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Add search_term method #2

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9e7def4
Add search_term method
gabrielandrade2 Jan 28, 2022
c4a1273
Update README.md
gabrielandrade2 Jan 28, 2022
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141 changes: 83 additions & 58 deletions README.md
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -16,32 +16,33 @@ Get CUI.
import umls_api

resp = umls_api.API(api_key='<UMLS_API_KEY_HERE>').get_cui(cui='C0007107')
print(res)
print(resp)
{
'pageCount': 1,
'pageNumber': 1,
'pageSize': 25,
'result': {
'atomCount': 247,
'atoms': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/atoms',
'attributeCount': 0,
'classType': 'Concept',
'cvMemberCount': 0,
'dateAdded': '09-30-1990',
'defaultPreferredAtom': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/atoms/preferred',
'definitions': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/definitions',
'majorRevisionDate': '06-25-2020',
'name': 'Malignant neoplasm of larynx',
'relationCount': 17,
'relations': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/relations',
'semanticTypes': [{
'name': 'Neoplastic Process',
'uri': 'https://uts-ws.nlm.nih.gov/rest/semantic-network/2020AB/TUI/T191'
}],
'status': 'R',
'suppressible': False,
'ui': 'C0007107'
}
'pageCount': 1,
'pageNumber': 1,
'pageSize': 25,
'result': {
'atomCount': 247,
'atoms': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/atoms',
'attributeCount': 0,
'classType': 'Concept',
'cvMemberCount': 0,
'dateAdded': '09-30-1990',
'defaultPreferredAtom': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/atoms/preferred',
'definitions': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/definitions',
'majorRevisionDate': '06-25-2020',
'name': 'Malignant neoplasm of larynx',
'relationCount': 17,
'relations': 'https://uts-ws.nlm.nih.gov/rest/content/2020AB/CUI/C0007107/relations',
'semanticTypes': [{
'name': 'Neoplastic Process',
'uri': 'https://uts-ws.nlm.nih.gov/rest/semantic-network/2020AB/TUI/T191'
}],
'status': 'R',
'suppressible': False,
'ui': 'C0007107'
}
}
```

Get TUI.
Expand All @@ -52,39 +53,63 @@ import umls_api
resp = umls_api.API(api_key='<UMLS_API_KEY_HERE>').get_tui(cui='T047')
print(resp)
{
'pageCount': 1,
'pageNumber': 1,
'pageSize': 25,
'result': {
'abbreviation': 'dsyn',
'childCount': 2,
'classType': 'SemanticType',
'definition': 'A condition which alters or interferes with a '
'normal process, state, or activity of an organism. '
'It is usually characterized by the abnormal '
"functioning of one or more of the host's systems, "
'parts, or organs. Included here is a complex of '
'symptoms descriptive of a disorder.',
'example': 'NONE',
'name': 'Disease or Syndrome',
'nonHuman': 'NONE',
'semanticTypeGroup': {
'abbreviation': 'DISO',
'classType': 'SemanticGroup',
'expandedForm': 'Disorders',
'semanticTypeCount': 12
},
'treeNumber': 'B2.2.1.2.1',
'ui': 'T047',
'usageNote': 'Any specific disease or syndrome that is modified by '
'such modifiers as "acute", "prolonged", etc. will '
'also be assigned to this type. If an anatomic '
'abnormality has a pathologic manifestation, then it '
'will be given this type as well as a type from the '
"'Anatomical Abnormality' hierarchy, e.g., "
'"Diabetic Cataract" will be double-typed for this '
'reason.'
}
'pageCount': 1,
'pageNumber': 1,
'pageSize': 25,
'result': {
'abbreviation': 'dsyn',
'childCount': 2,
'classType': 'SemanticType',
'definition': 'A condition which alters or interferes with a '
'normal process, state, or activity of an organism. '
'It is usually characterized by the abnormal '
"functioning of one or more of the host's systems, "
'parts, or organs. Included here is a complex of '
'symptoms descriptive of a disorder.',
'example': 'NONE',
'name': 'Disease or Syndrome',
'nonHuman': 'NONE',
'semanticTypeGroup': {
'abbreviation': 'DISO',
'classType': 'SemanticGroup',
'expandedForm': 'Disorders',
'semanticTypeCount': 12
},
'treeNumber': 'B2.2.1.2.1',
'ui': 'T047',
'usageNote': 'Any specific disease or syndrome that is modified by '
'such modifiers as "acute", "prolonged", etc. will '
'also be assigned to this type. If an anatomic '
'abnormality has a pathologic manifestation, then it '
'will be given this type as well as a type from the '
"'Anatomical Abnormality' hierarchy, e.g., "
'"Diabetic Cataract" will be double-typed for this '
'reason.'
}
}
```

Search term.

```python
import umls_api

resp = umls_api.API(api_key='<UMLS_API_KEY_HERE>').search_term('Malignant neoplasm of larynx')
print(resp)
{
'pageSize': 25,
'pageNumber': 1,
'result': {
'classType': 'searchResults',
'results': [
{
'ui': 'C0007107',
'rootSource': 'MTH',
'uri': 'https://uts-ws.nlm.nih.gov/rest/content/2021AB/CUI/C0007107',
'name': 'Malignant neoplasm of larynx'
}
]
}
}
```

Expand Down
28 changes: 23 additions & 5 deletions src/tests/test_api.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
UMLS_API_KEY = os.environ['UMLS_API_KEY']
CUI = 'C0007107'
TUI = 'T047'
TERM = 'Malignant neoplasm of larynx'


class TestAuth:
Expand Down Expand Up @@ -38,16 +39,13 @@ def test_get_cui(self):
'dateAdded': '09-30-1990',
'defaultPreferredAtom': str,
'definitions': str,
'majorRevisionDate': '06-25-2020',
'majorRevisionDate': str,
'name': 'Malignant neoplasm of larynx',
'relationCount': int,
'relations': str,
'semanticTypes': [{
'name': 'Neoplastic Process',
'uri': (
'https://uts-ws.nlm.nih.gov/rest/semantic-network/'
'2020AB/TUI/T191'
)
'uri': str,
}],
'status': str,
'suppressible': bool,
Expand Down Expand Up @@ -81,3 +79,23 @@ def test_get_tui(self):
'usageNote': str
}
})

def test_get_term(self):
result = umls_api.API(api_key=UMLS_API_KEY).term_search(TERM, umls_api.SearchType.NORMALIZED_STRING)

assert result == S({
'pageNumber': int,
'pageSize': int,
'result': {
'classType': 'searchResults',
'results': [
{
'ui': 'C0007107',
'rootSource': str,
'name': 'Malignant neoplasm of larynx',
'uri': str

}
]
}
})
22 changes: 22 additions & 0 deletions src/umls_api/api.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import requests
from lxml.html import fromstring
from cachetools import cached, TTLCache
from enum import Enum

TTL_7HRS = TTLCache(maxsize=2, ttl=25200)

Expand Down Expand Up @@ -34,6 +35,16 @@ def get_single_use_service_ticket(self):
return single_use_service_ticket


class SearchType(Enum):
EXACT = 'exact'
WORDS = 'words'
LEFT_TRUNCATION = 'leftTruncation'
RIGHT_TRUNCATION = 'rightTruncation'
APPROXIMATE = 'approximate'
NORMALIZED_STRING = 'normalizedString'
NORMALIZED_WORDS = 'normalizedWords'


class API:
BASE_URL = 'https://uts-ws.nlm.nih.gov/rest'

Expand All @@ -49,6 +60,17 @@ def get_tui(self, tui):
url = (f'{self.BASE_URL}/semantic-network/{self._version}/TUI/{tui}')
return self._get(url=url)

def term_search(self, term, searchType=None):
url = (f'{self.BASE_URL}/search/{self._version}/?string={term}')
if searchType is not None:
# Type checking
if not isinstance(searchType, SearchType):
raise ValueError('searchType must be an instance of SearchType Enum')
else:
url = url + (f'/&searchType={searchType.value}')

return self._get(url=url)

def _get(self, url):
ticket = self._auth.get_single_use_service_ticket()
resp = requests.get(url, params={'ticket': ticket})
Expand Down