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beat
beat.core
Commits
2bc5215d
Commit
2bc5215d
authored
Apr 17, 2019
by
André Anjos
💬
Browse files
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Merge branch '64_protocol_template' into 'master'
Protocol template See merge request
!67
parents
18c882ae
d1b03a6c
Pipeline
#29377
passed with stages
in 26 minutes and 47 seconds
Changes
21
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1
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21 changed files
with
845 additions
and
70 deletions
+845
-70
beat/core/database.py
beat/core/database.py
+20
-12
beat/core/protocoltemplate.py
beat/core/protocoltemplate.py
+123
-0
beat/core/schema/__init__.py
beat/core/schema/__init__.py
+5
-1
beat/core/schema/database/2.json
beat/core/schema/database/2.json
+107
-0
beat/core/schema/protocoltemplate/1.json
beat/core/schema/protocoltemplate/1.json
+58
-0
beat/core/scripts/migrate_db_to_v2.py
beat/core/scripts/migrate_db_to_v2.py
+158
-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_bcp.py
beat/core/test/test_bcp.py
+1
-1
beat/core/test/test_database.py
beat/core/test/test_database.py
+10
-4
beat/core/test/test_protocoltemplate.py
beat/core/test/test_protocoltemplate.py
+65
-0
beat/core/test/test_schema.py
beat/core/test/test_schema.py
+11
-28
beat/core/test/test_worker.py
beat/core/test/test_worker.py
+61
-21
beat/core/test/utils.py
beat/core/test/utils.py
+2
-2
conda/meta.yaml
conda/meta.yaml
+2
-1
No files found.
beat/core/database.py
View file @
2bc5215d
...
...
@@ -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/protocoltemplate.py
0 → 100644
View file @
2bc5215d
#!/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
beat/core/schema/__init__.py
View file @
2bc5215d
...
...
@@ -94,7 +94,11 @@ def load_schema(schema_name, version=1):
with
open
(
fname
,
"rb"
)
as
f
:
data
=
f
.
read
().
decode
()
schema
=
json
.
loads
(
data
)
try
:
schema
=
json
.
loads
(
data
)
except
json
.
errors
.
JSONDecodeError
:
print
(
"Invalid json:
\
n
{data}"
.
format
(
data
))
raise
basedir
=
os
.
path
.
realpath
(
os
.
path
.
dirname
(
fname
))
resolver
=
jsonschema
.
RefResolver
(
"file://"
+
basedir
+
"/"
,
schema
)
...
...
beat/core/schema/database/2.json
0 → 100644
View file @
2bc5215d
{
"$schema"
:
"http://json-schema.org/draft-04/schema#"
,
"title"
:
"Database descriptor v2"
,
"description"
:
"This schema defines the properties of a version 2 BEAT database"
,
"type"
:
"object"
,
"properties"
:
{
"root_folder"
:
{
"type"
:
"string"
,
"pattern"
:
"^((file://)?(/[^/]+)+|nfs://[a-z0-9._-]+:(/[^/]+)+)$"
},
"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/schema/protocoltemplate/1.json
0 → 100644
View file @
2bc5215d
{
"$schema"
:
"http://json-schema.org/draft-04/schema#"
,
"title"
:
"Database Protocol descriptor"
,
"description"
:
"This schema defines the properties of a BEAT database protocol"
,
"type"
:
"object"
,
"properties"
:
{
"description"
:
{
"$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
}
}
}
beat/core/scripts/migrate_db_to_v2.py
0 → 100644
View file @
2bc5215d
#!/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. #
# #
###################################################################################
"""Migrate a v1 database to v2
Usage:
%(prog)s [-v ... | --verbose ...] [--prefix=<path>][-f|--force]
<database_identifier>
%(prog)s (--help | -h)
%(prog)s (--version | -V)
Options:
-h, --help Show this screen
-V, --version Show version
-v, --verbose Increases the output verbosity level
-p, --prefix=<path> Path where the prefix is contained [default: .]
"""
import
os
import
sys
import
copy
from
docopt
import
docopt
from
..version
import
__version__
from
..database
import
Database
,
Storage
as
DBStorage
from
..protocoltemplate
import
ProtocolTemplate
,
Storage
as
PTStorage
from
..utils
import
setup_logging
def
main
(
argv
=
None
):
if
argv
is
None
:
argv
=
sys
.
argv
[
1
:]
prog
=
os
.
path
.
basename
(
sys
.
argv
[
0
])
completions
=
dict
(
prog
=
prog
,
version
=
__version__
)
args
=
docopt
(
__doc__
%
completions
,
argv
=
argv
,
options_first
=
True
,
version
=
"v%s"
%
__version__
,
)
logger
=
setup_logging
(
args
[
"--verbose"
],
__name__
,
__name__
)
prefix
=
args
[
"--prefix"
]
if
args
[
"--prefix"
]
is
not
None
else
"."
if
not
os
.
path
.
exists
(
prefix
):
logger
.
error
(
"Prefix not found at: '%s'"
,
prefix
)
return
1
database_identifier
=
args
[
"<database_identifier>"
]
database
=
Database
(
prefix
,
database_identifier
)
if
not
database
.
valid
:
logger
.
error
(
"Invalid database: '%s'"
,
"
\
n
"
.
join
(
database
.
errors
))
return
1
if
database
.
schema_version
!=
1
:
logger
.
error
(
"Can't migrate database is not v1"
)
return
1
db_name
,
db_version
=
database_identifier
.
split
(
"/"
)
new_db_name
=
f"
{
db_name
}
/
{
int
(
db_version
)
+
1
}
"
db_storage
=
DBStorage
(
prefix
,
new_db_name
)
if
db_storage
.
exists
():
logger
.
error
(
f"Database already exists:
{
new_db_name
}
"
)
return
1
database_json
=
copy
.
deepcopy
(
database
.
data
)
database_json
[
"schema_version"
]
=
2
database_json
[
"protocols"
]
=
[]
for
protocol
in
database
.
protocols
:
sets
=
database
.
sets
(
protocol
)
set_list
=
[]
views
=
{}
for
_
,
set_
in
sets
.
items
():
views
[
set_
[
"name"
]]
=
{
"view"
:
set_
[
"view"
],
"parameters"
:
set_
.
get
(
"parameters"
,
{}),
}
for
key
in
[
"template"
,
"view"
,
"parameters"
]:
if
key
in
set_
:
set_
.
pop
(
key
)
set_list
.
append
(
set_
)
template
=
{
"schema_version"
:
1
,
"sets"
:
set_list
}
pt_name
=
f"
{
protocol
}
/1"
pt_storage
=
PTStorage
(
prefix
,
pt_name
)
if
pt_storage
.
exists
():
logger
.
info
(
f"Protocol template already exists:
{
pt_name
}
"
)
else
:
protocol_template
=
ProtocolTemplate
(
prefix
,
template
)
if
not
protocol_template
.
valid
:
logger
.
error
(
"Invalid protocol created:"
,
"
\
n
"
.
join
(
protocol_template
.
errors
)
)
return
1
else
:
protocol_template
.
write
(
pt_storage
)
protocol_entry
=
{
"name"
:
protocol
,
"template"
:
pt_name
,
"views"
:
views
}
database_json
[
"protocols"
].
append
(
protocol_entry
)
new_database
=
Database
(
prefix
,
database_json
)
if
not
new_database
.
valid
:
logger
.
error
(
"Invalid database created:"
,
"
\
n
"
.
join
(
new_database
.
errors
))
return
1
else
:
new_database
.
code
=
database
.
code
new_database
.
description
=
(
database
.
description
if
database
.
description
is
not
None
else
""
)
new_database
.
write
(
db_storage
)
if
__name__
==
"__main__"
:
main
()
beat/core/test/prefix/databases/large/2.json
0 → 100644
View file @
2bc5215d
{
"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 @
2bc5215d
#!/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 @
2bc5215d
{
"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 @
2bc5215d
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 @
2bc5215d