Merge 3dedd2b into 234dff7

db/patches/2410_activity_v2_deprecations.sql

@@ -0,0 +1,21 @@
+/* Changes to create a modern version of the Activity */
+
+COMMENT ON COLUMN activity.duration
+  IS 'DEPRECATED - use activity_duration to document the time taken to perform the activity.';
+COMMENT ON COLUMN activity.data_usage
+  IS 'DEPRECATED - A description of the way in which input data were used for this activity.';
+COMMENT ON COLUMN activity.notes
+  IS 'DEPRECATED - Other information about this activity which might be useful for traceability or reproducability.';
+
+COMMENT ON COLUMN activity.output_artifacts
+  IS 'Deprecated outside of NCO assessment activities. The final output filenames from the process.';
+
+COMMENT ON COLUMN activity.methodology
+  IS 'The process of creating the resulting object from the input, in the author’s own words and in such a way that another expert partycould reproduce the output.';
+COMMENT ON COLUMN activity.visualization_software
+  IS 'Primary visualization software (with version) used.';
+
+COMMENT ON COLUMN activity.start_time
+  IS 'Time bounds used to restrict the input object. Optional, depending on applicability. If equal to end_time, indicates a temporal moment.';
+COMMENT ON COLUMN activity.end_time
+  IS 'Time bounds used to restrict the input object. Optional, depending on applicability. If equal to start_time, indicates a temporal moment.';

db/patches/2420_activity_v2_new_columns.sql

@@ -0,0 +1,30 @@
+/* New activity fields */
+
+ALTER table activity ADD COLUMN activity_duration interval;
+ALTER table activity ADD COLUMN source_access_date date;
+ALTER table activity ADD COLUMN interim_artifacts text;
+ALTER table activity ADD COLUMN source_modifications text;
+ALTER table activity ADD COLUMN modified_source_location text;
+ALTER table activity ADD COLUMN visualization_methodology text;
+ALTER table activity ADD COLUMN methodology_citation text;
+ALTER table activity ADD COLUMN methodology_contact text;
+ALTER table activity ADD COLUMN database_variables text;
+
+COMMENT ON COLUMN activity.activity_duration
+  IS 'Captures the time taken in the process to get from the source object to the final one.';
+COMMENT ON COLUMN activity.source_access_date
+  IS 'The date the parent resource was accessed.';
+COMMENT ON COLUMN activity.interim_artifacts
+  IS 'Deprecated outside of NCO assessment activities. The names of files created along the way to create the final product.';
+COMMENT ON COLUMN activity.source_modifications
+  IS 'A written description of modifications done to the source object.';
+COMMENT ON COLUMN activity.modified_source_location
+  IS 'The location of the modified source, if available.';
+COMMENT ON COLUMN activity.visualization_methodology
+  IS 'The process of creating the visual portion of the output object, if any and if distinguished from the main methodology.';
+COMMENT ON COLUMN activity.methodology_citation
+  IS 'The citation to the methodology, if it has been published.';
+COMMENT ON COLUMN activity.methodology_contact
+  IS 'The point of contact for the methodology, if any.';
+COMMENT ON COLUMN activity.database_variables
+  IS 'A list of Dataset Variables applied in this activity.';

db/patches/2430_activity_v2_spatial_extent.sql

@@ -0,0 +1,4 @@
+/* New activity field */
+
+ALTER TABLE activity ADD COLUMN spatial_extent json;
+COMMENT ON COLUMN activity.spatial_extent IS 'Spatial bounds used to restrict the input object. GeoJSON. Optional, depending on applicability.';

lib/Tuba.pm

@@ -258,7 +258,7 @@ sub startup {
                            )
                          ]x;
         for my $format (@supported_formats) {
-                $resource->get("(*$identifier).$format" => \@restrict => { format => $format } )
+                $resource->get("<*$identifier>.$format" => \@restrict => { format => $format } )
                          ->over(not_match => { $identifier => $reserved })
                          ->to('#show')->name("_show_${name}_$format");
         }

lib/Tuba/Activity.pm

@@ -7,6 +7,7 @@ Tuba::Activity : Controller class for books
 package Tuba::Activity;
 use Mojo::Base qw/Tuba::Controller/;
 use Tuba::DB::Objects qw/-nicknames/;
+use JSON::XS;
 
 sub list {
     my $c = shift;
@@ -19,6 +20,22 @@ sub show {
     $c->SUPER::show(@_);
 }
 
+sub create {
+    my $c = shift;
+    my $spatial_extent = $c->_spatial_extent;
+    my $error = _check_valid_geojson($spatial_extent) if $spatial_extent;
+    return $c->create_error($error) if $error;
+    $c->SUPER::create(@_);
+}
+
+sub update {
+    my $c = shift;
+    my $spatial_extent = $c->_spatial_extent;
+    my $error = _check_valid_geojson($spatial_extent) if $spatial_extent;
+    return $c->update_error($error) if $error;
+    $c->SUPER::update(@_);
+}
+
 sub make_tree_for_show {
     my $c = shift;
     my $obj = shift;
@@ -54,8 +71,30 @@ sub normalize_form_parameter {
 
 sub _default_order {
     my $c = shift;
-    return ( $c->SUPER::_default_order(), qw/methodology_publication_id methodology_contributor_id/ );
-
+    return ( qw/
+        identifier
+        methodology
+        visualization_methodology
+        methodology_citation
+        methodology_contact
+        activity_duration
+        source_access_date
+        source_modifications
+        modified_source_location
+        interim_artifacts
+        output_artifacts
+        computing_environment
+        software
+        visualization_software
+        start_time
+        end_time
+        database_variables
+        spatial_extent
+        data_usage
+        notes
+        methodology_publication_id
+        methodology_contributor_id/
+    );
 }
 
 sub update_rel_form {
@@ -109,5 +148,48 @@ sub update_rel {
     );
 }
 
+sub _spatial_extent {
+    my $c = shift;
+    return $c->param('spatial_extent') if $c->param('spatial_extent');
+
+    my $json = $c->req->json;
+    return unless $json;
+    return $json->{spatial_extent};
+
+}
+
+sub _check_valid_geojson {
+    my $spatial_param = shift;
+    my $valid_geojson_types = {
+        Point              => 1,
+        MultiPoint         => 1,
+        LineString         => 1,
+        MultiLineString    => 1,
+        Polygon            => 1,
+        MultiPolygon       => 1,
+        GeometryCollection => 1,
+        Feature            => 1,
+        FeatureCollection  => 1,
+    };
+    # parse valid JSON
+    my $error;
+    my $geojson = eval { JSON::XS->new->decode($spatial_param); };
+    if ($@ || (ref $geojson ne 'HASH')) {
+        $error = "Invalid geoJSON: could not parse json :".($@ || ref $geojson);
+    }
+    # check the field type exists
+    if ( !$error && $geojson->{'type'} ) {
+        # check the type value is valid
+        unless ( $valid_geojson_types->{ $geojson->{'type'} } ) {
+            $error = "Invalid geoJSON: Bad type '$geojson->{type}' not one of: " . join(', ', keys %$valid_geojson_types);
+        }
+    }
+    else {
+        $error = "Invalid geoJSON: missing type field" unless $error;
+    }
+
+    return $error;
+}
+
 1;
 

lib/Tuba/DB/Mixin/Object/Activity.pm

@@ -1,6 +1,7 @@
 package Tuba::DB::Object::Activity;
 # Tuba::DB::Mixin::Object::Activity
 use Tuba::Util qw[new_uuid];
+use JSON::XS;
 use strict;
 
 __PACKAGE__->meta->primary_key_generator(sub {
@@ -12,5 +13,17 @@ sub stringify {
     return $s->identifier;
 }
 
+sub bounding_box {
+    my $s = shift;
+
+    my $box;
+    if ( $s->spatial_extent ) {
+        my $j = JSON::XS->new->decode($s->spatial_extent);
+        $box = $j->{'bbox'} if $j->{'bbox'};
+    }
+
+    return $box;
+};
+
 1;
 

lib/Tuba/Generic.pm

@@ -39,7 +39,8 @@ sub update {
             $generic->delete_attr( { del_attr => $params->{delete_pub_attr}, audit_user => $c->user, audit_note => "Setting attributes" });
             $c->redirect_without_error('update_form');
         }
-        elsif ( exists $params->{new_attr_key} || /^attribute/ ~~ %$params ) {
+        # find any new attr keys or attribute_* keys
+        elsif ( exists $params->{new_attr_key} || grep { /^attribute/ } keys %$params ) {
             my $new_attributes = _collect_attributes($params);
             $generic->set_attr( { new_attrs => $new_attributes, audit_user => $c->user, audit_note => "Setting attributes" });
             $c->redirect_without_error('update_form');