def test_add_metrics_file(self):
hashfs_path = os.path.join(self.tmp_dir, 'objectsfs')
test_config = yaml_load('hdata/config.yaml')
local_repo = LocalRepository(test_config,
hashfs_path,
repo_type=MODELS)
spec_path = os.path.join(self.tmp_dir, 'model-ex.spec')
shutil.copy('hdata/dataset-ex.spec', spec_path)
spec_file = yaml_load(spec_path)
model = spec_file[DATASET_SPEC_KEY].copy()
del spec_file[DATASET_SPEC_KEY]
spec_file[MODEL_SPEC_KEY] = model
yaml_save(spec_file, spec_path)
metrics_file_path = os.path.join(self.tmp_dir, 'metrics.csv')
self.create_csv_file(metrics_file_path, {
'metric_a': 10,
'metric_b': 9
})
local_repo.add_metrics(spec_path, (), metrics_file_path)
test_spec_file = yaml_load(spec_path)
self.assertEqual(
test_spec_file[MODEL_SPEC_KEY]['metrics'].get('metric_a', ''),
10.0)
self.assertEqual(
test_spec_file[MODEL_SPEC_KEY]['metrics'].get('metric_b', ''), 9.0)
def export(self, bucket, tag, retry):
try:
categories_path, spec_name, _ = spec_parse(tag)
get_root_path()
if not self._tag_exists(tag):
return None, None
except InvalidGitRepositoryError:
log.error('You are not in an initialized ml-git repository.',
class_name=LOCAL_REPOSITORY_CLASS_NAME)
return None, None
except Exception as e:
log.error(e, class_name=LOCAL_REPOSITORY_CLASS_NAME)
return None, None
try:
self._checkout_ref(tag)
except Exception:
log.error('Unable to checkout to %s' % tag,
class_name=REPOSITORY_CLASS_NAME)
return None, None
local = LocalRepository(
self.__config, get_objects_path(self.__config, self.__repo_type),
self.__repo_type)
local.export_tag(get_metadata_path(self.__config, self.__repo_type),
tag, bucket, retry)
self._checkout_ref()
def test_fetch(self):
mdpath = os.path.join(self.tmp_dir, 'metadata-test')
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
config_spec = get_sample_config_spec(testbucketname, testprofile,
testregion)
dataset_spec = get_sample_spec(testbucketname)
specpath = os.path.join(mdpath, 'vision-computing', 'images',
'dataset-ex')
ensure_path_exists(specpath)
yaml_save(dataset_spec, os.path.join(specpath, 'dataset-ex.spec'))
manifestpath = os.path.join(specpath, 'MANIFEST.yaml')
yaml_save(
{
'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh':
{'imghires.jpg'}
}, manifestpath)
objectpath = os.path.join(self.tmp_dir, 'objects-test')
spec = 'vision-computing__images__dataset-ex__5'
r = LocalRepository(config_spec, objectpath)
r.fetch(mdpath, spec, None)
fs = set()
for root, dirs, files in os.walk(objectpath):
for file in files:
fs.add(file)
self.assertEqual(len(hs), len(fs))
self.assertTrue(len(hs.difference(fs)) == 0)
def status(self, spec, full_option, status_directory):
repo_type = self.__repo_type
try:
objects_path = get_objects_path(self.__config, repo_type)
repo = LocalRepository(self.__config, objects_path, repo_type)
log.info('%s: status of ml-git index for [%s]' % (repo_type, spec),
class_name=REPOSITORY_CLASS_NAME)
new_files, deleted_files, untracked_files, corruped_files, changed_files = repo.status(
spec, status_directory)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
if new_files is not None and deleted_files is not None and untracked_files is not None:
print('Changes to be committed:')
self._print_files(new_files, full_option, 'New file: ')
self._print_files(deleted_files, full_option, 'Deleted: ')
print('\nUntracked files:')
self._print_files(untracked_files, full_option)
print('\nCorrupted files:')
self._print_files(corruped_files, full_option)
if changed_files and len(changed_files) > 0:
print('\nChanges not staged for commit:')
self._print_files(changed_files, full_option)
def test_remote_fsck(self):
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
ohfs = MultihashFS(hfspath)
ohfs.put(HDATA_IMG_1)
s3 = boto3.resource(
's3',
region_name='us-east-1',
aws_access_key_id='fake_access_key',
aws_secret_access_key='fake_secret_key',
)
s3.Object(testbucketname, 'zdj7WWsMkELZSGQGgpm5VieCWV8NxY5n5XEP73H4E7eeDMA3A').delete()
self.assertRaises(botocore.exceptions.ClientError, lambda: self.check_delete(s3, testbucketname))
mdpath = os.path.join(self.tmp_dir, 'metadata-test')
dataset_spec = get_sample_spec(testbucketname)
specpath = os.path.join(mdpath, 'vision-computing', 'images', 'dataset-ex')
ensure_path_exists(specpath)
yaml_save(dataset_spec, os.path.join(specpath, 'dataset-ex.spec'))
manifestpath = os.path.join(specpath, 'MANIFEST.yaml')
yaml_save({'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh': {'imghires.jpg'}}, manifestpath)
fullspecpath = os.path.join(specpath, os.path.join(specpath, 'dataset-ex.spec'))
spec = 'vision-computing__images__dataset-ex__5'
c = yaml_load('hdata/config.yaml')
r = LocalRepository(c, hfspath)
ret = r.remote_fsck(mdpath, spec, fullspecpath, 2, True, True)
self.assertTrue(ret)
self.assertEqual(None, s3.Object(testbucketname, 'zdj7WWsMkELZSGQGgpm5VieCWV8NxY5n5XEP73H4E7eeDMA3A').load())
def remote_fsck(self, spec, retries=2, thorough=False, paranoid=False):
repo_type = self.__repo_type
try:
metadata_path = get_metadata_path(self.__config, repo_type)
objects_path = get_objects_path(self.__config, repo_type)
refs_path = get_refs_path(self.__config, repo_type)
ref = Refs(refs_path, spec, repo_type)
tag, sha = ref.branch()
categories_path = get_path_with_categories(tag)
self._checkout_ref(tag)
spec_path, spec_file = search_spec_file(self.__repo_type, spec,
categories_path)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
if spec_path is None:
return
full_spec_path = os.path.join(spec_path, spec_file)
r = LocalRepository(self.__config, objects_path, repo_type)
r.remote_fsck(metadata_path, tag, full_spec_path, retries, thorough,
paranoid)
# ensure first we're on master !
self._checkout_ref()
def test_mount_blobs(self):
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
s3 = boto3.resource(
's3',
region_name='eu-west-1',
aws_access_key_id='fake_access_key',
aws_secret_access_key='fake_secret_key',
)
keypath = 'zdj7We7Je5MRECsZUF7uptseHHPY29zGoqFsVHw6sbgv1MbWS'
file = os.path.join('hdata', keypath)
with open(file, 'rb') as f:
s3.Bucket(testbucketname).Object(keypath).put(file, Body=f)
c = yaml_load('hdata/config.yaml')
r = LocalRepository(c, hfspath)
s3store = S3Store(testbucketname, bucket)
links = {'Links': [{'Hash': keypath, 'Size': 16822}]}
with open(file, 'rb') as f:
self.assertEqual(f.read(), r._mount_blobs(s3store, links))
def test_get_ipld(self):
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
s3 = boto3.resource(
's3',
region_name='eu-west-1',
aws_access_key_id='fake_access_key',
aws_secret_access_key='fake_secret_key',
)
keypath = 'zdj7WdjnTVfz5AhTavcpsDT62WiQo4AeQy6s4UC1BSEZYx4NP'
file = os.path.join('hdata', keypath)
with open(file, 'rb') as f:
s3.Bucket(testbucketname).Object(keypath).put(file, Body=f)
c = yaml_load('hdata/config.yaml')
r = LocalRepository(c, hfspath)
s3store = S3Store(testbucketname, bucket)
links = {
'Links': [{
'Hash': 'zdj7WVyQ8wTdnDXsbg8wxwwFkt2Bzp95Tncsfg8PCgKXeLTye',
'Size': 16822
}]
}
self.assertEqual(links, r._get_ipld(s3store, keypath))
def unlock_file(self, spec, file_path):
repo_type = self.__repo_type
if not validate_config_spec_hash(self.__config):
log.error(
'.ml-git/config.yaml invalid. It should look something like this:\n%s'
% get_yaml_str(
get_sample_config_spec('somebucket', 'someprofile',
'someregion')),
class_name=REPOSITORY_CLASS_NAME)
return None
path, file = None, None
try:
refs_path = get_refs_path(self.__config, repo_type)
objects_path = get_objects_path(self.__config, repo_type)
index_path = get_index_path(self.__config, repo_type)
cache_path = get_cache_path(self.__config, repo_type)
ref = Refs(refs_path, spec, repo_type)
tag, sha = ref.branch()
categories_path = get_path_with_categories(tag)
path, file = search_spec_file(self.__repo_type, spec,
categories_path)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
if path is None:
return
spec_path = os.path.join(path, file)
spec_file = yaml_load(spec_path)
try:
mutability = spec_file[repo_type]['mutability']
if mutability not in Mutability.list():
log.error('Invalid mutability type.',
class_name=REPOSITORY_CLASS_NAME)
return
except Exception:
log.info(
'The spec does not have the \'mutability\' property set. Default: strict.',
class_name=REPOSITORY_CLASS_NAME)
return
if mutability != Mutability.STRICT.value:
try:
local = LocalRepository(self.__config, objects_path, repo_type)
local.unlock_file(path, file_path, index_path, objects_path,
spec, cache_path)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
else:
log.error(
'You cannot use this command for this entity because mutability cannot be strict.',
class_name=REPOSITORY_CLASS_NAME)
def test_add_metrics_wrong_entity(self):
hashfs_path = os.path.join(self.tmp_dir, 'objectsfs')
test_config = yaml_load('hdata/config.yaml')
local_repo = LocalRepository(test_config, hashfs_path)
spec_path = os.path.join(self.tmp_dir, 'dataset-ex.spec')
shutil.copy('hdata/dataset-ex.spec', spec_path)
local_repo.add_metrics(spec_path,
(('metric_a', '10'), ('metric_b', '9')), None)
test_spec_file = yaml_load(spec_path)
self.assertFalse('metrics' in test_spec_file[DATASET_SPEC_KEY])
def push(self, spec, retry=2, clear_on_fail=False):
repo_type = self.__repo_type
try:
objects_path = get_objects_path(self.__config, repo_type)
metadata_path = get_metadata_path(self.__config, repo_type)
refs_path = get_refs_path(self.__config, repo_type)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
met = Metadata(spec, metadata_path, self.__config, repo_type)
fields = met.git_user_config()
if None in fields.values():
log.error(
'Your name and email address need to be configured in git. '
'Please see the commands below:',
class_name=REPOSITORY_CLASS_NAME)
log.error('git config --global user.name \'Your Name\'',
class_name=REPOSITORY_CLASS_NAME)
log.error('git config --global user.email [email protected]',
class_name=REPOSITORY_CLASS_NAME)
return
if met.fetch() is False:
return
ref = Refs(refs_path, spec, repo_type)
tag, sha = ref.branch()
categories_path = get_path_with_categories(tag)
spec_path, spec_file = None, None
try:
spec_path, spec_file = search_spec_file(self.__repo_type, spec,
categories_path)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
if spec_path is None:
return
full_spec_path = os.path.join(spec_path, spec_file)
repo = LocalRepository(self.__config, objects_path, repo_type)
ret = repo.push(objects_path, full_spec_path, retry, clear_on_fail)
# ensure first we're on master !
met.checkout()
if ret == 0:
# push metadata spec to LocalRepository git repository
try:
met.push()
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
MultihashFS(objects_path).reset_log()
def _fetch(self, tag, samples, retries=2, bare=False):
repo_type = self.__repo_type
try:
objects_path = get_objects_path(self.__config, repo_type)
metadata_path = get_metadata_path(self.__config, repo_type)
# check if no data left untracked/uncommitted. othrewise, stop.
local_rep = LocalRepository(self.__config, objects_path, repo_type)
return local_rep.fetch(metadata_path, tag, samples, retries, bare)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
def test_get_update_cache(self):
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
ohfs = MultihashFS(hfspath)
key = ohfs.put(HDATA_IMG_1)
cachepath = os.path.join(self.tmp_dir, 'cachefs')
cache = Cache(cachepath, '', '')
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
c = get_sample_config_spec(testbucketname, testprofile, testregion)
r = LocalRepository(c, hfspath)
r._update_cache(cache, key)
self.assertTrue(os.path.exists(cache.get_keypath(key)))
self.assertEqual(self.md5sum(HDATA_IMG_1), self.md5sum(cache.get_keypath(key)))
def test_add_metrics_with_none_metrics_options(self):
hashfs_path = os.path.join(self.tmp_dir, 'objectsfs')
test_config = yaml_load('hdata/config.yaml')
local_repo = LocalRepository(test_config,
hashfs_path,
repo_type=MODELS)
spec_path = os.path.join(self.tmp_dir, 'model-ex.spec')
shutil.copy('hdata/dataset-ex.spec', spec_path)
spec_file = yaml_load(spec_path)
model = spec_file[DATASET_SPEC_KEY].copy()
del spec_file[DATASET_SPEC_KEY]
spec_file[MODEL_SPEC_KEY] = model
yaml_save(spec_file, spec_path)
local_repo.add_metrics(spec_path, (), None)
test_spec_file = yaml_load(spec_path)
self.assertFalse('metrics' in test_spec_file[MODEL_SPEC_KEY])
def create(self, kwargs):
artifact_name = kwargs['artifact_name']
categories = list(kwargs['category'])
version = int(kwargs['version_number'])
imported_dir = kwargs['import']
store_type = kwargs['store_type']
bucket_name = kwargs['bucket_name']
start_wizard = kwargs['wizard_config']
import_url = kwargs['import_url']
unzip_file = kwargs['unzip']
credentials_path = kwargs['credentials_path']
repo_type = self.__repo_type
try:
create_workspace_tree_structure(repo_type, artifact_name,
categories, store_type,
bucket_name, version, imported_dir,
kwargs['mutability'])
if start_wizard:
has_new_store, store_type, bucket, profile, endpoint_url, git_repo = start_wizard_questions(
repo_type)
if has_new_store:
store_add(store_type, bucket, profile, endpoint_url)
update_store_spec(repo_type, artifact_name, store_type, bucket)
remote_add(repo_type, git_repo)
if import_url:
self.create_config_store('gdrive', credentials_path)
local = LocalRepository(
self.__config, get_objects_path(self.__config, repo_type))
destine_path = os.path.join(repo_type, artifact_name, 'data')
local.import_file_from_url(destine_path, import_url,
StoreType.GDRIVE.value)
if unzip_file:
log.info('Unzipping files', CLASS_NAME=REPOSITORY_CLASS_NAME)
data_path = os.path.join(get_root_path(), repo_type,
artifact_name, 'data')
unzip_files_in_directory(data_path)
log.info("Project Created.", CLASS_NAME=REPOSITORY_CLASS_NAME)
except Exception as e:
if not isinstance(e, PermissionError):
clear(os.path.join(repo_type, artifact_name))
if isinstance(e, KeyboardInterrupt):
log.info("Create command aborted!",
class_name=REPOSITORY_CLASS_NAME)
else:
log.error(e, CLASS_NAME=REPOSITORY_CLASS_NAME)
def test_push(self):
mlgit_dir = os.path.join(self.tmp_dir, '.ml-git')
indexpath = os.path.join(mlgit_dir, 'index-test')
mdpath = os.path.join(mlgit_dir, 'metadata-test')
objectpath = os.path.join(mlgit_dir, 'objects-test')
specpath = os.path.join(mdpath, 'vision-computing/images/dataset-ex')
ensure_path_exists(specpath)
ensure_path_exists(indexpath)
shutil.copy('hdata/dataset-ex.spec', specpath + '/dataset-ex.spec')
shutil.copy('hdata/config.yaml', mlgit_dir + '/config.yaml')
manifestpath = os.path.join(specpath, 'MANIFEST.yaml')
yaml_save(
{
'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh':
{'imghires.jpg'}
}, manifestpath)
# adds chunks to ml-git Index
idx = MultihashIndex(specpath, indexpath, objectpath)
idx.add('data-test-push/', manifestpath)
fi = yaml_load(os.path.join(specpath, 'INDEX.yaml'))
self.assertTrue(len(fi) > 0)
self.assertTrue(os.path.exists(indexpath))
o = Objects(specpath, objectpath)
o.commit_index(indexpath, self.tmp_dir)
self.assertTrue(os.path.exists(objectpath))
c = yaml_load('hdata/config.yaml')
r = LocalRepository(c, objectpath)
r.push(objectpath, specpath + '/dataset-ex.spec')
s3 = boto3.resource(
's3',
region_name='eu-west-1',
aws_access_key_id='fake_access_key',
aws_secret_access_key='fake_secret_key',
)
for key in idx.get_index():
self.assertIsNotNone(s3.Object(testbucketname, key))
def test_add_metrics(self):
hashfs_path = os.path.join(self.tmp_dir, 'objectsfs')
test_config = yaml_load('hdata/config.yaml')
local_repo = LocalRepository(test_config,
hashfs_path,
repo_type=MODELS)
spec_path = os.path.join(self.tmp_dir, 'model-ex.spec')
shutil.copy('hdata/dataset-ex.spec', spec_path)
spec_file = yaml_load(spec_path)
model = spec_file[DATASET_SPEC_KEY].copy()
del spec_file[DATASET_SPEC_KEY]
spec_file[MODEL_SPEC_KEY] = model
yaml_save(spec_file, spec_path)
local_repo.add_metrics(spec_path,
(('metric_a', '10'), ('metric_b', '9')), None)
test_spec_file = yaml_load(spec_path)
self.assertTrue(test_spec_file[MODEL_SPEC_KEY]['metrics'].get(
'metric_a', '') == 10.0)
self.assertTrue(test_spec_file[MODEL_SPEC_KEY]['metrics'].get(
'metric_b', '') == 9.0)
def test_get_update_links_wspace(self):
wspath = os.path.join(self.tmp_dir, 'wspace')
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
ohfs = MultihashFS(hfspath)
key = ohfs.put(HDATA_IMG_1)
fidx = FullIndex(self.tmp_dir, self.tmp_dir)
cachepath = os.path.join(self.tmp_dir, 'cachefs')
cache = Cache(cachepath, '', '')
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
c = get_sample_config_spec(testbucketname, testprofile, testregion)
r = LocalRepository(c, hfspath)
r._update_cache(cache, key)
mfiles = {}
files = {DATA_IMG_1}
r._update_links_wspace(cache, fidx, files, key, wspath, mfiles, Status.u.name, 'strict')
wspace_file = os.path.join(wspath, DATA_IMG_1)
set_write_read(wspace_file)
self.assertTrue(os.path.exists(wspace_file))
self.assertEqual(self.md5sum(HDATA_IMG_1), self.md5sum(wspace_file))
st = os.stat(wspace_file)
fi = fidx.get_index()
for k, v in fi.items():
self.assertEqual(k, os.path.join('data', 'imghires.jpg'))
self.assertEqual(v['hash'], 'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh')
self.assertEqual(v['status'], 'u')
self.assertEqual(v['ctime'], st.st_ctime)
self.assertEqual(v['mtime'], st.st_mtime)
self.assertTrue(st.st_nlink == 2)
self.assertEqual(mfiles, {DATA_IMG_1: 'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh'})
def test_push(self):
indexpath = os.path.join(self.tmp_dir, 'index-test')
mdpath = os.path.join(self.tmp_dir, 'metadata-test')
objectpath = os.path.join(self.tmp_dir, 'objects-test')
specpath = os.path.join(mdpath, 'vision-computing/images/dataset-ex')
ensure_path_exists(indexpath)
ensure_path_exists(specpath)
shutil.copy('hdata/dataset-ex.spec', specpath + '/dataset-ex.spec')
manifestpath = os.path.join(specpath, 'MANIFEST.yaml')
yaml_save(files_mock, manifestpath)
idx = MultihashIndex(specpath, indexpath, objectpath)
idx.add('data-test-push-1/', manifestpath)
fidx = FullIndex(specpath, indexpath)
self.assertTrue(os.path.exists(indexpath))
c = yaml_load('hdata/config.yaml')
o = Objects(specpath, objectpath)
o.commit_index(indexpath, self.tmp_dir)
self.assertTrue(os.path.exists(objectpath))
r = LocalRepository(c, objectpath)
self.assertTrue(r.push(objectpath, specpath + '/dataset-ex.spec') == 0)
self.assertTrue(len(fidx.get_index()) == 1)
def test_import_files(self):
path_obj = os.path.join(self.tmp_dir, 'objects')
c = yaml_load('hdata/config.yaml')
r = LocalRepository(c, path_obj)
r.change_config_store(testprofile, testbucketname, 's3', region=None, endpoint_url=None)
r.import_files(None, None, self.tmp_dir, 2, '{}://{}'.format('s3', testbucketname))
for h in hs:
file_path = os.path.join(self.tmp_dir, h)
dir_file = os.path.join('hdata', h)
self.assertTrue(os.path.exists(file_path))
self.assertTrue(filecmp.cmp(dir_file, file_path))
def import_files(self, object, path, directory, retry, bucket):
err_msg = 'Invalid ml-git project!'
try:
root = get_root_path()
root_dir = os.path.join(root, directory)
except Exception:
log.error(err_msg, class_name=REPOSITORY_CLASS_NAME)
return
local = LocalRepository(
self.__config, get_objects_path(self.__config, self.__repo_type),
self.__repo_type)
bucket_name = bucket['bucket_name']
store_type = bucket['store_type']
local.change_config_store(bucket['profile'],
bucket_name,
store_type,
region=bucket['region'],
endpoint_url=bucket['endpoint_url'])
local.import_files(object, path, root_dir, retry,
'{}://{}'.format(store_type, bucket_name))
def commit(self, spec, specs, version=None, run_fsck=False, msg=None):
# Move chunks from index to .ml-git/objects
repo_type = self.__repo_type
try:
index_path = get_index_path(self.__config, repo_type)
objects_path = get_objects_path(self.__config, repo_type)
metadata_path = get_metadata_path(self.__config, repo_type)
refs_path = get_refs_path(self.__config, repo_type)
repo = LocalRepository(self.__config, objects_path, repo_type)
mutability, check_mutability = repo.get_mutability_from_spec(
spec, repo_type)
if not mutability:
return
if not check_mutability:
log.error('Spec mutability cannot be changed.',
class_name=REPOSITORY_CLASS_NAME)
return
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
ref = Refs(refs_path, spec, repo_type)
tag, sha = ref.branch()
categories_path = get_path_with_categories(tag)
manifest_path = os.path.join(metadata_path, categories_path, spec,
MANIFEST_FILE)
path, file = None, None
try:
path, file = search_spec_file(self.__repo_type, spec,
categories_path)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
if path is None:
return None, None, None
spec_path = os.path.join(path, file)
idx = MultihashIndex(spec, index_path, objects_path)
if version:
set_version_in_spec(version, spec_path, self.__repo_type)
idx.add_metadata(path, file)
# Check tag before anything to avoid creating unstable state
log.debug('Check if tag already exists',
class_name=REPOSITORY_CLASS_NAME)
m = Metadata(spec, metadata_path, self.__config, repo_type)
if not m.check_exists():
log.error('The %s has not been initialized' % self.__repo_type,
class_name=REPOSITORY_CLASS_NAME)
return
full_metadata_path, categories_sub_path, metadata = m.tag_exists(
index_path)
if metadata is None:
return None
log.debug('%s -> %s' % (index_path, objects_path),
class_name=REPOSITORY_CLASS_NAME)
# commit objects in index to ml-git objects
o = Objects(spec, objects_path)
changed_files, deleted_files = o.commit_index(index_path, path)
bare_mode = os.path.exists(
os.path.join(index_path, 'metadata', spec, 'bare'))
if not bare_mode:
manifest = m.get_metadata_manifest(manifest_path)
self._remove_deleted_files(idx, index_path, m, manifest, spec,
deleted_files)
m.remove_files_added_after_base_tag(manifest, path)
else:
tag, _ = ref.branch()
self._checkout_ref(tag)
# update metadata spec & README.md
# option --dataset-spec --labels-spec
tag, sha = m.commit_metadata(index_path, specs, msg, changed_files,
mutability, path)
# update ml-git ref spec HEAD == to new SHA-1 / tag
if tag is None:
return None
ref = Refs(refs_path, spec, repo_type)
ref.update_head(tag, sha)
# Run file check
if run_fsck:
self.fsck()
return tag
def _checkout(self,
tag,
samples,
retries=2,
force_get=False,
dataset=False,
labels=False,
bare=False):
repo_type = self.__repo_type
try:
cache_path = get_cache_path(self.__config, repo_type)
metadata_path = get_metadata_path(self.__config, repo_type)
objects_path = get_objects_path(self.__config, repo_type)
refs_path = get_refs_path(self.__config, repo_type)
# find out actual workspace path to save data
if not self._tag_exists(tag):
return None, None
categories_path, spec_name, _ = spec_parse(tag)
dataset_tag = None
labels_tag = None
root_path = get_root_path()
ws_path = os.path.join(root_path,
os.sep.join([repo_type, categories_path]))
ensure_path_exists(ws_path)
except Exception as e:
log.error(e, class_name=LOCAL_REPOSITORY_CLASS_NAME)
return None, None
ref = Refs(refs_path, spec_name, repo_type)
cur_tag, _ = ref.branch()
if cur_tag == tag:
log.info('already at tag [%s]' % tag,
class_name=REPOSITORY_CLASS_NAME)
return None, None
local_rep = LocalRepository(self.__config, objects_path, repo_type)
# check if no data left untracked/uncommitted. otherwise, stop.
if not force_get and local_rep.exist_local_changes(spec_name) is True:
return None, None
try:
self._checkout_ref(tag)
except Exception:
log.error('Unable to checkout to %s' % tag,
class_name=REPOSITORY_CLASS_NAME)
return None, None
spec_path = os.path.join(metadata_path, categories_path,
spec_name + '.spec')
if dataset is True:
dataset_tag = get_entity_tag(spec_path, repo_type, 'dataset')
if labels is True:
labels_tag = get_entity_tag(spec_path, repo_type, 'labels')
fetch_success = self._fetch(tag, samples, retries, bare)
if not fetch_success:
objs = Objects('', objects_path)
objs.fsck(remove_corrupted=True)
self._checkout_ref('master')
return None, None
try:
spec_index_path = os.path.join(
get_index_metadata_path(self.__config, repo_type), spec_name)
except Exception:
return
if os.path.exists(spec_index_path):
if os.path.exists(
os.path.join(spec_index_path, spec_name + '.spec')):
os.unlink(os.path.join(spec_index_path, spec_name + '.spec'))
if os.path.exists(os.path.join(spec_index_path, 'README.md')):
os.unlink(os.path.join(spec_index_path, 'README.md'))
try:
r = LocalRepository(self.__config, objects_path, repo_type)
r.checkout(cache_path, metadata_path, objects_path, ws_path, tag,
samples, bare)
except OSError as e:
self._checkout_ref('master')
if e.errno == errno.ENOSPC:
log.error(
'There is not enough space in the disk. Remove some files and try again.',
class_name=REPOSITORY_CLASS_NAME)
else:
log.error(
'An error occurred while creating the files into workspace: %s \n.'
% e,
class_name=REPOSITORY_CLASS_NAME)
return None, None
except Exception as e:
self._checkout_ref('master')
log.error(
'An error occurred while creating the files into workspace: %s \n.'
% e,
class_name=REPOSITORY_CLASS_NAME)
return None, None
m = Metadata('', metadata_path, self.__config, repo_type)
sha = m.sha_from_tag(tag)
ref.update_head(tag, sha)
# restore to master/head
self._checkout_ref('master')
return dataset_tag, labels_tag
def _checkout(self, tag, samples, options):
dataset = options['with_dataset']
labels = options['with_labels']
retries = options['retry']
force_get = options['force']
bare = options['bare']
version = options['version']
repo_type = self.__repo_type
try:
cache_path = get_cache_path(self.__config, repo_type)
metadata_path = get_metadata_path(self.__config, repo_type)
objects_path = get_objects_path(self.__config, repo_type)
refs_path = get_refs_path(self.__config, repo_type)
if not re.search(RGX_TAG_FORMAT, tag):
metadata_path = get_metadata_path(self.__config, repo_type)
metadata = Metadata(tag, metadata_path, self.__config,
repo_type)
tag = metadata.get_tag(tag, version)
if not tag:
return None, None
elif not self._tag_exists(tag):
return None, None
categories_path, spec_name, _ = spec_parse(tag)
root_path = get_root_path()
ws_path = os.path.join(root_path,
os.sep.join([repo_type, categories_path]))
except Exception as e:
log.error(e, class_name=LOCAL_REPOSITORY_CLASS_NAME)
return None, None
ref = Refs(refs_path, spec_name, repo_type)
cur_tag, _ = ref.branch()
if cur_tag == tag:
log.info('already at tag [%s]' % tag,
class_name=REPOSITORY_CLASS_NAME)
return None, None
local_rep = LocalRepository(self.__config, objects_path, repo_type)
# check if no data left untracked/uncommitted. otherwise, stop.
if not force_get and local_rep.exist_local_changes(spec_name) is True:
return None, None
try:
self._checkout_ref(tag)
except Exception:
log.error('Unable to checkout to %s' % tag,
class_name=REPOSITORY_CLASS_NAME)
return None, None
dataset_tag, labels_tag = self._get_related_tags(
categories_path, dataset, labels, metadata_path, repo_type,
spec_name)
fetch_success = self._fetch(tag, samples, retries, bare)
if not fetch_success:
objs = Objects('', objects_path)
objs.fsck(remove_corrupted=True)
self._checkout_ref()
return None, None
ensure_path_exists(ws_path)
try:
spec_index_path = os.path.join(
get_index_metadata_path(self.__config, repo_type), spec_name)
except Exception:
return
self._delete_spec_and_readme(spec_index_path, spec_name)
try:
r = LocalRepository(self.__config, objects_path, repo_type)
r.checkout(cache_path, metadata_path, ws_path, tag, samples, bare)
except OSError as e:
self._checkout_ref()
if e.errno == errno.ENOSPC:
log.error(
'There is not enough space in the disk. Remove some files and try again.',
class_name=REPOSITORY_CLASS_NAME)
else:
log.error(
'An error occurred while creating the files into workspace: %s \n.'
% e,
class_name=REPOSITORY_CLASS_NAME)
return None, None
except Exception as e:
self._checkout_ref()
log.error(
'An error occurred while creating the files into workspace: %s \n.'
% e,
class_name=REPOSITORY_CLASS_NAME)
return None, None
m = Metadata('', metadata_path, self.__config, repo_type)
sha = m.sha_from_tag(tag)
ref.update_head(tag, sha)
# restore to master/head
self._checkout_ref()
return dataset_tag, labels_tag
def test_get_update_links_wspace_with_duplicates(self):
wspath = os.path.join(self.tmp_dir, 'wspace')
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
ohfs = MultihashFS(hfspath)
key = ohfs.put(HDATA_IMG_1)
fidx = FullIndex(self.tmp_dir, self.tmp_dir)
cachepath = os.path.join(self.tmp_dir, 'cachefs')
cache = Cache(cachepath, '', '')
testbucketname = os.getenv('MLGIT_TEST_BUCKET', 'ml-git-datasets')
c = get_sample_config_spec(testbucketname, testprofile, testregion)
r = LocalRepository(c, hfspath)
r._update_cache(cache, key)
mfiles = {}
files = {DATA_IMG_1, DATA_IMG_2}
args = {
'obj_files': {
key: files
},
'key': key,
'mutability': 'strict',
'mfiles': mfiles,
'ws_path': wspath,
'cache': cache,
'fidx': fidx
}
r._update_links_wspace(key, Status.u.name, args)
wspace_file = os.path.join(wspath, DATA_IMG_1)
self.assertTrue(os.path.exists(wspace_file))
self.assertEqual(self.md5sum(HDATA_IMG_1), self.md5sum(wspace_file))
wspace_file = os.path.join(wspath, DATA_IMG_2)
self.assertTrue(os.path.exists(wspace_file))
self.assertEqual(self.md5sum(HDATA_IMG_1), self.md5sum(wspace_file))
st = os.stat(wspace_file)
self.assertTrue(st.st_nlink == 3)
self.assertEqual(
mfiles, {
DATA_IMG_1:
'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh',
DATA_IMG_2: 'zdj7WjdojNAZN53Wf29rPssZamfbC6MVerzcGwd9tNciMpsQh'
})
wspath = os.path.join(self.tmp_dir, 'wspace')
ensure_path_exists(wspath)
to_be_removed = os.path.join(wspath, 'to_be_removed')
with open(to_be_removed, 'w') as f:
f.write('DEAD\n')
hfspath = os.path.join(self.tmp_dir, 'objectsfs')
ohfs = MultihashFS(hfspath)
key = ohfs.put(HDATA_IMG_1)
fidx = FullIndex(self.tmp_dir, self.tmp_dir)
cachepath = os.path.join(self.tmp_dir, 'cachefs')
cache = Cache(cachepath, '', '')
c = yaml_load('hdata/config.yaml')
r = LocalRepository(c, hfspath)
r._update_cache(cache, key)
mfiles = {}
files = {DATA_IMG_1, DATA_IMG_2}
args = {
'obj_files': {
key: files
},
'key': key,
'mutability': 'strict',
'mfiles': mfiles,
'ws_path': wspath,
'cache': cache,
'fidx': fidx
}
r._update_links_wspace(key, Status.u.name, args)
r._remove_unused_links_wspace(wspath, mfiles)
self.assertFalse(os.path.exists(to_be_removed))
def add(self, spec, file_path, bump_version=False, run_fsck=False):
repo_type = self.__repo_type
is_shared_objects = 'objects_path' in self.__config[repo_type]
is_shared_cache = 'cache_path' in self.__config[repo_type]
if not validate_config_spec_hash(self.__config):
log.error(
'.ml-git/config.yaml invalid. It should look something like this:\n%s'
% get_yaml_str(
get_sample_config_spec('somebucket', 'someprofile',
'someregion')),
class_name=REPOSITORY_CLASS_NAME)
return None
path, file = None, None
try:
refs_path = get_refs_path(self.__config, repo_type)
index_path = get_index_path(self.__config, repo_type)
metadata_path = get_metadata_path(self.__config, repo_type)
cache_path = get_cache_path(self.__config, repo_type)
objects_path = get_objects_path(self.__config, repo_type)
repo = LocalRepository(self.__config, objects_path, repo_type)
mutability, check_mutability = repo.get_mutability_from_spec(
spec, repo_type)
sampling_flag = os.path.exists(
os.path.join(index_path, 'metadata', spec, 'sampling'))
if sampling_flag:
log.error(
'You cannot add new data to an entity that is based on a checkout with the --sampling option.',
class_name=REPOSITORY_CLASS_NAME)
return
if not mutability:
return
if not check_mutability:
log.error('Spec mutability cannot be changed.',
class_name=REPOSITORY_CLASS_NAME)
return
if not self._has_new_data(repo, spec):
return None
ref = Refs(refs_path, spec, repo_type)
tag, sha = ref.branch()
categories_path = get_path_with_categories(tag)
path, file = search_spec_file(self.__repo_type, spec,
categories_path)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return
if path is None:
return
spec_path = os.path.join(path, file)
if not self._is_spec_valid(spec_path):
return None
# Check tag before anything to avoid creating unstable state
log.debug('Repository: check if tag already exists',
class_name=REPOSITORY_CLASS_NAME)
m = Metadata(spec, metadata_path, self.__config, repo_type)
if not m.check_exists():
log.error('The %s has not been initialized' % self.__repo_type,
class_name=REPOSITORY_CLASS_NAME)
return
try:
m.update()
except Exception:
pass
# get version of current manifest file
manifest = self._get_current_manifest_file(m, tag)
try:
# adds chunks to ml-git Index
log.info('%s adding path [%s] to ml-git index' % (repo_type, path),
class_name=REPOSITORY_CLASS_NAME)
with change_mask_for_routine(is_shared_objects):
idx = MultihashIndex(spec, index_path, objects_path,
mutability, cache_path)
idx.add(path, manifest, file_path)
# create hard links in ml-git Cache
self.create_hard_links_in_cache(cache_path, index_path,
is_shared_cache, mutability, path,
spec)
except Exception as e:
log.error(e, class_name=REPOSITORY_CLASS_NAME)
return None
if bump_version and not increment_version_in_spec(
spec_path, self.__repo_type):
return None
idx.add_metadata(path, file)
self._check_corrupted_files(spec, repo)
# Run file check
if run_fsck:
self.fsck()