Merge pull request #249 from jeromekelleher/test_metadata

Test metadata

Author: jeromekelleher

sc2ts/alignments.py

@@ -119,11 +119,6 @@ def append(self, alignments, show_progress=False):
         self._flush(chunk)
         bar.close()
 
-    def __contains__(self, key):
-        with self.env.begin() as txn:
-            val = txn.get(key.encode())
-            return val is not None
-
     def __getitem__(self, key):
         with self.env.begin() as txn:
             val = txn.get(key.encode())

sc2ts/metadata.py

@@ -1,3 +1,4 @@
+import collections
 import logging
 import sqlite3
 import pathlib
@@ -13,14 +14,27 @@ def dict_factory(cursor, row):
     return {key: value for key, value in zip(col_names, row)}
 
 
-class MetadataDb:
+class MetadataDb(collections.abc.Mapping):
     def __init__(self, path):
         uri = f"file:{path}"
         uri += "?mode=ro"
         self.uri = uri
         self.conn = sqlite3.connect(uri, uri=True)
         self.conn.row_factory = dict_factory
 
+    @staticmethod
+    def import_csv(csv_path, db_path):
+        df = pd.read_csv(csv_path, sep="\t")
+        db_path = pathlib.Path(db_path)
+        if db_path.exists():
+            db_path.unlink()
+        with sqlite3.connect(db_path) as conn:
+            df.to_sql("samples", conn, index=False)
+            conn.execute(
+                "CREATE UNIQUE INDEX [ix_samples_strain] on 'samples' ([strain]);"
+            )
+            conn.execute("CREATE INDEX [ix_samples_date] on 'samples' ([date]);")
+
     def __enter__(self):
         return self
 
@@ -36,23 +50,23 @@ def __len__(self):
             row = self.conn.execute(sql).fetchone()
             return row["COUNT(*)"]
 
+    def __getitem__(self, key):
+        sql = "SELECT * FROM samples WHERE strain==?"
+        with self.conn:
+            result = self.conn.execute(sql, [key]).fetchone()
+            if result is None:
+                raise KeyError(f"strain {key} not in DB")
+            return result
+
+    def __iter__(self):
+        sql = "SELECT strain FROM samples"
+        with self.conn:
+            for result in self.conn.execute(sql):
+                yield result["strain"]
+
     def close(self):
         self.conn.close()
 
-    @staticmethod
-    def import_csv(csv_path, db_path):
-        df = pd.read_csv(
-            csv_path,
-            sep="\t",
-        )
-        db_path = pathlib.Path(db_path)
-        if db_path.exists():
-            db_path.unlink()
-        with sqlite3.connect(db_path) as conn:
-            df.to_sql("samples", conn, index=False)
-            conn.execute("CREATE INDEX [ix_samples_strain] on 'samples' ([strain]);")
-            conn.execute("CREATE INDEX [ix_samples_date] on 'samples' ([date]);")
-
     def get(self, date):
         sql = "SELECT * FROM samples WHERE date==?"
         with self.conn:

tests/conftest.py

@@ -0,0 +1,43 @@
+import pathlib
+import shutil
+import gzip
+
+import pytest
+
+import sc2ts
+
+
+@pytest.fixture
+def data_cache():
+    cache_path = pathlib.Path("tests/data/cache")
+    if not cache_path.exists():
+        cache_path.mkdir()
+    return cache_path
+
+
+@pytest.fixture
+def alignments_fasta(data_cache):
+    cache_path = data_cache / "alignments.fasta"
+    if not cache_path.exists():
+        with gzip.open("tests/data/alignments.fasta.gz") as src:
+            with open(cache_path, "wb") as dest:
+                shutil.copyfileobj(src, dest)
+    return cache_path
+
+
+@pytest.fixture
+def alignments_store(data_cache, alignments_fasta):
+    cache_path = data_cache / "alignments.db"
+    if not cache_path.exists():
+        with sc2ts.AlignmentStore(cache_path, "a") as a:
+            fasta = sc2ts.core.FastaReader(alignments_fasta)
+            a.append(fasta, show_progress=False)
+    return sc2ts.AlignmentStore(cache_path)
+
+@pytest.fixture
+def metadata_db(data_cache):
+    cache_path = data_cache / "metadata.db"
+    tsv_path = "tests/data/metadata.tsv"
+    if not cache_path.exists():
+        sc2ts.MetadataDb.import_csv(tsv_path, cache_path)
+    return sc2ts.MetadataDb(cache_path)

tests/test_alignments.py

@@ -1,7 +1,3 @@
-import pathlib
-import shutil
-import gzip
-
 import numpy as np
 import pytest
 from numpy.testing import assert_array_equal
@@ -10,34 +6,6 @@
 from sc2ts import core
 
 
-@pytest.fixture
-def data_cache():
-    cache_path = pathlib.Path("tests/data/cache")
-    if not cache_path.exists():
-        cache_path.mkdir()
-    return cache_path
-
-
-@pytest.fixture
-def alignments_fasta(data_cache):
-    cache_path = data_cache / "alignments.fasta"
-    if not cache_path.exists():
-        with gzip.open("tests/data/alignments.fasta.gz") as src:
-            with open(cache_path, "wb") as dest:
-                shutil.copyfileobj(src, dest)
-    return cache_path
-
-
-@pytest.fixture
-def alignments_store(data_cache, alignments_fasta):
-    cache_path = data_cache / "alignments.db"
-    if not cache_path.exists():
-        with sa.AlignmentStore(cache_path, "a") as a:
-            fasta = core.FastaReader(alignments_fasta)
-            a.append(fasta, show_progress=False)
-    return sa.AlignmentStore(cache_path)
-
-
 class TestAlignmentsStore:
     def test_info(self, alignments_store):
         assert "contains" in str(alignments_store)
@@ -117,7 +85,7 @@ def test_lowercase_nucleotide_missing(self, hap):
             [0, -2],
         ],
     )
-    def test_examples(self, a):
+    def test_error__examples(self, a):
         with pytest.raises(ValueError):
             sa.decode_alignment(np.array(a))
 

tests/test_metadata.py

@@ -0,0 +1,75 @@
+import pytest
+import pandas as pd
+
+
+class TestMetadataDb:
+    def test_known(self, metadata_db):
+        record = metadata_db["SRR11772659"]
+        assert record["strain"] == "SRR11772659"
+        assert record["date"] == "2020-01-19"
+        assert record["Viridian_pangolin"] == "A"
+
+    def test_missing_sequence(self, metadata_db):
+        # We include sequence that's not in the alignments DB
+        assert "ERR_MISSING" in metadata_db
+
+    def test_keys(self, metadata_db):
+        keys = list(metadata_db.keys())
+        assert "SRR11772659" in keys
+        assert len(set(keys)) == len(keys)
+        df = pd.read_csv("tests/data/metadata.tsv", sep="\t")
+        assert set(keys) == set(df["strain"])
+
+    def test_in(self, metadata_db):
+        assert "SRR11772659" in metadata_db
+        assert "DEFO_NOT_IN_DB" not in metadata_db
+
+    def test_get_all_days(self, metadata_db):
+        results = metadata_db.get_days()
+        assert results == [
+            "2020-01-01",
+            "2020-01-19",
+            "2020-01-24",
+            "2020-01-25",
+            "2020-01-28",
+            "2020-01-29",
+            "2020-01-30",
+            "2020-01-31",
+            "2020-02-01",
+            "2020-02-02",
+            "2020-02-03",
+            "2020-02-04",
+            "2020-02-05",
+            "2020-02-06",
+            "2020-02-07",
+            "2020-02-08",
+            "2020-02-09",
+            "2020-02-10",
+            "2020-02-11",
+            "2020-02-13",
+        ]
+
+    def test_get_days_greater(self, metadata_db):
+        results = metadata_db.get_days("2020-02-06")
+        assert results == [
+            "2020-02-07",
+            "2020-02-08",
+            "2020-02-09",
+            "2020-02-10",
+            "2020-02-11",
+            "2020-02-13",
+        ]
+
+    def test_get_days_none(self, metadata_db):
+        assert metadata_db.get_days("2022-02-06") == []
+
+    def test_get_first(self, metadata_db):
+        results = list(metadata_db.get("2020-01-01"))
+        assert len(results) == 1
+        assert results[0] == metadata_db["SRR14631544"]
+
+    def test_get_multi(self, metadata_db):
+        results = list(metadata_db.get("2020-02-11"))
+        assert len(results) == 2
+        for result in results:
+            assert result["date"] == "2020-02-11"