def cli(ctx, **kwds):
"""Generate a tool outline from supplied arguments.
"""
invalid = _validate_kwds(kwds)
if invalid:
return invalid
output = kwds.get("tool")
if not output:
output = "%s.xml" % kwds.get("id")
if not io.can_write_to_path(output, **kwds):
sys.exit(1)
tool_description = tool_builder.build(**kwds)
open(output, "w").write(tool_description.contents)
io.info("Tool written to %s" % output)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
open(macros_file, "w").write(tool_description.macro_contents)
else:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
def write_tool_description(ctx, tool_description, **kwds):
"""Write a tool description to the file system guided by supplied CLI kwds."""
tool_id = kwds.get("id")
output = kwds.get("tool")
if not output:
extension = "cwl" if kwds.get("cwl") else "xml"
output = "%s.%s" % (tool_id, extension)
if not io.can_write_to_path(output, **kwds):
ctx.exit(1)
io.write_file(output, tool_description.contents)
io.info("Tool written to %s" % output)
test_contents = tool_description.test_contents
if test_contents:
sep = "-" if "-" in tool_id else "_"
tests_path = "%s%stests.yml" % (kwds.get("id"), sep)
if not io.can_write_to_path(tests_path, **kwds):
ctx.exit(1)
io.write_file(tests_path, test_contents)
io.info("Tool tests written to %s" % tests_path)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
io.write_file(macros_file, tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
def _diff_in(ctx, working, realized_repository, **kwds):
path = realized_repository.path
shed_target_source = kwds.get("shed_target_source", None)
label_a = "_%s_" % (shed_target_source if shed_target_source else "local")
shed_target = kwds.get("shed_target", "B")
if "/" in shed_target:
shed_target = "custom_shed"
label_b = "_%s_" % shed_target
mine = os.path.join(working, label_a)
other = os.path.join(working, label_b)
tsi = tool_shed_client(ctx, read_only=True, **kwds)
# In order to download the tarball, require repository ID...
repo_id = realized_repository.find_repository_id(ctx, tsi)
if repo_id is None:
error(
"Repository [%s] does not exist in the targeted Tool Shed, can't do shed_diff"
% realized_repository.name)
# TODO - Should this return an error code which can be checked for in recursive mode?
return 0
download_tarball(ctx,
tsi,
realized_repository,
destination=other,
clean=True,
destination_is_pattern=False,
**kwds)
if shed_target_source:
new_kwds = kwds.copy()
new_kwds["shed_target"] = shed_target_source
tsi = tool_shed_client(ctx, read_only=True, **new_kwds)
download_tarball(ctx,
tsi,
realized_repository,
destination=mine,
clean=True,
destination_is_pattern=False,
**new_kwds)
else:
tar_path = build_tarball(path)
cmd_template = 'mkdir "%s"; tar -xzf "%s" -C "%s"; rm -rf %s'
shell(cmd_template % (mine, tar_path, mine, tar_path))
output = kwds.get("output", None)
raw = kwds.get("raw", False)
is_diff = 0
if not raw:
if output:
with open(output, "w") as f:
is_diff = diff_and_remove(working, label_a, label_b, f)
else:
is_diff = diff_and_remove(working, label_a, label_b, sys.stdout)
cmd = 'cd "%s"; diff -r %s %s' % (working, label_a, label_b)
if output:
cmd += ">> '%s'" % output
exit = shell(cmd) or is_diff
return exit
def write_tool_description(ctx, tool_description, **kwds):
"""Write a tool description to the file system guided by supplied CLI kwds."""
tool_id = kwds.get("id")
output = kwds.get("tool")
if not output:
extension = "cwl" if kwds.get("cwl") else "xml"
output = "%s.%s" % (tool_id, extension)
if not io.can_write_to_path(output, **kwds):
ctx.exit(1)
io.write_file(output, tool_description.contents)
io.info("Tool written to %s" % output)
test_contents = tool_description.test_contents
if test_contents:
sep = "-" if "-" in tool_id else "_"
tests_path = "%s%stests.yml" % (kwds.get("id"), sep)
if not io.can_write_to_path(tests_path, **kwds):
ctx.exit(1)
io.write_file(tests_path, test_contents)
io.info("Tool tests written to %s" % tests_path)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
io.write_file(macros_file, tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
def cli(ctx, **kwds):
"""Generate a tool outline from supplied arguments.
"""
invalid = _validate_kwds(kwds)
if invalid:
return invalid
output = kwds.get("tool")
if not output:
output = "%s.xml" % kwds.get("id")
if not io.can_write_to_path(output, **kwds):
sys.exit(1)
tool_description = tool_builder.build(**kwds)
open(output, "w").write(tool_description.contents)
io.info("Tool written to %s" % output)
macros = kwds["macros"]
macros_file = "macros.xml"
if macros and not os.path.exists(macros_file):
open(macros_file, "w").write(tool_description.macro_contents)
elif macros:
io.info(REUSING_MACROS_MESSAGE)
if tool_description.test_files:
if not os.path.exists("test-data"):
io.info("No test-data directory, creating one.")
io.shell("mkdir -p 'test-data'")
for test_file in tool_description.test_files:
io.info("Copying test-file %s" % test_file)
io.shell("cp '%s' 'test-data'" % test_file)
def test_upload_from_git(self):
with self._isolate() as f:
with self._git_configured():
dest = join(f, "single_tool")
self._copy_repo("single_tool", dest)
shell(" && ".join([
"cd %s" % dest,
"git init",
"git add .",
"git commit -m 'initial commit'"
]))
rev = git.rev(None, "single_tool")
upload_command = [
"shed_update", "--force_repository_creation",
"git+single_tool/.git"
]
upload_command.extend(self._shed_args())
self._check_exit_code(upload_command)
self._verify_single_uploaded(f, ["single_tool"])
model = self.mock_shed.model
repo_id = self.repository_by_name("single_tool")["id"]
message = model._repositories_msg[repo_id][0]
assert "planemo upload for repository " in message
assert "repository https://github.com/galaxyproject" in message
assert rev in message
def test_upload_from_git(self):
with self._isolate() as f:
with self._git_configured():
dest = join(f, "single_tool")
self._copy_repo("single_tool", dest)
shell(" && ".join([
"cd %s" % dest,
"git init",
"git add .",
"git commit -m 'initial commit'"
]))
rev = git.rev(None, "single_tool")
upload_command = [
"shed_update", "--force_repository_creation",
"git+single_tool/.git"
]
upload_command.extend(self._shed_args())
self._check_exit_code(upload_command)
self._verify_single_uploaded(f, ["single_tool"])
model = self.mock_shed.model
repo_id = self.repository_by_name("single_tool")["id"]
message = model._repositories_msg[repo_id][0]
assert "planemo upload for repository " in message
assert "repository https://github.com/galaxyproject" in message
assert rev in message
def _ensure_galaxy_repository_available(ctx):
workspace = ctx.workspace
gx_repo = os.path.join(workspace, "gx_repo")
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
remote_repo = "https://github.com/galaxyproject/galaxy"
shell("git clone --bare %s %s" % (remote_repo, gx_repo))
def _install_with_command(config_directory, command):
install_cmds = [
"cd %s" % config_directory,
command,
"cd galaxy-dev",
"type virtualenv >/dev/null 2>&1 && virtualenv .venv",
galaxy_run.ACTIVATE_COMMAND,
]
shell(";".join(install_cmds))
def _ensure_galaxy_repository_available(ctx):
workspace = ctx.workspace
gx_repo = os.path.join(workspace, "gx_repo")
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
remote_repo = "https://github.com/galaxyproject/galaxy"
shell("git clone --bare %s %s" % (remote_repo, gx_repo))
def _install_with_command(config_directory, command):
install_cmds = [
"cd %s" % config_directory,
command,
"cd galaxy-dev",
"type virtualenv >/dev/null 2>&1 && virtualenv .venv",
galaxy_run.ACTIVATE_COMMAND,
]
shell(";".join(install_cmds))
def kill(self):
if self._ctx.verbose:
shell(["ps", "ax"])
exists = os.path.exists(self.pid_file)
print("Killing pid file [%s]" % self.pid_file)
print("pid_file exists? [%s]" % exists)
if exists:
print("pid_file contents are [%s]" % open(self.pid_file, "r").read())
kill_pid_file(self.pid_file)
def _install_with_command(ctx, galaxy_root, env, kwds):
setup_venv_command = setup_venv(ctx, kwds)
env['__PYVENV_LAUNCHER__'] = ''
install_cmd = shell_join(
setup_venv_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd, cwd=galaxy_root, env=env)
def _install_with_command(ctx, command, galaxy_root, env, kwds):
setup_venv_command = setup_venv(ctx, kwds)
env['__PYVENV_LAUNCHER__'] = ''
install_cmd = shell_join(
command,
['cd', galaxy_root],
setup_venv_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd, env=env)
def _install_with_command(ctx, config_directory, command, env, kwds):
setup_venv_command = setup_venv(ctx, kwds)
env['__PYVENV_LAUNCHER__'] = ''
install_cmd = shell_join(
['cd', config_directory],
command,
['cd', 'galaxy-dev'],
setup_venv_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd, env=env)
def cli(ctx):
"""Download linuxbrew install and run it with ruby. Linuxbrew is a fork
of Homebrew (http://brew.sh/linuxbrew/).
For more information on installing linuxbrew and pre-requisites see
https://github.com/Homebrew/linuxbrew#installation.
Homebrew or linuxbrew are required in order to use the other commands
``brew`` and ``brew_shell``.
"""
fname = mkstemp('install_brew')
urllib.urlretrieve(INSTALL_SCRIPT, fname)
shell(["ruby", fname])
def cli(ctx):
"""Download linuxbrew install and run it with ruby. Linuxbrew is a fork
of Homebrew (http://brew.sh/linuxbrew/).
For more information on installing linuxbrew and pre-requisites see
https://github.com/Homebrew/linuxbrew#installation.
Homebrew or linuxbrew are required in order to use the other commands
``brew`` and ``brew_shell``.
"""
fname = mkstemp('install_brew')
urllib.urlretrieve(INSTALL_SCRIPT, fname)
shell(["ruby", fname])
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
galaxy_source = kwds.get('galaxy_source')
if galaxy_source and galaxy_source != DEFAULT_GALAXY_SOURCE:
sanitized_repo_name = "".join(
c if c.isalnum() else '_'
for c in kwds['galaxy_source']).rstrip()[:255]
gx_repo = os.path.join(workspace, "gx_repo_%s" % sanitized_repo_name)
else:
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# 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)
command = git.command_clone(ctx, remote_repo, gx_repo, mirror=True)
shell(command)
return gx_repo
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
remote_repo = _galaxy_source(kwds)
command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
shell(command)
return gx_repo
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
remote_repo = _galaxy_source(kwds)
command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
shell(command)
return gx_repo
def test_tar_from_git(self):
with self._isolate() as f:
dest = join(f, "single_tool")
self._copy_repo("single_tool", dest)
shell(" && ".join([
"cd single_tool", "git init", "git add .",
"git commit -m 'initial commit'"
]))
upload_command = [
"shed_update", "--force_repository_creation",
"git+single_tool/.git"
]
upload_command.extend(self._shed_args())
self._check_exit_code(upload_command)
self._verify_single_uploaded(f, ["single_tool"])
def kill(self):
"""Kill planemo container..."""
kill_command = docker_util.kill_command(
self.server_name,
**self.docker_target_kwds
)
return shell(kill_command)
def kill(self):
"""Kill planemo container..."""
kill_command = docker_util.kill_command(
self.server_name,
**self.docker_target_kwds
)
return shell(kill_command)
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_root, branch=branch)
exit_code = shell(command, env=env)
if exit_code != 0:
raise Exception("Failed to glone Galaxy via git")
_install_with_command(ctx, galaxy_root, env, kwds)
def test_tar_from_git(self):
with self._isolate() as f:
dest = join(f, "single_tool")
self._copy_repo("single_tool", dest)
shell(" && ".join([
"cd single_tool",
"git init",
"git add .",
"git commit -m 'initial commit'"
]))
upload_command = [
"shed_update", "--force_repository_creation",
"git+single_tool/.git"
]
upload_command.extend(self._shed_args())
self._check_exit_code(upload_command)
self._verify_single_uploaded(f, ["single_tool"])
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - but don't fail if not interweb, etc...
shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
else:
if cwl:
remote_repo = "https://github.com/common-workflow-language/galaxy"
else:
remote_repo = "https://github.com/galaxyproject/galaxy"
command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
shell(command)
return gx_repo
def __handle_upload(ctx, realized_repository, **kwds):
"""Upload a tool directory as a tarball to a tool shed.
"""
path = realized_repository.path
tar_path = kwds.get("tar", None)
if not tar_path:
tar_path = shed.build_tarball(path, **kwds)
if kwds["tar_only"]:
suffix = ""
if realized_repository.multiple:
name = realized_repository.config["name"]
suffix = "_%s" % name.replace("-", "_")
shell("cp %s shed_upload%s.tar.gz" % (tar_path, suffix))
return 0
tsi = shed.tool_shed_client(ctx, **kwds)
update_kwds = {}
message = kwds.get("message", None)
if message:
update_kwds["commit_message"] = message
# TODO: this needs to use realized repository
repo_id = realized_repository.find_repository_id(ctx, tsi)
if repo_id is None and kwds["force_repository_creation"]:
repo_id = realized_repository.create(ctx, tsi)
# failing to create the repo, give up
if repo_id is None:
return -1
# TODO: support updating repo information if it changes in the config file
try:
tsi.repositories.update_repository(repo_id, tar_path, **update_kwds)
except Exception as e:
exception_content = e.read()
try:
# Galaxy passes nice JSON messages as their errors, which bioblend
# blindly returns. Attempt to parse those.
upstream_error = json.loads(exception_content)
error(upstream_error['err_msg'])
except Exception as e2:
error("Could not update %s" % realized_repository.name)
error(exception_content)
error(e2.read())
return -1
info("Repository %s updated successfully." % realized_repository.name)
return 0
def _install_with_command(ctx, config_directory, command, env, kwds):
# TODO: --watchdog
pip_installs = []
if pip_installs:
pip_install_command = ['pip', 'install'] + pip_installs
else:
pip_install_command = ""
setup_venv_command = setup_venv(ctx, kwds)
install_cmd = shell_join(
['cd', config_directory],
command,
['cd', 'galaxy-dev'],
setup_venv_command,
pip_install_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd, env=env)
def _install_with_command(ctx, config_directory, command, env, kwds):
# TODO: --watchdog
pip_installs = []
if pip_installs:
pip_install_command = PIP_INSTALL_CMD % " ".join(pip_installs)
else:
pip_install_command = ""
setup_venv_command = setup_venv(ctx, kwds)
install_cmd = shell_join(
"cd %s" % config_directory,
command,
"cd galaxy-dev",
setup_venv_command,
pip_install_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd, env=env)
def _install_with_command(ctx, config_directory, command, env, kwds):
# TODO: --watchdog
pip_installs = []
if pip_installs:
pip_install_command = PIP_INSTALL_CMD % " ".join(pip_installs)
else:
pip_install_command = ""
setup_venv_command = setup_venv(ctx, kwds)
install_cmd = shell_join(
"cd %s" % config_directory,
command,
"cd galaxy-dev",
setup_venv_command,
pip_install_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd, env=env)
def cli(ctx, path, template=None, **kwds):
"""Initialize a new tool project (demo only right now).
"""
if template is None:
warn("Creating empty project, this function doesn't do much yet.")
if not os.path.exists(path):
os.makedirs(path)
if template is None:
return
tempdir = tempfile.mkdtemp()
try:
untar_args = UNTAR_ARGS % (tempdir)
untar_to(DOWNLOAD_URL, tempdir, untar_args)
shell("ls '%s'" % (tempdir))
shell("mv '%s/%s'/* '%s'" % (tempdir, template, path))
finally:
shutil.rmtree(tempdir)
def cli(ctx, path, template=None, **kwds):
"""Initialize a new tool project (demo only right now).
"""
if template is None:
warn("Creating empty project, this function doesn't do much yet.")
if not os.path.exists(path):
os.makedirs(path)
if template is None:
return
tempdir = tempfile.mkdtemp()
try:
untar_args = UNTAR_ARGS % (tempdir)
untar_to(DOWNLOAD_URL, tempdir, untar_args)
shell("ls '%s'" % (tempdir))
shell("mv '%s/%s'/* '%s'" % (tempdir, template, path))
finally:
shutil.rmtree(tempdir)
def upload_repository(ctx, realized_repository, **kwds):
"""Upload a tool directory as a tarball to a tool shed."""
path = realized_repository.path
tar_path = kwds.get("tar", None)
if not tar_path:
tar_path = build_tarball(path, **kwds)
if kwds.get("tar_only", False):
name = realized_repository.pattern_to_file_name("shed_upload.tar.gz")
shell("cp '%s' '%s'" % (tar_path, name))
return 0
shed_context = get_shed_context(ctx, **kwds)
update_kwds = {}
_update_commit_message(ctx, realized_repository, update_kwds, **kwds)
repo_id = handle_force_create(realized_repository, ctx, shed_context,
**kwds)
# failing to create the repo, give up
if repo_id is None:
return report_non_existent_repository(realized_repository)
if kwds.get("check_diff", False):
is_diff = diff_repo(ctx, realized_repository, **kwds) != 0
if not is_diff:
name = realized_repository.name
info("Repository [%s] not different, skipping upload." % name)
return 0
# TODO: support updating repo information if it changes in the config file
try:
shed_context.tsi.repositories.update_repository(
str(repo_id), tar_path, **update_kwds)
except Exception as e:
if isinstance(e, bioblend.ConnectionError) and e.status_code == 400 and \
e.body == '{"content_alert": "", "err_msg": "No changes to repository."}':
warn(
"Repository %s was not updated because there were no changes" %
realized_repository.name)
return 0
message = api_exception_to_message(e)
error("Could not update %s" % realized_repository.name)
error(message)
return -1
info("Repository %s updated successfully." % realized_repository.name)
return 0
def diff_in(ctx, working, path, **kwds):
shed_target_source = kwds.get("shed_target_source", None)
label_a = "_%s_" % (shed_target_source if shed_target_source else "local")
shed_target = kwds.get("shed_target", "B")
if "/" in shed_target:
shed_target = "custom_shed"
label_b = "_%s_" % shed_target
mine = os.path.join(working, label_a)
other = os.path.join(working, label_b)
tsi = shed.tool_shed_client(ctx, read_only=True, **kwds)
shed.download_tarball(
ctx,
tsi,
path,
destination=other,
clean=True,
**kwds
)
if shed_target_source:
new_kwds = kwds.copy()
new_kwds["shed_target"] = shed_target_source
tsi = shed.tool_shed_client(ctx, read_only=True, **new_kwds)
shed.download_tarball(
ctx,
tsi,
path,
destination=mine,
clean=True,
**new_kwds
)
else:
tar_path = shed.build_tarball(path)
cmd_template = 'mkdir "%s"; tar -xzf "%s" -C "%s"; rm -rf %s'
shell(cmd_template % (mine, tar_path, mine, tar_path))
cmd = 'cd "%s"; diff -r %s %s' % (working, label_a, label_b)
if kwds["output"]:
cmd += "> '%s'" % kwds["output"]
shell(cmd)
def upload_repository(ctx, realized_repository, **kwds):
"""Upload a tool directory as a tarball to a tool shed.
"""
path = realized_repository.path
tar_path = kwds.get("tar", None)
if not tar_path:
tar_path = build_tarball(path, **kwds)
if kwds.get("tar_only", False):
name = realized_repository.pattern_to_file_name("shed_upload.tar.gz")
shell("cp '%s' '%s'" % (tar_path, name))
return 0
shed_context = get_shed_context(ctx, **kwds)
update_kwds = {}
_update_commit_message(ctx, realized_repository, update_kwds, **kwds)
repo_id = realized_repository.find_repository_id(ctx, shed_context)
if repo_id is None and kwds["force_repository_creation"]:
repo_id = realized_repository.create(ctx, shed_context)
# failing to create the repo, give up
if repo_id is None:
name = realized_repository.name
error("Repository [%s] does not exist in the targeted Tool Shed." % name)
return 2
if kwds.get("check_diff", False):
is_diff = diff_repo(ctx, realized_repository, **kwds)
if not is_diff:
name = realized_repository.name
info("Repository [%s] not different, skipping upload." % name)
return 0
# TODO: support updating repo information if it changes in the config file
try:
shed_context.tsi.repositories.update_repository(
repo_id, tar_path, **update_kwds
)
except Exception as e:
message = api_exception_to_message(e)
error("Could not update %s" % realized_repository.name)
error(message)
return -1
info("Repository %s updated successfully." % realized_repository.name)
return 0
def upload_repository(ctx, realized_repository, **kwds):
"""Upload a tool directory as a tarball to a tool shed.
"""
path = realized_repository.path
tar_path = kwds.get("tar", None)
if not tar_path:
tar_path = build_tarball(path, **kwds)
if kwds.get("tar_only", False):
name = realized_repository.pattern_to_file_name("shed_upload.tar.gz")
shell("cp '%s' '%s'" % (tar_path, name))
return 0
shed_context = get_shed_context(ctx, **kwds)
update_kwds = {}
_update_commit_message(ctx, realized_repository, update_kwds, **kwds)
repo_id = realized_repository.find_repository_id(ctx, shed_context)
if repo_id is None and kwds["force_repository_creation"]:
repo_id = realized_repository.create(ctx, shed_context)
# failing to create the repo, give up
if repo_id is None:
name = realized_repository.name
error("Repository [%s] does not exist in the targeted Tool Shed." % name)
return 2
if kwds.get("check_diff", False):
is_diff = diff_repo(ctx, realized_repository, **kwds)
if not is_diff:
name = realized_repository.name
info("Repository [%s] not different, skipping upload." % name)
return 0
# TODO: support updating repo information if it changes in the config file
try:
shed_context.tsi.repositories.update_repository(
repo_id, tar_path, **update_kwds
)
except Exception as e:
message = api_exception_to_message(e)
error("Could not update %s" % realized_repository.name)
error(message)
return -1
info("Repository %s updated successfully." % realized_repository.name)
return 0
def _ensure_galaxy_repository_available(ctx, kwds):
workspace = ctx.workspace
cwl = kwds.get("cwl", False)
galaxy_source = kwds.get('galaxy_source')
if galaxy_source and galaxy_source != DEFAULT_GALAXY_SOURCE:
sanitized_repo_name = "".join(c if c.isalnum() else '_' for c in kwds['galaxy_source']).rstrip()[:255]
gx_repo = os.path.join(workspace, "gx_repo_%s" % sanitized_repo_name)
else:
gx_repo = os.path.join(workspace, "gx_repo")
if cwl:
gx_repo += "_cwl"
if os.path.exists(gx_repo):
# Attempt fetch - 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)
command = git.command_clone(ctx, remote_repo, gx_repo, mirror=True)
shell(command)
return gx_repo
def upload_repository(ctx, realized_repository, **kwds):
"""Upload a tool directory as a tarball to a tool shed."""
path = realized_repository.path
tar_path = kwds.get("tar", None)
if not tar_path:
tar_path = build_tarball(path, **kwds)
if kwds.get("tar_only", False):
name = realized_repository.pattern_to_file_name("shed_upload.tar.gz")
shell("cp '%s' '%s'" % (tar_path, name))
return 0
shed_context = get_shed_context(ctx, **kwds)
update_kwds = {}
_update_commit_message(ctx, realized_repository, update_kwds, **kwds)
repo_id = handle_force_create(realized_repository, ctx, shed_context, **kwds)
# failing to create the repo, give up
if repo_id is None:
return report_non_existent_repository(realized_repository)
if kwds.get("check_diff", False):
is_diff = diff_repo(ctx, realized_repository, **kwds) != 0
if not is_diff:
name = realized_repository.name
info("Repository [%s] not different, skipping upload." % name)
return 0
# TODO: support updating repo information if it changes in the config file
try:
shed_context.tsi.repositories.update_repository(
str(repo_id), tar_path, **update_kwds
)
except Exception as e:
if isinstance(e, bioblend.ConnectionError) and e.status_code == 400 and \
e.body == '{"content_alert": "", "err_msg": "No changes to repository."}':
warn("Repository %s was not updated because there were no changes" % realized_repository.name)
return 0
message = api_exception_to_message(e)
error("Could not update %s" % realized_repository.name)
error(message)
return -1
info("Repository %s updated successfully." % realized_repository.name)
return 0
def _install_with_command(ctx, config_directory, command, kwds):
# TODO: --watchdog
pip_installs = []
if kwds.get("cwl", False):
pip_installs.append("cwltool")
if pip_installs:
pip_install_command = PIP_INSTALL_CMD % " ".join(pip_installs)
else:
pip_install_command = ""
setup_venv_command = galaxy_run.setup_venv(ctx, kwds)
install_cmd = shell_join(
"cd %s" % config_directory,
command,
"cd galaxy-dev",
setup_venv_command,
pip_install_command,
galaxy_run.setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
shell(install_cmd)
def test_io_capture():
"""Test :func:`planemo.io.conditionally_captured_io`."""
with io.conditionally_captured_io(True, tee=False) as capture:
io.warn("Problem...")
assert_equal(capture[0]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.shell("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.communicate("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(False, tee=False) as capture:
io.communicate("echo 'Test...'")
assert capture is None
def test_io_capture():
"""Test :func:`planemo.io.conditionally_captured_io`."""
with io.conditionally_captured_io(True, tee=False) as capture:
io.warn("Problem...")
assert_equal(capture[0]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.shell("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(True, tee=False) as capture:
io.communicate("echo 'Problem...'")
assert_equal(capture[0]["data"], "echo 'Problem...'")
assert_equal(capture[1]["data"], "Problem...")
with io.conditionally_captured_io(False, tee=False) as capture:
io.communicate("echo 'Test...'")
assert capture is None
def shed_serve(ctx, install_args_list, **kwds):
"""Serve a daemon instance of Galaxy with specified repositories installed."""
with serve_daemon(ctx, **kwds) as config:
install_deps = not kwds.get("skip_dependencies", False)
print(INSTALLING_MESSAGE)
io.info(INSTALLING_MESSAGE)
for install_args in install_args_list:
install_args["install_tool_dependencies"] = install_deps
install_args["install_repository_dependencies"] = True
install_args["new_tool_panel_section_label"] = "Shed Installs"
config.install_repo(**install_args)
try:
config.wait_for_all_installed()
except Exception:
if ctx.verbose:
print("Failed to install tool repositories, Galaxy log:")
print(config.log_contents)
print("Galaxy root:")
io.shell(['ls', config.galaxy_root])
raise
yield config
def cli(ctx):
"""This command is used internally by planemo to assist in contineous testing
of tools with Travis CI (https://travis-ci.org/).
"""
build_dir = os.environ.get("TRAVIS_BUILD_DIR", None)
if not build_dir:
raise Exception("Failed to determine ${TRAVIS_BUILD_DIR}")
build_travis_dir = os.path.join(build_dir, ".travis")
if not os.path.exists(build_travis_dir):
os.makedirs(build_travis_dir)
build_bin_dir = os.path.join(build_travis_dir, "bin")
if not os.path.exists(build_bin_dir):
os.makedirs(build_bin_dir)
build_env_path = os.path.join(build_travis_dir, "env.sh")
template_vars = {
"BUILD_TRAVIS_DIR": build_travis_dir,
"BUILD_BIN_DIR": build_bin_dir,
"BUILD_ENV_PATH": build_env_path,
}
build_env = string.Template(BUILD_ENVIRONMENT_TEMPLATE).safe_substitute(
**template_vars
)
open(build_env_path, "a").write(build_env)
shell(FIX_EGGS_DIR)
shell(INSTALL_SAMTOOLS)
setup_file = os.path.join(build_travis_dir, SETUP_FILE_NAME)
if os.path.exists(setup_file):
shell(
". %s && bash -x %s" % (build_env_path, setup_file),
env=template_vars
)
def cli(ctx, path, template=None, **kwds):
"""(Experimental) Initialize a new tool project.
This is only a proof-of-concept demo right now.
"""
if template is None:
warn("Creating empty project, this function doesn't do much yet.")
if not os.path.exists(path):
os.makedirs(path)
if template is None:
return
tempdir = tempfile.mkdtemp()
try:
untar_args = UNTAR_ARGS % (tempdir)
untar_to(DOWNLOAD_URL, tempdir, untar_args)
template_dir = os.path.join(tempdir, template)
shell("ls '%s'" % (template_dir))
shell("mv '%s'/* '%s'" % (template_dir, path))
dot_files = [os.path.join(template_dir, f) for f in os.listdir(template_dir) if f.startswith(".")]
if len(dot_files) > 0:
dot_files_quoted = "'" + "' '".join(dot_files) + "'"
shell("mv %s '%s'" % (dot_files_quoted, path))
finally:
shutil.rmtree(tempdir)
def cli(ctx, path, template=None, **kwds):
"""(Experimental) Initialize a new tool project.
This is only a proof-of-concept demo right now.
"""
if template is None:
warn("Creating empty project, this function doesn't do much yet.")
if not os.path.exists(path):
os.makedirs(path)
if template is None:
return
tempdir = tempfile.mkdtemp()
try:
untar_args = UNTAR_ARGS % (tempdir)
untar_to(DOWNLOAD_URL, tempdir, untar_args)
template_dir = os.path.join(tempdir, template)
shell("ls '%s'" % (template_dir))
shell("mv '%s'/* '%s'" % (template_dir, path))
dot_files = [
os.path.join(template_dir, f) for f in os.listdir(template_dir)
if f.startswith(".")
]
if len(dot_files) > 0:
dot_files_quoted = "'" + "' '".join(dot_files) + "'"
shell("mv %s '%s'" % (dot_files_quoted, path))
finally:
shutil.rmtree(tempdir)
def __handle_upload(ctx, path, **kwds):
"""Upload a tool directory as a tarball to a tool shed.
"""
tar_path = kwds.get("tar", None)
if not tar_path:
tar_path = shed.build_tarball(path, **kwds)
if kwds["tar_only"]:
shell("cp %s shed_upload.tar.gz" % tar_path)
return 0
tsi = shed.tool_shed_client(ctx, **kwds)
update_kwds = {}
message = kwds.get("message", None)
if message:
update_kwds["commit_message"] = message
repo_id = __find_repository(ctx, tsi, path, **kwds)
if repo_id is None and kwds["force_repository_creation"]:
repo_id = __create_repository(ctx, tsi, path, **kwds)
# failing to create the repo, give up
if repo_id is None:
return -1
# TODO: support updating repo information if it changes in the config file
try:
tsi.repositories.update_repository(repo_id, tar_path, **update_kwds)
except Exception as e:
exception_content = e.read()
try:
# Galaxy passes nice JSON messages as their errors, which bioblend
# blindly returns. Attempt to parse those.
upstream_error = json.loads(exception_content)
error(upstream_error['err_msg'])
except Exception as e2:
error("Could not update %s" % path)
error(exception_content)
error(e2.read())
return -1
info("Repository %s updated successfully." % path)
return 0
def _install_with_command(ctx, galaxy_root, env, kwds):
setup_venv_command = setup_venv(ctx, kwds)
install_cmd = shell_join(
setup_venv_command,
setup_common_startup_args(),
COMMAND_STARTUP_COMMAND,
)
exit_code = shell(install_cmd, cwd=galaxy_root, env=env)
if exit_code != 0:
raise Exception("Failed to install Galaxy via command [%s]" % install_cmd)
if not os.path.exists(galaxy_root):
raise Exception("Failed to create Galaxy directory [%s]" % galaxy_root)
if not os.path.exists(os.path.join(galaxy_root, "lib")):
raise Exception("Failed to create Galaxy directory [%s], lib missing" % galaxy_root)
def cli(ctx):
"""Internal command for GitHub/TravisCI testing.
This command is used internally by planemo to assist in contineous testing
of tools with Travis CI (https://travis-ci.org/).
"""
build_dir = os.environ.get("TRAVIS_BUILD_DIR", None)
if not build_dir:
raise Exception("Failed to determine ${TRAVIS_BUILD_DIR}")
build_travis_dir = os.path.join(build_dir, ".travis")
if not os.path.exists(build_travis_dir):
os.makedirs(build_travis_dir)
build_bin_dir = os.path.join(build_travis_dir, "bin")
if not os.path.exists(build_bin_dir):
os.makedirs(build_bin_dir)
build_env_path = os.path.join(build_travis_dir, "env.sh")
template_vars = {
"BUILD_TRAVIS_DIR": build_travis_dir,
"BUILD_BIN_DIR": build_bin_dir,
"BUILD_ENV_PATH": build_env_path,
}
build_env = string.Template(BUILD_ENVIRONMENT_TEMPLATE).safe_substitute(
**template_vars
)
open(build_env_path, "a").write(build_env)
eggs_dir = os.path.join(os.getenv('HOME'), '.python-eggs')
if not os.path.exists(eggs_dir):
os.makedirs(eggs_dir, 0o700)
else:
os.chmod(eggs_dir, 0o700)
# samtools essentially required by Galaxy
shell(['wget', SAMTOOLS_URL])
shell(['sudo', 'dpkg', '-i', SAMTOOLS_DEB])
setup_file = os.path.join(build_travis_dir, SETUP_FILE_NAME)
if os.path.exists(setup_file):
shell(
". %s && bash -x %s" % (build_env_path, setup_file),
env=template_vars
)
def _copy_repo(self, name, dest):
repo = os.path.join(TEST_REPOS_DIR, name)
io.shell("cp -r '%s/.' '%s'" % (repo, dest))
def clone(*args, **kwds):
command = command_clone(*args, **kwds)
return io.shell(command)
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_root, branch=branch)
shell(command, env=env)
_install_with_command(ctx, galaxy_root, env, kwds)
def is_rev_dirty(ctx, directory):
cmd = "cd '%s' && git diff --quiet" % directory
return io.shell(cmd) != 0
def _diff_in(ctx, working, realized_repository, **kwds):
path = realized_repository.path
shed_target_source = kwds.get("shed_target_source")
label_a = "_%s_" % (shed_target_source if shed_target_source else "workingdir")
shed_target = kwds.get("shed_target", "B")
if "/" in shed_target:
shed_target = "custom_shed"
label_b = "_%s_" % shed_target
mine = os.path.join(working, label_a)
other = os.path.join(working, label_b)
shed_context = get_shed_context(ctx, read_only=True, **kwds)
# In order to download the tarball, require repository ID...
repo_id = realized_repository.find_repository_id(ctx, shed_context)
if repo_id is None:
error("shed_diff: Repository [%s] does not exist in the targeted Tool Shed."
% realized_repository.name)
# $ diff README.rst not_a_file 2&>1 /dev/null; echo $?
# 2
return 2
info("Diffing repository [%s]" % realized_repository.name)
download_tarball(
ctx,
shed_context,
realized_repository,
destination=other,
clean=True,
destination_is_pattern=False,
**kwds
)
if shed_target_source:
new_kwds = kwds.copy()
new_kwds["shed_target"] = shed_target_source
shed_context = get_shed_context(ctx, read_only=True, **new_kwds)
download_tarball(
ctx,
shed_context,
realized_repository,
destination=mine,
clean=True,
destination_is_pattern=False,
**new_kwds
)
else:
tar_path = build_tarball(path)
os.mkdir(mine)
shell(['tar', '-xzf', tar_path, '-C', mine])
shutil.rmtree(tar_path, ignore_errors=True)
output = kwds.get("output")
raw = kwds.get("raw", False)
xml_diff = 0
if not raw:
if output:
with open(output, "w") as f:
xml_diff = diff_and_remove(working, label_a, label_b, f)
else:
xml_diff = diff_and_remove(working, label_a, label_b, sys.stdout)
cmd = ['diff', '-r', label_a, label_b]
if output:
with open(output, 'ab') as fh:
raw_diff = shell(cmd, cwd=working, stdout=fh)
else:
raw_diff = shell(cmd, cwd=working)
exit = raw_diff or xml_diff
if not raw:
if xml_diff:
ctx.vlog("One or more shed XML file(s) different!")
if raw_diff:
ctx.vlog("One or more non-shed XML file(s) different.")
if not xml_diff and not raw_diff:
ctx.vlog("No differences.")
return exit
def _diff_in(ctx, working, realized_repository, **kwds):
path = realized_repository.path
shed_target_source = kwds.get("shed_target_source", None)
label_a = "_%s_" % (shed_target_source if shed_target_source else "local")
shed_target = kwds.get("shed_target", "B")
if "/" in shed_target:
shed_target = "custom_shed"
label_b = "_%s_" % shed_target
mine = os.path.join(working, label_a)
other = os.path.join(working, label_b)
tsi = tool_shed_client(ctx, read_only=True, **kwds)
# In order to download the tarball, require repository ID...
repo_id = realized_repository.find_repository_id(ctx, tsi)
if repo_id is None:
error("Repository [%s] does not exist in the targeted Tool Shed, can't do shed_diff"
% realized_repository.name)
# TODO - Should this return an error code which can be checked for in recursive mode?
return 0
download_tarball(
ctx,
tsi,
realized_repository,
destination=other,
clean=True,
destination_is_pattern=False,
**kwds
)
if shed_target_source:
new_kwds = kwds.copy()
new_kwds["shed_target"] = shed_target_source
tsi = tool_shed_client(ctx, read_only=True, **new_kwds)
download_tarball(
ctx,
tsi,
realized_repository,
destination=mine,
clean=True,
destination_is_pattern=False,
**new_kwds
)
else:
tar_path = build_tarball(path)
cmd_template = 'mkdir "%s"; tar -xzf "%s" -C "%s"; rm -rf %s'
shell(cmd_template % (mine, tar_path, mine, tar_path))
output = kwds.get("output", None)
raw = kwds.get("raw", False)
is_diff = 0
if not raw:
if output:
with open(output, "w") as f:
is_diff = diff_and_remove(working, label_a, label_b, f)
else:
is_diff = diff_and_remove(working, label_a, label_b, sys.stdout)
cmd = 'cd "%s"; diff -r %s %s' % (working, label_a, label_b)
if output:
cmd += ">> '%s'" % output
exit = shell(cmd) or is_diff
return exit
def is_rev_dirty(ctx, directory):
"""Check if specified git repository has uncommitted changes."""
# TODO: Use ENV instead of cd.
cmd = "cd '%s' && git diff --quiet" % directory
return io.shell(cmd) != 0
def _diff_in(ctx, working, realized_repository, **kwds):
path = realized_repository.path
shed_target_source = kwds.get("shed_target_source", None)
label_a = "_%s_" % (shed_target_source if shed_target_source else "workingdir")
shed_target = kwds.get("shed_target", "B")
if "/" in shed_target:
shed_target = "custom_shed"
label_b = "_%s_" % shed_target
mine = os.path.join(working, label_a)
other = os.path.join(working, label_b)
shed_context = get_shed_context(ctx, read_only=True, **kwds)
# In order to download the tarball, require repository ID...
repo_id = realized_repository.find_repository_id(ctx, shed_context)
if repo_id is None:
error("shed_diff: Repository [%s] does not exist in the targeted Tool Shed."
% realized_repository.name)
# $ diff README.rst not_a_file 2&>1 /dev/null; echo $?
# 2
return 2
info("Diffing repository [%s]" % realized_repository.name)
download_tarball(
ctx,
shed_context,
realized_repository,
destination=other,
clean=True,
destination_is_pattern=False,
**kwds
)
if shed_target_source:
new_kwds = kwds.copy()
new_kwds["shed_target"] = shed_target_source
shed_context = get_shed_context(ctx, read_only=True, **new_kwds)
download_tarball(
ctx,
shed_context,
realized_repository,
destination=mine,
clean=True,
destination_is_pattern=False,
**new_kwds
)
else:
tar_path = build_tarball(path)
cmd_template = 'mkdir "%s"; tar -xzf "%s" -C "%s"; rm -rf %s'
shell(cmd_template % (mine, tar_path, mine, tar_path))
output = kwds.get("output", None)
raw = kwds.get("raw", False)
xml_diff = 0
if not raw:
if output:
with open(output, "w") as f:
xml_diff = diff_and_remove(working, label_a, label_b, f)
else:
xml_diff = diff_and_remove(working, label_a, label_b, sys.stdout)
cmd = 'cd "%s"; diff -r %s %s' % (working, label_a, label_b)
if output:
cmd += " >> '%s'" % output
raw_diff = shell(cmd)
exit = raw_diff or xml_diff
if not raw:
if xml_diff:
ctx.vlog("One or more shed XML file(s) different!")
if raw_diff:
ctx.vlog("One or more non-shed XML file(s) different.")
if not xml_diff and not raw_diff:
ctx.vlog("No differences.")
return exit