From f58d6f8478d5eecd118ed521d6c5a2f619e5f212 Mon Sep 17 00:00:00 2001
From: Samuel Gaist <samuel.gaist@idiap.ch>
Date: Fri, 12 Apr 2019 17:32:57 +0200
Subject: [PATCH] [protocoltemplate] Implement ProcotolTemplate support
---
beat/core/protocoltemplate.py | 123 +++++++++++++++++++++++
beat/core/schema/protocoltemplate/1.json | 58 +++++++++++
beat/core/test/test_protocoltemplate.py | 65 ++++++++++++
3 files changed, 246 insertions(+)
create mode 100644 beat/core/protocoltemplate.py
create mode 100644 beat/core/schema/protocoltemplate/1.json
create mode 100644 beat/core/test/test_protocoltemplate.py
diff --git a/beat/core/protocoltemplate.py b/beat/core/protocoltemplate.py
new file mode 100644
index 00000000..11574f56
--- /dev/null
+++ b/beat/core/protocoltemplate.py
@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+###################################################################################
+# #
+# Copyright (c) 2019 Idiap Research Institute, http://www.idiap.ch/ #
+# Contact: beat.support@idiap.ch #
+# #
+# Redistribution and use in source and binary forms, with or without #
+# modification, are permitted provided that the following conditions are met: #
+# #
+# 1. Redistributions of source code must retain the above copyright notice, this #
+# list of conditions and the following disclaimer. #
+# #
+# 2. Redistributions in binary form must reproduce the above copyright notice, #
+# this list of conditions and the following disclaimer in the documentation #
+# and/or other materials provided with the distribution. #
+# #
+# 3. Neither the name of the copyright holder nor the names of its contributors #
+# may be used to endorse or promote products derived from this software without #
+# specific prior written permission. #
+# #
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND #
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED #
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE #
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE #
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL #
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR #
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER #
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, #
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE #
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. #
+# #
+###################################################################################
+
+
+"""
+================
+protocoltemplate
+================
+
+Validation of protocoltemplate
+
+Forward importing from :py:mod:`beat.backend.python.protocoltemplate`:
+:py:class:`beat.backend.python.protocoltemplate.Storage`
+"""
+
+import six
+
+from . import schema
+
+from beat.backend.python.protocoltemplate import Storage
+from beat.backend.python.protocoltemplate import (
+ ProtocolTemplate as BackendProtocolTemplate,
+)
+
+
+class ProtocolTemplate(BackendProtocolTemplate):
+ """Protocol template define the design of the database.
+
+
+ Parameters:
+
+ prefix (str): Establishes the prefix of your installation.
+
+ data (dict, str): The piece of data representing the protocol templates.
+ It must validate against the schema defined for protocol templates. If a
+ string is passed, it is supposed to be a valid path to protocol template
+ in the designated prefix area.
+
+ dataformat_cache (:py:class:`dict`, Optional): A dictionary mapping
+ dataformat names to loaded dataformats. This parameter is optional and,
+ if passed, may greatly speed-up protocol template loading times as
+ dataformats that are already loaded may be re-used. If you use this
+ parameter, you must guarantee that the cache is refreshed as appropriate
+ in case the underlying dataformats change.
+
+
+ Attributes:
+
+ name (str): The full, valid name of this protocol template
+
+ description (str): The short description string, loaded from the JSON
+ file if one was set.
+
+ documentation (str): The full-length docstring for this object.
+
+ storage (object): A simple object that provides information about file
+ paths for this protocol template
+
+ errors (list): A list containing errors found while loading this
+ protocol template.
+
+ data (dict): The original data for this protocol template, as loaded by
+ our JSON decoder.
+
+ """
+
+ def __init__(self, prefix, data, dataformat_cache=None):
+ super(ProtocolTemplate, self).__init__(prefix, data, dataformat_cache)
+
+ def _load(self, data, dataformat_cache):
+ """Loads the database"""
+
+ self._name = None
+ self.storage = None
+ self.dataformats = {} # preloaded dataformats
+
+ if isinstance(data, six.string_types): # user has passed a file pointer
+
+ self._name = data
+ self.storage = Storage(self.prefix, self._name)
+ data = self.storage.json.path
+ if not self.storage.json.exists():
+ self.errors.append(
+ "Protocol template declaration file not found: %s" % data
+ )
+ return
+
+ # this runs basic validation, including JSON loading if required
+ self.data, self.errors = schema.validate("protocoltemplate", data)
+ if self.errors:
+ return # don't proceed with the rest of validation
diff --git a/beat/core/schema/protocoltemplate/1.json b/beat/core/schema/protocoltemplate/1.json
new file mode 100644
index 00000000..07af41a7
--- /dev/null
+++ b/beat/core/schema/protocoltemplate/1.json
@@ -0,0 +1,58 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "title": "Database Protocol descriptor",
+ "description": "This schema defines the properties of a BEAT database protocol",
+
+ "type": "object",
+
+ "properties": {
+
+ "description": { "$ref": "../common/1.json#/definitions/description" },
+
+ "schema_version": { "const": 1 },
+
+ "sets": {
+ "type": "array",
+ "minItems": 1,
+ "uniqueItems": true,
+ "items": { "$ref": "#/definitions/set" }
+ }
+
+ },
+
+ "required": [
+ "schema_version", "sets"
+ ],
+
+ "additionalProperties": false,
+
+ "definitions": {
+
+ "identifier": {
+ "type": "string",
+ "pattern": "^[a-zA-Z_][a-zA-Z0-9_-]*$"
+ },
+
+ "set": {
+ "type": "object",
+ "properties": {
+ "name": { "$ref": "#/definitions/identifier" },
+ "outputs": {
+ "type": "object",
+ "patternProperties": {
+ "^[a-zA-Z_][a-zA-Z0-9_-]*$": {
+ "$ref": "../common/1.json#/definitions/reference"
+ }
+ },
+ "minProperties": 1,
+ "uniqueItems": true,
+ "additionalProperties": false
+ }
+ },
+ "required": ["name", "outputs"],
+ "additionalProperties": false
+ }
+
+ }
+
+}
diff --git a/beat/core/test/test_protocoltemplate.py b/beat/core/test/test_protocoltemplate.py
new file mode 100644
index 00000000..526a8560
--- /dev/null
+++ b/beat/core/test/test_protocoltemplate.py
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+###################################################################################
+# #
+# Copyright (c) 2019 Idiap Research Institute, http://www.idiap.ch/ #
+# Contact: beat.support@idiap.ch #
+# #
+# Redistribution and use in source and binary forms, with or without #
+# modification, are permitted provided that the following conditions are met: #
+# #
+# 1. Redistributions of source code must retain the above copyright notice, this #
+# list of conditions and the following disclaimer. #
+# #
+# 2. Redistributions in binary form must reproduce the above copyright notice, #
+# this list of conditions and the following disclaimer in the documentation #
+# and/or other materials provided with the distribution. #
+# #
+# 3. Neither the name of the copyright holder nor the names of its contributors #
+# may be used to endorse or promote products derived from this software without #
+# specific prior written permission. #
+# #
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND #
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED #
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE #
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE #
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL #
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR #
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER #
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, #
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE #
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. #
+# #
+###################################################################################
+
+
+import nose.tools
+from ..protocoltemplate import ProtocolTemplate
+
+from . import prefix, tmp_prefix
+from .utils import cleanup
+
+
+def test_export():
+ for protocol_name in [
+ "double",
+ "triple",
+ "two_sets",
+ "labelled",
+ "different_frequencies",
+ ]:
+ yield export, f"{protocol_name}/1"
+
+
+@nose.tools.with_setup(teardown=cleanup)
+def export(protocol_name):
+
+ obj = ProtocolTemplate(prefix, protocol_name)
+ nose.tools.assert_true(obj.valid, "\n * %s" % "\n * ".join(obj.errors))
+
+ obj.export(tmp_prefix)
+
+ # load from tmp_prefix and validates
+ exported = ProtocolTemplate(tmp_prefix, protocol_name)
+ nose.tools.assert_true(exported.valid, "\n * %s" % "\n * ".join(exported.errors))
--
GitLab