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beat
beat.core
Commits
183dc834
Commit
183dc834
authored
Apr 12, 2019
by
Samuel GAIST
Browse files
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[database] Implement v2
parent
99615244
Changes
11
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11 changed files
with
359 additions
and
16 deletions
+359
-16
beat/core/database.py
beat/core/database.py
+20
-12
beat/core/schema/database/2.json
beat/core/schema/database/2.json
+107
-0
beat/core/test/prefix/databases/large/2.json
beat/core/test/prefix/databases/large/2.json
+27
-0
beat/core/test/prefix/databases/large/2.py
beat/core/test/prefix/databases/large/2.py
+87
-0
beat/core/test/prefix/databases/simple/2.json
beat/core/test/prefix/databases/simple/2.json
+30
-0
beat/core/test/prefix/databases/simple/2.py
beat/core/test/prefix/databases/simple/2.py
+22
-0
beat/core/test/prefix/protocoltemplates/large/1.json
beat/core/test/prefix/protocoltemplates/large/1.json
+11
-0
beat/core/test/prefix/protocoltemplates/protocol/1.json
beat/core/test/prefix/protocoltemplates/protocol/1.json
+17
-0
beat/core/test/prefix/protocoltemplates/protocol2/1.json
beat/core/test/prefix/protocoltemplates/protocol2/1.json
+17
-0
beat/core/test/prefix/protocoltemplates/small/1.json
beat/core/test/prefix/protocoltemplates/small/1.json
+11
-0
beat/core/test/test_database.py
beat/core/test/test_database.py
+10
-4
No files found.
beat/core/database.py
View file @
183dc834
...
...
@@ -102,6 +102,15 @@ class Database(BackendDatabase):
def
__init__
(
self
,
prefix
,
data
,
dataformat_cache
=
None
):
super
(
Database
,
self
).
__init__
(
prefix
,
data
,
dataformat_cache
)
def
_validate_view
(
self
,
view_name
):
if
view_name
.
find
(
"."
)
!=
-
1
or
view_name
.
find
(
os
.
sep
)
!=
-
1
:
self
.
errors
.
append
(
"dataset views are required to sit inside the "
"database root folder, but `%s' is either in a "
"subdirectory or points to a python module, what is "
"unsupported by this version"
%
(
view_name
)
)
def
_load
(
self
,
data
,
dataformat_cache
):
"""Loads the database"""
...
...
@@ -150,7 +159,7 @@ class Database(BackendDatabase):
self
.
_validate_semantics
(
dataformat_cache
)
def
_validate_semantics
(
self
,
dataformat_cache
):
"""Validates all sematical aspects of the database"""
"""Validates all sema
n
tical aspects of the database"""
# all protocol names must be unique
protocol_names
=
[
k
[
"name"
]
for
k
in
self
.
data
[
"protocols"
]]
...
...
@@ -161,7 +170,7 @@ class Database(BackendDatabase):
# all set names within a protocol must be unique
for
protocol
in
self
.
data
[
"protocols"
]:
set_names
=
[
k
[
"name"
]
for
k
in
protocol
[
"sets"
]]
set_names
=
self
.
set_names
(
protocol
[
"name"
])
if
len
(
set_names
)
!=
len
(
set
(
set_names
)):
self
.
errors
.
append
(
"found different sets with the same name at protocol "
...
...
@@ -169,9 +178,9 @@ class Database(BackendDatabase):
)
# all outputs must have valid data types
for
_
set
in
protocol
[
"sets"
]
:
for
_
,
set_
in
self
.
sets
(
protocol
[
"name"
]).
items
()
:
for
key
,
value
in
_set
[
"outputs"
].
items
():
for
key
,
value
in
set_
[
"outputs"
].
items
():
if
value
in
self
.
dataformats
:
continue
...
...
@@ -191,17 +200,16 @@ class Database(BackendDatabase):
%
(
value
,
key
,
_set
[
"name"
],
set_
[
"name"
],
protocol
[
"name"
],
"
\
n
"
.
join
(
dataformat
.
errors
),
)
)
# all view names must be relative to the database root path
if
_set
[
"view"
].
find
(
"."
)
!=
-
1
or
_set
[
"view"
].
find
(
os
.
sep
)
!=
-
1
:
self
.
errors
.
append
(
"dataset views are required to sit inside the "
"database root folder, but `%s' is either in a "
"subdirectory or points to a python module, what is "
"unsupported by this version"
%
(
_set
[
"view"
],)
)
if
self
.
schema_version
==
1
:
self
.
_validate_view
(
set_
[
"view"
])
if
self
.
schema_version
!=
1
:
for
view
in
protocol
[
"views"
].
keys
():
self
.
_validate_view
(
view
)
beat/core/schema/database/2.json
0 → 100644
View file @
183dc834
{
"$schema"
:
"http://json-schema.org/draft-04/schema#"
,
"title"
:
"Database descriptor v2"
,
"description"
:
"This schema defines the properties of a version 2 BEAT database"
,
"type"
:
"object"
,
"properties"
:
{
"root_folder"
:
{
"type"
:
"string"
,
"pattern"
:
"^((file://)?(/[^/]+)+|nfs://[a-z0-9._-]+:(/[^/]+)+)$"
},
"protocols"
:
{
"type"
:
"array"
,
"minItems"
:
1
,
"uniqueItems"
:
true
,
"items"
:
{
"$ref"
:
"#/definitions/protocol"
}
},
"description"
:
{
"$ref"
:
"../common/1.json#/definitions/description"
},
"schema_version"
:
{
"const"
:
2
}
},
"required"
:
[
"root_folder"
,
"protocols"
,
"schema_version"
],
"additionalProperties"
:
false
,
"definitions"
:
{
"template_identifier"
:
{
"type"
:
"string"
,
"pattern"
:
"^[a-zA-Z0-9_-]+/[0-9]+$"
},
"protocol"
:
{
"type"
:
"object"
,
"properties"
:
{
"name"
:
{
"$ref"
:
"#/definitions/protocol_name"
},
"template"
:
{
"$ref"
:
"#/definitions/template_identifier"
},
"views"
:
{
"$ref"
:
"#/definitions/views"
}
},
"required"
:
[
"name"
,
"views"
,
"template"
],
"additionalProperties"
:
false
},
"protocol_name"
:
{
"type"
:
"string"
,
"pattern"
:
"^[a-zA-Z0-9_][
\\
.a-zA-Z0-9_-]*$"
},
"view_name"
:
{
"type"
:
"string"
,
"pattern"
:
"^[a-zA-Z_][a-zA-Z0-9_]*$"
},
"views"
:
{
"type"
:
"object"
,
"minProperties"
:
1
,
"uniqueItems"
:
true
,
"patternProperties"
:
{
"^[a-zA-Z_][a-zA-Z0-9_]*$"
:
{
"$ref"
:
"#/definitions/view"
}
}
},
"view"
:
{
"type"
:
"object"
,
"properties"
:
{
"view"
:
{
"$ref"
:
"#definitions/view_name"
},
"parameters"
:
{
"$ref"
:
"#/definitions/parameters"
}
},
"additionalProperties"
:
false
},
"parameters"
:
{
"type"
:
"object"
,
"patternProperties"
:
{
"^[a-zA-Z_][a-zA-Z0-9_-]*$"
:
{
"$ref"
:
"#/definitions/parameter_value"
}
}
},
"parameter_value"
:
{
"oneOf"
:
[
{
"type"
:
"string"
},
{
"type"
:
"number"
},
{
"type"
:
"boolean"
}
]
}
}
}
beat/core/test/prefix/databases/large/2.json
0 → 100644
View file @
183dc834
{
"root_folder"
:
"/tmp/path/not/set"
,
"protocols"
:
[
{
"name"
:
"large"
,
"template"
:
"large/1"
,
"views"
:
{
"data"
:
{
"view"
:
"LargeView"
,
"parameters"
:
{}
}
}
},
{
"name"
:
"small"
,
"template"
:
"small/1"
,
"views"
:
{
"data"
:
{
"view"
:
"SmallView"
,
"parameters"
:
{}
}
}
}
],
"schema_version"
:
2
,
"description"
:
""
}
beat/core/test/prefix/databases/large/2.py
0 → 100644
View file @
183dc834
#!/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
numpy
from
collections
import
namedtuple
from
beat.backend.python.database
import
View
# ----------------------------------------------------------
class
LargeView
(
View
):
def
__init__
(
self
):
super
(
LargeView
,
self
).
__init__
()
numpy
.
random
.
seed
(
0
)
# So it is kept reproducible
def
index
(
self
,
root_folder
,
parameters
):
Entry
=
namedtuple
(
"Entry"
,
[
"out"
])
entries
=
[]
for
i
in
range
(
0
,
1000
):
entries
.
append
(
Entry
(
numpy
.
int32
(
numpy
.
random
.
randint
(
100
,
size
=
(
1000
,)))))
return
entries
def
get
(
self
,
output
,
index
):
obj
=
self
.
objs
[
index
]
if
output
==
"out"
:
return
{
"value"
:
obj
.
out
}
# ----------------------------------------------------------
class
SmallView
(
View
):
def
__init__
(
self
):
super
(
SmallView
,
self
).
__init__
()
numpy
.
random
.
seed
(
0
)
# So it is kept reproducible
def
index
(
self
,
root_folder
,
parameters
):
Entry
=
namedtuple
(
"Entry"
,
[
"out"
])
entries
=
[]
for
i
in
range
(
0
,
1000
):
entries
.
append
(
Entry
(
numpy
.
int32
(
numpy
.
random
.
randint
(
0
,
100
))))
return
entries
def
get
(
self
,
output
,
index
):
obj
=
self
.
objs
[
index
]
if
output
==
"out"
:
return
{
"value"
:
obj
.
out
}
beat/core/test/prefix/databases/simple/2.json
0 → 100644
View file @
183dc834
{
"root_folder"
:
"/tmp/foo/bar"
,
"protocols"
:
[
{
"name"
:
"protocol"
,
"template"
:
"protocol/1"
,
"views"
:
{
"set"
:
{
"view"
:
"View"
},
"set2"
:
{
"view"
:
"View2"
}
}
},
{
"name"
:
"protocol2"
,
"template"
:
"protocol2/1"
,
"views"
:
{
"set"
:
{
"view"
:
"LargeView"
},
"set2"
:
{
"view"
:
"View2"
}
}
}
],
"schema_version"
:
2
}
beat/core/test/prefix/databases/simple/2.py
0 → 100644
View file @
183dc834
class
View
:
def
setup
(
self
,
root_folder
,
outputs
,
parameters
,
force_start_index
=
None
,
force_end_index
=
None
,
):
"""Initializes the database"""
return
True
def
done
(
self
):
"""Should return ``True``, when data is finished"""
return
True
def
next
(
self
):
"""Loads the next data block on ``outputs``"""
return
True
beat/core/test/prefix/protocoltemplates/large/1.json
0 → 100644
View file @
183dc834
{
"schema_version"
:
1
,
"sets"
:
[
{
"name"
:
"data"
,
"outputs"
:
{
"out"
:
"user/empty_1d_array_of_integers/1"
}
}
]
}
beat/core/test/prefix/protocoltemplates/protocol/1.json
0 → 100644
View file @
183dc834
{
"schema_version"
:
1
,
"sets"
:
[
{
"name"
:
"set"
,
"outputs"
:
{
"out"
:
"user/single_integer/1"
}
},
{
"name"
:
"set2"
,
"outputs"
:
{
"out"
:
"user/single_integer/1"
}
}
]
}
beat/core/test/prefix/protocoltemplates/protocol2/1.json
0 → 100644
View file @
183dc834
{
"schema_version"
:
1
,
"sets"
:
[
{
"name"
:
"set"
,
"outputs"
:
{
"out"
:
"user/single_integer/1"
}
},
{
"name"
:
"set2"
,
"outputs"
:
{
"out"
:
"user/single_integer/1"
}
}
]
}
beat/core/test/prefix/protocoltemplates/small/1.json
0 → 100644
View file @
183dc834
{
"schema_version"
:
1
,
"sets"
:
[
{
"name"
:
"data"
,
"outputs"
:
{
"out"
:
"user/single_integer/1"
}
}
]
}
beat/core/test/test_database.py
View file @
183dc834
...
...
@@ -41,15 +41,21 @@ from . import prefix, tmp_prefix
from
.utils
import
cleanup
@
nose
.
tools
.
with_setup
(
teardown
=
cleanup
)
def
test_export
():
for
i
in
range
(
1
,
3
):
yield
export
,
f"integers_db/
{
i
}
"
yield
export
,
f"simple/
{
i
}
"
yield
export
,
f"large/
{
i
}
"
@
nose
.
tools
.
with_setup
(
teardown
=
cleanup
)
def
export
(
db_name
):
name
=
"integers_db/1"
obj
=
Database
(
prefix
,
name
)
obj
=
Database
(
prefix
,
db_name
)
nose
.
tools
.
assert_true
(
obj
.
valid
,
"
\
n
* %s"
%
"
\
n
* "
.
join
(
obj
.
errors
))
obj
.
export
(
tmp_prefix
)
# load from tmp_prefix and validates
exported
=
Database
(
tmp_prefix
,
name
)
exported
=
Database
(
tmp_prefix
,
db_
name
)
nose
.
tools
.
assert_true
(
exported
.
valid
,
"
\
n
* %s"
%
"
\
n
* "
.
join
(
exported
.
errors
))
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