forked from microbiomedata/nmdc-schema
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #182 from microbiomedata/2027-berkeley-schema-fy24…
…-implement-migrator-that-removes-specific-slots Implement migrator that removes obsolete slots from `MassSpectrometry` documents
- Loading branch information
Showing
1 changed file
with
111 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,111 @@ | ||
from nmdc_schema.migrators.migrator_base import MigratorBase | ||
|
||
|
||
class Migrator(MigratorBase): | ||
r""" | ||
Migrates a database between two schemas. | ||
""" | ||
|
||
_from_version = "PR176" | ||
_to_version = "PR104" | ||
|
||
def upgrade(self) -> None: | ||
r""" | ||
Deletes specific fields from documents (whose `type` is `nmdc:MassSpectrometry`) residing in | ||
the `data_generation_set` collection. | ||
""" | ||
|
||
self.adapter.process_each_document( | ||
collection_name="data_generation_set", | ||
pipeline=[self.delete_obsolete_fields], | ||
) | ||
|
||
@staticmethod | ||
def delete_obsolete_fields(data_generation: dict) -> dict: | ||
r""" | ||
Deletes specific fields from a document representing a `DataGeneration` instance. | ||
If the document's `type` is not `nmdc:MassSpectrometry`, this function will not modify the document. | ||
If a target field exists and is empty, this function will delete the field. On the other hand, if a target | ||
field exists and is not empty, this function will not delete the field and will, instead, raise an exception. | ||
>>> m = Migrator() | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry'}) # no obsolete fields exist | ||
{'id': 123, 'type': 'nmdc:MassSpectrometry'} | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:NucleotideSequencing', | ||
... 'ncbi_project_name': ''}) # type is not relevant | ||
{'id': 123, 'type': 'nmdc:NucleotideSequencing', 'ncbi_project_name': ''} | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'ncbi_project_name': ''}) # single-valued, is empty | ||
{'id': 123, 'type': 'nmdc:MassSpectrometry'} | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'ncbi_project_name': None}) | ||
{'id': 123, 'type': 'nmdc:MassSpectrometry'} | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'gold_sequencing_project_identifiers': []}) # multivalued, is empty | ||
{'id': 123, 'type': 'nmdc:MassSpectrometry'} | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'gold_sequencing_project_identifiers': None}) | ||
{'id': 123, 'type': 'nmdc:MassSpectrometry'} | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'ncbi_project_name': 'a'}) # single-valued, is not empty | ||
Traceback (most recent call last): | ||
... | ||
ValueError: Field "ncbi_project_name" in document "123" is not empty (contains value "a"). | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'gold_sequencing_project_identifiers': ['a']}) # multivalued, is not empty | ||
Traceback (most recent call last): | ||
... | ||
ValueError: Field "gold_sequencing_project_identifiers" in document "123" is not empty (contains value "['a']"). | ||
>>> m.delete_obsolete_fields({'id': 123, 'type': 'nmdc:MassSpectrometry', | ||
... 'ncbi_project_name': None, | ||
... 'target_gene': '', | ||
... 'target_subfragment': '', | ||
... 'gold_sequencing_project_identifiers': None, | ||
... 'insdc_bioproject_identifiers': [], | ||
... 'insdc_experiment_identifiers': []}) # multiple obsolete fields | ||
{'id': 123, 'type': 'nmdc:MassSpectrometry'} | ||
""" | ||
|
||
# If this document's `type` is not "nmdc:MassSpectrometry", leave the document as-is. | ||
if data_generation["type"] != "nmdc:MassSpectrometry": | ||
return data_generation | ||
|
||
# List the names of the single-valued fields we want to delete. | ||
# Note: Their emptiness is represented by `None` or `""`. | ||
single_valued_fields_to_delete = [ | ||
"ncbi_project_name", | ||
"target_gene", | ||
"target_subfragment", | ||
] | ||
|
||
# List the names of the multivalued fields we want to delete. | ||
# Note: Their emptiness is represented by `None` or `[]`. | ||
multi_valued_fields_to_delete = [ | ||
"gold_sequencing_project_identifiers", | ||
"insdc_bioproject_identifiers", | ||
"insdc_experiment_identifiers", | ||
] | ||
|
||
# Combine the two lists. | ||
field_names = single_valued_fields_to_delete + multi_valued_fields_to_delete | ||
|
||
for field_name in field_names: | ||
# Check whether the field exists. | ||
if field_name in data_generation: | ||
value = data_generation[field_name] | ||
|
||
# Check whether the field is empty (using emptiness criteria appropriate for the field). | ||
if ( | ||
field_name in single_valued_fields_to_delete and value in [None, ""] | ||
) or ( | ||
field_name in multi_valued_fields_to_delete and value in [None, []] | ||
): | ||
del data_generation[field_name] | ||
else: | ||
document_id = data_generation["id"] | ||
raise ValueError( | ||
f'Field "{field_name}" in document "{document_id}" is not empty (contains value "{value}").' | ||
) | ||
|
||
return data_generation |