Merge pull request #55 from PGScatalog/dev

v0.4.1 patch

pgscatalog_utils/config.py

@@ -20,6 +20,16 @@
 logger = logging.getLogger(__name__)
 
 
+def headers() -> dict[str, str]:
+    if PGSC_CALC_VERSION is None:
+        raise Exception("Missing User-Agent when querying PGS Catalog")
+    else:
+        logger.info(f"User-Agent header: {PGSC_CALC_VERSION}")
+
+    header = {"User-Agent": PGSC_CALC_VERSION}
+    return header
+
+
 def setup_tmpdir(outdir, combine=False):
     if combine:
         work_dir = "work_combine"

pgscatalog_utils/download/Catalog.py

@@ -6,10 +6,10 @@
 
 import requests
 
-from pgscatalog_utils import __version__ as pgscatalog_utils_version
 from pgscatalog_utils import config
 from pgscatalog_utils.download.CatalogCategory import CatalogCategory
 from pgscatalog_utils.download.ScoringFile import ScoringFile
+from pgscatalog_utils.download.download_file import get_with_user_agent
 
 logger = logging.getLogger(__name__)
 
@@ -69,8 +69,8 @@ def get_download_urls(self) -> dict[str: ScoringFile]:
             case CatalogCategory.TRAIT | CatalogCategory.PUBLICATION:
                 # publications and traits have to query Catalog API again to grab score data
                 results: list[CatalogResult] = CatalogQuery(CatalogCategory.SCORE,
-                                                            accession=list(self.pgs_ids),
-                                                            pgsc_calc_version=config.PGSC_CALC_VERSION).get()
+                                                            accession=list(
+                                                                self.pgs_ids)).get()
                 for result in results:
                     for pgs in result.response.get("results"):
                         urls[pgs["id"]] = ScoringFile.from_result(pgs)
@@ -84,12 +84,9 @@ class CatalogQuery:
     """
     category: CatalogCategory
     accession: typing.Union[str, list[str]]
-    pgsc_calc_version: typing.Union[str, None]
     include_children: bool = False
     _rest_url_root: str = "https://www.pgscatalog.org/rest"
     _max_retries: int = 5
-    _version: str = pgscatalog_utils_version
-    _user_agent: dict[str: str] = field(init=False)
 
     def _resolve_query_url(self) -> typing.Union[str, list[str]]:
         child_flag: int = int(self.include_children)
@@ -109,16 +106,8 @@ def _resolve_query_url(self) -> typing.Union[str, list[str]]:
             case CatalogCategory.PUBLICATION, str():
                 return f"{self._rest_url_root}/publication/{self.accession}"
             case _:
-                raise Exception(f"Invalid CatalogCategory and accession type: {self.category}, type({self.accession})")
-
-    def __post_init__(self):
-        ua: str
-        if self.pgsc_calc_version:
-            ua = pgscatalog_utils_version
-        else:
-            ua = f"pgscatalog_utils/{self._version}"
-
-        self._user_agent = {"User-Agent": ua}
+                raise Exception(
+                    f"Invalid CatalogCategory and accession type: {self.category}, type({self.accession})")
 
     def _query_api(self, url: str):
         wait: int = 10
@@ -128,7 +117,7 @@ def _query_api(self, url: str):
         while retry < self._max_retries:
             try:
                 logger.info(f"Querying {url}")
-                r: requests.models.Response = requests.get(url, headers=self._user_agent)
+                r: requests.models.Response = get_with_user_agent(url)
                 r.raise_for_status()
                 results_json = r.json()
                 break

pgscatalog_utils/download/ScoringFileChecksum.py

@@ -15,7 +15,7 @@ def _generate_md5_checksum(filename: str, blocksize=4096) -> typing.Union[str, N
     """ Returns MD5 checksum for the given file. """
     md5 = hashlib.md5()
     try:
-        file = open(filename, 'rb')
+        file = open(config.OUTDIR.joinpath(filename), 'rb')
         with file:
             for block in iter(lambda: file.read(blocksize), b""):
                 md5.update(block)

pgscatalog_utils/download/download_file.py

@@ -1,5 +1,4 @@
 import logging
-import os
 import pathlib
 import time
 import urllib.parse
@@ -13,6 +12,10 @@
 logger = logging.getLogger(__name__)
 
 
+def get_with_user_agent(url: str) -> requests.Response:
+    return requests.get(url, headers=config.headers())
+
+
 def download_file(url: str, local_path: str, overwrite: bool, ftp_fallback: bool) -> None:
     if config.OUTDIR.joinpath(local_path).exists():
         if not overwrite:
@@ -25,7 +28,7 @@ def download_file(url: str, local_path: str, overwrite: bool, ftp_fallback: bool
     attempt: int = 0
 
     while attempt < config.MAX_RETRIES:
-        response: requests.Response = requests.get(url)
+        response: requests.Response = get_with_user_agent(url)
         match response.status_code:
             case 200:
                 with open(config.OUTDIR.joinpath(local_path), "wb") as f:
@@ -69,3 +72,4 @@ def _ftp_fallback_download(url: str, local_path: str) -> None:
             else:
                 logger.critical(f"Download failed: {e}")
                 raise Exception
+

pgscatalog_utils/download/download_scorefile.py

@@ -1,17 +1,16 @@
 import argparse
 import logging
-import os
 import pathlib
 import textwrap
 import typing
 
+from pgscatalog_utils import __version__ as version
 from pgscatalog_utils import config
-from pgscatalog_utils.download.CatalogCategory import CatalogCategory
 from pgscatalog_utils.download.Catalog import CatalogQuery, CatalogResult
+from pgscatalog_utils.download.CatalogCategory import CatalogCategory
 from pgscatalog_utils.download.GenomeBuild import GenomeBuild
 from pgscatalog_utils.download.ScoringFileDownloader import ScoringFileDownloader
 
-
 logger = logging.getLogger(__name__)
 
 
@@ -44,7 +43,11 @@ def download_scorefile() -> None:
 
     if args.pgsc_calc:
         config.PGSC_CALC_VERSION = args.pgsc_calc
-        logger.info(f"Setting user agent to {config.PGSC_CALC_VERSION} for PGS Catalog API queries")
+        logger.info(
+            f"Setting user agent to {config.PGSC_CALC_VERSION} for PGS Catalog API queries")
+    else:
+        config.PGSC_CALC_VERSION = f"pgscatalog_utils/{version}"
+        logger.warning(f"No user agent set, defaulting to {config.PGSC_CALC_VERSION}")
 
     config.OUTDIR = pathlib.Path(args.outdir).resolve()
     logger.info(f"Download directory: {config.OUTDIR}")
@@ -60,19 +63,19 @@ def download_scorefile() -> None:
         else:
             logger.debug("--trait set, querying traits")
         for term in args.efo:
-            results.append(CatalogQuery(CatalogCategory.TRAIT, term, include_children=inc_child,
-                                    pgsc_calc_version=config.PGSC_CALC_VERSION).get())
+            results.append(CatalogQuery(CatalogCategory.TRAIT, term,
+                                        include_children=inc_child).get())
 
     if args.pgp:
         logger.debug("--pgp set, querying publications")
         for term in args.pgp:
-            results.append(CatalogQuery(CatalogCategory.PUBLICATION, term, pgsc_calc_version=config.PGSC_CALC_VERSION).get())
+            results.append(CatalogQuery(CatalogCategory.PUBLICATION, term).get())
 
     if args.pgs:
         logger.debug("--id set, querying scores")
         results.append(
-            CatalogQuery(CatalogCategory.SCORE, args.pgs,
-                         pgsc_calc_version=config.PGSC_CALC_VERSION).get())  # pgs_lst: a list containing up to three flat lists
+            CatalogQuery(CatalogCategory.SCORE,
+                         args.pgs).get())  # pgs_lst: a list containing up to three flat lists
 
     flat_results = [element for sublist in results for element in sublist]
 

tests/test_combine.py

@@ -33,7 +33,7 @@ def test_fail_combine(scorefiles, tmp_path_factory):
 
 @pytest.fixture
 def _n_variants(pgs_accessions):
-    result = CatalogQuery(CatalogCategory.SCORE, accession=pgs_accessions, pgsc_calc_version=None).get()[0]
+    result = CatalogQuery(CatalogCategory.SCORE, accession=pgs_accessions).get()[0]
     json = result.response
     n: list[int] = jq.compile("[.results][][].variants_number").input(json).all()
     return sum(n)

tests/test_download.py

@@ -1,4 +1,5 @@
 import gzip
+import logging
 import os
 from unittest.mock import patch
 
@@ -7,6 +8,22 @@
 from pgscatalog_utils.download.download_scorefile import download_scorefile
 
 
+def test_checksum_validation(tmp_path, caplog):
+    out_dir = str(tmp_path.resolve())
+    pgs_id = 'PGS000001'
+    args: list[str] = ['download_scorefiles', '-i', pgs_id, '-b', 'GRCh38', '-o',
+                       out_dir, '-v']
+
+    with patch('sys.argv', args):
+        caplog.set_level(logging.INFO)
+        # Test download
+        download_scorefile()
+        hm_score_filename = f'{pgs_id}_hmPOS_GRCh38.txt.gz'
+        assert hm_score_filename in os.listdir(out_dir)
+        # make sure validation passed
+        assert "Checksum matches" in  [x.message for x in caplog.records]
+
+
 def test_download_scorefile_author(tmp_path):
     out_dir = str(tmp_path.resolve())
     pgs_id = 'PGS000001'
@@ -92,13 +109,11 @@ def test_download_trait(tmp_path):
 
 def test_query_publication():
     # publications are relatively static
-    query: list[CatalogResult] = CatalogQuery(CatalogCategory.PUBLICATION, accession="PGP000001",
-                                              pgsc_calc_version=None).get()
+    query: list[CatalogResult] = CatalogQuery(CatalogCategory.PUBLICATION, accession="PGP000001").get()
     assert not query[0].pgs_ids.difference({'PGS000001', 'PGS000002', 'PGS000003'})
 
 
 def test_query_trait():
     # new scores may be added to traits in the future
-    query: list[CatalogResult] = CatalogQuery(CatalogCategory.TRAIT, accession="EFO_0004329",
-                                              pgsc_calc_version=None).get()
+    query: list[CatalogResult] = CatalogQuery(CatalogCategory.TRAIT, accession="EFO_0004329").get()
     assert not {'PGS001901', 'PGS002115'}.difference(query[0].pgs_ids)