def diff(repo: Repository, dev, master):
"""Display diff of DEV commit/branch to MASTER commit/branch.
If no MASTER is specified, then the staging area branch HEAD will
will be used as the commit digest for MASTER. This operation will
return a diff which could be interpreted as if you were merging
the changes in DEV into MASTER.
TODO: VERIFY ORDER OF OUTPUT IS CORRECT.
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.commiting import get_staging_branch_head
from hangar.records.summarize import status
if dev not in repo.list_branches():
dev = expand_short_commit_digest(repo._env.refenv, dev)
if master is None:
master = get_staging_branch_head(repo._env.branchenv)
elif master not in repo.list_branches():
master = expand_short_commit_digest(repo._env.refenv, master)
diff_spec = repo.diff(master, dev)
buf = status(hashenv=repo._env.hashenv, branch_name=dev, diff=diff_spec.diff)
click.echo(buf.getvalue())
def test_full_from_short_commit_digest(two_commit_filled_samples_repo):
from hangar.records.commiting import expand_short_commit_digest
repo = two_commit_filled_samples_repo
history = repo.log(branch='master', return_contents=True)
commits = history['order']
for full_cmt in commits:
short_cmt = full_cmt[:18]
found_cmt = expand_short_commit_digest(repo._env.refenv, short_cmt)
assert found_cmt == full_cmt
with pytest.raises(KeyError, match='No matching commit hash found starting with'):
expand_short_commit_digest(repo._env.refenv, 'zzzzzzzzzzzzzzzzzzzzzzzzzzzz')
def test_full_from_short_commit_digest(written_two_cmt_repo):
from hangar.records.commiting import expand_short_commit_digest
repo = written_two_cmt_repo
history = repo.log(branch='master', return_contents=True)
commits = history['order']
for full_cmt in commits:
short_cmt = full_cmt[:18]
found_cmt = expand_short_commit_digest(repo._env.refenv, short_cmt)
assert found_cmt == full_cmt
with pytest.raises(KeyError):
expand_short_commit_digest(repo._env.refenv,
'zzzzzzzzzzzzzzzzzzzzzzzzzzzz')
def view_data(ctx, repo: Repository, column, sample, startpoint, format_, plugin):
"""Use a plugin to view the data of some SAMPLE in COLUMN at STARTPOINT.
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.heads import get_branch_head_commit, get_staging_branch_head
from hangar import external
kwargs = parse_custom_arguments(ctx.args)
if startpoint in repo.list_branches():
base_commit = get_branch_head_commit(repo._env.branchenv, startpoint)
elif startpoint:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
else:
branch_name = get_staging_branch_head(repo._env.branchenv)
base_commit = get_branch_head_commit(repo._env.branchenv, branch_name)
co = repo.checkout(commit=base_commit)
try:
aset = co.columns.get(column)
extension = format_.lstrip('.') if format_ else None
data = aset[sample]
try:
external.show(data, plugin=plugin, extension=extension, **kwargs)
except Exception as e:
raise click.ClickException(e)
except KeyError as e:
raise click.ClickException(e)
finally:
co.close()
def branch_create(repo: Repository, name, startpoint):
"""Create a branch with NAME at STARTPOINT (short-digest or branch)
If no STARTPOINT is provided, the new branch is positioned at the HEAD of
the staging area branch, automatically.
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.heads import get_branch_head_commit
from hangar.records.heads import get_staging_branch_head
branch_names = repo.list_branches()
if name in branch_names:
e = ValueError(f'branch name: {name} already exists')
raise click.ClickException(e)
try:
if startpoint is None:
branch = get_staging_branch_head(repo._env.branchenv)
base_commit = get_branch_head_commit(repo._env.branchenv, branch)
elif startpoint in branch_names:
base_commit = get_branch_head_commit(repo._env.branchenv, startpoint)
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
res = repo.create_branch(name, base_commit=base_commit)
except (KeyError, ValueError, RuntimeError) as e:
raise click.ClickException(e)
click.echo(f'Created BRANCH: {res.name} HEAD: {res.digest}')
def fetch_data(repo: Repository, remote, startpoint, column, nbytes, all_):
"""Get data from REMOTE referenced by STARTPOINT (short-commit or branch).
The default behavior is to only download a single commit's data or the HEAD
commit of a branch. Please review optional arguments for other behaviors.
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.heads import get_branch_head_commit
from hangar.records.heads import get_staging_branch_head
from hangar.utils import parse_bytes
if startpoint is None:
branch = get_staging_branch_head(repo._env.branchenv)
commit = get_branch_head_commit(repo._env.branchenv, branch)
elif startpoint in repo.list_branches():
commit = get_branch_head_commit(repo._env.branchenv, startpoint)
else:
commit = expand_short_commit_digest(repo._env.refenv, startpoint)
click.echo(f'Fetching data for commit: {commit}')
try:
max_nbytes = parse_bytes(nbytes)
except AttributeError:
max_nbytes = None
if len(column) == 0:
column = None
commits = repo.remote.fetch_data(remote=remote,
commit=commit,
column_names=column,
max_num_bytes=max_nbytes,
retrieve_all_history=all_)
click.echo(f'completed data for commits: {commits}')
def branch_create(ctx, name, startpoint):
"""Create a branch with NAME at STARTPOINT (short-digest or branch)
If no STARTPOINT is provided, the new branch is positioned at the HEAD of
the staging area branch, automatically.
"""
from hangar.records.heads import get_branch_head_commit, get_staging_branch_head
P = os.getcwd()
repo = Repository(path=P)
branch_names = repo.list_branches()
if name in branch_names:
raise ValueError(f'branch name: {name} already exists')
if startpoint is None:
branch = get_staging_branch_head(repo._env.branchenv)
base_commit = get_branch_head_commit(repo._env.branchenv, branch)
elif startpoint in branch_names:
base_commit = get_branch_head_commit(repo._env.branchenv, startpoint)
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
click.echo(f'BRANCH: ' +
repo.create_branch(name, base_commit=base_commit) +
f' HEAD: {base_commit}')
def export_data(ctx, repo: Repository, column, outdir, startpoint, sample,
format_, plugin):
"""Export COLUMN sample data as it existed a STARTPOINT to some format and path.
Specifying which sample to be exported is possible by using the switch
``--sample`` (without this, all the samples in the given column will be
exported). Since hangar supports both int and str datatype for the sample
name, specifying that while mentioning the sample name might be necessary
at times. It is possible to do that by separating the name and type by a
colon.
Example:
1. if the sample name is string of numeric 10 - ``str:10`` or ``10``
2. if the sample name is ``sample1`` - ``str:sample1`` or ``sample1``
3. if the sample name is an int, let say 10 - ``int:10``
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.heads import get_branch_head_commit, get_staging_branch_head
from hangar import external
kwargs = parse_custom_arguments(ctx.args)
if startpoint in repo.list_branches():
base_commit = get_branch_head_commit(repo._env.branchenv, startpoint)
elif startpoint:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
else:
branch_name = get_staging_branch_head(repo._env.branchenv)
base_commit = get_branch_head_commit(repo._env.branchenv, branch_name)
co = repo.checkout(commit=base_commit)
try:
aset = co.columns.get(column)
sampleNames = [sample] if sample is not None else list(aset.keys())
extension = format_.lstrip('.') if format_ else None
with aset, click.progressbar(sampleNames) as sNamesBar:
for sampleN in sNamesBar:
data = aset[sampleN]
formated_sampleN = f'{type(sampleN).__name__}:{sampleN}'
try:
external.save(data, outdir, formated_sampleN, extension,
plugin, **kwargs)
except Exception as e:
raise click.ClickException(e)
except KeyError as e:
raise click.ClickException(e)
finally:
co.close()
def log(repo: Repository, startpoint):
"""Display commit graph starting at STARTPOINT (short-digest or name)
If no argument is passed in, the staging area branch HEAD will be used as the
starting point.
"""
from hangar.records.commiting import expand_short_commit_digest
if startpoint is None:
click.echo(repo.log())
elif startpoint in repo.list_branches():
click.echo(repo.log(branch=startpoint))
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
click.echo(repo.log(commit=base_commit))
def log(ctx, startpoint):
"""Display commit graph starting at STARTPOINT (short-digest or name)
If no argument is passed in, the staging area branch HEAD will be used as the
starting point.
"""
P = os.getcwd()
repo = Repository(path=P)
if startpoint is None:
click.echo(repo.log())
elif startpoint in repo.list_branches():
click.echo(repo.log(branch=startpoint))
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
click.echo(repo.log(commit=base_commit))
def summary(repo: Repository, startpoint):
"""Display content summary at STARTPOINT (short-digest or branch).
If no argument is passed in, the staging area branch HEAD wil be used as the
starting point. In order to recieve a machine readable, and more complete
version of this information, please see the ``Repository.summary()`` method
of the API.
"""
from hangar.records.commiting import expand_short_commit_digest
if startpoint is None:
click.echo(repo.summary())
elif startpoint in repo.list_branches():
click.echo(repo.summary(branch=startpoint))
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
click.echo(repo.summary(commit=base_commit))
def fetch_data(ctx, remote, startpoint, aset, nbytes, all_):
"""Get data from REMOTE referenced by STARTPOINT (short-commit or branch).
The default behavior is to only download a single commit's data or the HEAD
commit of a branch. Please review optional arguments for other behaviors
"""
from hangar.records.heads import get_branch_head_commit, get_staging_branch_head
from hangar.utils import parse_bytes
P = os.getcwd()
repo = Repository(path=P)
if startpoint is None:
branch = get_staging_branch_head(repo._env.branchenv)
commit = get_branch_head_commit(repo._env.branchenv, branch)
click.echo(
f'No startpoint supplied, fetching data of HEAD: {commit} for BRANCH: {branch}'
)
elif startpoint in repo.list_branches():
commit = get_branch_head_commit(repo._env.branchenv, startpoint)
click.echo(
f'Fetching data for HEAD: {commit} of STARTPOINT BRANCH: {startpoint}'
)
else:
commit = expand_short_commit_digest(repo._env.refenv, startpoint)
click.echo(f'Fetching data for STARTPOINT HEAD: {commit}')
click.echo(f'aset argument: {aset}')
try:
max_nbytes = parse_bytes(nbytes)
click.echo(f'nbytes argument: {max_nbytes}')
except AttributeError:
max_nbytes = None
if len(aset) == 0:
aset = None
commits = repo.remote.fetch_data(remote=remote,
commit=commit,
arrayset_names=aset,
max_num_bytes=max_nbytes,
retrieve_all_history=all_)
click.echo(f'completed data for commits: {commits}')
def export_data(repo: Repository, startpoint, arrayset, out, sample, format_,
plugin):
"""export ARRAYSET sample data as it existed a STARTPOINT to some format and path.
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.heads import get_branch_head_commit
from hangar.cli.io import imsave
if startpoint in repo.list_branches():
base_commit = get_branch_head_commit(repo._env.branchenv, startpoint)
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
try:
co = repo.checkout(write=False, commit=base_commit)
arrayset = co.arraysets[arrayset]
if sample:
sampleNames = [sample]
else:
sampleNames = list(arrayset.keys())
if format_:
format_ = format_.lstrip('.')
outP = os.path.expanduser(os.path.normpath(out))
with arrayset as aset, click.progressbar(sampleNames) as sNamesBar:
for sampleN in sNamesBar:
if format_:
if sampleN.endswith(format_):
outFP = os.path.join(outP, f'{sampleN}')
else:
outFP = os.path.join(outP, f'{sampleN}.{format_}')
else:
outFP = os.path.join(outP, f'{sampleN}')
try:
data = aset[sampleN]
imsave(outFP, data)
except KeyError as e:
click.echo(e)
finally:
co.close()
def view_data(repo: Repository, startpoint, arrayset, sample, plugin):
"""Use a plugin to view the data of some SAMPLE in ARRAYSET at STARTPOINT.
"""
from hangar.records.commiting import expand_short_commit_digest
from hangar.records.heads import get_branch_head_commit
from hangar.cli.io import imshow, show
if startpoint in repo.list_branches():
base_commit = get_branch_head_commit(repo._env.branchenv, startpoint)
else:
base_commit = expand_short_commit_digest(repo._env.refenv, startpoint)
try:
co = repo.checkout(write=False, commit=base_commit)
arrayset = co.arraysets[arrayset]
try:
data = arrayset[sample]
imshow(data, plugin=plugin)
show()
except KeyError as e:
click.echo(e)
finally:
co.close()
