annotate env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyTools.py @ 4:79f47841a781 draft

"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"

"""
"""
import os

import six

from bioblend.galaxy.tools.inputs import (
    conditional,
    dataset,
    inputs,
    repeat,
)
from . import GalaxyTestBase, test_util


class TestGalaxyTools(GalaxyTestBase.GalaxyTestBase):

    def setUp(self):
        super(TestGalaxyTools, self).setUp()

    def test_get_tools(self):
        # Test requires target Galaxy is configured with at least one tool.
        tools = self.gi.tools.get_tools()
        self.assertGreater(len(tools), 0)
        self.assertTrue(all(map(self._assert_is_tool_rep, tools)))

    def test_get_tool_panel(self):
        # Test requires target Galaxy is configured with at least one tool
        # section.
        tool_panel = self.gi.tools.get_tool_panel()
        sections = [s for s in tool_panel if "elems" in s]
        self.assertGreater(len(sections), 0)
        self.assertTrue(all(map(self._assert_is_tool_rep, sections[0]["elems"])))

    def _assert_is_tool_rep(self, data):
        self.assertTrue(data["model_class"].endswith("Tool"))
        # Special tools like SetMetadataTool may have different model_class
        # than Tool - but they all seem to end in tool.

        for key in ["name", "id", "version"]:
            self.assertIn(key, data)
        return True

    def test_paste_content(self):
        history = self.gi.histories.create_history(name="test_paste_data history")
        paste_text = 'line 1\nline 2\rline 3\r\nline 4'
        tool_output = self.gi.tools.paste_content(paste_text, history["id"])
        self.assertEqual(len(tool_output["outputs"]), 1)
        # All lines in the resulting dataset should end with "\n"
        expected_contents = six.b("\n".join(paste_text.splitlines()) + "\n")
        self._wait_and_verify_dataset(tool_output['outputs'][0]['id'], expected_contents)
        # Same with space_to_tab=True
        tool_output = self.gi.tools.paste_content(paste_text, history["id"], space_to_tab=True)
        self.assertEqual(len(tool_output["outputs"]), 1)
        expected_contents = six.b("\n".join("\t".join(_.split()) for _ in paste_text.splitlines()) + "\n")
        self._wait_and_verify_dataset(tool_output['outputs'][0]['id'], expected_contents)

    def test_upload_file(self):
        history = self.gi.histories.create_history(name="test_upload_file history")

        fn = test_util.get_abspath("test_util.py")
        file_name = "test1"
        tool_output = self.gi.tools.upload_file(
            fn,
            # First param could be a regular path also of course...
            history_id=history["id"],
            file_name=file_name,
            dbkey="?",
            file_type="txt",
        )
        self._wait_for_and_verify_upload(tool_output, file_name, fn, expected_dbkey="?")

    def test_upload_file_dbkey(self):
        history = self.gi.histories.create_history(name="test_upload_file history")
        fn = test_util.get_abspath("test_util.py")
        file_name = "test1"
        dbkey = "hg19"
        tool_output = self.gi.tools.upload_file(
            fn,
            history_id=history["id"],
            file_name=file_name,
            dbkey=dbkey,
            file_type="txt",
        )
        self._wait_for_and_verify_upload(tool_output, file_name, fn, expected_dbkey=dbkey)

    @test_util.skip_unless_tool("random_lines1")
    def test_run_random_lines(self):
        # Run second test case from randomlines.xml
        history_id = self.gi.histories.create_history(name="test_run_random_lines history")["id"]
        with open(test_util.get_abspath(os.path.join("data", "1.bed"))) as f:
            contents = f.read()
        dataset_id = self._test_dataset(history_id, contents=contents)
        tool_inputs = inputs().set(
            "num_lines", "1"
        ).set(
            "input", dataset(dataset_id)
        ).set(
            "seed_source", conditional().set(
                "seed_source_selector", "set_seed"
            ).set(
                "seed", "asdf"
            )
        )
        tool_output = self.gi.tools.run_tool(
            history_id=history_id,
            tool_id="random_lines1",
            tool_inputs=tool_inputs
        )
        self.assertEqual(len(tool_output["outputs"]), 1)
        # TODO: Wait for results and verify has 1 line and is
        # chr5  131424298   131424460   CCDS4149.1_cds_0_0_chr5_131424299_f 0   +

    @test_util.skip_unless_tool("cat1")
    def test_run_cat1(self):
        history_id = self.gi.histories.create_history(name="test_run_cat1 history")["id"]
        dataset1_id = self._test_dataset(history_id, contents="1 2 3")
        dataset2_id = self._test_dataset(history_id, contents="4 5 6")
        dataset3_id = self._test_dataset(history_id, contents="7 8 9")
        tool_inputs = inputs().set(
            "input1", dataset(dataset1_id)
        ).set(
            "queries", repeat().instance(
                inputs().set("input2", dataset(dataset2_id))
            ).instance(
                inputs().set("input2", dataset(dataset3_id))
            )
        )
        tool_output = self.gi.tools.run_tool(
            history_id=history_id,
            tool_id="cat1",
            tool_inputs=tool_inputs
        )
        self.assertEqual(len(tool_output["outputs"]), 1)
        # TODO: Wait for results and verify it has 3 lines - 1 2 3, 4 5 6,
        # and 7 8 9.

    # This test doesn't work any more on Galaxy 16.10 because that release uses an old Conda 3.19.3
    @test_util.skip_unless_galaxy('release_17.01')
    def test_tool_dependency_install(self):
        installed_dependencies = self.gi.tools.install_dependencies('CONVERTER_fasta_to_bowtie_color_index')
        self.assertTrue(any(True for d in installed_dependencies if d.get('name') == 'bowtie' and d.get('dependency_type') == 'conda'), "installed_dependencies is %s" % installed_dependencies)

    def _wait_for_and_verify_upload(self, tool_output, file_name, fn, expected_dbkey="?"):
        self.assertEqual(len(tool_output["outputs"]), 1)
        output = tool_output['outputs'][0]
        self.assertEqual(output['name'], file_name)
        expected_contents = open(fn, "rb").read()
        self._wait_and_verify_dataset(output["id"], expected_contents)
        self.assertEqual(output["genome_build"], expected_dbkey)