Configuration tests for the last few upload enhancements.

test/functional/tools/sample_datatypes_conf.xml

@@ -24,5 +24,6 @@
     <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true" />
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" type_extension="bgzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
   </registration>
 </datatypes>

test/integration/test_check_upload_content_configuration.py

@@ -0,0 +1,112 @@
+"""Integration tests for check_upload_content configuraiton option."""
+
+from base import integration_util
+from base.populators import DatasetPopulator
+
+
+class BaseCheckUploadContentConfigurationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    def setUp(self):
+        super(BaseCheckUploadContentConfigurationTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
+
+
+class NonAdminsCannotPasteFilePathTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test(self):
+        payload = self.dataset_populator.upload_payload(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/1.RData', ext="binary"
+        )
+        create_response = self._post( "tools", data=payload )
+        # Ideally this would be 403 but the tool API endpoint isn't using
+        # the newer API decorator that handles those details.
+        assert create_response.status_code >= 400
+
+
+class AdminsCanPasteFilePathsTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test(self):
+        payload = self.dataset_populator.upload_payload(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/random-file',
+        )
+        create_response = self._post( "tools", data=payload )
+        # Ideally this would be 403 but the tool API endpoint isn't using
+        # the newer API decorator that handles those details.
+        assert create_response.status_code == 200
+
+
+class DefaultBinaryContentFiltersTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test_random_binary_allowed(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/random-file', file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_ext"] == "data", dataset
+
+    def test_gzipped_html_content_blocked_by_default(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/bad.html.gz', file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_size"] == 0
+
+
+class DisableContentCheckingTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+        config["check_upload_content"] = False
+
+    def test_gzipped_html_content_now_allowed(self):
+        self.dataset_populator.new_dataset(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/bad.html.gz', file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        # Same file was empty above!
+        assert dataset["file_size"] != 0
+
+
+class AutoDecompressTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test_auto_decompress_off(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/1.sam.gz', file_type="auto", auto_decompress=False, wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_ext"] == "data", dataset
+
+    def test_auto_decompress_on(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file:///Users/john/workspace/galaxy/test-data/1.sam.gz', file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_ext"] == "sam", dataset