--- /dev/null
+Arvados Code of Conduct
+=======================
+
+The Arvados Project is dedicated to providing a harassment-free experience for
+everyone. We do not tolerate harassment of participants in any form.
+
+This code of conduct applies to all Arvados Project spaces both online and off:
+Gitter chat, Redmine issues, wiki, mailing lists, forums, video chats, and any other
+Arvados spaces. Anyone who violates this code of conduct may be sanctioned or
+expelled from these spaces at the discretion of the Arvados Team.
+
+Some Arvados Project spaces may have additional rules in place, which will be
+made clearly available to participants. Participants are responsible for
+knowing and abiding by these rules.
+
+Harassment includes, but is not limited to:
+
+ - Offensive comments related to gender, gender identity and expression, sexual
+orientation, disability, mental illness, neuro(a)typicality, physical
+appearance, body size, age, race, or religion.
+ - Unwelcome comments regarding a person’s lifestyle choices and practices,
+including those related to food, health, parenting, drugs, and employment.
+ - Deliberate misgendering or use of [dead](https://www.quora.com/What-is-deadnaming/answer/Nancy-C-Walker)
+or rejected names.
+ - Gratuitous or off-topic sexual images or behaviour in spaces where they’re not
+appropriate.
+ - Physical contact and simulated physical contact (eg, textual descriptions like
+“\*hug\*” or “\*backrub\*”) without consent or after a request to stop.
+ - Threats of violence.
+ - Incitement of violence towards any individual, including encouraging a person
+to commit suicide or to engage in self-harm.
+ - Deliberate intimidation.
+ - Stalking or following.
+ - Harassing photography or recording, including logging online activity for
+harassment purposes.
+ - Sustained disruption of discussion.
+ - Unwelcome sexual attention.
+ - Pattern of inappropriate social contact, such as requesting/assuming
+inappropriate levels of intimacy with others
+ - Continued one-on-one communication after requests to cease.
+ - Deliberate “outing” of any aspect of a person’s identity without their consent
+except as necessary to protect vulnerable people from intentional abuse.
+ - Publication of non-harassing private communication.
+
+The Arvados Project prioritizes marginalized people’s safety over privileged
+people’s comfort. The Arvados Leadership Team will not act on complaints regarding:
+
+ - ‘Reverse’ -isms, including ‘reverse racism,’ ‘reverse sexism,’ and ‘cisphobia’
+ - Reasonable communication of boundaries, such as “leave me alone,” “go away,” or
+“I’m not discussing this with you.”
+ - Communicating in a [tone](http://geekfeminism.wikia.com/wiki/Tone_argument)
+you don’t find congenial
+
+Reporting
+---------
+
+If you are being harassed by a member of the Arvados Project, notice that someone
+else is being harassed, or have any other concerns, please contact the Arvados
+Project Team at contact@arvados.org. If person who is harassing
+you is on the team, they will recuse themselves from handling your incident. We
+will respond as promptly as we can.
+
+This code of conduct applies to Arvados Project spaces, but if you are being
+harassed by a member of Arvados Project outside our spaces, we still want to
+know about it. We will take all good-faith reports of harassment by Arvados Project
+members, especially the Arvados Team, seriously. This includes harassment
+outside our spaces and harassment that took place at any point in time. The
+abuse team reserves the right to exclude people from the Arvados Project based on
+their past behavior, including behavior outside Arvados Project spaces and
+behavior towards people who are not in the Arvados Project.
+
+In order to protect volunteers from abuse and burnout, we reserve the right to
+reject any report we believe to have been made in bad faith. Reports intended
+to silence legitimate criticism may be deleted without response.
+
+We will respect confidentiality requests for the purpose of protecting victims
+of abuse. At our discretion, we may publicly name a person about whom we’ve
+received harassment complaints, or privately warn third parties about them, if
+we believe that doing so will increase the safety of Arvados Project members or
+the general public. We will not name harassment victims without their
+affirmative consent.
+
+Consequences
+------------
+
+Participants asked to stop any harassing behavior are expected to comply
+immediately.
+
+If a participant engages in harassing behavior, the Arvados Team may
+take any action they deem appropriate, up to and including expulsion from all
+Arvados Project spaces and identification of the participant as a harasser to other
+Arvados Project members or the general public.
+
+This anti-harassment policy is based on the [example policy from the Geek
+Feminism wiki](http://geekfeminism.wikia.com/wiki/Community_anti-harassment/Policy),
+created by the Geek Feminism community.
--- /dev/null
+[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
+[comment]: # ()
+[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
+
+# Contributing
+
+Arvados is free software, which means it is free for all to use, learn
+from, and improve. We encourage contributions from the community that
+improve Arvados for everyone. Some examples of contributions are bug
+reports, bug fixes, new features, and scripts or documentation that help
+with using, administering, or installing Arvados. We also love to
+hear about Arvados success stories.
+
+Those interested in contributing should begin by joining the [Arvados community
+channel](https://gitter.im/arvados/community) and telling us about your interest.
+
+Contributers should also create an account at https://dev.arvados.org
+to be able to create and comment on bug tracker issues. The
+Arvados public bug tracker is located at
+https://dev.arvados.org/projects/arvados/issues .
+
+Contributers may also be interested in the [development road map](https://dev.arvados.org/issues/gantt?utf8=%E2%9C%93&set_filter=1&gantt=1&f%5B%5D=project_id&op%5Bproject_id%5D=%3D&v%5Bproject_id%5D%5B%5D=49&f%5B%5D=&zoom=1).
+
+# Development
+
+Git repositories for primary development are located at
+https://git.arvados.org/ and can also be browsed at
+https://dev.arvados.org/projects/arvados/repository . Every push to
+the master branch is also mirrored to Github at
+https://github.com/arvados/arvados .
+
+Visit [Hacking Arvados](https://dev.arvados.org/projects/arvados/wiki/Hacking) for
+detailed information about setting up an Arvados development
+environment, development process, coding standards, and notes about specific components.
+
+If you wish to build the Arvados documentation from a local git clone, see
+[doc/README.textile](doc/README.textile) for instructions.
+
+# Pull requests
+
+The preferred method for making contributions is through Github pull requests.
+
+This is the general contribution process:
+
+1. Fork the Arvados repository using the Github "Fork" button
+2. Clone your fork, make your changes, commit to your fork.
+3. Every commit message must have a DCO sign-off and every file must have a SPDX license (see below).
+4. Add yourself to the [AUTHORS](AUTHORS) file
+5. When your fork is ready, through Github, Create a Pull Request against `arvados:master`
+6. Notify the core team about your pull request through the [Arvados development
+channel](https://gitter.im/arvados/development) or by other means.
+7. A member of the core team will review the pull request. They may have questions or comments, or request changes.
+8. When the contribution is ready, a member of the core team will
+merge the pull request into the master branch, which will
+automatically resolve the pull request.
+
+The Arvados project does not require a contributor agreement in advance, but does require each commit message include a [Developer Certificate of Origin](https://dev.arvados.org/projects/arvados/wiki/Developer_Certificate_Of_Origin). Please ensure *every git commit message* includes `Arvados-DCO-1.1-Signed-off-by`. If you have already made commits without it, fix them with `git commit --amend` or `git rebase`.
+
+The Developer Certificate of Origin line looks like this:
+
+```
+Arvados-DCO-1.1-Signed-off-by: Joe Smith <joe.smith@example.com>
+```
+
+New files must also include `SPDX-License-Identifier` at the top with one of the three Arvados open source licenses. See [COPYING](COPYING) for details.
+
+# Continuous integration
+
+Continuous integration is hosted at https://ci.arvados.org/
+
+Currently, external contributers cannot trigger builds. We are investigating integration with Github pull requests for the future.
+
+[](https://ci.arvados.org/job/run-tests/)
+
+[](https://goreportcard.com/report/github.com/arvados/arvados)
AGPL-3.0: agpl-3.0.txt
Apache-2.0: apache-2.0.txt
CC-BY-SA-3.0: cc-by-sa-3.0.txt
+
+As a general rule, code in the sdk/ directory is licensed Apache-2.0,
+documentation in the doc/ directory is licensed CC-BY-SA-3.0, and
+everything else is licensed AGPL-3.0.
\ No newline at end of file
[comment]: # ()
[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
-[Arvados](https://arvados.org) is a free software distributed computing platform
-for bioinformatics, data science, and high throughput analysis of massive data
-sets. Arvados supports a variety of cloud, cluster and HPC environments.
+[](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) | [Installing Arvados](https://doc.arvados.org/install/index.html) | [Installing Client SDKs](https://doc.arvados.org/sdk/index.html) | [Report a bug](https://dev.arvados.org/projects/arvados/issues/new) | [Development and Contributing](CONTRIBUTING.md)
-Arvados consists of:
+<img align="right" src="doc/images/dax.png" height="240px">
-* *Keep*: a petabyte-scale content-addressed distributed storage system for managing and
- storing collections of files, accessible via HTTP and FUSE mount.
+[Arvados](https://arvados.org) is an open source platform for
+managing, processing, and sharing genomic and other large scientific
+and biomedical data. With Arvados, bioinformaticians run and scale
+compute-intensive workflows, developers create biomedical
+applications, and IT administrators manage large compute and storage
+resources.
-* *Crunch*: a Docker-based cluster and HPC workflow engine designed providing
- strong versioning, reproducibilty, and provenance of computations.
+The key components of Arvados are:
-* Related services and components including a web workbench for managing files
- and compute jobs, REST APIs, SDKs, and other tools.
+* *Keep*: Keep is the Arvados storage system for managing and storing large
+collections of files. Keep combines content addressing and a
+distributed storage architecture resulting in both high reliability
+and high throughput. Every file stored in Keep can be accurately
+verified every time it is retrieved. Keep supports the creation of
+collections as a flexible way to define data sets without having to
+re-organize or needlessly copy data. Keep works on a wide range of
+underlying filesystems and object stores.
-## Quick start
+* *Crunch*: Crunch is the orchestration system for running [Common Workflow Language](https://www.commonwl.org) workflows. It is
+designed to maintain data provenance and workflow
+reproducibility. Crunch automatically tracks data inputs and outputs
+through Keep and executes workflow processes in Docker containers. In
+a cloud environment, Crunch optimizes costs by scaling compute on demand.
+
+* *Workbench*: The Workbench web application allows users to interactively access
+Arvados functionality. It is especially helpful for querying and
+browsing data, visualizing provenance, and tracking the progress of
+workflows.
+
+* *Command Line tools*: The command line interface (CLI) provides convenient access to Arvados
+functionality in the Arvados platform from the command line.
+
+* *API and SDKs*: Arvados is designed to be integrated with existing infrastructure. All
+the services in Arvados are accessed through a RESTful API. SDKs are
+available for Python, Go, R, Perl, Ruby, and Java.
+
+# Quick start
To try out Arvados on your local workstation, you can use Arvbox, which
provides Arvados components pre-installed in a Docker container (requires
configure Arvbox to be accessible over a network and for other options see
http://doc.arvados.org/install/arvbox.html for details.
-## Documentation
+# Documentation
-Complete documentation, including a User Guide, Installation documentation and
-API documentation is available at http://doc.arvados.org/
+Complete documentation, including the [User Guide](https://doc.arvados.org/user/index.html), [Installation documentation](https://doc.arvados.org/install/index.html), [Administrator documentation](https://doc.arvados.org/admin/index.html) and
+[API documentation](https://doc.arvados.org/api/index.html) is available at http://doc.arvados.org/
If you wish to build the Arvados documentation from a local git clone, see
-doc/README.textile for instructions.
+[doc/README.textile](doc/README.textile) for instructions.
-## Community
+# Community
[](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
-The [arvados community channel](https://gitter.im/arvados/community)
+The [Arvados community channel](https://gitter.im/arvados/community)
channel at [gitter.im](https://gitter.im) is available for live
discussion and support.
-The
-[Arvados user mailing list](http://lists.arvados.org/mailman/listinfo/arvados)
-is a forum for general discussion, questions, and news about Arvados
-development. The
-[Arvados developer mailing list](http://lists.arvados.org/mailman/listinfo/arvados-dev)
-is a forum for more technical discussion, intended for developers and
-contributors to Arvados.
+The [Arvados developement channel](https://gitter.im/arvados/development)
+channel at [gitter.im](https://gitter.im) is used to coordinate development.
-## Development
+The [Arvados user mailing list](http://lists.arvados.org/mailman/listinfo/arvados)
+is used to announce new versions and other news.
-[](https://ci.arvados.org/job/run-tests/)
-[](https://goreportcard.com/report/github.com/arvados/arvados)
+All participants are expected to abide by the [Arvados Code of Conduct](CODE_OF_CONDUCT.md).
-The Arvados public bug tracker is located at https://dev.arvados.org/projects/arvados/issues
+# Reporting bugs
-Continuous integration is hosted at https://ci.arvados.org/
+[Report a bug](https://dev.arvados.org/projects/arvados/issues/new) on [dev.arvados.org](https://dev.arvados.org).
-Instructions for setting up a development environment and working on specific
-components can be found on the
-["Hacking Arvados" page of the Arvados wiki](https://dev.arvados.org/projects/arvados/wiki/Hacking).
+# Development and Contributing
-## Contributing
+See [CONTRIBUTING](CONTRIBUTING.md) for information about Arvados development and how to contribute to the Arvados project.
-When making a pull request, please ensure *every git commit message* includes a one-line [Developer Certificate of Origin](https://dev.arvados.org/projects/arvados/wiki/Developer_Certificate_Of_Origin). If you have already made commits without it, fix them with `git commit --amend` or `git rebase`.
+The [development road map](https://dev.arvados.org/issues/gantt?utf8=%E2%9C%93&set_filter=1&gantt=1&f%5B%5D=project_id&op%5Bproject_id%5D=%3D&v%5Bproject_id%5D%5B%5D=49&f%5B%5D=&zoom=1) outlines some of the project priorities over the next twelve months.
-## Licensing
+# Licensing
-Arvados is Free Software. See COPYING for information about Arvados Free
-Software licenses.
+Arvados is Free Software. See [COPYING](COPYING) for information about the open source licenses used in Arvados.
. "$VENVDIR/bin/activate"
# Needed for run_test_server.py which is used by certain (non-Python) tests.
- pip install --no-cache-dir PyYAML future \
- || fatal "pip install PyYAML failed"
+ pip install --no-cache-dir PyYAML future httplib2 \
+ || fatal "`pip install PyYAML future httplib2` failed"
# Preinstall libcloud if using a fork; otherwise nodemanager "pip
# install" won't pick it up by default.
do_install sdk/cli
do_install sdk/perl
do_install sdk/python pip
+ do_install sdk/python pip3
do_install sdk/ruby
do_install services/api
do_install services/arv-git-httpd go
'bin/arvados-cwl-runner',
],
# Note that arvados/build/run-build-packages.sh looks at this
- # file to determine what version of cwltool and schema-salad to build.
+ # file to determine what version of cwltool and schema-salad to
+ # build.
install_requires=[
'cwltool==1.0.20190831161204',
'schema-salad==4.5.20190815125611',
'mock>=1.0,<4',
'subprocess32>=3.5.1',
],
- zip_safe=True
- )
+ zip_safe=True,
+)
],
test_suite='tests',
tests_require=['pbr<1.7.0', 'mock>=1.0', 'python-pam'],
- zip_safe=False
- )
+ zip_safe=False,
+)
svc.api_token = token
svc.insecure = insecure
svc.request_id = request_id
+ svc.config = lambda: util.get_config_once(svc)
kwargs['http'].max_request_size = svc._rootDesc.get('maxRequestSize', 0)
kwargs['http'].cache = None
kwargs['http']._request_id = lambda: svc.request_id or util.new_request_id()
rid += chr(c+ord('a')-10)
n = n // 36
return rid
+
+def get_config_once(svc):
+ if not svc._rootDesc.get('resources')['configs']:
+ # Old API server version, no config export endpoint
+ return {}
+ if not hasattr(svc, '_cached_config'):
+ svc._cached_config = svc.configs().get().execute()
+ return svc._cached_config
LLFUSE_VERSION_0 = llfuse.__version__.startswith('0')
-from .fusedir import sanitize_filename, Directory, CollectionDirectory, TmpCollectionDirectory, MagicDirectory, TagsDirectory, ProjectDirectory, SharedDirectory, CollectionDirectoryBase
+from .fusedir import Directory, CollectionDirectory, TmpCollectionDirectory, MagicDirectory, TagsDirectory, ProjectDirectory, SharedDirectory, CollectionDirectoryBase
from .fusefile import StringFile, FuseArvadosFile
_logger = logging.getLogger('arvados.arvados_fuse')
return
e = self.operations.inodes.add_entry(Directory(
- llfuse.ROOT_INODE, self.operations.inodes))
+ llfuse.ROOT_INODE, self.operations.inodes, self.api.config))
dir_args[0] = e.inode
for name in self.args.mount_by_id:
# appear as underscores in the fuse mount.)
_disallowed_filename_characters = re.compile('[\x00/]')
-# '.' and '..' are not reachable if API server is newer than #6277
-def sanitize_filename(dirty):
- """Replace disallowed filename characters with harmless "_"."""
- if dirty is None:
- return None
- elif dirty == '':
- return '_'
- elif dirty == '.':
- return '_'
- elif dirty == '..':
- return '__'
- else:
- return _disallowed_filename_characters.sub('_', dirty)
-
class Directory(FreshBase):
"""Generic directory object, backed by a dict.
and the value referencing a File or Directory object.
"""
- def __init__(self, parent_inode, inodes):
+ def __init__(self, parent_inode, inodes, apiconfig):
"""parent_inode is the integer inode number"""
super(Directory, self).__init__()
raise Exception("parent_inode should be an int")
self.parent_inode = parent_inode
self.inodes = inodes
+ self.apiconfig = apiconfig
self._entries = {}
self._mtime = time.time()
- # Overriden by subclasses to implement logic to update the entries dict
- # when the directory is stale
+ def forward_slash_subst(self):
+ if not hasattr(self, '_fsns'):
+ self._fsns = None
+ config = self.apiconfig()
+ try:
+ self._fsns = config["Collections"]["ForwardSlashNameSubstitution"]
+ except KeyError:
+ # old API server with no FSNS config
+ self._fsns = '_'
+ else:
+ if self._fsns == '' or self._fsns == '/':
+ self._fsns = None
+ return self._fsns
+
+ def unsanitize_filename(self, incoming):
+ """Replace ForwardSlashNameSubstitution value with /"""
+ fsns = self.forward_slash_subst()
+ if isinstance(fsns, str):
+ return incoming.replace(fsns, '/')
+ else:
+ return incoming
+
+ def sanitize_filename(self, dirty):
+ """Replace disallowed filename characters according to
+ ForwardSlashNameSubstitution in self.api_config."""
+ # '.' and '..' are not reachable if API server is newer than #6277
+ if dirty is None:
+ return None
+ elif dirty == '':
+ return '_'
+ elif dirty == '.':
+ return '_'
+ elif dirty == '..':
+ return '__'
+ else:
+ fsns = self.forward_slash_subst()
+ if isinstance(fsns, str):
+ dirty = dirty.replace('/', fsns)
+ return _disallowed_filename_characters.sub('_', dirty)
+
+
+ # Overridden by subclasses to implement logic to update the
+ # entries dict when the directory is stale
@use_counter
def update(self):
pass
self._entries = {}
changed = False
for i in items:
- name = sanitize_filename(fn(i))
+ name = self.sanitize_filename(fn(i))
if name:
if name in oldentries and same(oldentries[name], i):
# move existing directory entry over
"""
- def __init__(self, parent_inode, inodes, collection):
- super(CollectionDirectoryBase, self).__init__(parent_inode, inodes)
+ def __init__(self, parent_inode, inodes, apiconfig, collection):
+ super(CollectionDirectoryBase, self).__init__(parent_inode, inodes, apiconfig)
+ self.apiconfig = apiconfig
self.collection = collection
def new_entry(self, name, item, mtime):
- name = sanitize_filename(name)
+ name = self.sanitize_filename(name)
if hasattr(item, "fuse_entry") and item.fuse_entry is not None:
if item.fuse_entry.dead is not True:
raise Exception("Can only reparent dead inode entry")
item.fuse_entry.dead = False
self._entries[name] = item.fuse_entry
elif isinstance(item, arvados.collection.RichCollectionBase):
- self._entries[name] = self.inodes.add_entry(CollectionDirectoryBase(self.inode, self.inodes, item))
+ self._entries[name] = self.inodes.add_entry(CollectionDirectoryBase(self.inode, self.inodes, self.apiconfig, item))
self._entries[name].populate(mtime)
else:
self._entries[name] = self.inodes.add_entry(FuseArvadosFile(self.inode, item, mtime))
def on_event(self, event, collection, name, item):
if collection == self.collection:
- name = sanitize_filename(name)
+ name = self.sanitize_filename(name)
_logger.debug("collection notify %s %s %s %s", event, collection, name, item)
with llfuse.lock:
if event == arvados.collection.ADD:
"""Represents the root of a directory tree representing a collection."""
def __init__(self, parent_inode, inodes, api, num_retries, collection_record=None, explicit_collection=None):
- super(CollectionDirectory, self).__init__(parent_inode, inodes, None)
+ super(CollectionDirectory, self).__init__(parent_inode, inodes, api.config, None)
self.api = api
self.num_retries = num_retries
self.collection_record_file = None
keep_client=api_client.keep,
num_retries=num_retries)
super(TmpCollectionDirectory, self).__init__(
- parent_inode, inodes, collection)
+ parent_inode, inodes, api_client.config, collection)
self.collection_record_file = None
self.populate(self.mtime())
""".lstrip()
def __init__(self, parent_inode, inodes, api, num_retries, pdh_only=False):
- super(MagicDirectory, self).__init__(parent_inode, inodes)
+ super(MagicDirectory, self).__init__(parent_inode, inodes, api.config)
self.api = api
self.num_retries = num_retries
self.pdh_only = pdh_only
e = self.inodes.add_entry(ProjectDirectory(
self.inode, self.inodes, self.api, self.num_retries, project[u'items'][0]))
else:
+ import sys
e = self.inodes.add_entry(CollectionDirectory(
self.inode, self.inodes, self.api, self.num_retries, k))
"""A special directory that contains as subdirectories all tags visible to the user."""
def __init__(self, parent_inode, inodes, api, num_retries, poll_time=60):
- super(TagsDirectory, self).__init__(parent_inode, inodes)
+ super(TagsDirectory, self).__init__(parent_inode, inodes, api.config)
self.api = api
self.num_retries = num_retries
self._poll = True
def __init__(self, parent_inode, inodes, api, num_retries, tag,
poll=False, poll_time=60):
- super(TagDirectory, self).__init__(parent_inode, inodes)
+ super(TagDirectory, self).__init__(parent_inode, inodes, api.config)
self.api = api
self.num_retries = num_retries
self.tag = tag
def __init__(self, parent_inode, inodes, api, num_retries, project_object,
poll=False, poll_time=60):
- super(ProjectDirectory, self).__init__(parent_inode, inodes)
+ super(ProjectDirectory, self).__init__(parent_inode, inodes, api.config)
self.api = api
self.num_retries = num_retries
self.project_object = project_object
elif self._full_listing or super(ProjectDirectory, self).__contains__(k):
return super(ProjectDirectory, self).__getitem__(k)
with llfuse.lock_released:
+ k2 = self.unsanitize_filename(k)
+ if k2 == k:
+ namefilter = ["name", "=", k]
+ else:
+ namefilter = ["name", "in", [k, k2]]
contents = self.api.groups().list(filters=[["owner_uuid", "=", self.project_uuid],
["group_class", "=", "project"],
- ["name", "=", k]],
- limit=1).execute(num_retries=self.num_retries)["items"]
+ namefilter],
+ limit=2).execute(num_retries=self.num_retries)["items"]
if not contents:
contents = self.api.collections().list(filters=[["owner_uuid", "=", self.project_uuid],
- ["name", "=", k]],
- limit=1).execute(num_retries=self.num_retries)["items"]
+ namefilter],
+ limit=2).execute(num_retries=self.num_retries)["items"]
if contents:
- name = sanitize_filename(self.namefn(contents[0]))
+ if len(contents) > 1 and contents[1]['name'] == k:
+ # If "foo/bar" and "foo[SUBST]bar" both exist, use
+ # "foo[SUBST]bar".
+ contents = [contents[1]]
+ name = self.sanitize_filename(self.namefn(contents[0]))
if name != k:
raise KeyError(k)
return self._add_entry(contents[0], name)
new_attrs = properties.get("new_attributes") or {}
old_attrs["uuid"] = ev["object_uuid"]
new_attrs["uuid"] = ev["object_uuid"]
- old_name = sanitize_filename(self.namefn(old_attrs))
- new_name = sanitize_filename(self.namefn(new_attrs))
+ old_name = self.sanitize_filename(self.namefn(old_attrs))
+ new_name = self.sanitize_filename(self.namefn(new_attrs))
# create events will have a new name, but not an old name
# delete events will have an old name, but not a new name
def __init__(self, parent_inode, inodes, api, num_retries, exclude,
poll=False, poll_time=60):
- super(SharedDirectory, self).__init__(parent_inode, inodes)
+ super(SharedDirectory, self).__init__(parent_inode, inodes, api.config)
self.api = api
self.num_retries = num_retries
self.current_user = api.users().current().execute(num_retries=num_retries)
import arvados_fuse as fuse
from . import run_test_server
+from .integration_test import IntegrationTest
from .mount_test_base import MountTestBase
logger = logging.getLogger('arvados.arv-mount')
llfuse.listdir(os.path.join(self.mounttmp, self.testcollection))
-class FuseUnitTest(unittest.TestCase):
+class SanitizeFilenameTest(MountTestBase):
def test_sanitize_filename(self):
+ pdir = fuse.ProjectDirectory(1, {}, self.api, 0, project_object=self.api.users().current().execute())
acceptable = [
"foo.txt",
".foo",
"//",
]
for f in acceptable:
- self.assertEqual(f, fuse.sanitize_filename(f))
+ self.assertEqual(f, pdir.sanitize_filename(f))
for f in unacceptable:
- self.assertNotEqual(f, fuse.sanitize_filename(f))
+ self.assertNotEqual(f, pdir.sanitize_filename(f))
# The sanitized filename should be the same length, though.
- self.assertEqual(len(f), len(fuse.sanitize_filename(f)))
+ self.assertEqual(len(f), len(pdir.sanitize_filename(f)))
# Special cases
- self.assertEqual("_", fuse.sanitize_filename(""))
- self.assertEqual("_", fuse.sanitize_filename("."))
- self.assertEqual("__", fuse.sanitize_filename(".."))
+ self.assertEqual("_", pdir.sanitize_filename(""))
+ self.assertEqual("_", pdir.sanitize_filename("."))
+ self.assertEqual("__", pdir.sanitize_filename(".."))
class FuseMagicTestPDHOnly(MountTestBase):
def test_with_default_by_id(self):
self.verify_pdh_only(skip_pdh_only=True)
+
+
+class SlashSubstitutionTest(IntegrationTest):
+ mnt_args = [
+ '--read-write',
+ '--mount-home', 'zzz',
+ ]
+
+ def setUp(self):
+ super(SlashSubstitutionTest, self).setUp()
+ self.api = arvados.safeapi.ThreadSafeApiCache(arvados.config.settings())
+ self.api.config = lambda: {"Collections": {"ForwardSlashNameSubstitution": "[SLASH]"}}
+ self.testcoll = self.api.collections().create(body={"name": "foo/bar/baz"}).execute()
+ self.testcolleasy = self.api.collections().create(body={"name": "foo-bar-baz"}).execute()
+ self.fusename = 'foo[SLASH]bar[SLASH]baz'
+
+ @IntegrationTest.mount(argv=mnt_args)
+ @mock.patch('arvados.util.get_config_once')
+ def test_slash_substitution_before_listing(self, get_config_once):
+ get_config_once.return_value = {"Collections": {"ForwardSlashNameSubstitution": "[SLASH]"}}
+ self.pool_test(os.path.join(self.mnt, 'zzz'), self.fusename)
+ self.checkContents()
+ @staticmethod
+ def _test_slash_substitution_before_listing(self, tmpdir, fusename):
+ with open(os.path.join(tmpdir, 'foo-bar-baz', 'waz'), 'w') as f:
+ f.write('xxx')
+ with open(os.path.join(tmpdir, fusename, 'waz'), 'w') as f:
+ f.write('foo')
+
+ @IntegrationTest.mount(argv=mnt_args)
+ @mock.patch('arvados.util.get_config_once')
+ def test_slash_substitution_after_listing(self, get_config_once):
+ get_config_once.return_value = {"Collections": {"ForwardSlashNameSubstitution": "[SLASH]"}}
+ self.pool_test(os.path.join(self.mnt, 'zzz'), self.fusename)
+ self.checkContents()
+ @staticmethod
+ def _test_slash_substitution_after_listing(self, tmpdir, fusename):
+ with open(os.path.join(tmpdir, 'foo-bar-baz', 'waz'), 'w') as f:
+ f.write('xxx')
+ os.listdir(tmpdir)
+ with open(os.path.join(tmpdir, fusename, 'waz'), 'w') as f:
+ f.write('foo')
+
+ def checkContents(self):
+ self.assertRegexpMatches(self.api.collections().get(uuid=self.testcoll['uuid']).execute()['manifest_text'], ' acbd18db') # md5(foo)
+ self.assertRegexpMatches(self.api.collections().get(uuid=self.testcolleasy['uuid']).execute()['manifest_text'], ' f561aaf6') # md5(xxx)
+
+ @IntegrationTest.mount(argv=mnt_args)
+ @mock.patch('arvados.util.get_config_once')
+ def test_slash_substitution_conflict(self, get_config_once):
+ self.testcollconflict = self.api.collections().create(body={"name": self.fusename}).execute()
+ get_config_once.return_value = {"Collections": {"ForwardSlashNameSubstitution": "[SLASH]"}}
+ self.pool_test(os.path.join(self.mnt, 'zzz'), self.fusename)
+ self.assertRegexpMatches(self.api.collections().get(uuid=self.testcollconflict['uuid']).execute()['manifest_text'], ' acbd18db') # md5(foo)
+ # foo/bar/baz collection unchanged, because it is masked by foo[SLASH]bar[SLASH]baz
+ self.assertEqual(self.api.collections().get(uuid=self.testcoll['uuid']).execute()['manifest_text'], '')
+ @staticmethod
+ def _test_slash_substitution_conflict(self, tmpdir, fusename):
+ with open(os.path.join(tmpdir, fusename, 'waz'), 'w') as f:
+ f.write('foo')
'apache-libcloud==2.5.0',
'subprocess32>=3.5.1',
],
- zip_safe=False
- )
+ zip_safe=False,
+)
],
test_suite='tests',
tests_require=['pbr<1.7.0', 'mock>=1.0'],
- zip_safe=False
- )
+ zip_safe=False,
+)
projects / arvados.git / commitdiff