Add more tests

docker/irods_client/Dockerfile

@@ -39,6 +39,7 @@ RUN apt-get install -y python3 git
 	# python3-pip \
 	# git
 
+# Work around for a bug in ubunto 22.04: https://github.com/pypa/setuptools/issues/3269#ref-issue-1217398136
 RUN wget https://bootstrap.pypa.io/get-pip.py
 RUN python3 get-pip.py
 RUN mkdir -p /ibridges/integration_test

docker/irods_client/testdata/example.r

@@ -0,0 +1,7 @@
+example{
+    writeLine("stderr", "Test output for errors.");
+    writeLine("stdout", "Input for this rule: *in");
+}
+
+input *in="This is a string or a path or etc"
+output ruleExecOut

docker/irods_client/tests/conftest.py

@@ -5,6 +5,14 @@
 import tomli
 
 from ibridges import Session
+from ibridges.irodsconnector.data_operations import (
+    create_collection,
+    get_collection,
+    get_dataobject,
+    upload,
+)
+from ibridges.irodsconnector.permissions import Permissions
+from ibridges.utils.path import IrodsPath
 
 # def pytest_addoption(parser):
     # parser.addoption("--configdir", action="store")
@@ -40,10 +48,29 @@ def config(config_dir):
 @pytest.fixture(scope="session")
 def session(irods_env, config):
     session = Session(irods_env=irods_env, password=config["password"])
+    ipath = IrodsPath(session, "~")
+    perm = Permissions(session, get_collection(session, ipath))
+    perm.set("own")
     yield session
     del session
 
 
 @pytest.fixture(scope="session")
 def testdata():
     return Path("/tmp/testdata")
+
+
+@pytest.fixture(scope="session")
+def collection(session):
+    return create_collection(session, IrodsPath(session, "~", "test_collection"))
+
+
+@pytest.fixture(scope="session")
+def dataobject(session, testdata):
+    ipath = IrodsPath(session, "~", "bunny.rtf")
+    upload(session, testdata/"bunny.rtf", IrodsPath(session, "~"), overwrite=True)
+    data_obj = get_dataobject(session, ipath)
+    perm = Permissions(session, data_obj)
+    perm.set("own")
+    yield data_obj
+    ipath.remove()

docker/irods_client/tests/test_data_ops.py

@@ -14,21 +14,21 @@
 
 
 def test_upload_download_dataset(session, testdata):
-    ipath = IrodsPath(session, "~", "bunny.rtf")
+    ipath = IrodsPath(session, "~", "plant.rtf")
     ipath.remove()
-    upload(session, testdata/"bunny.rtf", IrodsPath(session, "~"))
+    upload(session, testdata/"plant.rtf", IrodsPath(session, "~"))
     data_obj = get_dataobject(session, ipath)
     assert is_dataobject(data_obj)
     assert not is_collection(data_obj)
     with pytest.raises(ValueError):
         get_collection(session, ipath)
     print(session)
-    download(session, ipath, testdata/"bunny.rtf.copy", overwrite=True)
+    download(session, ipath, testdata/"plant.rtf.copy", overwrite=True)
     # with open(data_obj, "r") as handle:
         # data_irods = handle.read()
-    with open(testdata/"bunny.rtf.copy") as handle:
+    with open(testdata/"plant.rtf.copy") as handle:
         data_redownload = handle.read()
-    with open(testdata/"bunny.rtf") as handle:
+    with open(testdata/"plant.rtf") as handle:
         data_original = handle.read()
     assert data_original == data_redownload
     # assert data_irods == data_original

docker/irods_client/tests/test_meta.py

@@ -1,22 +1,10 @@
 import pytest
 from pytest import mark
 
-from ibridges.irodsconnector.data_operations import get_collection, get_dataobject, upload
+# 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(session, "~"))
-
-
-@pytest.fixture(scope="module")
-def dataobject(session, testdata):
-    ipath = IrodsPath(session, "~", "bunny.rtf")
-    upload(session, testdata/"bunny.rtf", IrodsPath(session, "~"), overwrite=True)
-    yield get_dataobject(session, ipath)
-    ipath.remove()
+# from ibridges.utils.path import IrodsPath
 
 
 @mark.parametrize("item_name", ["collection", "dataobject"])
@@ -67,10 +55,12 @@ def test_meta(item_name, request):
     meta.delete("x", "z")
     assert len(list(meta)) == 1
 
-    meta.delete("x")
+    meta.delete("x", None)
     assert len(list(meta)) == 0
 
     meta.add("x", "y")
+    meta.add("y", "z")
     meta.set("y", "x")
-    assert "x" not in meta
+    assert "x" in meta
+    assert ("y", "z") not in meta
     assert ("y", "x") in meta

docker/irods_client/tests/test_rules.py

@@ -0,0 +1,7 @@
+from ibridges.irodsconnector.rules import execute_rule
+
+
+def test_rules(session, testdata):
+    rule_fp = str(testdata/"example.r")
+    execute_rule(session, rule_fp, {})
+    execute_rule(session, rule_fp, {'*in': 4, '*another_val': '"Value"'})

docker/irods_client/tests/test_ticket.py

@@ -0,0 +1,34 @@
+from datetime import datetime
+
+import irods
+import pytest
+from pytest import mark
+
+from ibridges.irodsconnector.tickets import Tickets
+
+
+@mark.parametrize("item_name", ["collection", "dataobject"])
+@mark.parametrize("ticket_type", ["read", "write"])
+def test_tickets(item_name, ticket_type, session, request):
+    item = request.getfixturevalue(item_name)
+    ipath = item.path
+    tickets = Tickets(session)
+    tickets.clear()
+    assert len(tickets.all_tickets(update=True)) == 0
+
+    exp_date = datetime.today().strftime('%Y-%m-%d.%H:%M:%S')
+    tickets.create_ticket(str(ipath), ticket_type=ticket_type, expiry_string=exp_date)
+    assert len(tickets.all_tickets(update=True)) == 1
+    ticket_str = tickets.all_ticket_strings[0]
+    tick = tickets.get_ticket(ticket_str)
+    assert isinstance(tick, irods.ticket.Ticket)
+    ticket_data = tickets.all_tickets(update=True)[0]
+    assert ticket_data[0] == ticket_str
+    assert ticket_data[1] == ticket_type
+    assert ticket_data[2] == str(ipath)
+    # assert ticket_data[3] == exp_date
+    assert isinstance(ticket_data[3], str)
+    tickets.delete_ticket(tick)
+    assert len(tickets.all_tickets(update=True)) == 0
+    with pytest.raises(KeyError):
+        tickets.delete_ticket(tick, check=True)

ibridges/irodsconnector/meta.py

@@ -23,7 +23,7 @@ def __contains__(self, val: Union[str, Sequence]) -> bool:
         for meta in self:
             n_same = 0
             for i_attr, attr in enumerate(all_attrs):
-                if getattr(meta, attr) == val[i_attr]:
+                if getattr(meta, attr) == val[i_attr] or val[i_attr] is None:
                     n_same += 1
                 else:
                     break
@@ -62,6 +62,8 @@ def add(self, key: str, value: str, units: Optional[str] = None):
             CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME
         """
         try:
+            if (key, value, units) in self:
+                raise irods.exception.CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME()
             self.item.metadata.add(key, value, units)
         except irods.exception.CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME as error:
             raise ValueError("ADD META: Metadata already present") from error

ibridges/irodsconnector/permissions.py

@@ -1,6 +1,6 @@
 """ permission operations """
 from collections import defaultdict
-from typing import Iterator
+from typing import Iterator, Optional
 
 import irods.access
 import irods.collection
@@ -38,10 +38,17 @@ def __str__(self) -> str:
     @property
     def available_permissions(self) -> dict:
         """Get available permissions"""
-        return self.session.irods_session.available_permissions
+        return self.session.irods_session.available_permissions.codes
 
-    def set(self, perm: str, user: str = '', zone: str = '',
+    def set(self, perm: str, user: Optional[str] = None, zone: Optional[str] = None,
             recursive: bool = False, admin: bool = False) -> None:
         """Set permissions (ACL) for an iRODS collection or data object."""
+        if user is None:
+            user = self.session.username
+        if zone is None:
+            zone = self.session.zone
+        if perm == "null" and user == self.session.username and zone == self.session.zone:
+            raise ValueError("Cannot set your own permissions to null, because you would lose "
+                             "access to the object/collection.")
         acl = irods.access.iRODSAccess(perm, self.item.path, user, zone)
         self.session.irods_session.acls.set(acl, recursive=recursive, admin=admin)

ibridges/irodsconnector/tickets.py

@@ -103,6 +103,13 @@ def all_tickets(self, update: bool = False) -> list[tuple[str, str, str, str]]:
                                           ))
         return self._all_tickets
 
+    def clear(self):
+        self.all_tickets(update=True)
+        for tick_data in self._all_tickets:
+            tick_str = tick_data[0]
+            tick = self.get_ticket(tick_str)
+            self.delete_ticket(tick)
+
     def _id_to_path(self, itemid: str) -> str:
         """
         Given an iRODS item id (data object or collection) from the