Updated Schema with is_circular and type for assembly_sequence ✨ ✅

[dpopleton]

Both of these new values are properly updated in the assembly_sequence updater function. Full test coverage of all reasonable cases is provided in core_1
✨ ✅

[marcoooo]

there is no data in tests related to this feature. Shouldn't you add some?

[dpopleton]

there is no data in tests related to this feature. Shouldn't you add some?

Please check out the changes in the tests. There is full coverage for this feature.

[marcoooo]

there is no data in tests related to this feature. Shouldn't you add some?

Please check out the changes in the tests. There is full coverage for this feature.

I didn't see any data in new txt dump files with other values than chromosomal 0 doesn't that mean we don't have any data with a circular or non chromosomal sequence?

[dpopleton]

there is no data in tests related to this feature. Shouldn't you add some?

Please check out the changes in the tests. There is full coverage for this feature.

I didn't see any data in new txt dump files with other values than chromosomal 0 doesn't that mean we don't have any data with a circular or non chromosomal sequence?

See src/tests/databases/core_1/attrib_type.txt
and src/tests/databases/core_1/seq_region_attrib.txt
These are tested in test new organism which has three sequences. One is marked as circular, one is marked as not circular, while the third has no circular attribute.
These are each tested in that first test. Here is an example.
sequence = session.query(AssemblySequence).where(
(AssemblySequence.is_circular == 1) & (AssemblySequence.name == 'TEST1_seq')
).first()
assert sequence is not None
There is also a single test for sequence.type within the same logic. It does not need any additional data as it extracts from coord_system which is already present.
assert sequence.type == "primary_assembly"

[marcoooo]

there is no data in tests related to this feature. Shouldn't you add some?

Please check out the changes in the tests. There is full coverage for this feature.

I didn't see any data in new txt dump files with other values than chromosomal 0 doesn't that mean we don't have any data with a circular or non chromosomal sequence?

See src/tests/databases/core_1/attrib_type.txt and src/tests/databases/core_1/seq_region_attrib.txt These are tested in test new organism which has three sequences. One is marked as circular, one is marked as not circular, while the third has no circular attribute. These are each tested in that first test. Here is an example. sequence = session.query(AssemblySequence).where( (AssemblySequence.is_circular == 1) & (AssemblySequence.name == 'TEST1_seq') ).first() assert sequence is not None There is also a single test for sequence.type within the same logic. It does not need any additional data as it extracts from coord_system which is already present. assert sequence.type == "primary_assembly"

Ok, this is misunderstanding here, I meant there is no unit test in place to check we load / update the right values from test set.