => 'lookup', 'lookup_values' => 'C:Data entry complete/unverified,V:Verified,I:Data entry still in progress', 'default' => 'C'));
if (self::_check_module_active('occurrence_associations')) {
$retVal['useAssociations'] = array('display' => 'Use Associations', 'description' => 'Select if this import uses occurrence associations: implies two species records uploaded for each entry in the file.', 'datatype' => 'checkbox');
}
// default off
$retVal['occurrence_association:fkFilter:association_type:termlist_id'] = array('display' => 'Term list for association types', 'description' => 'Select the term list which will be used to match the association types.', 'datatype' => 'lookup', 'population_call' => 'direct:termlist:id:title');
$retVal['occurrence_2:fkFilter:taxa_taxon_list:taxon_list_id'] = array('display' => 'Second Species list', 'description' => 'Select the species checklist which will be used when attempting to match second species names.', 'datatype' => 'lookup', 'population_call' => 'direct:taxon_list:id:title', 'linked_to' => 'website_id', 'linked_filter_field' => 'website_id', 'filterIncludesNulls' => true);
$retVal['occurrence_2:record_status'] = array('display' => 'Record Status', 'description' => 'Select the initial status for second imported species records', 'datatype' => 'lookup', 'lookup_values' => 'C:Data entry complete/unverified,V:Verified,I:Data entry still in progress', 'default' => 'C');
return $retVal;
}
<div id="details">
<?php
echo $metadata;
?>
<fieldset>
<legend>Location details</legend>
<input type="hidden" name="location:id" value="<?php
echo html::initial_value($values, 'location:id');
?>
" />
<?php
echo data_entry_helper::text_input(array('label' => 'Name', 'fieldname' => 'location:name', 'default' => html::initial_value($values, 'location:name'), 'validation' => 'required', 'disabled' => $disabled));
echo data_entry_helper::text_input(array('label' => 'Code', 'fieldname' => 'location:code', 'default' => html::initial_value($values, 'location:code'), 'disabled' => $disabled));
echo data_entry_helper::select(array('label' => 'Type', 'fieldname' => 'location:location_type_id', 'default' => html::initial_value($values, 'location:location_type_id'), 'lookupValues' => $other_data['type_terms'], 'blankText' => '<Please select>', 'disabled' => $disabled));
echo data_entry_helper::textarea(array('label' => 'Comment', 'fieldname' => 'location:comment', 'default' => html::initial_value($values, 'location:comment'), 'disabled' => $disabled));
echo data_entry_helper::sref_and_system(array('label' => 'Spatial Ref', 'fieldname' => 'location:centroid_sref', 'geomFieldname' => 'location:centroid_geom', 'default' => html::initial_value($values, 'location:centroid_sref'), 'defaultGeom' => html::initial_value($values, 'location:centroid_geom'), 'systems' => spatial_ref::system_list(), 'defaultSystem' => html::initial_value($values, 'location:centroid_sref_system'), 'class' => 'control-width-3', 'validation' => 'required', 'disabled' => $disabled));
?>
<input type="hidden" name="location:boundary_geom" id="imp-boundary-geom" value="<?php
echo $boundary_geom;
?>
"/>
<p class="instruct">Zoom the map in by double-clicking then single click on the location's centre to set the
spatial reference. The more you zoom in, the more accurate the reference will be.</p>
<?php
$readAuth = data_entry_helper::get_read_auth(0 - $_SESSION['auth_user']->id, kohana::config('indicia.private_key'));
echo map_helper::map_panel(array('readAuth' => $readAuth, 'presetLayers' => array('osm'), 'editLayer' => true, 'layers' => array(), 'initial_lat' => 52, 'initial_long' => -2, 'initial_zoom' => 7, 'width' => 870, 'height' => 400, 'initialFeatureWkt' => $centroid_geom, 'standardControls' => $disabled_input === 'YES' ? array('layerSwitcher', 'panZoomBar') : array('layerSwitcher', 'panZoomBar', 'drawPolygon', 'drawLine', 'modifyFeature'), 'allowPolygonRecording' => true));
echo data_entry_helper::autocomplete(array('label' => 'Parent location', 'fieldname' => 'location:parent_id', 'table' => 'location', 'captionField' => 'name', 'valueField' => 'id', 'extraParams' => $readAuth, 'default' => html::initial_value($values, 'location:parent_id'), 'defaultCaption' => html::initial_value($values, 'parent:name'), 'disabled' => $disabled));
if ($this->auth->logged_in('CoreAdmin')) {
//Only core admin can create public locations.
echo data_entry_helper::checkbox(array('label' => 'Available to all websites', 'fieldname' => 'location:public', 'default' => html::initial_value($values, 'location:public'), 'disabled' => $disabled));
}
/**
* Allow a service request to triangulate between 2 systems. GET parameters are:
* from_sref
* from_system
* to_system
* to_precision (optional)
*/
public function convert_sref()
{
try {
$wkt = spatial_ref::sref_to_internal_wkt($_GET['from_sref'], $_GET['from_system']);
if (array_key_exists('precision', $_GET)) {
$precision = $_GET['precision'];
} else {
$precision = null;
}
if (array_key_exists('metresAccuracy', $_GET)) {
$metresAccuracy = $_GET['metresAccuracy'];
} else {
$metresAccuracy = null;
}
echo spatial_ref::internal_wkt_to_sref($wkt, $_GET['to_system'], $precision, null, $metresAccuracy);
} catch (Exception $e) {
$this->handle_error($e);
}
}
/**
* Define a form that is used to capture a set of predetermined values that apply to every record during an import.
*/
public function fixed_values_form()
{
$srefs = array();
$systems = spatial_ref::system_list();
foreach ($systems as $code => $title) {
$srefs[] = "{$code}:{$title}";
}
$sample_methods = array(":Defined in file");
$terms = $this->db->select('id, term')->from('list_termlists_terms')->where('termlist_external_key', 'indicia:sample_methods')->orderby('term', 'asc')->get()->result();
foreach ($terms as $term) {
$sample_methods[] = $term->id . ":" . $term->term;
}
$location_types = array(":No filter");
$terms = $this->db->select('id, term')->from('list_termlists_terms')->where('termlist_external_key', 'indicia:location_types')->orderby('term', 'asc')->get()->result();
foreach ($terms as $term) {
$location_types[] = $term->id . ':' . $term->term;
}
return array('website_id' => array('display' => 'Website', 'description' => 'Select the website to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:website:id:title'), 'survey_id' => array('display' => 'Survey', 'description' => 'Select the survey to import records into.', 'datatype' => 'lookup', 'population_call' => 'direct:survey:id:title', 'linked_to' => 'website_id', 'linked_filter_field' => 'website_id'), 'sample:entered_sref_system' => array('display' => 'Spatial Ref. System', 'description' => 'Select the spatial reference system used in this import file. Note, if you have a file with a mix of spatial reference systems then you need a ' . 'column in the import file which is mapped to the Sample Spatial Reference System field containing the spatial reference system code.', 'datatype' => 'lookup', 'lookup_values' => implode(',', $srefs)), 'sample:sample_method_id' => array('display' => 'Sample Method', 'description' => 'Select the sample method used for records in this import file. Note, if you have a file with a mix of sample methods then you need a ' . 'column in the import file which is mapped to the Sample Sample Method field, containing the sample method.', 'datatype' => 'lookup', 'lookup_values' => implode(',', $sample_methods)), 'fkFilter:location:location_type_id' => array('display' => 'Location Type', 'description' => 'If this import file includes samples which reference locations records, you can restrict the type of locations looked ' . 'up by setting this location type. It is not currently possible to use a column in the file to do this on a sample by sample basis.', 'datatype' => 'lookup', 'lookup_values' => implode(',', $location_types)));
}
/**
* Before submission, map vague dates to their underlying database fields.
*/
protected function preSubmit()
{
if (array_key_exists('date', $this->submission['fields'])) {
$vague_date = vague_date::string_to_vague_date($this->submission['fields']['date']['value']);
$this->submission['fields']['date_start']['value'] = $vague_date[0];
$this->submission['fields']['date_end']['value'] = $vague_date[1];
$this->submission['fields']['date_type']['value'] = $vague_date[2];
}
// Allow a sample to be submitted with a spatial ref and system but no Geom. If so we
// can work out the Geom
if (array_key_exists('entered_sref', $this->submission['fields']) && array_key_exists('entered_sref_system', $this->submission['fields']) && !(array_key_exists('geom', $this->submission['fields']) && $this->submission['fields']['geom']['value']) && $this->submission['fields']['entered_sref']['value'] && $this->submission['fields']['entered_sref_system']['value']) {
try {
$this->submission['fields']['geom']['value'] = spatial_ref::sref_to_internal_wkt($this->submission['fields']['entered_sref']['value'], $this->submission['fields']['entered_sref_system']['value']);
} catch (Exception $e) {
$this->errors['entered_sref'] = $e->getMessage();
}
}
return parent::presubmit();
}
/**
* Validate a spatial reference is a valid value for the system
*
* @param string sref
* @param string system
* @return boolean
* $todo Should we consider caching the system?
*/
public static function sref($sref, $system)
{
$system = $system[0];
return spatial_ref::is_valid($sref, $system);
}