Change integration tests to pytest

So far I have added session/resources/meta tests

Author: qubixes

docker/irods_client/Dockerfile

@@ -26,9 +26,9 @@ RUN apt-get update && \
     rm -rf /var/lib/apt/lists/* /tmp/*
 
 RUN mkdir -p /root/.irods
-COPY docker/irods_client/irods_environment.json /root/.irods
-RUN mkdir -p /root/.ibridges
-COPY docker/irods_client/ibridges_config.json /root/.ibridges
+# COPY docker/irods_client/irods_environment.json /root/.irods
+# RUN mkdir -p /root/.ibridges
+# COPY docker/irods_client/ibridges_config.json /root/.ibridges
 RUN mkdir -p /tmp
 ADD docker/irods_client/testdata /tmp/testdata/
 
@@ -41,11 +41,14 @@ RUN apt-get install -y python3 git
 
 RUN wget https://bootstrap.pypa.io/get-pip.py
 RUN python3 get-pip.py
-RUN mkdir -p /ibridges
+RUN mkdir -p /ibridges/integration_test
 ADD ibridges /ibridges/ibridges
+ADD docker/irods_client/tests ibridges/integration_test
+ADD docker/irods_client/environments/plain-irods ibridges/integration_test/environment
 ADD .git /ibridges/.git
 COPY pyproject.toml /ibridges
 RUN /usr/local/bin/pip3 install /ibridges
+RUN /usr/local/bin/pip3 install pytest tomli
 # COPY requirements.txt /iBridges-Gui/requirements_docker.txt
 # RUN pip3 install -r /iBridges-Gui/requirements_docker.txt
 COPY docker/irods_client/integration_test.py /ibridges/integration_test.py

docker/irods_client/entrypoint.sh

@@ -25,6 +25,8 @@ echo "iRODS is ready"
 # echo 'rods' | iinit
 # echo 'Authenticated as rods'
 
-python3 /ibridges/integration_test.py || echo "Failed"
+# python3 /ibridges/integration_test.py || echo "Failed"
+cd /ibridges/integration_test
+pytest .
 
 bash -c "until false; do sleep 2147483647d; done"

docker/irods_client/environments/plain-irods/config.toml

@@ -0,0 +1,5 @@
+password = "rods"
+server_version = "4.3.0"
+can_write_pam_pass = false
+resources = ["bundleResc", "demoResc"]
+free_resources = [false, false]

docker/irods_client/irods_environment.json renamed to docker/irods_client/environments/plain-irods/irods_environment.json

@@ -0,0 +1,49 @@
+import json
+from pathlib import Path
+
+import pytest
+import tomli
+
+from ibridges import Session
+
+# def pytest_addoption(parser):
+    # parser.addoption("--configdir", action="store")
+
+
+@pytest.fixture(scope="session")
+def config_dir(request):
+    # config_dir_name = request.config.option.configdir
+    # if config_dir_name is None:
+        # pytest.skip()
+    return Path("environment")
+
+
+@pytest.fixture(scope="session")
+def irods_env_file(config_dir):
+    return config_dir / "irods_environment.json"
+
+
+@pytest.fixture(scope="session")
+def irods_env(irods_env_file):
+    with open(irods_env_file, "r") as handle:
+        ienv = json.load(handle)
+    return ienv
+
+
+@pytest.fixture(scope="session")
+def config(config_dir):
+    with open(config_dir / "config.toml", "rb") as handle:
+        config_data = tomli.load(handle)
+    return config_data
+
+
+@pytest.fixture(scope="session")
+def session(irods_env, config):
+    session = Session(irods_env=irods_env, password=config["password"])
+    yield session
+    del session
+
+
+@pytest.fixture(scope="session")
+def testdata():
+    return Path("/tmp/testdata")

docker/irods_client/requirements.txt

@@ -0,0 +1,76 @@
+import pytest
+from pytest import mark
+
+from ibridges.irodsconnector.data_operations import get_collection, get_dataobject, upload
+from ibridges.irodsconnector.meta import MetaData
+from ibridges.utils.path import IrodsPath
+
+
+@pytest.fixture(scope="module")
+def collection(session):
+    return get_collection(session, IrodsPath("~"))
+
+
+@pytest.fixture(scope="module")
+def dataobject(session, testdata):
+    ipath = IrodsPath(session, "~", "bunny.rtf")
+    upload(session, testdata/"bunny.rtf", IrodsPath("~"), overwrite=True)
+    yield get_dataobject(session, ipath)
+    ipath.remove()
+
+
+@mark.parametrize("item_name", ["collection", "dataobject"])
+def test_meta(item_name, request):
+    item = request.getfixturevalue(item_name)
+    meta = MetaData(item)
+    meta.clear()
+
+    assert len(str(meta)) == 0
+    assert len(list(meta)) == 0
+
+    # Add key, value pair
+    meta.add("x", "y")
+    assert len(list(meta)) == 1
+    assert list(meta)[0].name == "x"
+    assert list(meta)[0].value == "y"
+    assert list(meta)[0].units is None
+    assert "x" in meta
+    assert ("x", "y") in meta
+    assert "y" not in meta
+    assert ("x", "z") not in meta
+    assert ("x", "y", "z") not in meta
+
+    # Same key, but different value
+    meta.add("x", "z")
+    assert len(list(meta)) == 2
+    assert len(str(meta).split("\n")) == 3  #\n at the end
+    assert ("x", "z") in meta
+
+    # Same key, value different units
+    meta.add("x", "z", "m")
+    assert len(list(meta)) == 3
+    assert ("x", "z", "m") in meta
+
+    # Test that we cannot add the same metadata twice
+    with pytest.raises(ValueError):
+        meta.add("x", "y")
+    with pytest.raises(ValueError):
+        meta.add("x", "z", "m")
+
+    # Cannot delete value with different units
+    assert ("x", "z", "kg") not in meta
+    with pytest.raises(KeyError):
+        meta.delete("x", "z", "kg")
+    meta.delete("x", "z", "m")
+    assert len(list(meta)) == 2
+
+    meta.delete("x", "z")
+    assert len(list(meta)) == 1
+
+    meta.delete("x")
+    assert len(list(meta)) == 0
+
+    meta.add("x", "y")
+    meta.set("y", "x")
+    assert "x" not in meta
+    assert ("y", "x") in meta

docker/irods_client/tests/conftest.py

@@ -0,0 +1,14 @@
+import irods
+
+from ibridges.irodsconnector.resources import Resources
+
+
+def test_resources(session, config):
+    resources = Resources(session)
+    resc_dict = resources.resources(update=True)
+    assert list(resc_dict) == config["resources"]
+    for i_resc, resc_name in enumerate(list(resc_dict)):
+        if config["free_resources"][i_resc]:
+            assert resources.get_free_space(resc_name) > 0
+        resc = resources.get_resource(resc_name)
+        assert isinstance(resc, irods.resource.iRODSResource)

docker/irods_client/tests/test_meta.py

@@ -0,0 +1,22 @@
+import pytest
+
+from ibridges import Session
+
+
+def test_session(session, config, irods_env):
+    assert session.has_valid_irods_session()
+    assert ".".join(str(x) for x in session.server_version) == config["server_version"]
+    assert session.home == irods_env["irods_home"]
+    assert session.default_resc == irods_env["irods_default_resource"]
+    assert session.host == irods_env["irods_host"]
+    assert session.port == irods_env["irods_port"]
+    assert session.username == irods_env["irods_user_name"]
+    assert session.zone == irods_env["irods_zone_name"]
+
+
+def test_pam_password(session, config, irods_env):
+    if not config["can_write_pam_pass"]:
+        pytest.xfail("This iRods server cannot write pam passwords.")
+    session._write_pam_password()
+    test_session = Session(irods_env)
+    assert test_session.has_valid_irods_session()

docker/irods_client/tests/test_resources.py

@@ -1,6 +1,6 @@
 """ metadata operations
 """
-from typing import Iterator, Optional
+from typing import Iterator, Optional, Sequence, Union
 
 import irods.exception
 import irods.meta
@@ -16,6 +16,21 @@ def __iter__(self) -> Iterator:
         for m in self.item.metadata.items():
             yield m
 
+    def __contains__(self, val: Union[str, Sequence]) -> bool:
+        if isinstance(val, str):
+            val = [val]
+        all_attrs = ["name", "value", "units"][:len(val)]
+        for meta in self:
+            n_same = 0
+            for i_attr, attr in enumerate(all_attrs):
+                if getattr(meta, attr) == val[i_attr]:
+                    n_same += 1
+                else:
+                    break
+            if n_same == len(val):
+                return True
+        return False
+
     def __repr__(self) -> str:
         """Create a sorted representation of the metadata"""
 
@@ -97,8 +112,12 @@ def delete(self, key: str, value: Optional[str], units: Optional[str] = None):
             else:
                 self.item.metadata.remove(key, value, units)
         except irods.exception.CAT_SUCCESS_BUT_WITH_NO_INFO as error:
-            raise ValueError(f"Cannot delete metadata with key '{key}', value '{value}'"
+            raise KeyError(f"Cannot delete metadata with key '{key}', value '{value}'"
                              f" and units '{units}' since it does not exist.") from error
         except irods.exception.CAT_NO_ACCESS_PERMISSION as error:
             raise ValueError("Cannot delete metadata due to insufficient permission for "
                              "path '{item.path}'.") from error
+
+    def clear(self):
+        for meta in self:
+            self.item.metadata.remove(meta)