openbel-api 0.4.0-java

data/app/openbel/api/schemas.rb

@@ -0,0 +1,34 @@
+require 'pathname'
+require 'multi_json'
+require 'json_schema'
+
+module OpenBEL
+  module Schemas
+
+    COMPILED_SCHEMAS = {}
+    SCHEMA_DIR = File.join(File.expand_path(File.dirname(__FILE__)), 'schemas')
+    SUFFIX     = ".schema.json"
+
+    def validate(data, type)
+      _get_schema(type).validate(data)
+    end
+
+    private
+
+    def _get_schema(type)
+      schemas = @@compiled ||= {}
+      schemas[type] ||= _compile_schema(type)
+    end
+
+    def _compile_schema(type)
+      path = (Pathname(SCHEMA_DIR) + "#{type}#{SUFFIX}").to_s
+      if File.exists? path
+        schema_data = MultiJson.load File.read(path)
+        JsonSchema.parse!(schema_data)
+      else
+        fail IOError.new "No schema file for type: #{type} at path: #{path}"
+      end
+    end
+  end
+end
+

data/app/openbel/api/schemas/annotation_collection.schema.json

@@ -0,0 +1,20 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "description": "DESCRIBE ANNOTATION COLLECTION",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "annotation_collection"
+  ],
+  "properties": {
+    "annotation_collection": {
+      "type": "array",
+      "minItems": 0,
+      "title": "",
+      "description": "",
+      "items": {
+        "$ref":"http://next.belframework.org/schemas/annotation_resource.schema.json"
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/annotation_resource.schema.json

@@ -0,0 +1,36 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Annotation",
+  "description": "A vocabulary of terms for describing evidence resources.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "annotation"
+  ],
+  "properties": {
+    "annotation": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": [
+        "rdf_uri",
+        "name",
+        "prefix",
+        "domain"
+      ],
+      "properties": {
+        "rdf_uri": {
+          "type": "string"
+        },
+        "name": {
+          "type": "string"
+        },
+        "prefix": {
+          "type": "string"
+        },
+        "domain": {
+          "type": "string"
+        }
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/annotation_value_collection.schema.json

@@ -0,0 +1,21 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Annotation Value Collection",
+  "description": "A collection of annotation value resources.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "annotation_value_collection"
+  ],
+  "properties": {
+    "annotation_value_collection": {
+      "type": "array",
+      "minItems": 0,
+      "title": "",
+      "description": "",
+      "items": {
+        "$ref":"http://next.belframework.org/schemas/annotation_value_resource.schema.json"
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/annotation_value_resource.schema.json

@@ -0,0 +1,35 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Annotation Value Resource",
+  "description": "A single annotation value within a BEL Annotation.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "annotation_value"
+  ],
+  "properties": {
+    "annotation_value": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": [
+        "type",
+        "identifier",
+        "name"
+      ],
+      "properties": {
+        "type": {
+          "type": "string"
+        },
+        "identifier": {
+          "type": "string"
+        },
+        "name": {
+          "type": "string"
+        },
+        "match_text": {
+          "type": "string"
+        }
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/completion_collection.schema.json

@@ -0,0 +1,21 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Completion Collection",
+  "description": "A collection of BEL expression completions.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "completion_collection"
+  ],
+  "properties": {
+    "completion_collection": {
+      "type": "array",
+      "minItems": 0,
+      "title": "",
+      "description": "",
+      "items": {
+        "$ref":"http://next.belframework.org/schemas/completion_resource.schema.json#/properties/completion"
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/completion_resource.schema.json

@@ -0,0 +1,146 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "Completion Resource",
+  "description": "A completion of a BEL expression.",
+  "type": "object",
+  "additionalProperties": false,
+  "required": [
+    "completion"
+  ],
+  "properties": {
+    "completion": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": [
+        "type",
+        "label",
+        "value",
+        "highlight",
+        "actions"
+      ],
+      "properties": {
+        "type": {
+          "enum": [
+            "function",
+            "namespace_prefix",
+            "namespace_value"
+          ]
+        },
+        "label": {
+          "type": "string"
+        },
+        "value": {
+          "type": "string"
+        },
+        "highlight": {
+          "oneOf": [
+            {
+              "type": "null"
+            },
+            {
+              "type": "object",
+              "required": [
+                "start_position",
+                "end_position",
+                "range_type"
+              ],
+              "properties": {
+                "start_position": {
+                  "type": "integer"
+                },
+                "end_position": {
+                  "type": "integer"
+                },
+                "range_type": {
+                  "enum": [
+                    "exclusive",
+                    "inclusive"
+                  ]
+                }
+              }
+            }
+          ]
+        },
+        "actions": {
+          "type": "array",
+          "items": {
+            "oneOf": [
+              {
+                "type": "object",
+                "required": [
+                  "delete"
+                ],
+                "properties": {
+                  "delete": {
+                    "type": "object",
+                    "required": [
+                      "start_position",
+                      "end_position",
+                      "range_type"
+                    ],
+                    "properties": {
+                      "start_position": {
+                        "type": "integer"
+                      },
+                      "end_position": {
+                        "type": "integer"
+                      },
+                      "range_type": {
+                        "enum": [
+                          "exclusive",
+                          "inclusive"
+                        ]
+                      }
+                    }
+                  }
+                }
+              },
+              {
+                "type": "object",
+                "required": [
+                  "insert"
+                ],
+                "properties": {
+                  "insert": {
+                    "type": "object",
+                    "required": [
+                      "position",
+                      "value"
+                    ],
+                    "properties": {
+                      "position": {
+                        "type": "integer"
+                      },
+                      "value": {
+                        "type": "string"
+                      }
+                    }
+                  }
+                }
+              },
+              {
+                "type": "object",
+                "required": [
+                  "move_cursor"
+                ],
+                "properties": {
+                  "move_cursor": {
+                    "type": "object",
+                    "required": [
+                      "position"
+                    ],
+                    "properties": {
+                      "position": {
+                        "type": "integer"
+                      }
+                    }
+                  }
+                }
+              }
+            ]
+          }
+        }
+      }
+    }
+  }
+}

data/app/openbel/api/schemas/evidence.schema.json

@@ -0,0 +1,198 @@
+{
+  "$schema":              "http://json-schema.org/draft-04/schema",
+  "description":          "DESCRIBE EVIDENCE",
+  "type":                 "object",
+  "additionalProperties": false,
+  "required":             ["evidence"],
+  "properties": {
+    "evidence": {
+      "type":                 "object",
+      "additionalProperties": false,
+      "required":             ["bel_statement", "citation"],
+      "properties": {
+        "bel_statement": {
+          "type":        "string",
+          "title":       "BEL Statement",
+          "description": "A BEL Statement is an expression that represents knowledge of the existence of biological entities and relationships between them that are known to be observed within a particular context, based on some source of prior knowledge such as a scientific publication or newly generated experimental data."
+        },
+        "citation": {
+          "type":        "object",
+          "title":       "Citation",
+          "description": "The citation specifies the written source where the biological knowledge was referenced.",
+          "required":    ["type", "id"],
+          "properties": {
+            "type": {
+              "type":        "string",
+              "enum":        ["PubMed", "Book", "Journal", "Online Resource", "Other"],
+              "title":       "Citation Type",
+              "description": "The citation type of the reference."
+            },
+            "id": {
+              "type":        ["string", "number"],
+              "title":       "Citation ID",
+              "description": "The citation identifier (PubMed ID, ISBN, DOI, URL) of the reference."
+            },
+            "name": {
+              "type":        ["string", "null"],
+              "title":       "Citation Name",
+              "description": "The citation name of the reference."
+            },
+            "date": {
+              "type":        ["string", "null"],
+              "title":       "Citation Date",
+              "description": "The citation date of the reference."
+            },
+            "authors": {
+              "type":        ["array", "null"],
+              "title":       "Citation Authors",
+              "description": "The citation authors of the reference.",
+              "items": {
+                "type":     "string",
+                "minItems": 0
+              }
+            },
+            "comment": {
+              "type":        ["string", "null"],
+              "title":       "Citation Comment",
+              "description": "The citation comment of the reference."
+            }
+          }
+        },
+        "experiment_context": {
+          "type":        ["array", "null"],
+          "title":       "Experiment Context",
+          "description": "An experiment context specifies the experiment's parameters where this interaction was observed.",
+          "items": {
+            "type":       "object",
+            "required":   ["name", "value"],
+            "properties": {
+              "name": {
+                "type":        "string",
+                "title":       "Annotation Type",
+                "description": "Annotation type listing - sourced from the BEL Annotation resource names"
+              },
+              "value": {
+                "type":        ["string", "number", "boolean", "array"],
+                "title":       "Annotations",
+                "description": "Annotations such as Homo sapiens, cancer, epithelial tissue sourced from the BEL Annotation resources",
+                "items": {
+                  "type": ["string", "number", "boolean"]
+                }
+              },
+              "uri": {
+                "type":        "string",
+                "title":       "Annotation URI",
+                "description": "URI for Annotation",
+                "format":      "uri",
+                "items": {
+                  "type":   "string",
+                  "format": "uri"
+                }
+              }
+            }
+          }
+        },
+        "summary_text": {
+          "type":        ["string", "null"],
+          "title":       "Summary Text",
+          "description": "Abstract from source text to provide support for this evidence"
+        },
+        "references": {
+          "type":        ["object", "null"],
+          "title":       "References",
+          "description": "The references section identifies annotation and namespace URIs.",
+          "properties": {
+            "annotations": {
+              "type":        ["array", "null"],
+              "title":       "Annotation references",
+              "description": "References to annotation resources.",
+              "item": {
+                "type": "object",
+                "properties": {
+                  "keyword": {
+                    "type":        "string",
+                    "title":       "Keyword",
+                    "description": "Keyword that identifies this annotation resource, but only in the context of this Evidence."
+                  },
+                  "uri": {
+                    "type":        "string",
+                    "format":      "uri",
+                    "title":       "URI",
+                    "description": "URI that identifies this annotation resource."
+                  }
+                },
+                "required": ["keyword", "uri"]
+              }
+            },
+            "namespaces": {
+              "type":        ["array", "null"],
+              "title":       "Namespace references",
+              "description": "References to namespace resources.",
+              "item": {
+                "type": "object",
+                "properties": {
+                  "keyword": {
+                    "type":        "string",
+                    "title":       "Keyword",
+                    "description": "Keyword that identifies this namespace resource, but only in the context of this Evidence."
+                  },
+                  "uri": {
+                    "type":        "string",
+                    "format":      "uri",
+                    "title":       "URI",
+                    "description": "URI that identifies this namespace resource."
+                  }
+                },
+                "required": ["keyword", "uri"]
+              }
+            }
+          }
+        },
+        "metadata": {
+          "type":        ["array", "null"],
+          "title":       "Evidence resource metadata",
+          "description": "Metadata that describes the evidence resource.",
+          "items": {
+            "oneOf": [
+              {
+                "type":       "object",
+                "required":   ["name", "value"],
+                "properties": {
+                  "name": {
+                    "type":        "string",
+                    "title":       "Name",
+                    "description": "The name of this metadata property."
+                  },
+                  "value": {
+                    "type":        ["array", "boolean", "number", "object", "string"],
+                    "title":       "Value",
+                    "description": "The value of this metadata property.",
+                    "items": {
+                      "type": ["array", "boolean", "integer", "number", "null", "object", "string"]
+                    }
+                  }
+                }
+              },
+              {
+                "type":        "object",
+                "required":    ["uri"],
+                "title":       "Annotation URI(s)",
+                "description": "URI(s) for Annotations",
+                "properties": {
+                  "uri": {
+                    "type":   ["string", "array"],
+                    "format": "uri",
+                    "items": {
+                      "type":   "string",
+                      "format": "uri"
+                    }
+                  }
+                }
+              }
+            ]
+          }
+        }
+      }
+    }
+  }
+}