Update schemas (#167)

* Added astrocyte, vasculature node types
* Updated datatypes.yaml, node.yaml, edge.yaml
* Removed unused types.json
* added schemas for enfoot, glialglial, neuromodulatory, synapse_astrocyte edge types
* Added missing properties
* Removed restrictions on additional properties
* Remove restriction on the number of populations/file
* Do not restrict the (u)int type used in indices

bluepysnap/schemas/circuit.yaml

@@ -2,7 +2,6 @@ title: SONATA Circuit Config
 description: schema for BBP SONATA circuit config
 required:
   - networks
-additionalProperties: false
 properties:
   version:
     type: number
@@ -17,7 +16,6 @@ properties:
     required:
       - nodes
       - edges
-    additionalProperties: false
     properties:
       nodes:
         $ref: "#/$defs/network_array"
@@ -37,7 +35,6 @@ $defs:
         type: string
       alternate_morphologies:
         type: object
-        additionalProperties: false
         properties:
           h5v1:
             type: string
@@ -60,7 +57,6 @@ $defs:
       type: object
       required:
         - populations
-      additionalProperties: false
       properties:
         edges_file:
           type: string

bluepysnap/schemas/definitions/datatypes.yaml

@@ -12,23 +12,50 @@ $typedefs:
   index_or_utf8:
       anyOf:
         - $ref: "#/$typedefs/utf8"
+        - $ref: "#/$typedefs/int8"
+        - $ref: "#/$typedefs/int16"
+        - $ref: "#/$typedefs/int32"
+        - $ref: "#/$typedefs/int64"
+        - $ref: "#/$typedefs/uint8"
+        - $ref: "#/$typedefs/uint16"
         - $ref: "#/$typedefs/uint32"
+        - $ref: "#/$typedefs/uint64"
 
   float32:
     $ref: "#/$typedefs/general"
     properties:
       datatype:
         const: float32
+  int8:
+    $ref: "#/$typedefs/general"
+    properties:
+      datatype:
+        const: int8
   int16:
     $ref: "#/$typedefs/general"
     properties:
       datatype:
         const: int16
+  int32:
+    $ref: "#/$typedefs/general"
+    properties:
+      datatype:
+        const: int32
   int64:
     $ref: "#/$typedefs/general"
     properties:
       datatype:
         const: int64
+  uint8:
+    $ref: "#/$typedefs/general"
+    properties:
+      datatype:
+        const: uint8
+  uint16:
+    $ref: "#/$typedefs/general"
+    properties:
+      datatype:
+        const: uint16
   uint32:
     $ref: "#/$typedefs/general"
     properties:

bluepysnap/schemas/definitions/edge.yaml

@@ -3,7 +3,6 @@ description: schema definitions that apply to all edge files
 $edge_file_defs:
   indices_id_mapping:
     type: object
-    additionalProperties: false
     properties:
       node_id_to_ranges:
         $ref: "#/$typedefs/uint64"
@@ -28,7 +27,6 @@ $edge_file_defs:
       - edges
     properties:
       edges:
-        maxProperties: 1
         minProperties: 1
         type: object
         patternProperties:
@@ -40,11 +38,9 @@ $edge_file_defs:
               - edge_type_id
               - source_node_id
               - target_node_id
-            additionalProperties: false
             properties:
               indices:  # Note that this is optional
                 type: object
-                additionalProperties: false
                 properties:
                   target_to_source:
                     $ref: "#/$edge_file_defs/indices_id_mapping"
@@ -61,7 +57,6 @@ $edge_file_defs:
 
               "0":
                 type: object
-                # additionalProperties: false
                 patternProperties:
                   # For docs, these would likely need to be changed actual property names.
                   # Best probably combine each to a definition like "#/edge_field_defs/..._xyz"
@@ -72,38 +67,68 @@ $edge_file_defs:
                     $ref: "#/$typedefs/uint32"
                   ^(a|e)fferent_(section|segment)_(pos|offset)$:
                     $ref: "#/$typedefs/float32"
+                  ^astrocyte_center_(x|y|z)$:
+                    $ref: "#/$typedefs/float32"
+                  ^astrocyte_(section|segment)_id$:
+                    $ref: "#/$typedefs/uint32"
+                  ^endfoot_compartment_(length|diameter|perimeter)$:
+                    $ref: "#/$typedefs/float32"
+                  ^endfoot_surface_(x|y|z)$:
+                    $ref: "#/$typedefs/float32"
+                  ^neuromod_(dtc|strength)$:
+                    $ref: "#/$typedefs/float32"
+                  ^vasculature_(section|segment)_id$:
+                    $ref: "#/$typedefs/uint32"
                 properties:
+                  astrocyte_section_pos:
+                    $ref: "#/$typedefs/float32"
+                  astrocyte_segment_offset:
+                    $ref: "#/$typedefs/float32"
                   conductance:
                     $ref: "#/$typedefs/float32"
+                  conductance_scale_factor:
+                    $ref: "#/$typedefs/float32"
                   decay_time:
                     $ref: "#/$typedefs/float32"
+                  delay:
+                    $ref: "#/$typedefs/float32"
                   depression_time:
                     $ref: "#/$typedefs/float32"
+                  endfoot_id:
+                    $ref: "#/$typedefs/uint64"
                   facilitation_time:
                     $ref: "#/$typedefs/float32"
-                  u_syn:
-                    $ref: "#/$typedefs/float32"
                   n_rrp_vesicles:
                     $ref: "#/$typedefs/uint32"
                   spine_length:
                     $ref: "#/$typedefs/float32"
-                  syn_type_id:
-                    $ref: "#/$typedefs/uint32"
-                  delay:
-                    $ref: "#/$typedefs/float32"
-                  # Optional properties
                   spine_morphology:
-                    $ref: "#/$typedefs/uint32"
+                    $ref: "#/$typedefs/index_or_utf8"
                   spine_psd_id:
                     $ref: "#/$typedefs/int64"
                   spine_sharding_id:
                     $ref: "#/$typedefs/int64"
-                  conductance_scale_factor:
-                    $ref: "#/$typedefs/float32"
+                  syn_type_id:
+                    $ref: "#/$typedefs/uint32"
+                  synapse_id:
+                    $ref: "#/$typedefs/uint64"
+                    required:
+                      - attributes
+                    properties:
+                      attributes:
+                        type: object
+                        required:
+                          - edge_population
+                        properties:
+                          edge_population:
+                            type: string
                   u_hill_coefficient:
                     $ref: "#/$typedefs/float32"
+                  u_syn:
+                    $ref: "#/$typedefs/float32"
                   "@library":
                     type: object
-                    properties:
-                      spine_morphology:
+                    patternProperties:
+                      # "" is used as a wild card for field name
+                      "":
                         $ref: "#/$typedefs/utf8"

bluepysnap/schemas/definitions/node.yaml

@@ -6,7 +6,6 @@ $node_file_defs:
       - nodes
     properties:
       nodes:
-        maxProperties: 1
         minProperties: 1
         type: object
         patternProperties:
@@ -16,65 +15,75 @@ $node_file_defs:
             required:
               - "0"
               - node_type_id
-            additionalProperties: false
             properties:
               node_type_id:
                 $ref: "#/$typedefs/int64"
               "0":
-                #additionalProperties: false
                 type: object
                 properties:
-                  mtype:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  morphology:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  model_template:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  model_type:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  morph_class:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  etype:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  mtype:
-                    $ref: "#/$typedefs/index_or_utf8"
-                  synapse_class:
-                    $ref: "#/$typedefs/index_or_utf8"
                   dynamics_params:
                     type: object
                     required:
                       - threshold_current
                       - holding_current
-                    additionalProperties: false
                     properties:
-                      threshold_current:
+                      AIS_scaler:
                         $ref: "#/$typedefs/float32"
                       holding_current:
                         $ref: "#/$typedefs/float32"
+                      input_resistance:
+                        $ref: "#/$typedefs/float32"
+                      threshold_current:
+                        $ref: "#/$typedefs/float32"
+                  etype:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  exc-mini_frequency:
+                    $ref: "#/$typedefs/float32"
+                  hemisphere:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  inh-mini_frequency:
+                    $ref: "#/$typedefs/float32"
                   layer:
                     $ref: "#/$typedefs/index_or_utf8"
                   me_combo:
                     $ref: "#/$typedefs/index_or_utf8"
-                  region:
+                  model_template:
                     $ref: "#/$typedefs/index_or_utf8"
-                  exc-mini_frequency:
-                    $ref: "#/$typedefs/float32"
-                  inh-mini_frequency:
+                  model_type:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  morphology:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  morph_class:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  mtype:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  radius:
                     $ref: "#/$typedefs/float32"
-                  hemisphere:
+                  region:
                     $ref: "#/$typedefs/index_or_utf8"
+                  section_id:
+                    $ref: "#/$typedefs/uint32"
+                  segment_id:
+                    $ref: "#/$typedefs/uint32"
+                  synapse_class:
+                    $ref: "#/$typedefs/index_or_utf8"
+                  type:
+                    $ref: "#/$typedefs/int32"
                   "@library":
                     type: object
                     patternProperties:
                       # "" is used as a wild card for field name
                       "":
                         $ref: "#/$typedefs/utf8"
                 patternProperties:
-                  ^(x|y|z)$:
+                  ^(start_|end_)?(x|y|z)$:
+                    $ref: "#/$typedefs/float32"
+                  ^(start|end)_diameter$:
                     $ref: "#/$typedefs/float32"
+                  ^(start|end)_node$:
+                    $ref: "#/$typedefs/uint64"
                   ^rotation_angle_(x|y|z)axis$:
                     $ref: "#/$typedefs/float32"
-                  # Optional
                   ^orientation_(w|x|y|z)$:
                     $ref: "#/$typedefs/float32"
 

bluepysnap/schemas/edge/endfoot.yaml

@@ -0,0 +1,21 @@
+title: Edges - endfoot
+description: schema for endfoot edge types
+allOf: [{ $ref: "#/$edge_file_defs/edges_file_root" }]
+properties:
+  edges:
+    patternProperties:
+      # "" is used as a wild card for population name
+      "":
+        properties:
+          "0":
+            required:
+              - endfoot_id
+              - endfoot_surface_x
+              - endfoot_surface_y
+              - endfoot_surface_z
+              - vasculature_section_id
+              - vasculature_segment_id
+              - astrocyte_section_id
+              - endfoot_compartment_length
+              - endfoot_compartment_diameter
+              - endfoot_compartment_perimeter

bluepysnap/schemas/edge/glialglial.yaml

@@ -0,0 +1,34 @@
+title: Edges - glialglial
+description: schema for glialglial edge types
+allOf: [{ $ref: "#/$edge_file_defs/edges_file_root" }]
+properties:
+  edges:
+    patternProperties:
+      # "" is used as a wild card for population name
+      "":
+        properties:
+          "0":
+            required:
+              - afferent_center_x
+              - afferent_center_y
+              - afferent_center_z
+              - afferent_surface_x
+              - afferent_surface_y
+              - afferent_surface_z
+              - afferent_section_id
+              - afferent_section_pos
+              - afferent_section_type
+              - afferent_segment_id
+              - afferent_segment_offset
+              - efferent_center_x
+              - efferent_center_y
+              - efferent_center_z
+              - efferent_surface_x
+              - efferent_surface_y
+              - efferent_surface_z
+              - efferent_section_id
+              - efferent_section_pos
+              - efferent_section_type
+              - efferent_segment_id
+              - efferent_segment_offset
+              - spine_length

bluepysnap/schemas/edge/neuromodulatory.yaml

@@ -0,0 +1,17 @@
+title: Edges - neuromodulatory
+description: schema for neuromodulatory edge types
+allOf: [{ $ref: "#/$edge_file_defs/edges_file_root" }]
+properties:
+  edges:
+    patternProperties:
+      # "" is used as a wild card for population name
+      "":
+        properties:
+          "0":
+            required:
+              - afferent_section_id
+              - afferent_section_pos
+              - afferent_segment_id
+              - delay
+              - neuromod_dtc
+              - neuromod_strength