How to use the resolwe.flow.models.Collection function in resolwe

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github genialis / resolwe / resolwe / flow / views.py View on Github external
def create(self, request, *args, **kwargs):
        """Create a resource."""
        collections = request.data.get('collections', [])

        # check that user has permissions on all collections that Data
        # object will be added to
        for collection_id in collections:
            try:
                collection = Collection.objects.get(pk=collection_id)
            except Collection.DoesNotExist:
                return Response({'collections': ['Invalid pk "{}" - object does not exist.'.format(collection_id)]},
                                status=status.HTTP_400_BAD_REQUEST)

            if not request.user.has_perm('add_collection', obj=collection):
                if request.user.is_authenticated():
                    raise exceptions.PermissionDenied
                else:
                    raise exceptions.NotFound

        # translate processe's slug to id
        process_slug = request.data.get('process', None)
        process_query = Process.objects.filter(slug=process_slug)
        process_query = get_objects_for_user(request.user, 'view_process', process_query)
        try:
            process = process_query.latest()
        except Process.DoesNotExist:
github genialis / resolwe / resolwe / flow / views.py View on Github external
def create(self, request, *args, **kwargs):
        """Create a resource."""
        collections = request.data.get('collections', [])

        # check that user has permissions on all collections that Data
        # object will be added to
        for collection_id in collections:
            try:
                collection = Collection.objects.get(pk=collection_id)
            except Collection.DoesNotExist:
                return Response({'collections': ['Invalid pk "{}" - object does not exist.'.format(collection_id)]},
                                status=status.HTTP_400_BAD_REQUEST)

            if not request.user.has_perm('add_collection', obj=collection):
                if request.user.is_authenticated():
                    raise exceptions.PermissionDenied
                else:
                    raise exceptions.NotFound

        # translate processe's slug to id
        process_slug = request.data.get('process', None)
        process_query = Process.objects.filter(slug=process_slug)
        process_query = get_objects_for_user(request.user, 'view_process', process_query)
        try:
            process = process_query.latest()
github genialis / resolwe / resolwe / flow / models.py View on Github external
"""Postgres model for storing entities."""

    class Meta(BaseCollection.Meta):
        """Entity Meta options."""

        permissions = (
            ("view_entity", "Can view entity"),
            ("edit_entity", "Can edit entity"),
            ("share_entity", "Can share entity"),
            ("download_entity", "Can download files from entity"),
            ("add_entity", "Can add data objects to entity"),
            ("owner_entity", "Is owner of the entity"),
        )

    #: list of collections to which entity belongs
    collections = models.ManyToManyField(Collection)


def iterate_fields(fields, schema, path_prefix=None):
    """Iterate over all field values sub-fields.

    This will iterate over all field values. Some fields defined in the schema
    might not be visited.

    :param fields: field values to iterate over
    :type fields: dict
    :param schema: schema to iterate over
    :type schema: dict
    :return: (field schema, field value)
    :rtype: tuple

    """
github genialis / resolwe / resolwe / flow / management / commands / genesis_migrate.py View on Github external
def clear_database(self):
        """Clear data base."""
        for model in [Collection, Data, Process, Storage, DescriptorSchema,
                      GroupObjectPermission, UserObjectPermission]:
            model.objects.all().delete()
github genialis / resolwe / resolwe / flow / views / data.py View on Github external
ResolweCheckSlugMixin,
    ParametersMixin,
    viewsets.GenericViewSet,
):
    """API view for :class:`Data` objects."""

    qs_collection_ds = DescriptorSchema.objects.select_related("contributor")
    qs_collection = Collection.objects.select_related("contributor")
    qs_collection = qs_collection.prefetch_related(
        "data", "entity_set", Prefetch("descriptor_schema", queryset=qs_collection_ds),
    )

    qs_descriptor_schema = DescriptorSchema.objects.select_related("contributor")

    qs_entity_col_ds = DescriptorSchema.objects.select_related("contributor")
    qs_entity_col = Collection.objects.select_related("contributor")
    qs_entity_col = qs_entity_col.prefetch_related(
        "data", "entity_set", Prefetch("descriptor_schema", queryset=qs_entity_col_ds),
    )
    qs_entity_ds = DescriptorSchema.objects.select_related("contributor")
    qs_entity = Entity.objects.select_related("contributor")
    qs_entity = qs_entity.prefetch_related(
        "data",
        Prefetch("collection", queryset=qs_entity_col),
        Prefetch("descriptor_schema", queryset=qs_entity_ds),
    )

    qs_process = Process.objects.select_related("contributor")

    queryset = Data.objects.select_related("contributor").prefetch_related(
        Prefetch("collection", queryset=qs_collection),
        Prefetch("descriptor_schema", queryset=qs_descriptor_schema),
github genialis / resolwe / resolwe / flow / management / commands / genesis_migrate.py View on Github external
new.started = data[u'date_start']
            new.finished = data[u'date_finish']
        elif u'date_finish' in data:
            new.started = data[u'date_finish']
            new.finished = data[u'date_finish']
        elif u'date_start' in data:
            new.started = data[u'date_start']
            new.finished = data[u'date_start']
        else:
            new.started = datetime.fromtimestamp(0)
            new.finished = datetime.fromtimestamp(0)
        new.save()

        for case_id in data[u'case_ids']:
            try:
                collection = Collection.objects.get(pk=self.id_mapping[u'collection'][str(case_id)])
            except KeyError:
                self.missing_collections.add(str(case_id))
                continue
            collection.data.add(new)

        for field_schema, fields, path in iterate_fields(data[u'output'], data[u'output_schema'], ''):
            if 'type' in field_schema and field_schema['type'].startswith('basic:json:'):
                self.storage_index[fields[field_schema['name']]] = {
                    'id': new.pk,
                    'path': path,
                }

        self.migrate_permissions(new, data)

        self.id_mapping['data'][str(data[u'_id'])] = new.pk
github genialis / resolwe / resolwe / flow / views / collection.py View on Github external
class BaseCollectionViewSet(
    ResolweCreateModelMixin,
    mixins.RetrieveModelMixin,
    ResolweUpdateModelMixin,
    mixins.DestroyModelMixin,
    mixins.ListModelMixin,
    ResolwePermissionsMixin,
    ResolweCheckSlugMixin,
    ParametersMixin,
    viewsets.GenericViewSet,
):
    """Base API view for :class:`Collection` objects."""

    qs_descriptor_schema = DescriptorSchema.objects.select_related("contributor")

    queryset = Collection.objects.select_related("contributor").prefetch_related(
        Prefetch("descriptor_schema", queryset=qs_descriptor_schema),
    )

    filter_class = CollectionFilter
    permission_classes = (get_permissions_class(),)

    ordering_fields = (
        "contributor",
        "contributor__first_name",
        "contributor__last_name",
        "created",
        "id",
        "modified",
        "name",
    )
    ordering = "id"