fetch tissue type from original sample #3979
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| @@ -345,6 +345,16 @@ def get_sample_ids_by_case_id(self, case_id: str = None) -> Iterator[str]: | |||
| for link in case.links: | |||
| yield link.sample.internal_id | |||
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| def get_original_sample_ids_by_case_id(self, case_id: str = None) -> Iterator[str]: | |||
| """Return original sample ids (go to original sample id for downloaded samples) from case id.""" | |||
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Suggested change
| """Return original sample ids (go to original sample id for downloaded samples) from case id.""" | |
| """Return original sample id from case id.""" |
| @@ -345,6 +345,16 @@ def get_sample_ids_by_case_id(self, case_id: str = None) -> Iterator[str]: | |||
| for link in case.links: | |||
| yield link.sample.internal_id | |||
|
|
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| def get_original_sample_ids_by_case_id(self, case_id: str = None) -> Iterator[str]: | |||
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How about a unit test for this function?
ChrOertlin
reviewed
Nov 28, 2024
Comment on lines
+348
to
+356
| def get_original_sample_ids_by_case_id(self, case_id: str = None) -> Iterator[str]: | ||
| """Return original sample ids (go to original sample id for downloaded samples) from case id.""" | ||
| case: Case = self.get_case_by_internal_id(internal_id=case_id) | ||
| self._is_case_found(case=case, case_id=case_id) | ||
| for link in case.links: | ||
| if link.sample.from_sample: | ||
| original_sample: Sample = link.sample.from_sample | ||
| yield original_sample.internal_id | ||
| yield link.sample.internal_id |
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I don't think we require.a yield here as we only fetch one id it seems?
Suggested change
| def get_original_sample_ids_by_case_id(self, case_id: str = None) -> Iterator[str]: | |
| """Return original sample ids (go to original sample id for downloaded samples) from case id.""" | |
| case: Case = self.get_case_by_internal_id(internal_id=case_id) | |
| self._is_case_found(case=case, case_id=case_id) | |
| for link in case.links: | |
| if link.sample.from_sample: | |
| original_sample: Sample = link.sample.from_sample | |
| yield original_sample.internal_id | |
| yield link.sample.internal_id | |
| def get_original_sample_ids_by_case_id(self, case_id: str = None) -> str: | |
| """Return original sample ids (go to original sample id for downloaded samples) from case id.""" | |
| case: Case = self.get_case_by_internal_id(internal_id=case_id) | |
| self._is_case_found(case=case, case_id=case_id) | |
| for link in case.links: | |
| if link.sample.from_sample: | |
| original_sample: Sample = link.sample.from_sample | |
| return original_sample.internal_id | |
| return link.sample.internal_id |
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