Rich type representation in Attributes (#700)

* Replace info with with Attributes close #607
Attributes message is moved to metadata.proto
info field was replaced for messages that had it with the field 'attributes'
renamed the 'vals' field to 'attr'
added to the available types in an attribute value message ('int32', 'int64', 'bool', 'double', 'null')
Added attributes to the Variant Annotation Set message and RNA expression messages.

* Remove references to info and update JSON example
Remove unused package

* Add attributes to reference/sets
Close #537

* Bump reused tag number
Remove unused import

* Merge for genotypes list

* Add maps and lists as possible attributes

* Add analysis and program, reorder

* Move messages to common
Merge assay_metadata in order to support as attributes.

* Clean up imports
Add tests that show basic attributes examples

* Update compiled proto
Remove assay metadata from tests

doc/source/api/assaymetadata.rst

@@ -28,7 +28,7 @@ Attribute             Notes
 *description*         * additional, unstructured information about this Experiment
 *created*             * the time the record was created, in ISO8601
 *updated*             * the time the record was updated, in ISO8601
-*info*                * additional, structured information
+*attributes*          * additional, structured information
 ===================== ==========================================================
 
 .. _assaymetadata_analysis:
@@ -55,5 +55,5 @@ Attribute             Notes
 *description*         * additional, unstructured information about this Analysis
 *created*             * the time the record was created, in ISO8601
 *updated*             * the time the record was updated, in ISO8601
-*info*                * additional, structured information
+*attributes*          * additional, structured information
 ===================== ==========================================================

doc/source/api/biometadata.rst

@@ -41,7 +41,7 @@ Attribute             Notes
 *individualId*        * the *id* of the *Individual* this Biosample was derived from
 *created*             * the time the record was created, in ISO8601
 *updated*             * the time the record was updated, in ISO8601
-*info*                * additional, structured information
+*attributes*          * additional, structured information
 ===================== ==========================================================
 
 .. _biometadata_Individual:
@@ -73,5 +73,5 @@ Attribute             Notes
 *sex*                 * OntologyTerm for the genetic sex of this individual.
 *created*             * the time the record was created, in ISO8601
 *updated*             * the time the record was updated, in ISO8601
-*info*                * additional, structured information
+*attributes*          * additional, structured information
 ===================== ==========================================================

doc/source/appendix/json_intro.rst

@@ -31,7 +31,7 @@ For example, here is the schema definition for Variants (with comments removed):
     int64 end = 8;
     string reference_bases = 9;
     repeated string alternate_bases = 10;
-    map<string, google.protobuf.ListValue> info = 11;
+    Attributes attributes = 13;
     repeated Call calls = 12;
   }
 
@@ -53,10 +53,21 @@ Here is a serialized variant in JSON. It's a bit of an edge case in some respect
           "C",
           "CTATCTT"
       ],
-      "info": {
-          "variantfacts": ["is_interesting", "is_long"],
-          "numberOfPapers": ["11"]
-      },
+      "attributes": {
+          "attr": {
+              "numberOfPapers": {
+                  "values": [
+                      {"int32Value": 11}
+                  ]
+              },
+              "variantFacts": {
+                  "values": [
+                      {"stringValue": "is_long"},
+                      {"stringValue": "is_interesting"}
+                  ]
+              }
+          }
+      }
   }
 
 Things to notice: