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Merge pull request #41 from microbiomedata/40-re-id-logic-for-metatra…
…nscriptomes 40 re id logic for metatranscriptomes
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@@ -7,3 +7,5 @@ htmlcov/ | |
| attic | ||
| .idea/ | ||
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| configs/.local_napa_config.toml | ||
| nmdc_automation/re_iding/scripts/data/dryrun_data/ | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,112 @@ | ||
| # -*- coding: utf-8 -*- | ||
| """Client for the NMDC API.""" | ||
| # TODO: move all of this to a separate project nmdc-common. But for now, just | ||
| # copy it here. | ||
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| import logging | ||
| import requests | ||
| from typing import Optional | ||
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| logging.basicConfig(level=logging.INFO) | ||
| logger = logging.getLogger(__name__) | ||
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| class NmdcApi: | ||
| """ | ||
| Basic API Client for GET requests. | ||
| """ | ||
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| def __init__(self, api_base_url): | ||
| if not api_base_url.endswith("/"): | ||
| api_base_url += "/" | ||
| self.base_url = api_base_url | ||
| self.headers = {'accept': 'application/json', 'Content-Type': 'application/json'} | ||
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| def get_biosamples_part_of_study(self, study_id: str) -> list[dict]: | ||
| """ | ||
| Get the biosamples that are part of a study. | ||
| """ | ||
| biosample_records = [] | ||
| params = { | ||
| 'filter': '{"part_of": "'+study_id+'"}', | ||
| 'max_page_size': '1000', | ||
| } | ||
| url = self.base_url + "nmdcschema/biosample_set" | ||
| response = requests.get(url, params=params, headers=self.headers) | ||
| response.raise_for_status() | ||
| biosample_records.extend(response.json()["resources"]) | ||
| # Get the next page of results, if any | ||
| while response.json().get("next_page_token") is not None: | ||
| params['page_token'] = response.json()["next_page_token"] | ||
| response = requests.get(url, params=params, headers=self.headers) | ||
| response.raise_for_status() | ||
| biosample_records.extend(response.json()["resources"]) | ||
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| return biosample_records | ||
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| def get_omics_processing_records_part_of_study(self, study_id: str) -> list[dict]: | ||
| """ | ||
| Get the OmicsProcessing records that are part of a study. | ||
| """ | ||
| omics_processing_records = [] | ||
| params = { | ||
| 'filter': '{"part_of": "'+study_id+'"}', | ||
| 'max_page_size': '1000', | ||
| } | ||
| url = self.base_url + "nmdcschema/omics_processing_set" | ||
| response = requests.get(url, params=params, headers=self.headers) | ||
| response.raise_for_status() | ||
| omics_processing_records.extend(response.json()["resources"]) | ||
| # Get the next page of results, if any | ||
| while response.json().get("next_page_token") is not None: | ||
| params['page_token'] = response.json()["next_page_token"] | ||
| response = requests.get(url, params=params, headers=self.headers) | ||
| response.raise_for_status() | ||
| omics_processing_records.extend(response.json()["resources"]) | ||
| return omics_processing_records | ||
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| def get_workflow_activities_informed_by(self, workflow_activity_set: str, | ||
| informed_by_id: str) -> list[dict]: | ||
| """ | ||
| Retrieve workflow activity record(s) for the given workflow | ||
| activity set and informed by a given OmicsProcessing ID. | ||
| """ | ||
| params = { | ||
| 'filter': '{"was_informed_by": "'+informed_by_id+'"}', | ||
| } | ||
| url = self.base_url + "nmdcschema/" + workflow_activity_set | ||
| response = requests.get(url, params=params, headers=self.headers) | ||
| logger.info(response.url) | ||
| response.raise_for_status() | ||
| workflow_activity_record = response.json()["resources"] | ||
| return workflow_activity_record | ||
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| def get_data_object(self, data_object_id: str) -> Optional[dict]: | ||
| """ | ||
| Retrieve a data object record by ID. | ||
| """ | ||
| url = self.base_url + "nmdcschema/data_object_set/" + data_object_id | ||
| try: | ||
| response = requests.get(url, headers=self.headers) | ||
| response.raise_for_status() | ||
| data_object_record = response.json() | ||
| except requests.exceptions.HTTPError as err: | ||
| if err.response.status_code == 404: | ||
| return None | ||
| else: | ||
| raise | ||
| return data_object_record | ||
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| def get_data_objects_by_description(self, description: str): | ||
| """ | ||
| Retrieve data object records by description. | ||
| """ | ||
| params = { | ||
| 'filter': '{"description.search": "'+description+'"}', | ||
| } | ||
| url = self.base_url + "data_objects" | ||
| response = requests.get(url, params=params, headers=self.headers) | ||
| response.raise_for_status() | ||
| data_object_records = response.json()["results"] | ||
| return data_object_records |
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