fix: support virtool-workflow==6.0.0-alpha

Author: ReeceHoffmann

Dockerfile

@@ -27,7 +27,7 @@ ENV PATH="/root/.local/bin:${PATH}"
 COPY --from=prep /build/bowtie2/* /usr/local/bin/
 COPY --from=prep /build/pigz-2.8/pigz /usr/local/bin/pigz
 COPY --from=rust /build/target/wheels/count_nucleotides_and_seqs*.whl ./
-COPY fixtures.py workflow.py pyproject.toml poetry.lock ./
+COPY workflow.py pyproject.toml poetry.lock ./
 RUN poetry export > requirements.txt
 RUN pip install --upgrade pip
 RUN pip install -r requirements.txt

fixtures.py

@@ -12,16 +12,18 @@ authors = [
 
 [tool.poetry.dependencies]
 python = "~3.10"
-virtool-workflow = "^5.4.2"
+virtool-workflow = "6.0.0a7"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.2"
 pytest-aiohttp = "^1.0.5"
 pytest-asyncio = "^0.21.1"
 pytest-datafiles = "^2.0.1"
+pytest-mock = "^3.12.0"
 
 [tool.pytest.ini_options]
 markers = ["asyncio_mode: auto"]
+asyncio_mode = "auto"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

poetry.lock

@@ -2,18 +2,22 @@
 from types import SimpleNamespace
 
 import pytest
+from virtool_workflow.data.subtractions import WFNewSubtraction
 
 from workflow import compute_gc_and_count, decompress
 
-ARABIDOPSIS_PATH = Path(__file__).parent / "files/arabidopsis_thaliana.fa.gz"
+ARABIDOPSIS_PATH = Path(__file__).parent / "files/subtraction.fa.gz"
+
+
 
 
 @pytest.mark.datafiles(ARABIDOPSIS_PATH)
-async def test_decompress_and_compute_gc(datafiles, tmpdir):
-    input_path = Path(datafiles) / "arabidopsis_thaliana.fa.gz"
+async def test_decompress_and_compute_gc(datafiles, tmpdir, mocker):
     fasta_path = Path(tmpdir) / "decompress.fa"
 
-    await decompress(fasta_path, input_path)
+    new_subtraction = WFNewSubtraction(id="foo", delete=mocker.Mock(), finalize=mocker.Mock(), name="bar", nickname="baz", path=Path(tmpdir), upload=mocker.Mock())
+
+    await decompress(fasta_path, new_subtraction, 1)
 
     assert fasta_path.is_file()
 

pyproject.toml

@@ -4,41 +4,66 @@
 from types import SimpleNamespace
 
 import count_nucleotides_and_seqs
+from pyfixtures import fixture
 from virtool_core.utils import compress_file, decompress_file, is_gzipped
 from virtool_workflow import hooks, step
-from virtool_workflow.api.subtractions import SubtractionProvider
+from virtool_workflow.data.subtractions import WFNewSubtraction
 from virtool_workflow.runtime.run_subprocess import RunSubprocess
 
 
 @hooks.on_failure
-async def delete_subtraction(subtraction_provider: SubtractionProvider):
+async def delete_subtraction(new_subtraction: WFNewSubtraction):
     """Delete the subtraction in the case of a failure."""
-    await subtraction_provider.delete()
+    await new_subtraction.delete()
 
 
-@step
+@fixture
+async def bowtie_index_path(work_path: Path) -> Path:
+    """The output directory for the subtraction's Bowtie2 index."""
+    path = work_path / "bowtie"
+    await asyncio.to_thread(path.mkdir)
+
+    return path
+
+
+@fixture
+async def decompressed_fasta_path(work_path: Path) -> Path:
+    """The path to the input FASTA file for the subtraction."""
+    return work_path / "subtraction.fa"
+
+
+@fixture
+def intermediate() -> SimpleNamespace:
+    """A namespace for intermediate variables."""
+    return SimpleNamespace()
+
+
+@step(name="Decompress FASTA")
 async def decompress(
-    fasta_path: Path,
-    input_path: Path,
+    decompressed_fasta_path: Path,
+    new_subtraction: WFNewSubtraction,
+    proc: int,
 ):
-    """
-    Ensure the input FASTA data is decompressed.
-
-    """
-    if is_gzipped(input_path):
+    """Ensure the input FASTA data is decompressed."""
+    if await asyncio.to_thread(is_gzipped, new_subtraction.fasta_path):
         await asyncio.to_thread(
             decompress_file,
-            input_path,
-            fasta_path,
+            new_subtraction.fasta_path,
+            decompressed_fasta_path,
+            processes=proc,
         )
     else:
-        await asyncio.to_thread(shutil.copyfile, input_path, fasta_path)
+        await asyncio.to_thread(
+            shutil.copyfile, new_subtraction.fasta_path, decompressed_fasta_path
+        )
 
 
-@step(name="Compute GC and count")
-async def compute_gc_and_count(fasta_path: Path, intermediate: SimpleNamespace):
+@step(name="Compute GC and Count")
+async def compute_gc_and_count(
+    decompressed_fasta_path: Path, intermediate: SimpleNamespace
+):
     """Compute the GC and count."""
-    a, t, g, c, n, count = count_nucleotides_and_seqs.run(str(fasta_path))
+    a, t, g, c, n, count = count_nucleotides_and_seqs.run(str(decompressed_fasta_path))
 
     nucleotides = {
         "a": int(a),
@@ -59,50 +84,46 @@ async def compute_gc_and_count(fasta_path: Path, intermediate: SimpleNamespace):
 
 @step
 async def build_index(
-    fasta_path: Path,
-    intermediate: SimpleNamespace,
+    bowtie_index_path: Path,
+    decompressed_fasta_path: Path,
     proc: int,
     run_subprocess: RunSubprocess,
-    work_path: Path,
 ):
     """Build a Bowtie2 index."""
-    bowtie_path = work_path / "index-build"
-    bowtie_path.mkdir()
-
-    command = [
-        "bowtie2-build",
-        "-f",
-        "--threads",
-        str(proc),
-        str(fasta_path),
-        str(bowtie_path) + "/subtraction",
-    ]
-
-    await run_subprocess(command)
-
-    intermediate.bowtie_path = bowtie_path
+    await run_subprocess(
+        [
+            "bowtie2-build",
+            "-f",
+            "--threads",
+            str(proc),
+            decompressed_fasta_path,
+            str(bowtie_index_path) + "/subtraction",
+        ]
+    )
 
 
 @step
 async def finalize(
-    fasta_path: Path,
+    bowtie_index_path: Path,
+    decompressed_fasta_path: Path,
     intermediate: SimpleNamespace,
+    new_subtraction: WFNewSubtraction,
     proc: int,
-    subtraction_provider: SubtractionProvider,
+    work_path: Path,
 ):
     """Compress and subtraction data."""
-    compressed_path = fasta_path.parent / "subtraction.fa.gz"
+    compressed_path = work_path / "subtraction.fa.gz"
 
     await asyncio.to_thread(
         compress_file,
-        fasta_path,
+        decompressed_fasta_path,
         compressed_path,
-        proc,
+        processes=proc,
     )
 
-    await subtraction_provider.upload(compressed_path)
+    await new_subtraction.upload(compressed_path)
 
-    for path in intermediate.bowtie_path.glob("*.bt2"):
-        await subtraction_provider.upload(path)
+    for path in bowtie_index_path.glob("*.bt2"):
+        await new_subtraction.upload(path)
 
-    await subtraction_provider.finalize(intermediate.gc, intermediate.count)
+    await new_subtraction.finalize(intermediate.gc, intermediate.count)