From ca009dc385947fd6fac83a15c2b65086ae3fbbe4 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 18 Nov 2018 01:13:04 +0100 Subject: [PATCH 01/11] Do not skip client build for planemo serve Fix https://github.com/galaxyproject/planemo/issues/845 . --- planemo/commands/cmd_serve.py | 1 + planemo/commands/cmd_shed_serve.py | 1 + planemo/galaxy/__init__.py | 6 ++++-- planemo/galaxy/config.py | 7 +++---- planemo/galaxy/serve.py | 6 ++++-- tests/test_cmd_serve.py | 15 ++++++++++++--- 6 files changed, 25 insertions(+), 11 deletions(-) diff --git a/planemo/commands/cmd_serve.py b/planemo/commands/cmd_serve.py index ccd39c00a..d1322278e 100644 --- a/planemo/commands/cmd_serve.py +++ b/planemo/commands/cmd_serve.py @@ -39,4 +39,5 @@ def cli(ctx, uris, **kwds): """ paths = uris_to_paths(ctx, uris) runnables = for_paths(paths) + kwds['galaxy_skip_client_build'] = False galaxy_serve(ctx, runnables, **kwds) diff --git a/planemo/commands/cmd_shed_serve.py b/planemo/commands/cmd_shed_serve.py index 09ead8afc..bd3c4193f 100644 --- a/planemo/commands/cmd_shed_serve.py +++ b/planemo/commands/cmd_shed_serve.py @@ -30,6 +30,7 @@ def cli(ctx, paths, **kwds): install these artifacts, and serve a Galaxy instances that can be logged into and explored interactively. """ + kwds['galaxy_skip_client_build'] = False install_args_list = shed.install_arg_lists(ctx, paths, **kwds) with shed_serve(ctx, install_args_list, **kwds) as config: io.info("Galaxy running with tools installed at %s" % config.galaxy_url) diff --git a/planemo/galaxy/__init__.py b/planemo/galaxy/__init__.py index 136c62e00..a2f99d4f5 100644 --- a/planemo/galaxy/__init__.py +++ b/planemo/galaxy/__init__.py @@ -7,8 +7,10 @@ run_galaxy_command, setup_venv, ) -from .serve import serve as galaxy_serve -from .serve import shed_serve +from .serve import ( + serve as galaxy_serve, + shed_serve +) __all__ = ( "galaxy_config", diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index 23a383256..d2c0c21cb 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -351,9 +351,9 @@ def local_galaxy_config(ctx, runnables, for_tests=False, **kwds): def config_join(*args): return os.path.join(config_directory, *args) - install_env = { - 'GALAXY_SKIP_CLIENT_BUILD': '1', - } + install_env = {} + if kwds.get('galaxy_skip_client_build', True): + install_env['GALAXY_SKIP_CLIENT_BUILD'] = '1' if install_galaxy: _build_eggs_cache(ctx, install_env, kwds) _install_galaxy(ctx, config_directory, install_env, kwds) @@ -484,7 +484,6 @@ def config_join(*args): env["GALAXY_TEST_UPLOAD_ASYNC"] = "false" env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini") env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1" - env["GALAXY_SKIP_CLIENT_BUILD"] = "1" # Following are needed in 18.01 to prevent Galaxy from changing log and pid. # https://github.com/galaxyproject/planemo/issues/788 env["GALAXY_LOG"] = log_file diff --git a/planemo/galaxy/serve.py b/planemo/galaxy/serve.py index 531f28de0..607586bb3 100644 --- a/planemo/galaxy/serve.py +++ b/planemo/galaxy/serve.py @@ -5,8 +5,10 @@ import os import time -from planemo import io -from planemo import network_util +from planemo import ( + io, + network_util +) from .config import galaxy_config from .ephemeris_sleep import sleep from .run import ( diff --git a/tests/test_cmd_serve.py b/tests/test_cmd_serve.py index 74bcebb11..7f9707739 100644 --- a/tests/test_cmd_serve.py +++ b/tests/test_cmd_serve.py @@ -2,6 +2,8 @@ import time import uuid +import requests + from planemo import network_util from planemo.galaxy import api from planemo.io import kill_pid_file @@ -34,14 +36,21 @@ def test_serve(self): @skip_if_environ("PLANEMO_SKIP_PYTHON3") @skip_unless_executable("python3") def test_serve_python3(self): - extra_args = ['--galaxy_python_version', '3', - '--galaxy_branch', 'release_18.09'] + extra_args = [ + "--galaxy_python_version", "3", + "--galaxy_branch", "release_18.09"] self._launch_thread_and_wait(self._run, extra_args) + # Check that the client was correctly built + url = "http://localhost:%d/static/scripts/libs/require.js" % int(self._port) + r = requests.get(url) + assert r.status_code == 200 @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS") @mark.tests_galaxy_branch def test_serve_daemon(self): - extra_args = ["--daemon", "--pid_file", self._pid_file] + extra_args = [ + "--daemon", + "--pid_file", self._pid_file] self._launch_thread_and_wait(self._run, extra_args) user_gi = self._user_gi assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0 From 31510231fa2ce7d6ff1e4c1c51272275154a09ee Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 18 Nov 2018 01:49:17 +0100 Subject: [PATCH 02/11] Convert an existing gx_repo from bare to mirror Follow-up on commit ec16ee7a4bc9fb8c2adb25c0b91743fc16391570 . --- planemo/galaxy/config.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index d2c0c21cb..a7aaf4aaf 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -1272,7 +1272,10 @@ def _ensure_galaxy_repository_available(ctx, kwds): if cwl: gx_repo += "_cwl" if os.path.exists(gx_repo): - # Attempt fetch - but don't fail if not interweb, etc... + # Convert the git repository from bare to mirror, if needed + shell(['git', '--git-dir', gx_repo, 'config', 'remote.origin.fetch', '+refs/*:refs/*']) + shell(['git', '--git-dir', gx_repo, 'config', 'remote.origin.mirror', 'true']) + # Attempt remote update - but don't fail if not interweb, etc... shell("git --git-dir %s remote update >/dev/null 2>&1" % gx_repo) else: remote_repo = _galaxy_source(kwds) From 0a25da8b3bf8332dea381f97012985e1f3ab450e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 20 Nov 2018 17:57:00 +0100 Subject: [PATCH 03/11] Install Galaxy when the directory specified with ``--galaxy_root` does not exist or is empty. Raise an `Exception` if `--galaxy_root` specifies an existing directory and `--install_galaxy` is set. Remove unused `_shed_tool_conf()` function and `FAILED_TO_FIND_GALAXY_EXCEPTION` constant. --- planemo/cli.py | 2 - planemo/galaxy/config.py | 83 ++++++++++++++++------------------------ planemo/galaxy/run.py | 6 --- planemo/io.py | 4 +- planemo/options.py | 2 +- 5 files changed, 36 insertions(+), 61 deletions(-) diff --git a/planemo/cli.py b/planemo/cli.py index 08454ead2..e4f13daf9 100644 --- a/planemo/cli.py +++ b/planemo/cli.py @@ -200,8 +200,6 @@ def handle_blended_options(*args, **kwds): EXCLUSIVE_OPTIONS_LIST = [ - ("galaxy_root", "galaxy_branch"), - ("galaxy_root", "galaxy_source"), ] diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index a7aaf4aaf..a71318de0 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -45,7 +45,6 @@ DISTRO_TOOLS_ID_TO_PATH ) from .run import ( - DOWNLOAD_GALAXY, setup_common_startup_args, setup_venv, ) @@ -186,11 +185,18 @@ class = StreamHandler DEFAULT_GALAXY_SOURCE = "https://github.com/galaxyproject/galaxy" CWL_GALAXY_SOURCE = "https://github.com/common-workflow-language/galaxy" +# TODO: Mac-y curl variant of this. +DOWNLOAD_GALAXY = ( + "wget -q https://codeload.github.com/galaxyproject/galaxy/tar.gz/" +) + DOWNLOADS_URL = ("https://raw.githubusercontent.com/" "jmchilton/galaxy-downloads/master/") DOWNLOADABLE_MIGRATION_VERSIONS = [141, 127, 120, 117] MIGRATION_PER_VERSION = { - "master": 141, + "dev": 145, + "master": 142, + "18.09": 142, "18.05": 141, "18.01": 140, "17.09": 135, @@ -203,10 +209,6 @@ class = StreamHandler COMMAND_STARTUP_COMMAND = "./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}" -FAILED_TO_FIND_GALAXY_EXCEPTION = ( - "Failed to find Galaxy root directory - please explicitly specify one " - "with --galaxy_root." -) CLEANUP_IGNORE_ERRORS = True DEFAULT_GALAXY_BRAND = 'Configured by Planemo' @@ -337,8 +339,13 @@ def local_galaxy_config(ctx, runnables, for_tests=False, **kwds): test_data_dir=test_data_dir, **kwds ) - galaxy_root = _check_galaxy(ctx, **kwds) - install_galaxy = galaxy_root is None + galaxy_root = _find_galaxy_root(ctx, **kwds) + install_galaxy = kwds.get("install_galaxy", False) + if galaxy_root is not None: + if os.path.isdir(galaxy_root) and not os.listdir(galaxy_root): + os.rmdir(galaxy_root) + if os.path.isdir(galaxy_root) and install_galaxy: + raise Exception("%s is an existing non-empty directory, cannot install Galaxy again" % galaxy_root) # Duplicate block in docker variant above. if kwds.get("mulled_containers", False) and not kwds.get("docker", False): @@ -354,10 +361,11 @@ def config_join(*args): install_env = {} if kwds.get('galaxy_skip_client_build', True): install_env['GALAXY_SKIP_CLIENT_BUILD'] = '1' - if install_galaxy: - _build_eggs_cache(ctx, install_env, kwds) - _install_galaxy(ctx, config_directory, install_env, kwds) + if galaxy_root is None: galaxy_root = config_join("galaxy-dev") + if not os.path.isdir(galaxy_root): + _build_eggs_cache(ctx, install_env, kwds) + _install_galaxy(ctx, galaxy_root, install_env, kwds) server_name = "planemo%d" % random.randint(0, 100000) # Once we don't have to support earlier than 18.01 - try putting these files @@ -933,7 +941,7 @@ def kill(self): def startup_command(self, ctx, **kwds): """Return a shell command used to startup this instance. - Among other common planmo kwds, this should respect the + Among other common planemo kwds, this should respect the ``daemon`` keyword. """ daemon = kwds.get("daemon", False) @@ -1074,19 +1082,6 @@ def _file_name_to_migration_version(name): return -1 -def _check_galaxy(ctx, **kwds): - """Find specified Galaxy root or ``None``. - - Return value of ``None`` indicates it should be installed automatically - by planemo. - """ - install_galaxy = kwds.get("install_galaxy", None) - galaxy_root = None - if not install_galaxy: - galaxy_root = _find_galaxy_root(ctx, **kwds) - return galaxy_root - - def _find_galaxy_root(ctx, **kwds): root_prop = "galaxy_root" cwl = kwds.get("cwl", False) @@ -1181,37 +1176,26 @@ def _tool_conf_entry_for(tool_paths): return tool_definitions -def _shed_tool_conf(install_galaxy, config_directory): - # TODO: There is probably a reason this is split up like this but I have - # no clue why I did it and not documented on the commit message. - if install_galaxy: - config_dir = os.path.join(config_directory, "galaxy-dev", "config") - else: - config_dir = config_directory - return os.path.join(config_dir, "shed_tool_conf.xml") - - -def _install_galaxy(ctx, config_directory, env, kwds): +def _install_galaxy(ctx, galaxy_root, env, kwds): if not kwds.get("no_cache_galaxy", False): - _install_galaxy_via_git(ctx, config_directory, env, kwds) + _install_galaxy_via_git(ctx, galaxy_root, env, kwds) else: - _install_galaxy_via_download(ctx, config_directory, env, kwds) + _install_galaxy_via_download(ctx, galaxy_root, env, kwds) -def _install_galaxy_via_download(ctx, config_directory, env, kwds): +def _install_galaxy_via_download(ctx, galaxy_root, env, kwds): + tmpdir = mkdtemp() branch = _galaxy_branch(kwds) - tar_cmd = "tar -zxvf %s" % branch - command = DOWNLOAD_GALAXY + "%s; %s | tail" % (branch, tar_cmd) - if branch != "dev": - command = command + "; ln -s galaxy-%s galaxy-dev" % (branch) - _install_with_command(ctx, config_directory, command, env, kwds) + command = DOWNLOAD_GALAXY + "%s -O - | tar -C '%s' -xvz | tail && mv '%s' '%s'" % \ + (branch, tmpdir, os.path.join(tmpdir, 'galaxy-' + branch), galaxy_root) + _install_with_command(ctx, command, galaxy_root, env, kwds) -def _install_galaxy_via_git(ctx, config_directory, env, kwds): +def _install_galaxy_via_git(ctx, galaxy_root, env, kwds): gx_repo = _ensure_galaxy_repository_available(ctx, kwds) branch = _galaxy_branch(kwds) - command = git.command_clone(ctx, gx_repo, "galaxy-dev", branch=branch) - _install_with_command(ctx, config_directory, command, env, kwds) + command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch) + _install_with_command(ctx, command, galaxy_root, env, kwds) def _build_eggs_cache(ctx, env, kwds): @@ -1246,13 +1230,12 @@ def _galaxy_source(kwds): return source -def _install_with_command(ctx, config_directory, command, env, kwds): +def _install_with_command(ctx, command, galaxy_root, env, kwds): setup_venv_command = setup_venv(ctx, kwds) env['__PYVENV_LAUNCHER__'] = '' install_cmd = shell_join( - ['cd', config_directory], command, - ['cd', 'galaxy-dev'], + ['cd', galaxy_root], setup_venv_command, setup_common_startup_args(), COMMAND_STARTUP_COMMAND, diff --git a/planemo/galaxy/run.py b/planemo/galaxy/run.py index b34d2226d..2c9f21767 100644 --- a/planemo/galaxy/run.py +++ b/planemo/galaxy/run.py @@ -26,11 +26,6 @@ ) -# TODO: Mac-y curl variant of this. -DOWNLOAD_GALAXY = ( - "wget https://codeload.github.com/galaxyproject/galaxy/tar.gz/" -) - CACHED_VIRTUAL_ENV_COMMAND = ("if [ -d .venv ] || [ -f dist-eggs.ini ]; " "then GALAXY_VIRTUAL_ENV=.venv; " "else GALAXY_VIRTUAL_ENV=%s; fi") @@ -116,6 +111,5 @@ def run_galaxy_command(ctx, command, env, action): __all__ = ( "setup_venv", "run_galaxy_command", - "DOWNLOAD_GALAXY", "setup_common_startup_args", ) diff --git a/planemo/io.py b/planemo/io.py index 735af6953..47f9205be 100644 --- a/planemo/io.py +++ b/planemo/io.py @@ -84,8 +84,8 @@ def warn(message, *args): def shell_join(*args): - """Join potentially empty commands together with ;.""" - return "; ".join(args_to_str(_) for _ in args if _) + """Join potentially empty commands together with '&&'.""" + return " && ".join(args_to_str(_) for _ in args if _) def write_file(path, content, force=True): diff --git a/planemo/options.py b/planemo/options.py index 60d26a03b..443a006b9 100644 --- a/planemo/options.py +++ b/planemo/options.py @@ -145,7 +145,7 @@ def galaxy_root_option(): use_global_config=True, extra_global_config_vars=["galaxy_root"], use_env_var=True, - type=click.Path(exists=True, file_okay=False, resolve_path=True), + type=click.Path(file_okay=False, dir_okay=True, resolve_path=True), help="Root of development galaxy directory to execute command with.", ) From e7d4b4914f9eb9379b5ba17251a222154ef565ad Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 21 Nov 2018 00:12:11 +0100 Subject: [PATCH 04/11] Run all ServeTestCase tests with the same ``galaxy_root`` directory to not rebuild the Galaxy client every time. --- tests/test_cmd_serve.py | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/tests/test_cmd_serve.py b/tests/test_cmd_serve.py index 7f9707739..1f686d7cd 100644 --- a/tests/test_cmd_serve.py +++ b/tests/test_cmd_serve.py @@ -1,4 +1,6 @@ import os +import shutil +import tempfile import time import uuid @@ -26,6 +28,20 @@ class ServeTestCase(CliTestCase): + @classmethod + def setUpClass(cls): + cls.galaxy_root = tempfile.mkdtemp() + + @classmethod + def tearDownClass(cls): + shutil.rmtree(cls.galaxy_root) + + def setUp(self): + super(ServeTestCase, self).setUp() + self._port = network_util.get_free_port() + self._pid_file = os.path.join(self._home, "test.pid") + self._serve_artifact = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml") + @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS") @skip_if_environ("PLANEMO_SKIP_PYTHON2") @mark.tests_galaxy_branch @@ -123,12 +139,6 @@ def _test_serve_profile(self, *db_options): with cli_daemon_galaxy(self._runner, self._pid_file, self._port, serve_cmd): assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 1 - def setUp(self): - super(ServeTestCase, self).setUp() - self._port = network_util.get_free_port() - self._pid_file = os.path.join(self._home, "test.pid") - self._serve_artifact = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml") - @property def _user_gi(self): admin_gi = api.gi(self._port) @@ -150,10 +160,10 @@ def _run(self, serve_args=[], serve_cmd="serve"): def _serve_command_list(self, serve_args=[], serve_cmd="serve"): test_cmd = [ serve_cmd, + "--galaxy_root", self.galaxy_root, "--galaxy_branch", target_galaxy_branch(), "--no_dependency_resolution", - "--port", - str(self._port), + "--port", str(self._port), self._serve_artifact, ] test_cmd.extend(serve_args) From 1397f35e456f670c82985696efe190dd11fd340f Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 21 Nov 2018 10:49:59 +0100 Subject: [PATCH 05/11] Fix broken shell command Various tests produced the following error: ``` Set $GALAXY_VIRTUAL_ENV to /home/travis/.planemo/gx_venv /bin/sh: 1: if [ -e "$GALAXY_VIRTUAL_ENV" ]; : not found run command exited with return code 127 ``` Introduced in commit 434099e81314b41c4d9f5bd89dcc78f6513e9141 . --- planemo/galaxy/run.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/planemo/galaxy/run.py b/planemo/galaxy/run.py index 2c9f21767..3fedac492 100644 --- a/planemo/galaxy/run.py +++ b/planemo/galaxy/run.py @@ -14,14 +14,14 @@ # Activate galaxy's virtualenv if present (needed for tests say but not for # server because run.sh does this). -ACTIVATE_COMMAND = '[ -e "$GALAXY_VIRTUAL_ENV" ] && . "$GALAXY_VIRTUAL_ENV"/bin/activate' +ACTIVATE_COMMAND = 'if [ -e "$GALAXY_VIRTUAL_ENV" ]; then . "$GALAXY_VIRTUAL_ENV"/bin/activate; fi' CREATE_COMMAND_TEMPLATE = string.Template( 'if [ ! -e "$GALAXY_VIRTUAL_ENV" ]; then $create_virtualenv; fi', ) PRINT_VENV_COMMAND = shell_join( r'echo "Set \$GALAXY_VIRTUAL_ENV to $GALAXY_VIRTUAL_ENV"', - ('if [ -e "$GALAXY_VIRTUAL_ENV" ]; ', - 'then echo "Virtual environment directory exists."; ', + ('if [ -e "$GALAXY_VIRTUAL_ENV" ]; ' + 'then echo "Virtual environment directory exists."; ' 'else echo "Virtual environment directory does not exist."; fi'), ) From 2fd42de23aae8fb7a03f8ca7825df6b9b759d98a Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Wed, 21 Nov 2018 12:17:09 +0100 Subject: [PATCH 06/11] Remove unneeded `--galaxy_branch` option in 4 tests Fix wrong tool version in workflow. --- tests/data/wf2.ga | 4 ++-- tests/test_cmd_test.py | 4 ---- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/tests/data/wf2.ga b/tests/data/wf2.ga index 804d56e0b..4ac0356d4 100644 --- a/tests/data/wf2.ga +++ b/tests/data/wf2.ga @@ -82,9 +82,9 @@ "tool_errors": null, "tool_id": "cat", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/john/workspace/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", - "tool_version": "1.0.0", + "tool_version": "1.0", "type": "tool", "user_outputs": [] } } -} \ No newline at end of file +} diff --git a/tests/test_cmd_test.py b/tests/test_cmd_test.py index fd264d603..e35b3cc89 100644 --- a/tests/test_cmd_test.py +++ b/tests/test_cmd_test.py @@ -29,7 +29,6 @@ def test_workflow_test_simple_yaml(self): test_command = self.append_profile_argument_if_needed(test_command) test_command += [ "--no_dependency_resolution", - "--galaxy_branch", "release_18.01", # Much better workflow output detection than master for now (pre-release of 18.01) "--extra_tools", random_lines, "--extra_tools", cat, test_artifact, @@ -49,7 +48,6 @@ def test_workflow_test_simple_ga(self): test_command = self.append_profile_argument_if_needed(test_command) test_command += [ "--no_dependency_resolution", - "--galaxy_branch", "release_18.01", # Much better workflow output detection than master for now (pre-release of 18.01) "--extra_tools", cat, test_artifact, ] @@ -72,7 +70,6 @@ def test_workflow_test_distro_tool(self): test_command = self.append_profile_argument_if_needed(test_command) test_command += [ "--no_dependency_resolution", - "--galaxy_branch", "release_18.01", # Much better workflow output detection than master for now (pre-release of 18.01) test_artifact, ] # try: @@ -95,7 +92,6 @@ def test_workflow_test_collection_inputs(self): test_command = self.append_profile_argument_if_needed(test_command) test_command += [ "--no_dependency_resolution", - "--galaxy_branch", "release_18.01", # Much better workflow output detection than master for now (pre-release of 18.01) "--extra_tools", cat_list, test_artifact, ] From e163f443fc98ab080078e49015e9764de3922e93 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 23 Nov 2018 13:19:45 +0000 Subject: [PATCH 07/11] Remove redundant ``os.makerdirs()`` call --- tests/test_cmd_training_generate_from_wf.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/test_cmd_training_generate_from_wf.py b/tests/test_cmd_training_generate_from_wf.py index 72e6f17b4..558ae93da 100644 --- a/tests/test_cmd_training_generate_from_wf.py +++ b/tests/test_cmd_training_generate_from_wf.py @@ -14,8 +14,6 @@ def create_tutorial_dir(topic_n, tuto_n): topic_dir = os.path.join("topics", topic_n) tuto_dir = os.path.join(topic_dir, "tutorials", tuto_n) metadata_path = os.path.join(topic_dir, "metadata.yaml") - if not os.path.isdir(topic_dir): - os.makedirs(topic_dir) if not os.path.isdir(tuto_dir): os.makedirs(tuto_dir) if not os.path.exists(metadata_path): From e71791c6a55d1a6bb6ae369966a0d1ab93375c9a Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 23 Nov 2018 13:22:34 +0000 Subject: [PATCH 08/11] Set ``server_name`` before using it Otherwise the `pid_file` is set to the wrong filename, preventing `LocalGalaxyConfig.kill()` from working when running Galaxy under Python 3. Follow-up to https://github.com/galaxyproject/planemo/pull/874 . --- planemo/galaxy/config.py | 11 ++++++----- planemo/galaxy/serve.py | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index a71318de0..8e78e6984 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -367,7 +367,12 @@ def config_join(*args): _build_eggs_cache(ctx, install_env, kwds) _install_galaxy(ctx, galaxy_root, install_env, kwds) - server_name = "planemo%d" % random.randint(0, 100000) + if parse_version(kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION) >= parse_version('3'): + # on python 3 we use gunicorn, + # which requires 'main' as server name + server_name = 'main' + else: + server_name = "planemo%d" % random.randint(0, 100000) # Once we don't have to support earlier than 18.01 - try putting these files # somewhere better than with Galaxy. log_file = "%s.log" % server_name @@ -407,10 +412,6 @@ def config_join(*args): ) _ensure_directory(shed_tool_path) port = _get_port(kwds) - if parse_version(kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION) >= parse_version('3'): - # on python 3 we use gunicorn, - # which requires 'main' as server name - server_name = 'main' template_args = dict( port=port, host=kwds.get("host", "127.0.0.1"), diff --git a/planemo/galaxy/serve.py b/planemo/galaxy/serve.py index 607586bb3..896097ff1 100644 --- a/planemo/galaxy/serve.py +++ b/planemo/galaxy/serve.py @@ -41,7 +41,7 @@ def _serve(ctx, runnables, **kwds): with galaxy_config(ctx, runnables, **kwds) as config: cmd = config.startup_command(ctx, **kwds) - action = "Starting galaxy" + action = "Starting Galaxy" exit_code = run_galaxy_command( ctx, cmd, From 01cd29142b81169f5ee98c59bdf11b76ca84b74d Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 23 Nov 2018 18:23:16 +0000 Subject: [PATCH 09/11] Update ``random_lines1`` tool from galaxy repo for Python 3 compatibility. --- .../demo/random_lines_two_pass.py | 177 ++++++++++++------ project_templates/demo/randomlines.xml | 11 +- scripts/tool_index.json | 2 +- 3 files changed, 127 insertions(+), 63 deletions(-) diff --git a/project_templates/demo/random_lines_two_pass.py b/project_templates/demo/random_lines_two_pass.py index 25ba02d1c..3dc8467cb 100644 --- a/project_templates/demo/random_lines_two_pass.py +++ b/project_templates/demo/random_lines_two_pass.py @@ -1,71 +1,134 @@ #!/usr/bin/env python -#Dan Blankenberg -#Selects N random lines from a file and outputs to another file, maintaining original line order -#allows specifying a seed -#does two passes to determine line offsets/count, and then to output contents +# Dan Blankenberg +# Selects N random lines from a file and outputs to another file, maintaining original line order +# allows specifying a seed +# does two passes to determine line offsets/count, and then to output contents +from __future__ import print_function -import optparse, random +import optparse +import random +from math import ( + ceil, + log +) -def get_random_by_subtraction( line_offsets, num_lines ): - while len( line_offsets ) > num_lines: - del line_offsets[ random.randint( 0, len( line_offsets ) - 1 ) ] + +def randint(a, b): + return a + int(random.random() * (b + 1 - a)) + + +def sample(population, k): + """Copied straight from python 2.7.""" + + # Sampling without replacement entails tracking either potential + # selections (the pool) in a list or previous selections in a set. + + # When the number of selections is small compared to the + # population, then tracking selections is efficient, requiring + # only a small set and an occasional reselection. For + # a larger number of selections, the pool tracking method is + # preferred since the list takes less space than the + # set and it doesn't suffer from frequent reselections. + + n = len(population) + if not 0 <= k <= n: + raise ValueError("sample larger than population") + result = [None] * k + setsize = 21 # size of a small set minus size of an empty list + if k > 5: + setsize += 4 ** ceil(log(k * 3, 4)) # table size for big sets + if n <= setsize or hasattr(population, "keys"): + # An n-length list is smaller than a k-length set, or this is a + # mapping type so the other algorithm wouldn't work. + pool = list(population) + for i in range(k): # invariant: non-selected at [0,n-i) + j = int(random.random() * (n - i)) + result[i] = pool[j] + pool[j] = pool[n - i - 1] # move non-selected item into vacancy + else: + try: + selected = set() + selected_add = selected.add + for i in range(k): + j = int(random.random() * n) + while j in selected: + j = int(random.random() * n) + selected_add(j) + result[i] = population[j] + except (TypeError, KeyError): # handle (at least) sets + if isinstance(population, list): + raise + return sample(tuple(population), k) + return result + + +def get_random_by_subtraction(line_offsets, num_lines): + while len(line_offsets) > num_lines: + del line_offsets[randint(0, len(line_offsets) - 1)] return line_offsets -def get_random_by_sample( line_offsets, num_lines ): - line_offsets = random.sample( line_offsets, num_lines ) + +def get_random_by_sample(line_offsets, num_lines): + line_offsets = sample(line_offsets, num_lines) line_offsets.sort() return line_offsets -def get_random( line_offsets, num_lines ): - if num_lines > ( len( line_offsets ) / 2 ): - return get_random_by_subtraction( line_offsets, num_lines ) + +def get_random(line_offsets, num_lines): + if num_lines > (len(line_offsets) / 2): + return get_random_by_subtraction(line_offsets, num_lines) else: - return get_random_by_sample( line_offsets, num_lines ) + return get_random_by_sample(line_offsets, num_lines) + def __main__(): - #Parse Command Line parser = optparse.OptionParser() - parser.add_option( '-s', '--seed', dest='seed', action='store', type="string", default=None, help='Set the random seed.' ) + parser.add_option('-s', '--seed', dest='seed', action='store', type="string", default=None, help='Set the random seed.') (options, args) = parser.parse_args() - - assert len( args ) == 3, "Invalid command line specified." - - input = open( args[0], 'rb' ) - output = open( args[1], 'wb' ) - num_lines = int( args[2] ) - assert num_lines > 0, "You must select at least one line." - - if options.seed is not None: - random.seed( options.seed ) - - #get line offsets - line_offsets = [] - teller = input.tell - readliner = input.readline - appender = line_offsets.append - while True: - offset = teller() - if readliner(): - appender( offset ) - else: - break - - total_lines = len( line_offsets ) - assert num_lines <= total_lines, "Error: asked to select more lines (%i) than there were in the file (%i)." % ( num_lines, total_lines ) - - #get random line offsets - line_offsets = get_random( line_offsets, num_lines ) - - #write out random lines - seeker = input.seek - writer = output.write - for line_offset in line_offsets: - seeker( line_offset ) - writer( readliner() ) - input.close() - output.close() - print "Kept %i of %i total lines." % ( num_lines, total_lines ) + + assert len(args) == 3, "Invalid command line specified." + + with open(args[0], 'rb') as input, open(args[1], 'wb') as output: + num_lines = int(args[2]) + assert num_lines > 0, "You must select at least one line." + + if options.seed is not None: + seed_int = int("".join([str(ord(_)) for _ in options.seed])) + try: + # Select version 1, which results in the same seed for python 2 and 3 + random.seed(seed_int, version=1) + except TypeError: + # We're on python 2.X, which doesn't know the version argument + random.seed(seed_int) + + # get line offsets + line_offsets = [] + teller = input.tell + readliner = input.readline + appender = line_offsets.append + while True: + offset = teller() + if readliner(): + appender(offset) + else: + break + + total_lines = len(line_offsets) + assert num_lines <= total_lines, "Error: asked to select more lines (%i) than there were in the file (%i)." % (num_lines, total_lines) + + # get random line offsets + line_offsets = get_random(line_offsets, num_lines) + + # write out random lines + seeker = input.seek + writer = output.write + for line_offset in line_offsets: + seeker(line_offset) + writer(readliner()) + print("Kept %i of %i total lines." % (num_lines, total_lines)) if options.seed is not None: - print 'Used random seed of "%s".' % options.seed - -if __name__=="__main__": __main__() + print('Used random seed of "%s".' % options.seed) + + +if __name__ == "__main__": + __main__() diff --git a/project_templates/demo/randomlines.xml b/project_templates/demo/randomlines.xml index 526c66d4b..d686651e0 100644 --- a/project_templates/demo/randomlines.xml +++ b/project_templates/demo/randomlines.xml @@ -1,9 +1,10 @@ - + from a file - random_lines_two_pass.py "${input}" "${out_file1}" "${num_lines}" - #if str( $seed_source.seed_source_selector ) == "set_seed": - --seed "${seed_source.seed}" - #end if + +python '$__tool_directory__/random_lines_two_pass.py' '${input}' '${out_file1}' 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null, "config_file": "/Users/john/workspace/galaxy/lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml", "description": "", "labels": [], "edam_operations": [], "form_style": "regular", "edam_topics": [], "panel_section_id": null, "version": "2.4.1", "link": "/tool_runner?tool_id=CONVERTER_SMILES_to_inchi", "target": "galaxy_main", "min_width": -1, "model_class": "Tool", "id": "CONVERTER_SMILES_to_inchi", "name": "SMILES to InChI"}, {"panel_section_name": "Convert Formats", "config_file": "/Users/john/workspace/galaxy/tools/filters/axt_to_fasta.xml", "description": "Converts an AXT formatted file to FASTA format", "labels": [], "edam_operations": ["operation_3434"], "form_style": "regular", "edam_topics": [], "panel_section_id": "convert", "version": "1.0.0", "link": "/tool_runner?tool_id=axt_to_fasta", "target": "galaxy_main", "min_width": -1, "model_class": "Tool", "id": "axt_to_fasta", "name": "AXT to FASTA"}, {"panel_section_name": "Text Manipulation", "config_file": "/Users/john/workspace/galaxy/tools/filters/fixedValueColumn.xml", "description": "to an existing dataset", "labels": [], "edam_operations": [], "form_style": "regular", "edam_topics": [], "panel_section_id": "textutil", "version": "1.0.0", "link": "/tool_runner?tool_id=addValue", "target": "galaxy_main", "min_width": -1, "model_class": "Tool", "id": "addValue", "name": "Add column"}, {"panel_section_name": "Fetch Alignments", "config_file": "/Users/john/workspace/galaxy/tools/maf/maf_split_by_species.xml", "description": "by Species", "labels": [], "edam_operations": [], "form_style": "regular", "edam_topics": [], "panel_section_id": "fetchAlign", "version": "1.0.0", "link": "/tool_runner?tool_id=MAF_split_blocks_by_species1", "target": "galaxy_main", "min_width": -1, "model_class": "Tool", "id": "MAF_split_blocks_by_species1", "name": "Split MAF blocks"}] From af4f7c7e7addbb51303a3eb9dfba2ac2d4c187cc Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 23 Nov 2018 18:40:32 +0000 Subject: [PATCH 10/11] Default host to 127.0.0.1 Fix the following traceback: ``` Problem serving Galaxy Traceback (most recent call last): File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/serve.py", line 22, in serve return _serve(ctx, runnables, **kwds) File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/serve.py", line 43, in _serve cmd = config.startup_command(ctx, **kwds) File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/config.py", line 963, in startup_command host=kwds['host'], KeyError: 'host' ``` --- planemo/galaxy/config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index 8e78e6984..477f569b1 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -960,7 +960,7 @@ def startup_command(self, ctx, **kwds): # We need to start under gunicorn self.env['APP_WEBSERVER'] = 'gunicorn' self.env['GUNICORN_CMD_ARGS'] = "--bind={host}:{port} --name={server_name}".format( - host=kwds['host'], + host=kwds.get('host', '127.0.0.1'), port=kwds['port'], server_name=self.server_name, ) From a022c3fd519aa734bbdb5c7ebcedeeb1665c2162 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 23 Nov 2018 22:44:19 +0000 Subject: [PATCH 11/11] Pass ``--dev-wheels`` also when serving Galaxy --- planemo/galaxy/config.py | 1 + tests/test_cmd_serve.py | 8 +++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py index 477f569b1..10c7f90c6 100644 --- a/planemo/galaxy/config.py +++ b/planemo/galaxy/config.py @@ -968,6 +968,7 @@ def startup_command(self, ctx, **kwds): return shell_join( cd_to_galaxy_command, setup_venv_command, + setup_common_startup_args(), run_script, ) diff --git a/tests/test_cmd_serve.py b/tests/test_cmd_serve.py index 1f686d7cd..f3a89afab 100644 --- a/tests/test_cmd_serve.py +++ b/tests/test_cmd_serve.py @@ -53,8 +53,7 @@ def test_serve(self): @skip_unless_executable("python3") def test_serve_python3(self): extra_args = [ - "--galaxy_python_version", "3", - "--galaxy_branch", "release_18.09"] + "--galaxy_python_version", "3"] self._launch_thread_and_wait(self._run, extra_args) # Check that the client was correctly built url = "http://localhost:%d/static/scripts/libs/require.js" % int(self._port) @@ -96,7 +95,10 @@ def test_serve_workflow(self): @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS") @mark.tests_galaxy_branch def test_shed_serve(self): - extra_args = ["--daemon", "--pid_file", self._pid_file, "--shed_target", "toolshed"] + extra_args = [ + "--daemon", + "--pid_file", self._pid_file, + "--shed_target", "toolshed"] fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc") self._serve_artifact = fastqc_path self._launch_thread_and_wait(self._run_shed, extra_args)