Merge branch 'release/0.18.1'

CHANGES.rst

@@ -2,6 +2,23 @@ Changelog
 =========
 
 
+0.18.1 (2021-04-13)
+~~~~~~~~~~~~~~~~~~~
+
+Bug fixes and minor changes
+---------------------------
+
++ `#82`_: Change the search result in the case of multiple fields from
+  list to tuple.
+
++ `#76`_, `#81`_: work around an issue in icat.server using `DISTINCT`
+  in search queries for multiple fields.
+
+.. _#76: https://github.com/icatproject/python-icat/issues/76
+.. _#81: https://github.com/icatproject/python-icat/pull/81
+.. _#82: https://github.com/icatproject/python-icat/pull/82
+
+
 0.18.0 (2021-03-29)
 ~~~~~~~~~~~~~~~~~~~
 
@@ -32,8 +49,8 @@ Bug fixes and minor changes
 + `#80`_: add :exc:`TypeError` as additional ancestor of
   :exc:`icat.exception.EntityTypeError`.
 
-.. _#76: https://github.com/icatproject/python-icat/pull/76
-.. _#78: https://github.com/icatproject/python-icat/issues/78
+.. _#76: https://github.com/icatproject/python-icat/issues/76
+.. _#78: https://github.com/icatproject/python-icat/pull/78
 .. _#79: https://github.com/icatproject/python-icat/pull/79
 .. _#80: https://github.com/icatproject/python-icat/pull/80
 

doc/src/tutorial-search.rst

@@ -374,15 +374,15 @@ values of the matching objects.  Listing the names of all datasets::
   [e201215, e201216, e208339, e208341, e208342, e208945, e208946, e208947]
 
 As the name of that keyword argument suggests, we may also search for
-multiple attributes at once.  The result will be a list of attribute
+multiple attributes at once.  The result will be a tuple of attribute
 values rather then a single value for each object found in the query.
 This requires an ICAT server version 4.11 or newer though::
 
   >>> query = Query(client, "Dataset", attributes=["investigation.name", "name", "complete", "type.name"])
   >>> print(query)
   SELECT i.name, o.name, o.complete, t.name FROM Dataset o JOIN o.investigation AS i JOIN o.type AS t
   >>> client.search(query)
-  [[08100122-EF, e201215, False, raw], [08100122-EF, e201216, False, raw], [10100601-ST, e208339, False, raw], [10100601-ST, e208341, False, raw], [10100601-ST, e208342, False, raw], [12100409-ST, e208945, False, raw], [12100409-ST, e208946, False, raw], [12100409-ST, e208947, True, analyzed]]
+  [(08100122-EF, e201215, False, raw), (08100122-EF, e201216, False, raw), (10100601-ST, e208339, False, raw), (10100601-ST, e208341, False, raw), (10100601-ST, e208342, False, raw), (12100409-ST, e208945, False, raw), (12100409-ST, e208946, False, raw), (12100409-ST, e208947, True, analyzed)]
   
 There are also some aggregate functions that may be applied to search
 results.  Let's count all datasets::

icat/client.py

@@ -287,18 +287,25 @@ def getEntityClass(self, name):
     def getEntity(self, obj):
         """Get the corresponding :class:`icat.entity.Entity` for an object.
 
-        if obj is a `fieldSet`, return the list of fields.  If obj is
-        any other Suds instance object, create a new entity object
+        if obj is a `fieldSet`, return a tuple of the fields.  If obj
+        is any other Suds instance object, create a new entity object
         with :meth:`~icat.client.Client.new`.  Otherwise do nothing
         and return obj unchanged.
         
         :param obj: either a Suds instance object or anything.
         :type obj: :class:`suds.sudsobject.Object` or any type
         :return: the new entity object or obj.
-        :rtype: :class:`list` or :class:`icat.entity.Entity` or any type
+        :rtype: :class:`tuple` or :class:`icat.entity.Entity` or any type
+
+        .. versionchanged:: 0.18.0
+            add support of `fieldSet`.
+
+        .. versionchanged:: 0.18.1
+            changed the return type from :class:`list` to
+            :class:`tuple` in the case of `fieldSet`.
         """
         if obj.__class__.__name__ == 'fieldSet':
-            return obj.fields
+            return tuple(obj.fields)
         elif isinstance(obj, suds.sudsobject.Object):
             return self.new(obj)
         else:

icat/query.py

@@ -199,7 +199,7 @@ def setAttributes(self, attributes):
             value or a list of attribute values respectively for each
             matching entity object.  If attributes is :const:`None`,
             the result will be the list of matching objects instead.
-        :type attributes: :class:`str` or :class:`list` of :class:`str`
+        :type attributes: :class:`str` or iterable of :class:`str`
         :raise ValueError: if any name in `attributes` is not valid or
             if multiple attributes are provided, but the ICAT server
             does not support this.
@@ -261,7 +261,7 @@ def setOrder(self, order):
             any item in the list may also be a tuple of an attribute
             name and an order direction, the latter being either "ASC"
             or "DESC" for ascending or descending order respectively.
-        :type order: :class:`list` or :class:`bool`
+        :type order: iterable or :class:`bool`
         :raise ValueError: if `order` contains invalid attributes that
             either do not exist or contain one to many relationships.
         """
@@ -415,8 +415,12 @@ def __str__(self):
         else:
             res = "o"
         if self.aggregate:
-            for fct in reversed(self.aggregate.split(':')):
-                res = "%s(%s)" % (fct, res)
+            if len(self.attributes) > 1 and self.aggregate == "DISTINCT":
+                # See discussion in #76
+                res = "%s %s" % (self.aggregate, res)
+            else:
+                for fct in reversed(self.aggregate.split(':')):
+                    res = "%s(%s)" % (fct, res)
         base = "SELECT %s FROM %s o" % (res, self.entity.BeanName)
         joins = ""
         for obj in sorted(subst.keys()):

python-icat.spec

@@ -251,6 +251,7 @@ rm -rf %{buildroot}
 %endif
 %doc %{_docdir}/%{name}
 %exclude %{_docdir}/%{name}/examples
+%exclude %{_docdir}/%{name}/man
 %exclude %{_docdir}/%{name}/tutorial
 
 %files examples

tests/test_06_client.py

@@ -55,21 +55,21 @@ def test_logout_no_session_error(client):
 
 @pytest.mark.parametrize(("query", "result"), [
     pytest.param("SELECT o.name, o.title, o.startDate FROM Investigation o",
-                 [["08100122-EF", "Durol single crystal",
-                   datetime.datetime(2008, 3, 13, 11, 39, 42, tzinfo=cet)],
-                  ["10100601-ST", "Ni-Mn-Ga flat cone",
-                   datetime.datetime(2010, 9, 30, 12, 27, 24, tzinfo=cest)],
-                  ["12100409-ST", "NiO SC OF1 JUH HHL",
-                   datetime.datetime(2012, 7, 26, 17, 44, 24, tzinfo=cest)]],
+                 [("08100122-EF", "Durol single crystal",
+                   datetime.datetime(2008, 3, 13, 11, 39, 42, tzinfo=cet)),
+                  ("10100601-ST", "Ni-Mn-Ga flat cone",
+                   datetime.datetime(2010, 9, 30, 12, 27, 24, tzinfo=cest)),
+                  ("12100409-ST", "NiO SC OF1 JUH HHL",
+                   datetime.datetime(2012, 7, 26, 17, 44, 24, tzinfo=cest))],
                  marks=pytest.mark.skipif("cet is None",
                                           reason="require datetime.timezone")),
     ("SELECT i.name, ds.name FROM Dataset ds JOIN ds.investigation AS i "
      "WHERE i.startDate < '2011-01-01'",
-     [["08100122-EF", "e201215"],
-      ["08100122-EF", "e201216"],
-      ["10100601-ST", "e208339"],
-      ["10100601-ST", "e208341"],
-      ["10100601-ST", "e208342"]]),
+     [("08100122-EF", "e201215"),
+      ("08100122-EF", "e201216"),
+      ("10100601-ST", "e208339"),
+      ("10100601-ST", "e208341"),
+      ("10100601-ST", "e208342")]),
 ])
 def test_search_mulitple_fields(client, query, result):
     """Search for mutliple fields.
@@ -148,8 +148,8 @@ def test_assertedSearch_unique_mulitple_fields(client):
         pytest.skip("search for multiple fields not supported by this server")
     query = ("SELECT i.name, i.title, i.startDate FROM Investigation i "
              "WHERE i.name = '08100122-EF'")
-    result = ["08100122-EF", "Durol single crystal",
-              datetime.datetime(2008, 3, 13, 11, 39, 42, tzinfo=cet)]
+    result = ("08100122-EF", "Durol single crystal",
+              datetime.datetime(2008, 3, 13, 11, 39, 42, tzinfo=cet))
     r = client.assertedSearch(query)[0]
     assert isinstance(r, Sequence)
     assert r == result

tests/test_06_query.py

@@ -452,14 +452,14 @@ def test_query_mulitple_attributes(client):
     if not client._has_wsdl_type('fieldSet'):
         pytest.skip("search for multiple fields not supported by this server")
 
-    results = [["08100122-EF", "Durol single crystal",
-                datetime.datetime(2008, 3, 13, 10, 39, 42, tzinfo=tzinfo)],
-               ["10100601-ST", "Ni-Mn-Ga flat cone",
-                datetime.datetime(2010, 9, 30, 10, 27, 24, tzinfo=tzinfo)],
-               ["12100409-ST", "NiO SC OF1 JUH HHL",
-                datetime.datetime(2012, 7, 26, 15, 44, 24, tzinfo=tzinfo)]]
+    results = [("08100122-EF", "Durol single crystal",
+                datetime.datetime(2008, 3, 13, 10, 39, 42, tzinfo=tzinfo)),
+               ("10100601-ST", "Ni-Mn-Ga flat cone",
+                datetime.datetime(2010, 9, 30, 10, 27, 24, tzinfo=tzinfo)),
+               ("12100409-ST", "NiO SC OF1 JUH HHL",
+                datetime.datetime(2012, 7, 26, 15, 44, 24, tzinfo=tzinfo))]
     query = Query(client, "Investigation",
-                  attributes=["name", "title", "startDate"], order=True)
+                  attributes=("name", "title", "startDate"), order=True)
     print(str(query))
     res = client.search(query)
     assert res == results
@@ -470,13 +470,13 @@ def test_query_mulitple_attributes_related_obj(client):
     if not client._has_wsdl_type('fieldSet'):
         pytest.skip("search for multiple fields not supported by this server")
 
-    results = [["08100122-EF", "e201215"],
-               ["08100122-EF", "e201216"],
-               ["10100601-ST", "e208339"],
-               ["10100601-ST", "e208341"],
-               ["10100601-ST", "e208342"]]
+    results = [("08100122-EF", "e201215"),
+               ("08100122-EF", "e201216"),
+               ("10100601-ST", "e208339"),
+               ("10100601-ST", "e208341"),
+               ("10100601-ST", "e208342")]
     query = Query(client, "Dataset",
-                  attributes=["investigation.name", "name"], order=True,
+                  attributes=("investigation.name", "name"), order=True,
                   conditions={"investigation.startDate":  "< '2011-01-01'"})
     print(str(query))
     res = client.search(query)
@@ -490,10 +490,37 @@ def test_query_mulitple_attributes_oldicat_valueerror(client):
         pytest.skip("search for multiple fields is supported by this server")
 
     with pytest.raises(ValueError) as err:
-        query = Query(client, "Investigation", attributes=["name", "title"])
+        query = Query(client, "Investigation", attributes=("name", "title"))
     err_pattern = r"\bICAT server\b.*\bnot support\b.*\bmultiple attributes\b"
     assert re.search(err_pattern, str(err.value))
 
+def test_query_mulitple_attributes_distinct(client):
+    """Combine DISTINCT with a query for multiple attributes.
+
+    This requires a special handling due to some quirks in the
+    icat.server query poarser.  Support for this has been added in
+    #81.
+    """
+    if not client._has_wsdl_type('fieldSet'):
+        pytest.skip("search for multiple fields not supported by this server")
+
+    # Try the query without DISTINCT first so that we can verify the effect.
+    query = Query(client, "InvestigationUser",
+                  attributes=("investigation.name", "role"),
+                  conditions={"investigation.name": "= '08100122-EF'"})
+    print(str(query))
+    res = client.search(query)
+    query = Query(client, "InvestigationUser",
+                  attributes=("investigation.name", "role"),
+                  conditions={"investigation.name": "= '08100122-EF'"},
+                  aggregate="DISTINCT")
+    print(str(query))
+    res_dist = client.search(query)
+    # The search with DISTINCT yields less items, but if we eliminate
+    # duplicates, the result set is the same:
+    assert len(res) > len(res_dist)
+    assert set(res) == set(res_dist)
+
 @pytest.mark.skipif(Version(pytest.__version__) < "3.9.0",
                     reason="pytest.deprecated_call() does not work properly")
 def test_query_deprecated_kwarg_attribute(client):