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monarch-initiative · Sep 20, 2024 · b071835 · b071835
1 parent cd1e971
commit b071835
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Showing 9 changed files with 9 additions and 25 deletions.
diff --git a/tests/agents/conftest.py b/tests/agents/conftest.py
@@ -5,6 +5,7 @@
 from curate_gpt.wrappers.ontology import ONTOLOGY_MODEL_PATH
 from tests import INPUT_DBS
 
+
 # TODO: this has to be reviewed, isolate more, dont use one db for multiple tests
 # - the current setup does not allow reset
 # - set collection is v vulnerable, easier setting/creating new col for each test

diff --git a/tests/wrappers/test_bioportal.py b/tests/wrappers/test_bioportal.py
@@ -2,12 +2,11 @@
 
 import pytest
 
-from curate_gpt import ChromaDBAdapter
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.ontology.bioportal_wrapper import BioportalWrapper
 from curate_gpt.wrappers.ontology.ontology_wrapper import OntologyWrapper
 from tests import OUTPUT_DIR
-from tests.utils.helper import create_db_dir, setup_db, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir, setup_db
 
 TEMP_OAKVIEW_DB = OUTPUT_DIR / "bioportal_tmp"
 

diff --git a/tests/wrappers/test_clinvar.py b/tests/wrappers/test_clinvar.py
@@ -1,21 +1,17 @@
 import logging
-import os
-import shutil
-import tempfile
 import time
 
 import pytest
 import requests
 import yaml
 
-from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.clinical.clinvar_wrapper import ClinVarWrapper
 from tests import INPUT_DIR, OUTPUT_DIR
 from tests.store.conftest import requires_openai_api_key
-from tests.utils.helper import create_db_dir, setup_db, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir, setup_db
 
 TEMP_DB = OUTPUT_DIR / "obj_tmp"
 

diff --git a/tests/wrappers/test_evidence_agent.py b/tests/wrappers/test_evidence_agent.py
@@ -8,10 +8,9 @@
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers import BaseWrapper
 from curate_gpt.wrappers.literature import PubmedWrapper, WikipediaWrapper
-
 from tests import OUTPUT_DIR
 from tests.store.conftest import requires_openai_api_key
-from tests.utils.helper import create_db_dir, setup_db, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir, setup_db
 
 TEMP_PUBMED_DB = OUTPUT_DIR / "pmid_tmp"
 

diff --git a/tests/wrappers/test_ncbi_biosample.py b/tests/wrappers/test_ncbi_biosample.py
@@ -1,12 +1,8 @@
 import logging
-import os
-import shutil
-import tempfile
 import time
 
 import yaml
 
-from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.investigation.ncbi_biosample_wrapper import NCBIBiosampleWrapper

diff --git a/tests/wrappers/test_ontology.py b/tests/wrappers/test_ontology.py
@@ -9,7 +9,7 @@
 from curate_gpt.wrappers.ontology.ontology_wrapper import OntologyWrapper
 from tests import INPUT_DIR, OUTPUT_DIR
 from tests.store.conftest import requires_openai_api_key
-from tests.utils.helper import create_db_dir, setup_db, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir, setup_db
 
 TEMP_OAK_OBJ = OUTPUT_DIR / "oak_tmp_obj"
 TEMP_OAK_IND = OUTPUT_DIR / "oak_tmp_ind"

diff --git a/tests/wrappers/test_pmc.py b/tests/wrappers/test_pmc.py
@@ -1,17 +1,15 @@
 import logging
-import shutil
 import time
 
 import pytest
 import yaml
 
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.chat_agent import ChatAgent
-from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.literature.pmc_wrapper import PMCWrapper
 from tests import INPUT_DIR, OUTPUT_DIR
-from tests.utils.helper import create_db_dir, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir
 
 TEMP_PMC_SEARCH = OUTPUT_DIR / "pmc_search"
 TEMP_PMC_CHAT = OUTPUT_DIR / "pmc_chat"

diff --git a/tests/wrappers/test_pubmed.py b/tests/wrappers/test_pubmed.py
@@ -1,17 +1,14 @@
 import logging
-import os
-import shutil
-import tempfile
 import time
 
 import pytest
-from curate_gpt import ChromaDBAdapter
+
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.literature import PubmedWrapper
 from tests import OUTPUT_DIR
 from tests.store.conftest import requires_openai_api_key
-from tests.utils.helper import create_db_dir, setup_db, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir, setup_db
 
 TEMP_PUBMED_SEARCH = OUTPUT_DIR / "pmid_tmp"
 TEMP_PUBMED_CHAT = OUTPUT_DIR / "pmid_tmp"

diff --git a/tests/wrappers/test_wikipedia.py b/tests/wrappers/test_wikipedia.py
@@ -1,16 +1,14 @@
 import logging
-import shutil
 import time
 
 import pytest
 import yaml
 
-from curate_gpt import ChromaDBAdapter
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.literature import WikipediaWrapper
 from tests import OUTPUT_DIR
 from tests.store.conftest import requires_openai_api_key
-from tests.utils.helper import create_db_dir, setup_db, DEBUG_MODE
+from tests.utils.helper import DEBUG_MODE, create_db_dir, setup_db
 
 TEMP_Wikipedia_DB = OUTPUT_DIR / "wp_tmp"