Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
nomad-FAIR
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package registry
Container registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Service Desk
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
nomad-lab
nomad-FAIR
Commits
971beb83
Commit
971beb83
authored
6 years ago
by
Markus Scheidgen
Browse files
Options
Downloads
Patches
Plain Diff
Refactored coe_repo with new datamodel.
parent
82220c0b
No related branches found
No related tags found
1 merge request
!23
Merge new upload file structure
Changes
4
Show whitespace changes
Inline
Side-by-side
Showing
4 changed files
nomad/coe_repo.py
+107
-42
107 additions, 42 deletions
nomad/coe_repo.py
nomad/datamodel.py
+76
-0
76 additions, 0 deletions
nomad/datamodel.py
tests/test_api.py
+1
-3
1 addition, 3 deletions
tests/test_api.py
tests/test_coe_repo.py
+26
-89
26 additions, 89 deletions
tests/test_coe_repo.py
with
210 additions
and
134 deletions
nomad/coe_repo.py
+
107
−
42
View file @
971beb83
...
@@ -35,14 +35,17 @@ This module also provides functionality to add parsed calculation data to the db
...
@@ -35,14 +35,17 @@ This module also provides functionality to add parsed calculation data to the db
.. autofunction:: add_upload
.. autofunction:: add_upload
"""
"""
from
typing
import
List
,
Type
import
itertools
import
itertools
import
json
import
datetime
from
passlib.hash
import
bcrypt
from
passlib.hash
import
bcrypt
from
sqlalchemy
import
Column
,
Integer
,
String
,
Boolean
,
DateTime
,
ForeignKey
,
Enum
from
sqlalchemy
import
Column
,
Integer
,
String
,
Boolean
,
DateTime
,
ForeignKey
,
Enum
,
Table
from
sqlalchemy.orm
import
relationship
from
sqlalchemy.orm
import
relationship
from
sqlalchemy.ext.declarative
import
declarative_base
from
sqlalchemy.ext.declarative
import
declarative_base
from
sqlalchemy.dialects.postgresql
import
BYTEA
from
sqlalchemy.dialects.postgresql
import
BYTEA
from
nomad
import
utils
,
infrastructure
from
nomad
import
utils
,
infrastructure
,
datamodel
from
nomad.repo
import
RepoCalc
from
nomad.repo
import
RepoCalc
...
@@ -177,16 +180,13 @@ def add_calculation(upload, coe_upload, calc: RepoCalc, calc_meta_data: dict) ->
...
@@ -177,16 +180,13 @@ def add_calculation(upload, coe_upload, calc: RepoCalc, calc_meta_data: dict) ->
# user relations
# user relations
owner_user_id
=
calc_meta_data
.
get
(
'
_uploader
'
,
int
(
upload
.
user_id
))
owner_user_id
=
calc_meta_data
.
get
(
'
_uploader
'
,
int
(
upload
.
user_id
))
ownership
=
Ownership
(
calc_id
=
coe_calc
.
calc_id
,
user_id
=
owner_user_id
)
coe_calc
.
owners
.
append
(
repo_db
.
query
(
User
).
get
(
owner_user_id
))
repo_db
.
add
(
ownership
)
for
coauthor_id
in
calc_meta_data
.
get
(
'
coauthors
'
,
[]):
for
coauthor_id
in
calc_meta_data
.
get
(
'
coauthors
'
,
[]):
coauthorship
=
CoAuthorship
(
calc_id
=
coe_calc
.
calc_id
,
user_id
=
int
(
coauthor_id
))
coe_calc
.
coauthors
.
append
(
repo_db
.
query
(
User
).
get
(
coauthor_id
))
repo_db
.
add
(
coauthorship
)
for
shared_with_id
in
calc_meta_data
.
get
(
'
shared_with
'
,
[]):
for
shared_with_id
in
calc_meta_data
.
get
(
'
shared_with
'
,
[]):
shareship
=
Shareship
(
calc_id
=
coe_calc
.
calc_id
,
user_id
=
int
(
shared_with_id
))
coe_calc
.
shared_with
.
append
(
repo_db
.
query
(
User
).
get
(
shared_with_id
))
repo_db
.
add
(
shareship
)
# datasets
# datasets
for
dataset_id
in
calc_meta_data
.
get
(
'
datasets
'
,
[]):
for
dataset_id
in
calc_meta_data
.
get
(
'
datasets
'
,
[]):
...
@@ -203,13 +203,32 @@ def add_calculation(upload, coe_upload, calc: RepoCalc, calc_meta_data: dict) ->
...
@@ -203,13 +203,32 @@ def add_calculation(upload, coe_upload, calc: RepoCalc, calc_meta_data: dict) ->
citation
=
Citation
(
value
=
reference
,
kind
=
'
EXTERNAL
'
)
citation
=
Citation
(
value
=
reference
,
kind
=
'
EXTERNAL
'
)
repo_db
.
add
(
citation
)
repo_db
.
add
(
citation
)
metadata_citation
=
MetaDataCitation
(
coe_calc
.
citations
.
append
(
citation
)
calc_id
=
coe_calc
.
calc_id
,
citation
=
citation
)
repo_db
.
add
(
metadata_citation
)
class
Calc
(
Base
):
# type: ignore
calc_citation_association
=
Table
(
'
metadata_citations
'
,
Base
.
metadata
,
Column
(
'
calc_id
'
,
Integer
,
ForeignKey
(
'
calculations.calc_id
'
)),
Column
(
'
citation_id
'
,
Integer
,
ForeignKey
(
'
citations.citation_id
'
)))
ownership
=
Table
(
'
ownerships
'
,
Base
.
metadata
,
Column
(
'
calc_id
'
,
Integer
,
ForeignKey
(
'
calculations.calc_id
'
)),
Column
(
'
user_id
'
,
Integer
,
ForeignKey
(
'
users.user_id
'
)))
co_authorship
=
Table
(
'
coauthorships
'
,
Base
.
metadata
,
Column
(
'
calc_id
'
,
Integer
,
ForeignKey
(
'
calculations.calc_id
'
)),
Column
(
'
user_id
'
,
Integer
,
ForeignKey
(
'
users.user_id
'
)))
shareship
=
Table
(
'
shareships
'
,
Base
.
metadata
,
Column
(
'
calc_id
'
,
Integer
,
ForeignKey
(
'
calculations.calc_id
'
)),
Column
(
'
user_id
'
,
Integer
,
ForeignKey
(
'
users.user_id
'
)))
class
Calc
(
Base
,
datamodel
.
Calc
):
# type: ignore
__tablename__
=
'
calculations
'
__tablename__
=
'
calculations
'
calc_id
=
Column
(
Integer
,
primary_key
=
True
,
autoincrement
=
True
)
calc_id
=
Column
(
Integer
,
primary_key
=
True
,
autoincrement
=
True
)
...
@@ -217,6 +236,56 @@ class Calc(Base): # type: ignore
...
@@ -217,6 +236,56 @@ class Calc(Base): # type: ignore
upload
=
relationship
(
'
Upload
'
)
upload
=
relationship
(
'
Upload
'
)
checksum
=
Column
(
String
)
checksum
=
Column
(
String
)
calc_meta_data
=
relationship
(
'
CalcMetaData
'
,
uselist
=
False
)
user_meta_data
=
relationship
(
'
UserMetaData
'
,
uselist
=
False
)
citations
=
relationship
(
'
Citation
'
,
secondary
=
calc_citation_association
)
owners
=
relationship
(
'
User
'
,
secondary
=
ownership
)
coauthors
=
relationship
(
'
User
'
,
secondary
=
co_authorship
)
shared_with
=
relationship
(
'
User
'
,
secondary
=
shareship
)
@classmethod
def
create_from
(
cls
,
obj
):
repo_db
=
infrastructure
.
repository_db
return
repo_db
.
query
(
Calc
).
filter_by
(
calc_id
=
int
(
obj
.
pid
)).
first
()
@property
def
mainfile
(
self
)
->
str
:
return
self
.
calc_meta_data
.
location
@property
def
pid
(
self
):
return
self
.
calc_id
@property
def
comment
(
self
)
->
str
:
return
self
.
user_meta_data
.
label
@property
def
calc_hash
(
self
)
->
str
:
return
self
.
checksum
@property
def
references
(
self
)
->
List
[
str
]:
return
list
(
citation
.
value
for
citation
in
self
.
citations
if
citation
.
kind
==
'
EXTERNAL
'
)
@property
def
uploader
(
self
)
->
'
User
'
:
assert
len
(
self
.
owners
)
==
1
,
'
A calculation can only have one owner.
'
return
self
.
owners
[
0
]
@property
def
with_embargo
(
self
)
->
bool
:
return
self
.
user_meta_data
.
permission
==
1
@property
def
chemical_formula
(
self
)
->
str
:
return
self
.
calc_meta_data
.
chemical_formula
@property
def
filenames
(
self
)
->
List
[
str
]:
filenames
=
self
.
calc_meta_data
.
filenames
.
decode
(
'
utf-8
'
)
return
json
.
loads
(
filenames
)
def
set_value
(
self
,
topic_cid
:
int
,
value
:
str
)
->
None
:
def
set_value
(
self
,
topic_cid
:
int
,
value
:
str
)
->
None
:
if
value
is
None
:
if
value
is
None
:
return
return
...
@@ -304,43 +373,47 @@ class Topics(Base): # type: ignore
...
@@ -304,43 +373,47 @@ class Topics(Base): # type: ignore
topic
=
Column
(
String
)
topic
=
Column
(
String
)
class
Upload
(
Base
):
# type: ignore
class
Upload
(
Base
,
datamodel
.
Upload
):
# type: ignore
__tablename__
=
'
uploads
'
__tablename__
=
'
uploads
'
upload_id
=
Column
(
Integer
,
primary_key
=
True
,
autoincrement
=
True
)
upload_id
=
Column
(
Integer
,
primary_key
=
True
,
autoincrement
=
True
)
upload_name
=
Column
(
String
)
upload_name
=
Column
(
String
)
user_id
=
Column
(
Integer
,
ForeignKey
(
'
users.user_id
'
))
user_id
=
Column
(
Integer
,
ForeignKey
(
'
users.user_id
'
))
user
=
relationship
(
'
User
'
)
is_processed
=
Column
(
Boolean
)
is_processed
=
Column
(
Boolean
)
created
=
Column
(
DateTime
)
created
=
Column
(
DateTime
)
user
=
relationship
(
'
User
'
)
calcs
=
relationship
(
'
Calc
'
)
class
Session
(
Base
):
# type: ignore
@classmethod
__tablename__
=
'
sessions
'
def
create_from
(
cls
,
obj
):
return
Upload
.
from_upload_hash
(
obj
.
upload_hash
)
token
=
Column
(
String
,
primary_key
=
True
)
user_id
=
Column
(
String
)
class
Ownership
(
Base
):
# type: ignore
__tablename__
=
'
ownerships
'
calc_id
=
Column
(
Integer
,
ForeignKey
(
'
calculations.calc_id
'
),
primary_key
=
True
)
@staticmethod
user_id
=
Column
(
Integer
,
ForeignKey
(
'
users.user_id
'
),
primary_key
=
True
)
def
from_upload_hash
(
upload_hash
)
->
'
Upload
'
:
repo_db
=
infrastructure
.
repository_db
uploads
=
repo_db
.
query
(
Upload
).
filter_by
(
upload_name
=
upload_hash
)
assert
uploads
.
count
()
<=
1
,
'
Upload hash/name must be unique
'
return
uploads
.
first
()
@property
def
upload_hash
(
self
):
return
self
.
upload_name
class
CoAuthorship
(
Base
):
# type: ignore
@property
__tablename__
=
'
coauthorships
'
def
uploader
(
self
)
->
'
User
'
:
return
self
.
user
calc_id
=
Column
(
Integer
,
ForeignKey
(
'
calculations.calc_id
'
),
primary_key
=
True
)
@property
user_id
=
Column
(
Integer
,
ForeignKey
(
'
users.user_id
'
),
primary_key
=
True
)
def
upload_time
(
self
)
->
Type
[
datetime
.
datetime
]:
return
self
.
created
class
S
hareship
(
Base
):
# type: ignore
class
S
ession
(
Base
):
# type: ignore
__tablename__
=
'
s
hareship
s
'
__tablename__
=
'
s
ession
s
'
calc_id
=
Column
(
Integer
,
ForeignKey
(
'
calculations.calc_id
'
)
,
primary_key
=
True
)
token
=
Column
(
String
,
primary_key
=
True
)
user_id
=
Column
(
Integer
,
ForeignKey
(
'
users.user_id
'
),
primary_key
=
True
)
user_id
=
Column
(
String
)
class
CalcSet
(
Base
):
# type: ignore
class
CalcSet
(
Base
):
# type: ignore
...
@@ -358,14 +431,6 @@ class Citation(Base): # type: ignore
...
@@ -358,14 +431,6 @@ class Citation(Base): # type: ignore
kind
=
Column
(
Enum
(
'
INTERNAL
'
,
'
EXTERNAL
'
,
name
=
'
citation_kind_enum
'
))
kind
=
Column
(
Enum
(
'
INTERNAL
'
,
'
EXTERNAL
'
,
name
=
'
citation_kind_enum
'
))
class
MetaDataCitation
(
Base
):
# type: ignore
__tablename__
=
'
metadata_citations
'
calc_id
=
Column
(
Integer
,
ForeignKey
(
'
calculations.calc_id
'
),
primary_key
=
True
)
citation_id
=
Column
(
Integer
,
ForeignKey
(
'
citations.citation_id
'
),
primary_key
=
True
)
citation
=
relationship
(
'
Citation
'
)
class
LoginException
(
Exception
):
class
LoginException
(
Exception
):
pass
pass
...
...
This diff is collapsed.
Click to expand it.
nomad/datamodel.py
0 → 100644
+
76
−
0
View file @
971beb83
# Copyright 2018 Markus Scheidgen
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an"AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
This module contains classes that allow to represent and manipulate the core
nomad data entities on a high level of abstraction independent from their representation
in the coe repository db, the elastic index, json-files, or archive data. It is not
about representing every detail, but those parts that are directly involved in
api, processing, migration, mirroring, or other
'
infrastructure
'
operations.
"""
from
typing
import
Type
,
TypeVar
,
Union
,
Iterable
,
cast
import
datetime
T
=
TypeVar
(
'
T
'
)
class
Entity
:
@classmethod
def
create_from
(
cls
:
Type
[
T
],
obj
)
->
T
:
raise
NotImplementedError
def
to
(
self
,
entity_cls
:
Type
[
T
])
->
T
:
if
(
isinstance
(
self
,
entity_cls
)):
return
cast
(
T
,
self
)
else
:
return
cast
(
T
,
cast
(
Type
[
Entity
],
entity_cls
).
create_from
(
self
))
class
Calc
(
Entity
):
@property
def
pid
(
self
)
->
Union
[
int
,
str
]:
raise
NotImplementedError
@property
def
mainfile
(
self
)
->
str
:
raise
NotImplementedError
@property
def
upload
(
self
)
->
'
Upload
'
:
raise
NotImplementedError
class
Upload
(
Entity
):
@property
def
upload_uuid
(
self
)
->
str
:
return
'
<not assigned>
'
@property
def
upload_hash
(
self
)
->
str
:
raise
NotImplementedError
@property
def
upload_time
(
self
)
->
Type
[
datetime
.
datetime
]:
raise
NotImplementedError
@property
def
uploader
(
self
):
raise
NotImplementedError
@property
def
calcs
(
self
)
->
Iterable
[
Calc
]:
raise
NotImplementedError
This diff is collapsed.
Click to expand it.
tests/test_api.py
+
1
−
3
View file @
971beb83
...
@@ -222,9 +222,7 @@ class TestUploads:
...
@@ -222,9 +222,7 @@ class TestUploads:
upload
=
self
.
assert_upload
(
rv
.
data
)
upload
=
self
.
assert_upload
(
rv
.
data
)
empty_upload
=
upload
[
'
calcs
'
][
'
pagination
'
][
'
total
'
]
==
0
empty_upload
=
upload
[
'
calcs
'
][
'
pagination
'
][
'
total
'
]
==
0
assert_coe_upload
(
assert_coe_upload
(
upload
[
'
upload_hash
'
],
empty
=
empty_upload
,
meta_data
=
meta_data
)
upload
[
'
upload_hash
'
],
proc_infra
[
'
repository_db
'
],
empty
=
empty_upload
,
meta_data
=
meta_data
)
def
test_get_command
(
self
,
client
,
test_user_auth
,
no_warn
):
def
test_get_command
(
self
,
client
,
test_user_auth
,
no_warn
):
rv
=
client
.
get
(
'
/uploads/command
'
,
headers
=
test_user_auth
)
rv
=
client
.
get
(
'
/uploads/command
'
,
headers
=
test_user_auth
)
...
...
This diff is collapsed.
Click to expand it.
tests/test_coe_repo.py
+
26
−
89
View file @
971beb83
...
@@ -13,11 +13,9 @@
...
@@ -13,11 +13,9 @@
# limitations under the License.
# limitations under the License.
import
pytest
import
pytest
import
json
import
datetime
import
datetime
from
nomad.coe_repo
import
User
,
Calc
,
CalcMetaData
,
StructRatio
,
Upload
,
add_upload
,
\
from
nomad.coe_repo
import
User
,
Calc
,
Upload
,
add_upload
UserMetaData
,
Citation
,
MetaDataCitation
,
Shareship
,
CoAuthorship
,
Ownership
from
tests.processing.test_data
import
processed_upload
# pylint: disable=unused-import
from
tests.processing.test_data
import
processed_upload
# pylint: disable=unused-import
from
tests.processing.test_data
import
uploaded_id
# pylint: disable=unused-import
from
tests.processing.test_data
import
uploaded_id
# pylint: disable=unused-import
...
@@ -41,97 +39,36 @@ def test_password_authorize(test_user):
...
@@ -41,97 +39,36 @@ def test_password_authorize(test_user):
assert_user
(
user
,
test_user
)
assert_user
(
user
,
test_user
)
def
assert_coe_upload
(
upload_hash
,
repository_db
,
empty
=
False
,
meta_data
=
{}):
def
assert_coe_upload
(
upload_hash
,
empty
=
False
,
meta_data
=
{}):
coe_uploads
=
repository_db
.
query
(
Upload
).
filter_by
(
upload_name
=
upload_hash
)
coe_upload
=
Upload
.
from_upload_hash
(
upload_hash
)
if
empty
:
if
empty
:
assert
coe_upload
s
.
count
()
==
0
assert
coe_upload
is
None
else
:
else
:
assert
coe_uploads
.
count
()
==
1
assert
len
(
coe_upload
.
calcs
)
>
0
coe_upload
=
coe_uploads
.
first
()
for
calc
in
coe_upload
.
calcs
:
coe_upload_id
=
coe_upload
.
upload_id
assert_coe_calc
(
calc
,
meta_data
=
meta_data
)
one_calc_exist
=
False
for
calc
in
repository_db
.
query
(
Calc
).
filter_by
(
origin_id
=
coe_upload_id
):
one_calc_exist
=
True
assert
calc
.
origin_id
==
coe_upload_id
assert_coe_calc
(
calc
,
repository_db
,
meta_data
=
meta_data
)
if
'
_upload_time
'
in
meta_data
:
if
'
_upload_time
'
in
meta_data
:
assert
coe_upload
.
created
.
isoformat
()[:
26
]
==
meta_data
[
'
_upload_time
'
]
assert
coe_upload
.
created
.
isoformat
()[:
26
]
==
meta_data
[
'
_upload_time
'
]
assert
one_calc_exist
def
assert_coe_calc
(
calc
,
repository_db
,
meta_data
=
{}):
calc_id
=
calc
.
calc_id
calc_meta_data
=
repository_db
.
query
(
CalcMetaData
).
filter_by
(
calc_id
=
calc_id
).
first
()
assert
calc_meta_data
is
not
None
assert
calc_meta_data
.
calc
is
not
None
assert
calc_meta_data
.
chemical_formula
is
not
None
filenames
=
calc_meta_data
.
filenames
.
decode
(
'
utf-8
'
)
assert
len
(
json
.
loads
(
filenames
))
==
5
# struct ratio
struct_ratio
=
repository_db
.
query
(
StructRatio
).
filter_by
(
calc_id
=
calc_id
).
first
()
assert
struct_ratio
is
not
None
assert
struct_ratio
.
chemical_formula
==
calc_meta_data
.
chemical_formula
assert
struct_ratio
.
formula_units
==
1
# pid
if
'
_pid
'
in
meta_data
:
assert
calc_id
==
int
(
meta_data
[
'
_pid
'
])
# checksum
if
'
_checksum
'
in
meta_data
:
calc
.
checksum
==
meta_data
[
'
_checksum
'
]
# comments
def
assert_coe_calc
(
calc
:
Calc
,
meta_data
=
{}):
comment
=
repository_db
.
query
(
UserMetaData
).
filter_by
(
assert
int
(
calc
.
pid
)
==
int
(
meta_data
.
get
(
'
_pid
'
,
calc
.
pid
))
label
=
meta_data
.
get
(
'
comment
'
,
'
not existing comment
'
),
assert
calc
.
calc_hash
==
meta_data
.
get
(
'
_checksum
'
,
calc
.
calc_hash
)
calc_id
=
calc_id
).
first
()
if
'
comment
'
in
meta_data
:
assert
comment
is
not
None
else
:
assert
comment
is
None
# references
if
'
references
'
in
meta_data
:
for
reference
in
meta_data
[
'
references
'
]:
citation
=
repository_db
.
query
(
Citation
).
filter_by
(
value
=
reference
,
kind
=
'
EXTERNAL
'
).
first
()
assert
citation
is
not
None
assert
repository_db
.
query
(
MetaDataCitation
).
filter_by
(
citation_id
=
citation
.
citation_id
,
calc_id
=
calc_id
).
first
()
is
not
None
else
:
repository_db
.
query
(
MetaDataCitation
).
filter_by
(
calc_id
=
calc_id
).
first
()
is
None
# coauthors
if
'
coauthors
'
in
meta_data
:
for
coauthor
in
meta_data
[
'
coauthors
'
]:
assert
repository_db
.
query
(
CoAuthorship
).
filter_by
(
user_id
=
coauthor
,
calc_id
=
calc_id
).
first
()
is
not
None
else
:
assert
repository_db
.
query
(
CoAuthorship
).
filter_by
(
calc_id
=
calc_id
).
first
()
is
None
# coauthors
if
'
shared_with
'
in
meta_data
:
for
coauthor
in
meta_data
[
'
shared_with
'
]:
assert
repository_db
.
query
(
Shareship
).
filter_by
(
user_id
=
coauthor
,
calc_id
=
calc_id
).
first
()
is
not
None
else
:
assert
repository_db
.
query
(
Shareship
).
filter_by
(
calc_id
=
calc_id
).
first
()
is
None
# ownership
# calc data
owners
=
repository_db
.
query
(
Ownership
).
filter_by
(
calc_id
=
calc_id
)
assert
len
(
calc
.
filenames
)
==
5
assert
owners
.
count
()
==
1
assert
calc
.
chemical_formula
is
not
None
if
'
_uploader
'
in
meta_data
:
assert
owners
.
first
().
user_id
==
meta_data
[
'
_uploader
'
]
# embargo/restriction/permission
# user meta data
user_meta_data
=
repository_db
.
query
(
UserMetaData
).
filter_by
(
assert
calc
.
comment
==
meta_data
.
get
(
'
comment
'
,
None
)
calc_id
=
calc_meta_data
.
calc_id
).
first
()
assert
sorted
(
calc
.
references
)
==
sorted
(
meta_data
.
get
(
'
references
'
,
[]))
assert
user_meta_data
is
not
None
assert
calc
.
uploader
is
not
None
assert
user_meta_data
.
permission
==
(
1
if
meta_data
.
get
(
'
with_embargo
'
,
False
)
else
0
)
assert
calc
.
uploader
.
user_id
==
meta_data
.
get
(
'
_uploader
'
,
calc
.
uploader
.
user_id
)
assert
sorted
(
user
.
user_id
for
user
in
calc
.
coauthors
)
==
sorted
(
meta_data
.
get
(
'
coauthors
'
,
[]))
assert
sorted
(
user
.
user_id
for
user
in
calc
.
shared_with
)
==
sorted
(
meta_data
.
get
(
'
shared_with
'
,
[]))
assert
calc
.
with_embargo
==
meta_data
.
get
(
'
with_embargo
'
,
False
)
@pytest.mark.timeout
(
10
)
@pytest.mark.timeout
(
10
)
...
@@ -140,11 +77,11 @@ def test_add_upload(clean_repository_db, processed_upload):
...
@@ -140,11 +77,11 @@ def test_add_upload(clean_repository_db, processed_upload):
processed_upload
.
upload_hash
=
str
(
1
)
processed_upload
.
upload_hash
=
str
(
1
)
add_upload
(
processed_upload
)
add_upload
(
processed_upload
)
assert_coe_upload
(
processed_upload
.
upload_hash
,
clean_repository_db
,
empty
=
empty
)
assert_coe_upload
(
processed_upload
.
upload_hash
,
empty
=
empty
)
processed_upload
.
upload_hash
=
str
(
2
)
processed_upload
.
upload_hash
=
str
(
2
)
add_upload
(
processed_upload
)
add_upload
(
processed_upload
)
assert_coe_upload
(
processed_upload
.
upload_hash
,
clean_repository_db
,
empty
=
empty
)
assert_coe_upload
(
processed_upload
.
upload_hash
,
empty
=
empty
)
@pytest.mark.timeout
(
10
)
@pytest.mark.timeout
(
10
)
...
@@ -157,10 +94,10 @@ def test_add_upload_metadata(clean_repository_db, processed_upload, other_test_u
...
@@ -157,10 +94,10 @@ def test_add_upload_metadata(clean_repository_db, processed_upload, other_test_u
'
references
'
:
[
'
http://external.ref/one
'
,
'
http://external.ref/two
'
],
'
references
'
:
[
'
http://external.ref/one
'
,
'
http://external.ref/two
'
],
'
_uploader
'
:
other_test_user
.
user_id
,
'
_uploader
'
:
other_test_user
.
user_id
,
'
coauthors
'
:
[
test_user
.
user_id
],
'
coauthors
'
:
[
test_user
.
user_id
],
'
_checksum
'
:
1
,
'
_checksum
'
:
'
1
'
,
'
_upload_time
'
:
datetime
.
datetime
.
now
().
isoformat
(),
'
_upload_time
'
:
datetime
.
datetime
.
now
().
isoformat
(),
'
_pid
'
:
256
'
_pid
'
:
256
}
}
add_upload
(
processed_upload
,
meta_data
=
meta_data
)
add_upload
(
processed_upload
,
meta_data
=
meta_data
)
assert_coe_upload
(
processed_upload
.
upload_hash
,
clean_repository_db
,
empty
=
empty
,
meta_data
=
meta_data
)
assert_coe_upload
(
processed_upload
.
upload_hash
,
empty
=
empty
,
meta_data
=
meta_data
)
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment