def test_init() -> None:
my_dict = {d.id: d for d in DATA}
rm1: ResultMap[Data] = ResultMap(my_dict)
rm2: ResultMap[Data] = ResultMap(DATA)
assert rm1 == rm2
def run(self) -> ResultMap[GalaxyRole]:
"""Run the stage."""
galaxy_api = GalaxyAPI()
it_roles = galaxy_api.search_roles(limit=self.config.count)
if not self.config.progress:
return ResultMap(it_roles)
return ResultMap(tqdm(
it_roles, desc='Searching roles', total=self.config.count))
def test_unstructure() -> None:
rm = ResultMap(DATA)
d = rm.unstructure()
assert d == {
'test': {
'id': 'test',
'val': 1
},
'tset': {
'id': 'tset',
'val': -1
}
}
def run(
self, extract_versions: ResultMap[RepoVersions],
clone: ResultMap[GitRepo]
) -> ResultMap[RepoDiffMetrics]:
results = []
repos_to_bumps: Dict[GitRepo, List[Tuple[Version, Version]]]
repos_to_bumps = defaultdict(list)
for repo_id, repo_versions in extract_versions.items():
repos_to_bumps[clone[repo_id]].extend(
zip(repo_versions.versions, repo_versions.versions[1:]))
repo_list: Iterable[Tuple[GitRepo, List[Tuple[Version, Version]]]]
bump_pbar: Optional[tqdm]
repo_list = [(r, b) for r, b in repos_to_bumps.items() if b]
if self.config.progress:
repo_list = tqdm(
repo_list, desc='Extract structural diffs',
unit=' repos')
bump_pbar = tqdm(
desc='Extract structural diffs', unit=' version pairs',
total=sum(len(rb[1]) for rb in repos_to_bumps.items()))
else:
bump_pbar = None
for repo_path, versions in repo_list:
results.append(self.diff_repo(repo_path, versions, bump_pbar))
if bump_pbar is not None:
bump_pbar.close()
self.export_to_csv(results)
return ResultMap(results)
def test_stage_run_empty_input(config: CloneConfig, mock_clone: None) -> None:
stage = Clone(config)
prev: ResultMap[GalaxyRole] = ResultMap([])
paths = stage.run(prev)
assert not paths
def run(self, analyze_versions: ResultMap[AnalyzedRepoVersions],
clone: ResultMap[GitRepoPath],
discover: ResultMap[GalaxyRole]) -> ResultMap[RepoVersionDiffs]:
results = []
repos_to_versions: Iterable[AnalyzedRepoVersions] = (
analyze_versions.values())
if self.config.progress:
repos_to_versions = tqdm(repos_to_versions,
desc='Extract commits between versions',
unit=' repos')
# TODO(ROpdebee): Would be nice if we could speed this up a bit,
# currently takes 1-2s per repository. Likely due to
# the diffing, haven't profiled yet though. Caching
# should already massively help on consecutive runs
# though.
for repo_versions in repos_to_versions:
diff = RepoVersionDiffs.create(
repo_versions,
git.Repo(self.config.output_directory /
clone[repo_versions.id].path))
results.append(diff)
self.export_to_csv(results, clone, discover)
return ResultMap(results)
def test_iter(data: List[Data]) -> None:
rm: ResultMap[Data] = ResultMap(data)
keys = set()
for k in rm:
keys.add(k)
assert keys == {d.id for d in data}
def run(self, first_stage: ResultMap[MyModel],
second_stage: ResultMap[NewData]) -> ResultMap[NewData]:
transformed = []
for m in first_stage.values():
for n in second_stage.values():
transformed.append(NewData(m.string + ' ' + n.id))
return ResultMap(transformed)
def run(
self,
extract_role_metadata: ResultMap[GalaxyMetadata],
extract_git_metadata: ResultMap[GitRepoMetadata],
clone: ResultMap[GitRepo]
) -> ResultMap[MultiStructuralRoleModel]:
"""Run the stage."""
role_repos = self.get_role_repositories(extract_role_metadata, clone, extract_git_metadata)
num_revs = sum(len(revs) for (_, _, revs) in role_repos)
if not self.config.commits:
num_revs += len(role_repos)
task_list: Iterable[Tuple[GitRepo, str, List[Tuple[str, str]]]]
rev_pbar: Optional[tqdm]
if self.config.progress:
task_list = tqdm(
role_repos, desc='Extract structural models',
unit=' repos')
rev_pbar = tqdm(
desc='Extract structural models', unit=' revs',
total=num_revs)
else:
task_list = role_repos
rev_pbar = None
results: List[MultiStructuralRoleModel] = []
failures = 0
for repo, role_name, revs in task_list:
git_repo_obj = git.Repo(self.config.output_directory / 'Repositories' / repo.path)
save_branch = git_repo_obj.active_branch
role_models = []
try:
for sha1, rev in revs:
model = self.extract(git_repo_obj, role_name, sha1, rev, rev_pbar)
if model is None:
failures += 1
else:
role_models.append(model)
# Also extract for the latest commit if we're extracting tags.
if not self.config.commits:
save_branch.checkout(force=True)
model = self.extract(git_repo_obj, role_name, 'HEAD', 'HEAD', rev_pbar)
if model is None:
failures += 1
else:
role_models.append(model)
finally:
# Make sure to reset the repo to the HEAD from before
save_branch.checkout(force=True)
results.append(MultiStructuralRoleModel(role_name, role_models))
if rev_pbar is not None:
rev_pbar.close()
print(f'{failures} roles failed to load')
return ResultMap(results)
def test_report_empty(config: CloneConfig,
capsys: _pytest.capture.CaptureFixture) -> None:
stage = Clone(config)
results: ResultMap[GitRepoPath] = ResultMap([])
stage.report_results(results)
captured = capsys.readouterr()
assert 'Cloned 0 ' in captured.out
assert str(config.output_directory) in captured.out
def run(self, galaxy_scrape: ResultMap[GalaxyAPIPage]
) -> ResultMap[GalaxyMetadata]:
"""Run the stage."""
metadata_map = MetadataMap(list(galaxy_scrape._storage.values()))
metadata_map.verify_schema()
num_roles = cast(int, galaxy_scrape['roles/1'].response['count'])
meta = GalaxyMetadata.from_metamap(metadata_map)
return ResultMap([meta])
def run(
self, extract_structural_models: ResultMap[MultiStructuralRoleModel]
) -> ResultMap[StructuralRoleEvolution]:
"""Run the stage."""
models_it: Iterable[
MultiStructuralRoleModel] = extract_structural_models.values()
if self.config.progress:
models_it = tqdm(models_it, desc='Extract structural diffs')
return ResultMap(map(StructuralRoleEvolution.create, models_it))
def test_report(config: CloneConfig, resource: TextIO,
capsys: _pytest.capture.CaptureFixture) -> None:
stage = Clone(config)
data = json.load(resource)
results: ResultMap[GitRepoPath] = ResultMap.structure(
data, ResultMap[GitRepoPath])
stage.report_results(results)
captured = capsys.readouterr()
assert 'Cloned 100 ' in captured.out
assert str(config.output_directory) in captured.out
def load_from_dataset(self) -> ResultMap[GalaxyMetadata]:
"""Load the results of a previous run from the dataset.
Raises `CacheMiss` when not found in the dataset.
"""
dataset_dir_path = self.config.output_directory / self.dataset_dir_name
try:
return ResultMap(
[GalaxyMetadata.lazy_load('dummy', dataset_dir_path)])
except:
raise CacheMiss()
def run(self) -> ResultMap[GalaxyAPIPage]:
"""Run the stage."""
all_results: List[GalaxyAPIPage] = []
for name, url in API_URLS.items():
pages = self.load_pages(name, url)
all_results.extend(pages)
# Might happen that some roles in the role page fail to load because
# of 500 Internal Server Error at Galaxy side. Can't fix this. The
# role page includes more information though, and we've got both the
# role search and the roles themselves. Any roles in the search page
# that aren't present in the role pages need to be loaded separately
# too. We'll give these incremental page numbers.
all_results = self.import_missing_roles(all_results)
return ResultMap(all_results)
def test_stage_run(config: CloneConfig, progress: bool, resource: TextIO,
mock_clone: None) -> None:
config.progress = progress
stage = Clone(config)
data = json.load(resource)
prev: ResultMap[GalaxyRole] = ResultMap.structure(data,
ResultMap[GalaxyRole])
paths = stage.run(prev)
assert len(paths) == 2
for id_, path in paths.items():
assert not path.path.is_absolute()
assert (config.output_directory / path.path).exists()
assert path.owner == path.path.parent.name == prev[id_].github_user
assert path.name == path.path.name == prev[id_].github_repo
assert path.id == id_
def run(self, discover: ResultMap[GalaxyRole]) -> ResultMap[GitRepoPath]:
"""Run the stage: Clone the repositories."""
repo_paths = set()
roles: Iterable[GalaxyRole] = discover.values()
if self.config.progress:
roles = tqdm(roles, desc='Cloning repos')
for role in roles:
user, repo = role.github_user, role.github_repo
try:
path = self.clone(user, repo)
except CloneException as exc: # pragma: no cover
tqdm.write(f'Failed to clone repository {user}/{repo}: {exc}')
continue
repo_paths.add(
GitRepoPath(role.github_user, role.github_repo, role.id, path))
return ResultMap(repo_paths)
def run(self, extract_role_metadata: ResultMap[GalaxyMetadata]) -> ResultMap[GitRepo]:
"""Run the stage: Clone the repositories."""
repo_paths = set()
repos: Iterable[Repository] = extract_role_metadata['dummy'].repositories.values()
if self.config.progress:
repos = tqdm(repos, desc='Cloning repos')
for repo in repos:
try:
user, repo_name = self._parse_info(repo)
path = self.clone(user, repo_name, repo)
except CloneException as exc: # pragma: no cover
tqdm.write(f'Failed to clone repository {repo.github_url}: {exc}')
continue
repo_paths.add(GitRepo(
user, repo_name, XrefID(Repository, repo.entity_id), path))
return ResultMap(repo_paths)
def run(self) -> ResultMap[NewData]:
return ResultMap([NewData(self.config.option)])
def run(self) -> ResultMap[NewData]:
return ResultMap([NewData('append'), NewData('test')])
def run(self) -> ResultMap[MyModel]:
return ResultMap(TEST_DATA_RUN)
@attr.s(auto_attribs=True)
class MyModel(Model):
"""Test model for stage result type."""
number: int
string: str
boolean: bool
@property
def id(self) -> str:
return self.string
CACHE_NAME = 'cache.json'
TEST_DATA_CACHE = ResultMap(
[MyModel(1, 'test', False),
MyModel(2, 'test2', True)])
TEST_DATA_RUN = ResultMap(
[MyModel(3, 'Ran', False),
MyModel(4, 'Ran 2', True)])
CONFIG = MainConfig()
# Forward declarations of classes created in fixtures.
if TYPE_CHECKING:
class MyStage(Stage[MyModel, MainConfig]):
has_run: bool
has_reported: bool
reported_data: ResultMap[MyModel]
def run(self, clone: ResultMap[GitRepo]) -> ResultMap[GitRepoMetadata]:
repos: Iterable[GitRepo] = clone.values()
if self.config.progress:
repos = tqdm(repos, total=len(clone))
return ResultMap(map(self.extract_meta, repos))
def test_len(data: List[Data]) -> None:
rm: ResultMap[Data] = ResultMap(data)
assert len(rm) == len(data)
def test_get_item() -> None:
rm: ResultMap[Data] = ResultMap(DATA)
assert rm['test'] == DATA[0]
assert rm['tset'] == DATA[1]
def test_get_empty() -> None:
rm: ResultMap[Data] = ResultMap([])
with pytest.raises(KeyError):
rm['test']
def run(self, first_stage: ResultMap[MyModel]) -> ResultMap[NewData]:
transformed = [
NewData(m.string * m.number) for m in first_stage.values()
]
return ResultMap(transformed)
def test_structure() -> None:
d = {'test': {'id': 'test', 'val': 1}, 'tset': {'id': 'tset', 'val': -1}}
rm: ResultMap[Data] = ResultMap.structure(d, ResultMap[Data])
assert rm == ResultMap(DATA)
def test_get_nonexistant() -> None:
rm: ResultMap[Data] = ResultMap(DATA)
with pytest.raises(KeyError):
rm['doesnt_exist']
def run(
self, extract_versions: ResultMap[RepoVersions]
) -> ResultMap[AnalyzedRepoVersions]:
return ResultMap(
AnalyzedRepoVersions(repo_versions)
for repo_versions in extract_versions.values())