Tripal 4 tripal collections YAML file and Sequence Length and Checksu…

…m fields in : tv4g1-1509-sequence-fields
pdtouch · Oct 18, 2023 · cef5845 · cef5845
1 parent 9d97811
commit cef5845
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Showing 3 changed files with 153 additions and 22 deletions.
diff --git a/tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml b/tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml
@@ -1069,8 +1069,8 @@ fields:
 
     -   name: mrna_sequence
         content_type: mRNA
-        label: Sequence
-        type: chado_text_type
+        label: Sequence Residues
+        type: chado_sequence_default
         description: One or more molecular sequences, possibly with associated annotation.
         cardinality: 1
         required: false
@@ -1096,7 +1096,7 @@ fields:
     -   name: mrna_sequence_length
         content_type: mRNA
         label: Sequence Length
-        type: chado_integer_type
+        type: chado_sequence_length_default
         description: The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.
         cardinality: 1
         required: false
@@ -1119,6 +1119,32 @@ fields:
               region: content
               weight: 25
 
+    -   name: mrna_sequence_md5_checksum
+        content_type: mRNA
+        label: Sequence MD5 Checksum
+        type: chado_sequence_checksum_default
+        description: The 32-character checksum of the sequence, calculated using the MD5 algorithm.
+        cardinality: 1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                base_column: md5checksum
+        settings:
+            termIdSpace: data
+            termAccession: "2190"
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 30
+          form:
+            default:
+              region: content
+              weight: 30
+
     -   name: mrna_organism
         content_type: mRNA
         label: Organism
@@ -2168,7 +2194,7 @@ fields:
 
     -   name: qtl_unique_name
         content_type: QTL
-        label: Uniquen Name
+        label: Unique Name
         type: chado_text_type
         description: A name that uniquely identifies the QTL within the organism.
         cardinality: 1
@@ -2194,8 +2220,8 @@ fields:
 
     -   name: qtl_sequence
         content_type: QTL
-        label: Sequence
-        type: chado_text_type
+        label: Sequence Residues
+        type: chado_sequence_default
         description: One or more molecular sequences, possibly with associated annotation.
         cardinality: 1
         required: false
@@ -2221,7 +2247,7 @@ fields:
     -   name: qtl_sequence_length
         content_type: QTL
         label: Sequence Length
-        type: chado_integer_type
+        type: chado_sequence_length_default
         description: The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.
         cardinality: 1
         required: false
@@ -2244,6 +2270,33 @@ fields:
               region: content
               weight: 25
 
+    -   name: qtl_md5_checksum
+        content_type: QTL
+        label: Sequence MD5 Checksum
+        type: chado_sequence_checksum_default
+        description: The 32-character checksum of the sequence, calculated using the MD5 algorithm.
+        cardinality: 1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                base_column: md5checksum
+        settings:
+            termIdSpace: data
+            termAccession: "2190"
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 30
+          form:
+            default:
+              region: content
+              weight: 30
+
+
     -   name: qtl_organism
         content_type: QTL
         label: Organism
@@ -2379,7 +2432,7 @@ fields:
               region: content
               weight: 10
 
-    -   name: sequence_variant_uniquene_name
+    -   name: sequence_variant_unique_name
         content_type: sequence_variant
         label: Unique Name
         type: chado_text_type
@@ -2407,8 +2460,8 @@ fields:
 
     -   name: sequence_variant_sequence
         content_type: sequence_variant
-        label: Sequence
-        type: chado_text_type
+        label: Sequence Residues
+        type: chado_sequence_default
         description: One or more molecular sequences, possibly with associated annotation.
         cardinality: 1
         required: false
@@ -2434,7 +2487,7 @@ fields:
     -   name: sequence_variant_sequence_length
         content_type: sequence_variant
         label: Sequence Length
-        type: chado_integer_type
+        type: chado_sequence_length_default
         description: The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.
         cardinality: 1
         required: false
@@ -2457,6 +2510,32 @@ fields:
               region: content
               weight: 25
 
+    -   name: sequence_variant_md5_checksum
+        content_type: sequence_variant
+        label: Sequence MD5 Checksum
+        type: chado_sequence_checksum_default
+        description: The 32-character checksum of the sequence, calculated using the MD5 algorithm.
+        cardinality: 1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                base_column: md5checksum
+        settings:
+            termIdSpace: data
+            termAccession: "2190"
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 30
+          form:
+            default:
+              region: content
+              weight: 30
+
     -   name: sequence_variant_organism
         content_type: sequence_variant
         label: Organism
@@ -2620,8 +2699,8 @@ fields:
 
     -   name: genetic_marker_sequence
         content_type: genetic_marker
-        label: Sequence
-        type: chado_text_type
+        label: Sequence Residues
+        type: chado_sequence_default
         description: One or more molecular sequences, possibly with associated annotation.
         cardinality: 1
         required: false
@@ -2647,7 +2726,7 @@ fields:
     -   name: genetic_marker_sequence_length
         content_type: genetic_marker
         label: Sequence Length
-        type: chado_integer_type
+        type: chado_sequence_length_default
         description: The size (length) of a sequence, subsequence or region in a sequence,or range(s) of lengths.
         cardinality: 1
         required: false
@@ -2670,6 +2749,32 @@ fields:
               region: content
               weight: 25
 
+    -   name: genetic_marker_md5_checksum
+        content_type: genetic_marker
+        label: Sequence MD5 Checksum
+        type: chado_sequence_checksum_default
+        description: The 32-character checksum of the sequence, calculated using the MD5 algorithm.
+        cardinality: 1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                base_column: md5checksum
+        settings:
+            termIdSpace: data
+            termAccession: "2190"
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 30
+          form:
+            default:
+              region: content
+              weight: 30
+
     -   name: genetic_marker_organism
         content_type: genetic_marker
         label: Organism
@@ -2807,7 +2912,7 @@ fields:
 
     -   name: phenotypic_marker_unique_name
         content_type: phenotypic_marker
-        label: Uniquen Name
+        label: Unique Name
         type: chado_text_type
         description: A name that uniquely identifies the heritable phenotypic marker within the organism.
         cardinality: 1
@@ -2833,8 +2938,8 @@ fields:
 
     -   name: phenotypic_marker_sequence
         content_type: phenotypic_marker
-        label: Sequence
-        type: chado_text_type
+        label: Sequence Residues
+        type: chado_sequence_default
         description: One or more molecular sequences, possibly with associated annotation.
         cardinality: 1
         required: false
@@ -2857,10 +2962,10 @@ fields:
               region: content
               weight: 20
 
-    -   name: phenotypic_marker_seqlen
+    -   name: phenotypic_marker_length
         content_type: phenotypic_marker
         label: Sequence Length
-        type: chado_integer_type
+        type: chado_sequence_length_default
         description: The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths.
         cardinality: 1
         required: false
@@ -2883,6 +2988,32 @@ fields:
               region: content
               weight: 25
 
+    -   name: phenotypic_marker_md5_checksum
+        content_type: phenotypic_marker
+        label: Sequence MD5 Checksum
+        type: chado_sequence_checksum_default
+        description: The 32-character checksum of the sequence, calculated using the MD5 algorithm.
+        cardinality: 1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: feature
+                base_column: md5checksum
+        settings:
+            termIdSpace: data
+            termAccession: "2190"
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 30
+          form:
+            default:
+              region: content
+              weight: 30
+
     -   name: phenotypic_marker_organism
         content_type: phenotypic_marker
         label: Organism

diff --git a/tripal_chado/src/Plugin/Field/FieldType/ChadoSequenceChecksumDefault.php b/tripal_chado/src/Plugin/Field/FieldType/ChadoSequenceChecksumDefault.php
@@ -79,12 +79,12 @@ public static function tripalTypes($field_definition) {
         'chado_column' => 'feature_id'
     ]);
     $properties[] =  new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'seqlen', $seqlen_term, [
-      'action' => 'store',
+      'action' => 'read_value',
       'chado_column' => 'seqlen',
       'chado_table' => 'feature'
     ]);
     $properties[] =  new ChadoBpCharStoragePropertyType($entity_type_id, self::$id, 'md5checksum', $md5checksum_term, $md5_checksum_len, [
-      'action' => 'store',
+      'action' => 'read_value',
       'chado_column' => 'md5checksum',
       'chado_table' => 'feature'
     ]);

diff --git a/tripal_chado/src/Plugin/Field/FieldType/ChadoSequenceLengthDefault.php b/tripal_chado/src/Plugin/Field/FieldType/ChadoSequenceLengthDefault.php
@@ -73,7 +73,7 @@ public static function tripalTypes($field_definition) {
         'chado_column' => 'feature_id'
     ]);
     $properties[] =  new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'seqlen', $seqlen_term, [
-      'action' => 'store',
+      'action' => 'read_value',
       'chado_column' => 'seqlen',
       'chado_table' => 'feature'
     ]);