More upload API tests.

test/api/test_tools_upload.py

@@ -7,6 +7,10 @@
 
 from galaxy.tools.verify.test_data import TestDataResolver
 
+ONE_TO_SIX_WITH_SPACES = "1 2 3\n4 5 6\n"
+ONE_TO_SIX_WITH_TABS = "1\t2\t3\n4\t5\t6\n"
+ONE_TO_SIX_ON_WINDOWS = "1\t2\t3\r4\t5\t6\r"
+
 
 class ToolsUploadTestCase(api.ApiTestCase):
 
@@ -21,26 +25,26 @@ def test_upload1_paste(self):
             self._assert_has_keys(create_response.json(), 'outputs')
 
     def test_upload_posix_newline_fixes(self):
-        windows_content = "1\t2\t3\r4\t5\t6\r"
-        posix_content = windows_content.replace("\r", "\n")
+        windows_content = ONE_TO_SIX_ON_WINDOWS
         result_content = self._upload_and_get_content(windows_content)
-        self.assertEquals(result_content, posix_content)
+        self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS)
 
     def test_upload_disable_posix_fix(self):
-        windows_content = "1\t2\t3\r4\t5\t6\r"
+        windows_content = ONE_TO_SIX_ON_WINDOWS
         result_content = self._upload_and_get_content(windows_content, to_posix_lines=None)
         self.assertEquals(result_content, windows_content)
 
     def test_upload_tab_to_space(self):
-        table = "1 2 3\n4 5 6\n"
+        table = ONE_TO_SIX_WITH_SPACES
         result_content = self._upload_and_get_content(table, space_to_tab="Yes")
-        self.assertEquals(result_content, "1\t2\t3\n4\t5\t6\n")
+        self.assertEquals(result_content, ONE_TO_SIX_WITH_TABS)
 
     def test_upload_tab_to_space_off_by_default(self):
-        table = "1 2 3\n4 5 6\n"
+        table = ONE_TO_SIX_WITH_SPACES
         result_content = self._upload_and_get_content(table)
         self.assertEquals(result_content, table)
 
+    @skip_without_datatype("rdata")
     def test_rdata_not_decompressed(self):
         # Prevent regression of https://github.com/galaxyproject/galaxy/issues/753
         rdata_path = TestDataResolver().get_filename("1.RData")
@@ -185,6 +189,72 @@ def test_upload_multiple_files_3(self):
             assert datasets[1]["file_ext"] == "txt"
             assert datasets[1]["genome_build"] == "hg18", datasets
 
+    def test_upload_multiple_files_space_to_tab(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.upload_payload(history_id,
+                content=ONE_TO_SIX_WITH_SPACES,
+                file_type="tabular",
+                dbkey="hg19",
+                extra_inputs={
+                    "files_0|file_type": "txt",
+                    "files_0|space_to_tab": "Yes",
+                    "files_1|url_paste": ONE_TO_SIX_WITH_SPACES,
+                    "files_1|NAME": "SecondOutputName",
+                    "files_1|file_type": "txt",
+                    "files_2|url_paste": ONE_TO_SIX_WITH_SPACES,
+                    "files_2|NAME": "ThirdOutputName",
+                    "files_2|file_type": "txt",
+                    "files_2|space_to_tab": "Yes",
+                    "file_count": "3",
+                }
+            )
+            run_response = self.dataset_populator.tools_post(payload)
+            self.dataset_populator.wait_for_tool_run(history_id, run_response)
+            datasets = run_response.json()["outputs"]
+
+            assert len(datasets) == 3, datasets
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
+            assert content == ONE_TO_SIX_WITH_TABS
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
+            assert content == ONE_TO_SIX_WITH_SPACES
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[2])
+            assert content == ONE_TO_SIX_WITH_TABS
+
+    def test_multiple_files_posix_lines(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.upload_payload(history_id,
+                content=ONE_TO_SIX_ON_WINDOWS,
+                file_type="tabular",
+                dbkey="hg19",
+                extra_inputs={
+                    "files_0|file_type": "txt",
+                    "files_0|to_posix_lines": "Yes",
+                    "files_1|url_paste": ONE_TO_SIX_ON_WINDOWS,
+                    "files_1|NAME": "SecondOutputName",
+                    "files_1|file_type": "txt",
+                    "files_1|to_posix_lines": None,
+                    "files_2|url_paste": ONE_TO_SIX_ON_WINDOWS,
+                    "files_2|NAME": "ThirdOutputName",
+                    "files_2|file_type": "txt",
+                    "file_count": "3",
+                }
+            )
+            run_response = self.dataset_populator.tools_post(payload)
+            self.dataset_populator.wait_for_tool_run(history_id, run_response)
+            datasets = run_response.json()["outputs"]
+
+            assert len(datasets) == 3, datasets
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[0])
+            assert content == ONE_TO_SIX_WITH_TABS
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[1])
+            assert content == ONE_TO_SIX_ON_WINDOWS
+
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=datasets[2])
+            assert content == ONE_TO_SIX_WITH_TABS
+
     def _velvet_upload(self, history_id, extra_inputs):
         payload = self.dataset_populator.upload_payload(
             history_id,