Trim tests

tests/integration/test_cli/test_cli.py

@@ -1,12 +1,10 @@
 """Tests the command-line interface."""
 import unittest
 
-import inflection
 from click.testing import CliRunner
 
-import tests.integration.test_knowledge_engines.test_cases as extract_cases
 from talisman.cli import main
-from tests import CASES_DIR, OUTPUT_DIR
+from tests import OUTPUT_DIR
 from tests.integration.test_knowledge_engines.test_enrichment import PEX
 
 CACHE_DB = str(OUTPUT_DIR / "cli_cache.db")
@@ -27,86 +25,6 @@ def test_main_help(self):
         self.assertIn("halo", out)
         self.assertEqual(0, result.exit_code)
 
-    def test_extract(self):
-        for case in extract_cases.CASES:
-            template, input_name = case
-            input_file = str(CASES_DIR / f"{input_name}.txt")
-            fmts = ["yaml", "html", "md"]
-            if template == "recipe":
-                fmts.append("owl")
-            for fmt in fmts:
-                output_file = str(CLI_OUTPUT_DIR / f"{input_name}.{fmt}")
-                cmd = [
-                    "--cache-db",
-                    CACHE_DB,
-                    "extract",
-                    "-t",
-                    template,
-                    input_file,
-                    "-O",
-                    fmt,
-                    "-o",
-                    output_file,
-                ]
-                print(cmd)
-                result = self.runner.invoke(main, cmd)
-                self.assertEqual(0, result.exit_code)
-                out = result.stdout
-                print(out)
-
-    def test_pubmed_extract(self):
-        cases = [
-            ("PMID:32044947", "treatment.DiseaseTreatmentSummary"),
-        ]
-        for pmid, template in cases:
-            for fmt in ["yaml", "html"]:
-                output_file = str(CLI_OUTPUT_DIR / f"pmid-{pmid}-{template}.{fmt}")
-                cmd = [
-                    "--cache-db",
-                    CACHE_DB,
-                    "pubmed-extract",
-                    "-t",
-                    template,
-                    pmid,
-                    "-O",
-                    fmt,
-                    "-o",
-                    output_file,
-                ]
-                print(cmd)
-                result = self.runner.invoke(main, cmd)
-                self.assertEqual(0, result.exit_code)
-                out = result.stdout
-                print(out)
-
-    def test_search_and_extract(self):
-        cases = [
-            ("treatment.DiseaseTreatmentSummary", "COVID-19", ["review"]),
-        ]
-        for template, term, keywords in cases:
-            for fmt in ["yaml", "html"]:
-                safe_term = inflection.underscore(term)
-                output_file = str(CLI_OUTPUT_DIR / f"{template}-search-{safe_term}.{fmt}")
-                cmd = [
-                    "--cache-db",
-                    CACHE_DB,
-                    "search-and-extract",
-                    "-t",
-                    template,
-                    term,
-                    "-O",
-                    fmt,
-                    "-o",
-                    output_file,
-                ]
-                for kw in keywords:
-                    cmd.extend(["-k", kw])
-                print(cmd)
-                result = self.runner.invoke(main, cmd)
-                self.assertEqual(0, result.exit_code)
-                out = result.stdout
-                print(out)
-
     def test_enrichment(self):
         ids = [id for id, _ in PEX]
         cmd = ["enrichment"] + ids