[ORCA-284] External Test Testing & [ORCA-287] OmeXmlSchemaTest Bug fix

setup.cfg

@@ -77,6 +77,7 @@ testing =
     hypothesis~=4.0
     nbmake~=1.3
     pytest-xdist[psutil]~=3.1
+    docker~=6.1.3
 
 # Dependencies for development (used by Pipenv)
 dev =

src/dcqc/tests/bioformats_info_test.py

@@ -15,6 +15,8 @@ def generate_process(self) -> Process:
             "-nopix",
             "-novalid",
             "-nocore",
+            "-format",
+            "OMETiff",
             f"'{path.name}'",
         ]
         process = Process(

src/dcqc/tests/ome_xml_schema_test.py

@@ -13,6 +13,9 @@ def generate_process(self) -> Process:
         command_args = [
             "/opt/bftools/xmlvalid",
             f"'{path.name}'",
+            "|",
+            "grep",
+            "'No validation errors found.'",
         ]
         process = Process(
             container="quay.io/sagebionetworks/bftools:latest",

tests/conftest.py

@@ -55,16 +55,32 @@ def _get_data(filename: str) -> Path:
 @pytest.fixture
 def test_files(get_data):
     txt_path = get_data("test.txt")
+    date_path = get_data("test_contains_word_date.txt")
+    ome_tiff_path = get_data("single-channel.ome.tif")
     jsonld_path = get_data("example.jsonld")
     tiff_path = get_data("circuit.tif")
     fastq1_path = get_data("fastq1.fastq")
     fastq2_path = get_data("fastq2.fastq.gz")
     syn_path = "syn://syn50555279"
     tiff_dirty_datetime_path = get_data("test_image_dirty_datetime.tif")
+    tiff_date_in_tag_path = get_data("date_tag.tif")
+    invalid_xml_ome_tiff_path = get_data("invalid_xml.ome.tif")
+    invalid_xml_metadata = {
+        "file_type": "tiff",
+        "md5_checksum": "a2550a887091d51351d547c8beae8f0c",
+    }
     good_metadata = {
         "file_type": "txt",
         "md5_checksum": "14758f1afd44c09b7992073ccf00b43d",
     }
+    date_txt_metadata = {
+        "file_type": "txt",
+        "md5_checksum": "9cee1b0e8c4d051fabea82b62ae69404",
+    }
+    ome_tiff_metadata = {
+        "file_type": "ome-tiff",
+        "md5_checksum": "293e46687fa6543a2e8189f1698cc5d0",
+    }
     bad_metadata = {
         "file_type": "tiff",
         "md5_checksum": "definitelynottherightmd5checksum",
@@ -83,7 +99,13 @@ def test_files(get_data):
         "md5_checksum": "28a9ee7d0e994d494068ce8d6cda0268",
     }
     test_files = {
+        "date_in_tag_tiff": File(tiff_date_in_tag_path.as_posix(), tiff_metadata),
         "good": File(txt_path.as_posix(), good_metadata),
+        "date_txt": File(date_path.as_posix(), date_txt_metadata),
+        "ome_tiff": File(ome_tiff_path.as_posix(), ome_tiff_metadata),
+        "invalid_xml_tiff": File(
+            invalid_xml_ome_tiff_path.as_posix(), invalid_xml_metadata
+        ),
         "bad": File(txt_path.as_posix(), bad_metadata),
         "tiff": File(tiff_path.as_posix(), tiff_metadata),
         "fastq1": File(fastq1_path.as_posix(), fastq_metadata),