diff --git a/beat/web/databases/__init__.py b/beat/web/databases/__init__.py
index 93a15eb13994a4273d1626fb9e0113696b6fb263..e02b17d61b4a852e86e2da01954be6715046aae8 100644
--- a/beat/web/databases/__init__.py
+++ b/beat/web/databases/__init__.py
@@ -25,4 +25,4 @@
# #
###############################################################################
-default_app_config = 'beat.web.databases.apps.DatabasesConfig'
+default_app_config = "beat.web.databases.apps.DatabasesConfig"
diff --git a/beat/web/databases/admin.py b/beat/web/databases/admin.py
index 261c0f36aeba4e27414b2a61cf25cf311c2e8515..5af35497aba64ae2ba0339ee12bbd030c10b212a 100755
--- a/beat/web/databases/admin.py
+++ b/beat/web/databases/admin.py
@@ -25,11 +25,18 @@
# #
###############################################################################
+import simplejson as json
from django import forms
from django.contrib import admin
from django.core.files.base import ContentFile
-
+from ..common.admin import notify_by_email
+from ..common.models import Shareable
+from ..common.texts import Messages
+from ..ui.forms import CodeMirrorJSONFileField
+from ..ui.forms import CodeMirrorPythonFileField
+from ..ui.forms import CodeMirrorRSTFileField
+from ..ui.forms import NameField
from .models import Database as DatabaseModel
from .models import DatabaseProtocol as DatabaseProtocolModel
from .models import DatabaseSet as DatabaseSetModel
@@ -38,20 +45,6 @@ from .models import DatabaseSetTemplate as DatabaseSetTemplateModel
from .models import DatabaseSetTemplateOutput as DatabaseSetTemplateOutputModel
from .models import validate_database
-from ..ui.forms import (
- CodeMirrorJSONFileField,
- CodeMirrorRSTFileField,
- CodeMirrorPythonFileField,
- NameField,
-)
-
-from ..common.texts import Messages
-from ..common.admin import notify_by_email
-from ..common.models import Shareable
-
-import simplejson as json
-
-
# ------------------------------------------------
diff --git a/beat/web/databases/api.py b/beat/web/databases/api.py
index b076cb2ec4d35daf45c3dd1722907f2c4ff810f3..0763fda57db6bdd9de807d8033179f2afc450c2a 100755
--- a/beat/web/databases/api.py
+++ b/beat/web/databases/api.py
@@ -25,26 +25,24 @@
# #
###############################################################################
-import os
import json
import logging
+import os
-from rest_framework.response import Response
-from rest_framework import permissions as drf_permissions
from rest_framework import exceptions as drf_exceptions
+from rest_framework import permissions as drf_permissions
from rest_framework import views
-
-from .models import Database
-from .models import DatabaseSetTemplate
-
-from .serializers import DatabaseSerializer, DatabaseCreationSerializer
+from rest_framework.response import Response
from ..common import is_true
from ..common import permissions as beat_permissions
from ..common.api import ListCreateBaseView
from ..common.utils import ensure_html
-
from ..dataformats.serializers import ReferencedDataFormatSerializer
+from .models import Database
+from .models import DatabaseSetTemplate
+from .serializers import DatabaseCreationSerializer
+from .serializers import DatabaseSerializer
logger = logging.getLogger(__name__)
diff --git a/beat/web/databases/apps.py b/beat/web/databases/apps.py
index fd94461ab2849a1702de37129f7232f0690b97ad..64bdd0887ae9030166167f1ced80bd4326ca7fba 100644
--- a/beat/web/databases/apps.py
+++ b/beat/web/databases/apps.py
@@ -25,13 +25,16 @@
# #
###############################################################################
-from ..common.apps import CommonAppConfig
from django.utils.translation import ugettext_lazy as _
+from ..common.apps import CommonAppConfig
+
+
class DatabasesConfig(CommonAppConfig):
- name = 'beat.web.databases'
- verbose_name = _('Databases')
+ name = "beat.web.databases"
+ verbose_name = _("Databases")
def ready(self):
super(DatabasesConfig, self).ready()
- from . import signals
+
+ from . import signals # noqa: F401
diff --git a/beat/web/databases/exceptions.py b/beat/web/databases/exceptions.py
index d49916f3cef3126b98b971cade8dbabf5d928e93..23f16d2d60c32d64210dc4deb9fd1dc95dee5d00 100644
--- a/beat/web/databases/exceptions.py
+++ b/beat/web/databases/exceptions.py
@@ -28,8 +28,8 @@
"""
Database specific exceptions
"""
-
from ..common.exceptions import BaseCreationError
+
class DatabaseCreationError(BaseCreationError):
pass
diff --git a/beat/web/databases/migrations/0001_initial.py b/beat/web/databases/migrations/0001_initial.py
index c4f746df379e16e8f70cdabecf5d5de6e9d96baf..15a26287fcaaa9a18981241bf14abc38dc9ca710 100644
--- a/beat/web/databases/migrations/0001_initial.py
+++ b/beat/web/databases/migrations/0001_initial.py
@@ -27,99 +27,269 @@
from __future__ import unicode_literals
-from django.db import migrations, models
-import beat.web.code.models
-import beat.web.databases.models
from django.conf import settings
+from django.db import migrations
+from django.db import models
+
+import beat.web.code.models
import beat.web.common.models
+import beat.web.databases.models
class Migration(migrations.Migration):
dependencies = [
- ('dataformats', '0001_initial'),
+ ("dataformats", "0001_initial"),
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
- ('team', '0001_initial'),
+ ("team", "0001_initial"),
]
operations = [
migrations.CreateModel(
- name='Database',
+ name="Database",
fields=[
- ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
- ('sharing', models.CharField(default='P', max_length=1, choices=[('P', 'Private'), ('S', 'Shared'), ('A', 'Public'), ('U', 'Usable')])),
- ('name', models.CharField(help_text='The name for this object (space-like characters will be automatically replaced by dashes)', max_length=200)),
- ('version', models.PositiveIntegerField(default=1, help_text='The version of this object (an integer starting from 1)')),
- ('short_description', models.CharField(default='', help_text='Describe the object succinctly (try to keep it under 80 characters)', max_length=100, blank=True)),
- ('creation_date', models.DateTimeField(auto_now_add=True, verbose_name='Creation date')),
- ('hash', models.CharField(help_text='Hashed value of the object contents (<a href="https://docs.python.org/2/library/hashlib.html">SHA256, hexadecimal digest</a>). This field is auto-generated and managed by the platform.', max_length=64, editable=False)),
- ('declaration_file', models.FileField(db_column='declaration', upload_to=beat.web.common.models.get_contribution_declaration_filename, storage=beat.web.databases.models.DatabaseStorage(), max_length=200, blank=True, null=True)),
- ('description_file', models.FileField(db_column='description', upload_to=beat.web.common.models.get_contribution_description_filename, storage=beat.web.databases.models.DatabaseStorage(), max_length=200, blank=True, null=True)),
- ('source_code_file', models.FileField(db_column='source_code', upload_to=beat.web.code.models.get_contribution_source_code_filename, storage=beat.web.databases.models.DatabaseStorage(), max_length=200, blank=True, null=True)),
- ('fork_of', models.ForeignKey(related_name='forks', blank=True, to='databases.Database', null=True, on_delete=models.SET_NULL)),
- ('previous_version', models.ForeignKey(related_name='next_versions', blank=True, to='databases.Database', null=True, on_delete=models.CASCADE)),
- ('shared_with', models.ManyToManyField(related_name='shared_databases', to=settings.AUTH_USER_MODEL, blank=True)),
- ('shared_with_team', models.ManyToManyField(related_name='shared_databases', to='team.Team', blank=True)),
+ (
+ "id",
+ models.AutoField(
+ verbose_name="ID",
+ serialize=False,
+ auto_created=True,
+ primary_key=True,
+ ),
+ ),
+ (
+ "sharing",
+ models.CharField(
+ default="P",
+ max_length=1,
+ choices=[
+ ("P", "Private"),
+ ("S", "Shared"),
+ ("A", "Public"),
+ ("U", "Usable"),
+ ],
+ ),
+ ),
+ (
+ "name",
+ models.CharField(
+ help_text="The name for this object (space-like characters will be automatically replaced by dashes)",
+ max_length=200,
+ ),
+ ),
+ (
+ "version",
+ models.PositiveIntegerField(
+ default=1,
+ help_text="The version of this object (an integer starting from 1)",
+ ),
+ ),
+ (
+ "short_description",
+ models.CharField(
+ default="",
+ help_text="Describe the object succinctly (try to keep it under 80 characters)",
+ max_length=100,
+ blank=True,
+ ),
+ ),
+ (
+ "creation_date",
+ models.DateTimeField(
+ auto_now_add=True, verbose_name="Creation date"
+ ),
+ ),
+ (
+ "hash",
+ models.CharField(
+ help_text='Hashed value of the object contents (<a href="https://docs.python.org/2/library/hashlib.html">SHA256, hexadecimal digest</a>). This field is auto-generated and managed by the platform.',
+ max_length=64,
+ editable=False,
+ ),
+ ),
+ (
+ "declaration_file",
+ models.FileField(
+ db_column="declaration",
+ upload_to=beat.web.common.models.get_contribution_declaration_filename,
+ storage=beat.web.databases.models.DatabaseStorage(),
+ max_length=200,
+ blank=True,
+ null=True,
+ ),
+ ),
+ (
+ "description_file",
+ models.FileField(
+ db_column="description",
+ upload_to=beat.web.common.models.get_contribution_description_filename,
+ storage=beat.web.databases.models.DatabaseStorage(),
+ max_length=200,
+ blank=True,
+ null=True,
+ ),
+ ),
+ (
+ "source_code_file",
+ models.FileField(
+ db_column="source_code",
+ upload_to=beat.web.code.models.get_contribution_source_code_filename,
+ storage=beat.web.databases.models.DatabaseStorage(),
+ max_length=200,
+ blank=True,
+ null=True,
+ ),
+ ),
+ (
+ "fork_of",
+ models.ForeignKey(
+ related_name="forks",
+ blank=True,
+ to="databases.Database",
+ null=True,
+ on_delete=models.SET_NULL,
+ ),
+ ),
+ (
+ "previous_version",
+ models.ForeignKey(
+ related_name="next_versions",
+ blank=True,
+ to="databases.Database",
+ null=True,
+ on_delete=models.CASCADE,
+ ),
+ ),
+ (
+ "shared_with",
+ models.ManyToManyField(
+ related_name="shared_databases",
+ to=settings.AUTH_USER_MODEL,
+ blank=True,
+ ),
+ ),
+ (
+ "shared_with_team",
+ models.ManyToManyField(
+ related_name="shared_databases", to="team.Team", blank=True
+ ),
+ ),
],
),
migrations.CreateModel(
- name='DatabaseOutput',
+ name="DatabaseOutput",
fields=[
- ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
- ('name', models.CharField(max_length=200)),
- ('dataformat', models.ForeignKey(related_name='database_outputs', to='dataformats.DataFormat', on_delete=models.CASCADE)),
+ (
+ "id",
+ models.AutoField(
+ verbose_name="ID",
+ serialize=False,
+ auto_created=True,
+ primary_key=True,
+ ),
+ ),
+ ("name", models.CharField(max_length=200)),
+ (
+ "dataformat",
+ models.ForeignKey(
+ related_name="database_outputs",
+ to="dataformats.DataFormat",
+ on_delete=models.CASCADE,
+ ),
+ ),
],
),
migrations.CreateModel(
- name='DatabaseProtocol',
+ name="DatabaseProtocol",
fields=[
- ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
- ('name', models.CharField(max_length=200, blank=True)),
- ('database', models.ForeignKey(related_name='protocols', to='databases.Database', on_delete=models.CASCADE)),
+ (
+ "id",
+ models.AutoField(
+ verbose_name="ID",
+ serialize=False,
+ auto_created=True,
+ primary_key=True,
+ ),
+ ),
+ ("name", models.CharField(max_length=200, blank=True)),
+ (
+ "database",
+ models.ForeignKey(
+ related_name="protocols",
+ to="databases.Database",
+ on_delete=models.CASCADE,
+ ),
+ ),
],
- options={
- 'ordering': ['name'],
- },
+ options={"ordering": ["name"]},
),
migrations.CreateModel(
- name='DatabaseSet',
+ name="DatabaseSet",
fields=[
- ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
- ('name', models.CharField(max_length=200, blank=True)),
- ('protocol', models.ForeignKey(related_name='sets', to='databases.DatabaseProtocol', on_delete=models.CASCADE)),
+ (
+ "id",
+ models.AutoField(
+ verbose_name="ID",
+ serialize=False,
+ auto_created=True,
+ primary_key=True,
+ ),
+ ),
+ ("name", models.CharField(max_length=200, blank=True)),
+ (
+ "protocol",
+ models.ForeignKey(
+ related_name="sets",
+ to="databases.DatabaseProtocol",
+ on_delete=models.CASCADE,
+ ),
+ ),
],
),
migrations.CreateModel(
- name='DatabaseSetTemplate',
+ name="DatabaseSetTemplate",
fields=[
- ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
- ('name', models.CharField(unique=True, max_length=200)),
+ (
+ "id",
+ models.AutoField(
+ verbose_name="ID",
+ serialize=False,
+ auto_created=True,
+ primary_key=True,
+ ),
+ ),
+ ("name", models.CharField(unique=True, max_length=200)),
],
),
migrations.AddField(
- model_name='databaseset',
- name='template',
- field=models.ForeignKey(related_name='sets', to='databases.DatabaseSetTemplate', on_delete=models.CASCADE),
+ model_name="databaseset",
+ name="template",
+ field=models.ForeignKey(
+ related_name="sets",
+ to="databases.DatabaseSetTemplate",
+ on_delete=models.CASCADE,
+ ),
),
migrations.AddField(
- model_name='databaseoutput',
- name='template',
- field=models.ForeignKey(related_name='outputs', to='databases.DatabaseSetTemplate', on_delete=models.CASCADE),
+ model_name="databaseoutput",
+ name="template",
+ field=models.ForeignKey(
+ related_name="outputs",
+ to="databases.DatabaseSetTemplate",
+ on_delete=models.CASCADE,
+ ),
),
migrations.AlterUniqueTogether(
- name='databaseset',
- unique_together=set([('protocol', 'name', 'template')]),
+ name="databaseset", unique_together=set([("protocol", "name", "template")]),
),
migrations.AlterUniqueTogether(
- name='databaseprotocol',
- unique_together=set([('database', 'name')]),
+ name="databaseprotocol", unique_together=set([("database", "name")]),
),
migrations.AlterUniqueTogether(
- name='databaseoutput',
- unique_together=set([('template', 'name', 'dataformat')]),
+ name="databaseoutput",
+ unique_together=set([("template", "name", "dataformat")]),
),
migrations.AlterUniqueTogether(
- name='database',
- unique_together=set([('name', 'version')]),
+ name="database", unique_together=set([("name", "version")]),
),
]
diff --git a/beat/web/databases/migrations/0002_scheduler_addons.py b/beat/web/databases/migrations/0002_scheduler_addons.py
index 4e9fe7730a13d272c124dba88c1e581f787e614d..b7202d09898f18832071f10ccad8a2494e7f6572 100644
--- a/beat/web/databases/migrations/0002_scheduler_addons.py
+++ b/beat/web/databases/migrations/0002_scheduler_addons.py
@@ -23,31 +23,32 @@
# with the BEAT platform. If not, see http://www.gnu.org/licenses/. #
# #
###############################################################################
-
from __future__ import unicode_literals
-from django.db import migrations, models
+import logging
-from ...common.models import get_declaration
+from django.db import migrations
+from django.db import models
+from ...common.models import get_declaration
from ..models import validate_database
-import logging
logger = logging.getLogger(__name__)
def refresh_databases(apps, schema_editor):
- '''Refreshes each database so datasets/outputs are recreated'''
+ """Refreshes each database so datasets/outputs are recreated"""
Database = apps.get_model("databases", "Database")
DatabaseSetOutput = apps.get_model("databases", "DatabaseSetOutput")
Database.declaration = property(get_declaration)
- Database.fullname = lambda self: '%s/%d' % (self.name, self.version)
+ Database.fullname = lambda self: "%s/%d" % (self.name, self.version)
- if Database.objects.count(): print('')
+ if Database.objects.count():
+ print("")
- for db in Database.objects.order_by('id'):
+ for db in Database.objects.order_by("id"):
print("Refreshing protocols for database `%s'..." % db.fullname())
core = validate_database(db.declaration)
core.name = db.fullname()
@@ -55,36 +56,62 @@ def refresh_databases(apps, schema_editor):
for set in proto.sets.all():
for output in set.template.outputs.all():
try:
- DatabaseSetOutput(template=output, set=set,
- hash=core.hash_output(proto.name, set.name,
- output.name)).save()
+ DatabaseSetOutput(
+ template=output,
+ set=set,
+ hash=core.hash_output(proto.name, set.name, output.name),
+ ).save()
except KeyError:
- logger.warn('Database output %s/%d.%s.%s.%s does ' \
- 'not exist' % (db.name, db.version, proto.name,
- set.name, output.name))
+ logger.warn(
+ "Database output %s/%d.%s.%s.%s does "
+ "not exist"
+ % (db.name, db.version, proto.name, set.name, output.name)
+ )
continue
class Migration(migrations.Migration):
dependencies = [
- ('dataformats', '0001_initial'),
- ('databases', '0001_initial'),
+ ("dataformats", "0001_initial"),
+ ("databases", "0001_initial"),
]
operations = [
- migrations.RenameModel('DatabaseOutput', 'DatabaseSetTemplateOutput'),
+ migrations.RenameModel("DatabaseOutput", "DatabaseSetTemplateOutput"),
migrations.AlterUniqueTogether(
- name='databasesettemplateoutput',
- unique_together=set([('template', 'name')]),
+ name="databasesettemplateoutput",
+ unique_together=set([("template", "name")]),
),
migrations.CreateModel(
- name='DatabaseSetOutput',
+ name="DatabaseSetOutput",
fields=[
- ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
- ('hash', models.CharField(unique=True, max_length=64)),
- ('set', models.ForeignKey(related_name='outputs', to='databases.DatabaseSet', on_delete=models.CASCADE)),
- ('template', models.ForeignKey(related_name='instances', to='databases.DatabaseSetTemplateOutput', on_delete=models.CASCADE)),
+ (
+ "id",
+ models.AutoField(
+ verbose_name="ID",
+ serialize=False,
+ auto_created=True,
+ primary_key=True,
+ ),
+ ),
+ ("hash", models.CharField(unique=True, max_length=64)),
+ (
+ "set",
+ models.ForeignKey(
+ related_name="outputs",
+ to="databases.DatabaseSet",
+ on_delete=models.CASCADE,
+ ),
+ ),
+ (
+ "template",
+ models.ForeignKey(
+ related_name="instances",
+ to="databases.DatabaseSetTemplateOutput",
+ on_delete=models.CASCADE,
+ ),
+ ),
],
),
migrations.RunPython(refresh_databases),
diff --git a/beat/web/databases/migrations/0003_auto_20160704_1316.py b/beat/web/databases/migrations/0003_auto_20160704_1316.py
index 575732e942c2085e146b3697b3c75e0c1ff578b5..deb0e0444de508aa9f72abe602a35ff5076af03c 100644
--- a/beat/web/databases/migrations/0003_auto_20160704_1316.py
+++ b/beat/web/databases/migrations/0003_auto_20160704_1316.py
@@ -8,12 +8,11 @@ from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
- ('databases', '0002_scheduler_addons'),
+ ("databases", "0002_scheduler_addons"),
]
operations = [
migrations.AlterModelOptions(
- name='database',
- options={'ordering': ['name', '-version']},
+ name="database", options={"ordering": ["name", "-version"]},
),
]
diff --git a/beat/web/databases/migrations/0004_beat_backend_python_1_5_x.py b/beat/web/databases/migrations/0004_beat_backend_python_1_5_x.py
index 35960a975d955dcf8a600f0075bf1465193de8d5..3aac3b1490ddf7a6dc03594548ca808b63748d02 100644
--- a/beat/web/databases/migrations/0004_beat_backend_python_1_5_x.py
+++ b/beat/web/databases/migrations/0004_beat_backend_python_1_5_x.py
@@ -2,24 +2,22 @@
# Generated by Django 1.9.13 on 2018-01-25 09:06
from __future__ import unicode_literals
-from django.db import migrations, models
+from django.db import migrations
+from django.db import models
class Migration(migrations.Migration):
dependencies = [
- ('databases', '0003_auto_20160704_1316'),
+ ("databases", "0003_auto_20160704_1316"),
]
operations = [
- migrations.RemoveField(
- model_name='databasesetoutput',
- name='hash',
- ),
+ migrations.RemoveField(model_name="databasesetoutput", name="hash",),
migrations.AddField(
- model_name='databaseset',
- name='hash',
- field=models.CharField(default='', max_length=64),
+ model_name="databaseset",
+ name="hash",
+ field=models.CharField(default="", max_length=64),
preserve_default=False,
),
]
diff --git a/beat/web/databases/migrations/0005_databaseset_data_migration.py b/beat/web/databases/migrations/0005_databaseset_data_migration.py
index 44a24f1c840357d8442504e1f56b9a3d9fcbbdd4..4dc4fa249ceef4fd3bcd466549c978d57c415a7f 100644
--- a/beat/web/databases/migrations/0005_databaseset_data_migration.py
+++ b/beat/web/databases/migrations/0005_databaseset_data_migration.py
@@ -2,33 +2,42 @@
# Generated by Django 1.9.13 on 2018-01-25 09:06
from __future__ import unicode_literals
-from django.db import migrations, models
+from django.db import migrations
from beat.backend.python.hash import hashDataset
def compute_hashes(apps, schema_editor):
- '''Refreshes each database so datasets/outputs are recreated'''
+ """Refreshes each database so datasets/outputs are recreated"""
DatabaseSet = apps.get_model("databases", "DatabaseSet")
if DatabaseSet.objects.count():
- print('')
-
- for db_set in DatabaseSet.objects.order_by('id'):
- print("Computing hashes for database set '%s/%d/%s/%s'..." % \
- (db_set.protocol.database.name, db_set.protocol.database.version,
- db_set.protocol.name, db_set.name))
-
- db_set.hash = hashDataset('%s/%d' % (db_set.protocol.database.name, db_set.protocol.database.version),
- db_set.protocol.name, db_set.name)
+ print("")
+
+ for db_set in DatabaseSet.objects.order_by("id"):
+ print(
+ "Computing hashes for database set '%s/%d/%s/%s'..."
+ % (
+ db_set.protocol.database.name,
+ db_set.protocol.database.version,
+ db_set.protocol.name,
+ db_set.name,
+ )
+ )
+
+ db_set.hash = hashDataset(
+ "%s/%d" % (db_set.protocol.database.name, db_set.protocol.database.version),
+ db_set.protocol.name,
+ db_set.name,
+ )
db_set.save()
class Migration(migrations.Migration):
dependencies = [
- ('databases', '0004_beat_backend_python_1_5_x'),
+ ("databases", "0004_beat_backend_python_1_5_x"),
]
operations = [
diff --git a/beat/web/databases/migrations/0006_databaseset_hash_unique.py b/beat/web/databases/migrations/0006_databaseset_hash_unique.py
index 8ce33badee0597b74533ae8b930218e7847362e5..51dab6b5c20d0924ddfca8615636c7a158d0f1a6 100644
--- a/beat/web/databases/migrations/0006_databaseset_hash_unique.py
+++ b/beat/web/databases/migrations/0006_databaseset_hash_unique.py
@@ -2,19 +2,20 @@
# Generated by Django 1.9.13 on 2018-01-25 09:06
from __future__ import unicode_literals
-from django.db import migrations, models
+from django.db import migrations
+from django.db import models
class Migration(migrations.Migration):
dependencies = [
- ('databases', '0005_databaseset_data_migration'),
+ ("databases", "0005_databaseset_data_migration"),
]
operations = [
migrations.AlterField(
- model_name='databaseset',
- name='hash',
+ model_name="databaseset",
+ name="hash",
field=models.CharField(max_length=64, unique=True),
preserve_default=False,
),
diff --git a/beat/web/databases/migrations/0007_add_accessibility_date.py b/beat/web/databases/migrations/0007_add_accessibility_date.py
index 802aa1bcd0b7e903e6d51b88638784a6f78aff4d..d128d33a77a664e95182896c5fc0fbcab8c5c640 100644
--- a/beat/web/databases/migrations/0007_add_accessibility_date.py
+++ b/beat/web/databases/migrations/0007_add_accessibility_date.py
@@ -2,7 +2,8 @@
# Generated by Django 1.11.25 on 2020-02-12 11:22
from __future__ import unicode_literals
-from django.db import migrations, models
+from django.db import migrations
+from django.db import models
class Migration(migrations.Migration):
diff --git a/beat/web/databases/models.py b/beat/web/databases/models.py
index bc51fa22a63f0078daf978aa9f0a674d81f30415..6df73c4ce799a1b3831bdac4ae6d4c591c5cedf3 100755
--- a/beat/web/databases/models.py
+++ b/beat/web/databases/models.py
@@ -26,38 +26,32 @@
###############################################################################
import os
-
-import simplejson
-
from datetime import datetime
-from django.db import models
+import simplejson
from django.conf import settings
-from django.urls import reverse
+from django.db import models
from django.db.models import Q
+from django.urls import reverse
import beat.core.database
from beat.backend.python.hash import hashDataset
-from ..dataformats.models import DataFormat
-
+from ..code.models import get_contribution_source_code_filename
+from ..code.models import get_source_code
+from ..code.models import set_source_code
+from ..common import storage
from ..common.models import Versionable
from ..common.models import VersionableManager
-from ..common.storage import OverwriteStorage
-from ..common import storage
-
from ..common.models import get_contribution_declaration_filename
from ..common.models import get_contribution_description_filename
-from ..code.models import get_contribution_source_code_filename
-
-from ..common.models import get_description
-from ..common.models import set_description
from ..common.models import get_declaration
-from ..common.models import set_declaration
from ..common.models import get_declaration_string
-from ..code.models import get_source_code
-from ..code.models import set_source_code
-
+from ..common.models import get_description
+from ..common.models import set_declaration
+from ..common.models import set_description
+from ..common.storage import OverwriteStorage
+from ..dataformats.models import DataFormat
# ----------------------------------------------------------
diff --git a/beat/web/databases/serializers.py b/beat/web/databases/serializers.py
index 56d35a078887d1bb3633ce1830f33aaafa062f7a..c6c3ff4598d869d175b7b8754977dbf10d077d7f 100644
--- a/beat/web/databases/serializers.py
+++ b/beat/web/databases/serializers.py
@@ -26,16 +26,14 @@
###############################################################################
from django.conf import settings
-
from rest_framework import serializers
-from ..common.serializers import VersionableSerializer
-from ..common import fields as beat_fields
+import beat.core.database
-from .models import Database
+from ..common import fields as beat_fields
+from ..common.serializers import VersionableSerializer
from .exceptions import DatabaseCreationError
-
-import beat.core.database
+from .models import Database
class DatabaseSerializer(VersionableSerializer):
diff --git a/beat/web/databases/signals.py b/beat/web/databases/signals.py
index 8732721847a19858f54ae6762b378a4d4b2e8705..8dde23a02afb94818b261d43d37133092d6b8ba6 100755
--- a/beat/web/databases/signals.py
+++ b/beat/web/databases/signals.py
@@ -30,11 +30,12 @@ from django.db import models
from django.dispatch import receiver
from ..dataformats.models import DataFormat
-
-from .models import Database, DatabaseProtocol, DatabaseSet
-from .models import DatabaseSetTemplate, DatabaseSetTemplateOutput
+from .models import Database
+from .models import DatabaseProtocol
+from .models import DatabaseSet
from .models import DatabaseSetOutput
-
+from .models import DatabaseSetTemplate
+from .models import DatabaseSetTemplateOutput
from .models import validate_database
@@ -94,18 +95,17 @@ def refresh_protocols(sender, instance, **kwargs):
core.name = instance.fullname()
protocols = DatabaseProtocol.objects.filter(
- database__name=instance.name,
- database__version=instance.version,
+ database__name=instance.name, database__version=instance.version,
)
existing = set((k.name, k.set_template_basename()) for k in protocols)
- new_objects = set([(k,v['template']) for k,v in core.protocols.items()])
+ new_objects = set([(k, v["template"]) for k, v in core.protocols.items()])
for protocol_name, template in existing - new_objects:
# notice: no need to worry, this will clean-up all the rest
protocols.get(name__iexact=protocol_name).delete()
- json_protocols = dict([(k,v) for k,v in core.protocols.items()])
+ json_protocols = dict([(k, v) for k, v in core.protocols.items()])
for protocol_name, template in new_objects - existing:
protocol = DatabaseProtocol(name=protocol_name, database=instance)
@@ -114,12 +114,12 @@ def refresh_protocols(sender, instance, **kwargs):
json_protocol = json_protocols[protocol_name]
# creates all the template sets, outputs, etc for the first time
- for set_attr in json_protocol['sets']:
+ for set_attr in json_protocol["sets"]:
- tset_name = json_protocol['template'] + '__' + set_attr['template']
+ tset_name = json_protocol["template"] + "__" + set_attr["template"]
dataset_template = DatabaseSetTemplate.objects.filter(name=tset_name)
- if not dataset_template: #create
+ if not dataset_template: # create
dataset_template = DatabaseSetTemplate(name=tset_name)
dataset_template.save()
else:
@@ -127,78 +127,70 @@ def refresh_protocols(sender, instance, **kwargs):
# Create the database set
dataset = DatabaseSet.objects.filter(
- name = set_attr['name'],
- template = dataset_template,
- protocol = protocol,
+ name=set_attr["name"], template=dataset_template, protocol=protocol,
)
- if not dataset: #create
+ if not dataset: # create
dataset = DatabaseSet.objects.create(
- name = set_attr['name'],
- template = dataset_template,
- protocol = protocol,
+ name=set_attr["name"],
+ template=dataset_template,
+ protocol=protocol,
)
# Create the database set template output
- for output_name, format_name in set_attr['outputs'].items():
- if len(format_name.split('/')) != 3:
+ for output_name, format_name in set_attr["outputs"].items():
+ if len(format_name.split("/")) != 3:
raise SyntaxError(
- "Dataformat should be named following the " \
- "style `<username>/<format>/<version>', the " \
+ "Dataformat should be named following the "
+ "style `<username>/<format>/<version>', the "
"value `%s' is not valid" % (format_name,)
)
- (author, name, version) = format_name.split('/')
+ (author, name, version) = format_name.split("/")
dataformats = DataFormat.objects.filter(
- author__username=author,
- name=name,
- version=version,
+ author__username=author, name=name, version=version,
)
# TODO: Remove this when validation works (see comments)
if len(dataformats) != 1:
raise SyntaxError(
- "Could not find dataformat named `%s' to set" \
- "output `%s' of template `%s' for protocol" \
- "`%s' of database `%s'", (
+ "Could not find dataformat named `%s' to set"
+ "output `%s' of template `%s' for protocol"
+ "`%s' of database `%s'",
+ (
format_name,
- output_name,
- dataset_template.name,
- protocol_name,
- instance.name,
- )
+ output_name,
+ dataset_template.name,
+ protocol_name,
+ instance.name,
+ ),
)
return
- database_template_output = \
- DatabaseSetTemplateOutput.objects.filter(
+ database_template_output = DatabaseSetTemplateOutput.objects.filter(
+ name=output_name,
+ template=dataset_template,
+ dataformat=dataformats[0],
+ )
+
+ if not database_template_output: # create
+ database_template_output = DatabaseSetTemplateOutput(
name=output_name,
template=dataset_template,
dataformat=dataformats[0],
)
-
- if not database_template_output: # create
- database_template_output = \
- DatabaseSetTemplateOutput(
- name=output_name,
- template=dataset_template,
- dataformat=dataformats[0],
- )
database_template_output.save()
else:
- database_template_output = \
- database_template_output[0]
+ database_template_output = database_template_output[0]
# Create the database set output
- dataset_output = \
- DatabaseSetOutput.objects.filter(template=database_template_output,
- set=dataset,
- )
+ dataset_output = DatabaseSetOutput.objects.filter(
+ template=database_template_output, set=dataset,
+ )
- if not dataset_output: # create
+ if not dataset_output: # create
dataset_output = DatabaseSetOutput(
- template=database_template_output,
- set=dataset,
+ template=database_template_output, set=dataset,
)
dataset_output.save()
@@ -210,8 +202,9 @@ def refresh_protocols(sender, instance, **kwargs):
@receiver(models.signals.post_delete, sender=DatabaseSet)
def delete_empty_template_sets(sender, **kwargs):
- instance = kwargs['instance']
+ instance = kwargs["instance"]
try:
- if not instance.template.sets.all(): instance.template.delete()
- except:
+ if not instance.template.sets.all():
+ instance.template.delete()
+ except Exception: # nosec
pass
diff --git a/beat/web/databases/templates/databases/list.html b/beat/web/databases/templates/databases/list.html
index 8eb2bc1742e38f5ddecc56312bedf11941e78e25..82918f6199789a71294411edfe718341d87556f4 100644
--- a/beat/web/databases/templates/databases/list.html
+++ b/beat/web/databases/templates/databases/list.html
@@ -2,21 +2,21 @@
{% comment %}
* Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
* Contact: beat.support@idiap.ch
- *
+ *
* This file is part of the beat.web module of the BEAT platform.
- *
+ *
* Commercial License Usage
* Licensees holding valid commercial BEAT licenses may use this file in
* accordance with the terms contained in a written agreement between you
* and Idiap. For further information contact tto@idiap.ch
- *
+ *
* Alternatively, this file may be used under the terms of the GNU Affero
* Public License version 3 as published by the Free Software and appearing
* in the file LICENSE.AGPL included in the packaging of this file.
* The BEAT platform is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE.
- *
+ *
* You should have received a copy of the GNU Affero Public License along
* with the BEAT platform. If not, see http://www.gnu.org/licenses/.
{% endcomment %}
diff --git a/beat/web/databases/templates/databases/panels/actions.html b/beat/web/databases/templates/databases/panels/actions.html
index 3d231514a4058a56bd2ad3cf30e2aca4d4944acd..5bd21774ba1b752250ef2635a93fb04e43852d42 100644
--- a/beat/web/databases/templates/databases/panels/actions.html
+++ b/beat/web/databases/templates/databases/panels/actions.html
@@ -1,21 +1,21 @@
{% comment %}
* Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
* Contact: beat.support@idiap.ch
- *
+ *
* This file is part of the beat.web module of the BEAT platform.
- *
+ *
* Commercial License Usage
* Licensees holding valid commercial BEAT licenses may use this file in
* accordance with the terms contained in a written agreement between you
* and Idiap. For further information contact tto@idiap.ch
- *
+ *
* Alternatively, this file may be used under the terms of the GNU Affero
* Public License version 3 as published by the Free Software and appearing
* in the file LICENSE.AGPL included in the packaging of this file.
* The BEAT platform is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE.
- *
+ *
* You should have received a copy of the GNU Affero Public License along
* with the BEAT platform. If not, see http://www.gnu.org/licenses/.
{% endcomment %}
diff --git a/beat/web/databases/templates/databases/panels/table.html b/beat/web/databases/templates/databases/panels/table.html
index f0e0c3a8fda4263444d785bcedb17b06cecbf599..1a16d0eaf8b1c73b6bfbca736f7307252e893fb8 100644
--- a/beat/web/databases/templates/databases/panels/table.html
+++ b/beat/web/databases/templates/databases/panels/table.html
@@ -1,21 +1,21 @@
{% comment %}
* Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/
* Contact: beat.support@idiap.ch
- *
+ *
* This file is part of the beat.web module of the BEAT platform.
- *
+ *
* Commercial License Usage
* Licensees holding valid commercial BEAT licenses may use this file in
* accordance with the terms contained in a written agreement between you
* and Idiap. For further information contact tto@idiap.ch
- *
+ *
* Alternatively, this file may be used under the terms of the GNU Affero
* Public License version 3 as published by the Free Software and appearing
* in the file LICENSE.AGPL included in the packaging of this file.
* The BEAT platform is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE.
- *
+ *
* You should have received a copy of the GNU Affero Public License along
* with the BEAT platform. If not, see http://www.gnu.org/licenses/.
{% endcomment %}
diff --git a/beat/web/databases/templatetags/database_tags.py b/beat/web/databases/templatetags/database_tags.py
index c12366b44d4b0c1d7396de11951722d89c2bf676..fb476bf7dd6f014438eabe547bd0f00c0460c24f 100644
--- a/beat/web/databases/templatetags/database_tags.py
+++ b/beat/web/databases/templatetags/database_tags.py
@@ -28,13 +28,12 @@
from django import template
-
register = template.Library()
-@register.inclusion_tag('databases/panels/table.html', takes_context=True)
+@register.inclusion_tag("databases/panels/table.html", takes_context=True)
def database_table(context, objects, id):
- '''Composes a database list table
+ """Composes a database list table
This panel primarily exists for user's database list page.
@@ -44,18 +43,14 @@ def database_table(context, objects, id):
id: The HTML id to set on the generated table. This is handy for the
filter functionality normally available on list pages.
- '''
+ """
- return dict(
- request=context['request'],
- objects=objects,
- panel_id=id,
- )
+ return dict(request=context["request"], objects=objects, panel_id=id,)
-@register.inclusion_tag('databases/panels/actions.html', takes_context=True)
+@register.inclusion_tag("databases/panels/actions.html", takes_context=True)
def database_actions(context, object, display_count):
- '''Composes the action buttons for a particular database
+ """Composes the action buttons for a particular database
This panel primarily exists for showing action buttons for a given
database taking into consideration it is being displayed for a given user.
@@ -68,9 +63,5 @@ def database_actions(context, object, display_count):
display the number of protocols as a button (useful for the list
view)
- '''
- return dict(
- request=context['request'],
- object=object,
- display_count=display_count,
- )
+ """
+ return dict(request=context["request"], object=object, display_count=display_count,)
diff --git a/beat/web/databases/tests.py b/beat/web/databases/tests.py
index bd04208f3ac5f306a58ad7afeba13f4d6c5ef9b6..53b11da9223f7adfea074f3d8a77b15e0978574f 100644
--- a/beat/web/databases/tests.py
+++ b/beat/web/databases/tests.py
@@ -26,20 +26,17 @@
###############################################################################
import json
+from datetime import datetime
+from datetime import timedelta
-from datetime import datetime, timedelta
-
-from django.contrib.auth.models import User
from django.conf import settings
+from django.contrib.auth.models import User
from django.urls import reverse
-from .models import Database
-
-from ..dataformats.models import DataFormat
-
from ..common.testutils import BaseTestCase
from ..common.testutils import tearDownModule # noqa test runner will call it
-
+from ..dataformats.models import DataFormat
+from .models import Database
TEST_PWD = "1234" # nosec
diff --git a/beat/web/databases/views.py b/beat/web/databases/views.py
index b2e22661ff6f14fe271bf932755d341adb9ab823..66a5431d8023f2ae77fc9c91b432ed1484c5d4c7 100644
--- a/beat/web/databases/views.py
+++ b/beat/web/databases/views.py
@@ -39,30 +39,31 @@ def view(request, name, version=None):
if version is not None:
version = int(version)
- database = Database.objects.for_user(request.user, True).get(name__iexact=name,
- version=version)
+ database = Database.objects.for_user(request.user, True).get(
+ name__iexact=name, version=version
+ )
else:
- database = Database.objects.for_user(request.user, True).filter(name__iexact=name).order_by('-version')[0]
- except:
+ database = (
+ Database.objects.for_user(request.user, True)
+ .filter(name__iexact=name)
+ .order_by("-version")[0]
+ )
+ except Database.DoesNotExist:
raise Http404
# Render the page
- return render(request,
- 'databases/view.html',
- {'database': database})
+ return render(request, "databases/view.html", {"database": database})
def ls(request):
- '''List all accessible databases to the request user'''
+ """List all accessible databases to the request user"""
# orders databases so that the latest information is displayed first
- objects = Database.objects.for_user(request.user, True).order_by('-creation_date')
+ objects = Database.objects.for_user(request.user, True).order_by("-creation_date")
objects = Database.filter_latest_versions(objects)
- return render(request,
- 'databases/list.html',
- dict(
- objects=objects,
- author=request.user,
- owner=True,
- ))
+ return render(
+ request,
+ "databases/list.html",
+ dict(objects=objects, author=request.user, owner=True,),
+ )