class Project(object):
DVC_DIR = '.dvc'
def __init__(self, root_dir):
from dvc.logger import Logger
from dvc.config import Config
from dvc.state import LinkState, State
from dvc.lock import Lock
from dvc.scm import SCM
from dvc.cache import Cache
from dvc.data_cloud import DataCloud
from dvc.updater import Updater
from dvc.prompt import Prompt
self.root_dir = os.path.abspath(os.path.realpath(root_dir))
self.dvc_dir = os.path.join(self.root_dir, self.DVC_DIR)
self.config = Config(self.dvc_dir)
self.scm = SCM(self.root_dir)
self.lock = Lock(self.dvc_dir)
# NOTE: storing state and link_state in the repository itself to avoid
# any possible state corruption in 'shared cache dir' scenario.
self.state = State(self)
self.link_state = LinkState(self)
core = self.config._config[Config.SECTION_CORE]
self.logger = Logger(core.get(Config.SECTION_CORE_LOGLEVEL, None))
self.cache = Cache(self)
self.cloud = DataCloud(self, config=self.config._config)
self.updater = Updater(self.dvc_dir)
self.prompt = Prompt()
self._ignore()
self.updater.check()
@staticmethod
def init(root_dir=os.curdir, no_scm=False, force=False):
"""
Initiate dvc project in directory.
Args:
root_dir: Path to project's root directory.
Returns:
Project instance.
Raises:
KeyError: Raises an exception.
"""
import shutil
from dvc.scm import SCM, Base
from dvc.config import Config
root_dir = os.path.abspath(root_dir)
dvc_dir = os.path.join(root_dir, Project.DVC_DIR)
scm = SCM(root_dir)
if type(scm) == Base and not no_scm:
msg = "{} is not tracked by any supported scm tool(e.g. git)."
raise InitError(msg.format(root_dir))
if os.path.isdir(dvc_dir):
if not force:
msg = "'{}' exists. Use '-f' to force."
raise InitError(msg.format(os.path.relpath(dvc_dir)))
shutil.rmtree(dvc_dir)
os.mkdir(dvc_dir)
config = Config.init(dvc_dir)
proj = Project(root_dir)
scm.add([config.config_file])
if scm.ignore_file():
scm.add([os.path.join(dvc_dir, scm.ignore_file())])
return proj
def destroy(self):
import shutil
for stage in self.stages():
stage.remove()
shutil.rmtree(self.dvc_dir)
def _ignore(self):
flist = [
self.state.state_file, self.lock.lock_file,
self.config.config_local_file, self.updater.updater_file
]
if self.cache.local.cache_dir.startswith(self.root_dir):
flist += [self.cache.local.cache_dir]
self.scm.ignore_list(flist)
def install(self):
self.scm.install()
def to_dvc_path(self, path):
return os.path.relpath(path, self.root_dir)
def _check_output_duplication(self, outs):
from dvc.exceptions import OutputDuplicationError
for stage in self.stages():
for o in stage.outs:
for out in outs:
if o.path == out.path and o.stage.path != out.stage.path:
stages = [o.stage.relpath, out.stage.relpath]
raise OutputDuplicationError(o.path, stages)
def add(self, fname, recursive=False):
fnames = []
if recursive and os.path.isdir(fname):
fnames = []
for root, dirs, files in os.walk(fname):
for f in files:
path = os.path.join(root, f)
if Stage.is_stage_file(path):
continue
if os.path.basename(path) == self.scm.ignore_file():
continue
if self.scm.is_tracked(path):
continue
fnames.append(path)
else:
fnames = [fname]
stages = []
for f in fnames:
stage = Stage.loads(project=self, outs=[f], add=True)
self._check_output_duplication(stage.outs)
stage.save()
stage.dump()
stages.append(stage)
return stages
def remove(self, target, outs_only=False):
stage = Stage.load(self, target)
if outs_only:
stage.remove_outs()
else:
stage.remove()
return stage
def lock_stage(self, target, unlock=False):
stage = Stage.load(self, target)
stage.locked = False if unlock else True
stage.dump()
return stage
def move(self, from_path, to_path):
import dvc.output as Output
from_out = Output.loads_from(Stage(self, cwd=os.curdir),
[from_path])[0]
found = False
for stage in self.stages():
for out in stage.outs:
if out.path != from_out.path:
continue
if not stage.is_data_source:
msg = 'Dvcfile \'{}\' is not a data source.'
raise DvcException(msg.format(stage.rel_path))
found = True
to_out = Output.loads_from(out.stage, [to_path], out.cache,
out.metric)[0]
out.move(to_out)
stage_base = os.path.basename(stage.path)
stage_base = stage_base.rstrip(Stage.STAGE_FILE_SUFFIX)
stage_dir = os.path.dirname(stage.path)
from_base = os.path.basename(from_path)
to_base = os.path.basename(to_path)
if stage_base == from_base:
os.unlink(stage.path)
path = to_base + Stage.STAGE_FILE_SUFFIX
stage.path = os.path.join(stage_dir, path)
stage.dump()
if not found:
msg = 'Unable to find dvcfile with output \'{}\''
raise DvcException(msg.format(from_path))
def run(self,
cmd=None,
deps=[],
outs=[],
outs_no_cache=[],
metrics_no_cache=[],
fname=Stage.STAGE_FILE,
cwd=os.curdir,
no_exec=False,
overwrite=False):
stage = Stage.loads(project=self,
fname=fname,
cmd=cmd,
cwd=cwd,
outs=outs,
outs_no_cache=outs_no_cache,
metrics_no_cache=metrics_no_cache,
deps=deps,
overwrite=overwrite)
self._check_output_duplication(stage.outs)
if not no_exec:
stage.run()
stage.dump()
return stage
def imp(self, url, out):
stage = Stage.loads(project=self, cmd=None, deps=[url], outs=[out])
self._check_output_duplication(stage.outs)
stage.run()
stage.dump()
return stage
def _reproduce_stage(self, stages, node, force, dry, interactive):
stage = stages[node]
if stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependecies are not ' \
'going to be reproduced.'
self.logger.warn(msg.format(stage.relpath))
stage = stage.reproduce(force=force, dry=dry, interactive=interactive)
if not stage:
return []
if not dry:
stage.dump()
return [stage]
def reproduce(self,
target,
recursive=True,
force=False,
dry=False,
interactive=False):
import networkx as nx
stage = Stage.load(self, target)
G = self.graph()[1]
stages = nx.get_node_attributes(G, 'stage')
node = os.path.relpath(stage.path, self.root_dir)
if not interactive:
config = self.config
core = config._config[config.SECTION_CORE]
interactive = core.get(config.SECTION_CORE_INTERACTIVE, False)
if recursive:
return self._reproduce_stages(G, stages, node, force, dry,
interactive)
return self._reproduce_stage(stages, node, force, dry, interactive)
def _reproduce_stages(self, G, stages, node, force, dry, interactive):
import networkx as nx
result = []
for n in nx.dfs_postorder_nodes(G, node):
try:
result += self._reproduce_stage(stages, n, force, dry,
interactive)
except Exception as ex:
raise ReproductionError(stages[n].relpath, ex)
return result
def _cleanup_unused_links(self, all_stages):
used = []
for stage in all_stages:
for out in stage.outs:
used.append(out.path)
self.link_state.remove_unused(used)
def checkout(self, target=None):
all_stages = self.active_stages()
if target:
stages = [Stage.load(self, target)]
else:
stages = all_stages
self._cleanup_unused_links(all_stages)
for stage in stages:
if stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependecies are not ' \
'going to be checked out.'
self.logger.warn(msg.format(stage.relpath))
stage.checkout()
def _used_cache(self, target=None, all_branches=False, active=True):
cache = {}
cache['local'] = []
cache['s3'] = []
cache['gs'] = []
cache['hdfs'] = []
cache['ssh'] = []
for branch in self.scm.brancher(all_branches=all_branches):
if target:
stages = [Stage.load(self, target)]
elif active:
stages = self.active_stages()
else:
stages = self.stages()
for stage in stages:
if active and not target and stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependecies are ' \
'not going to be pushed/pulled/fetched.'
self.logger.warn(msg.format(stage.relpath))
for out in stage.outs:
if not out.use_cache or not out.info:
continue
info = out.dumpd()
info['branch'] = branch
cache[out.path_info['scheme']] += [info]
return cache
def _do_gc(self, typ, func, clist):
removed = func(clist)
if not removed:
self.logger.info("No unused {} cache to remove.".format(typ))
def gc(self, all_branches=False, cloud=False, remote=None):
clist = self._used_cache(target=None,
all_branches=all_branches,
active=False)
self._do_gc('local', self.cache.local.gc, clist)
if self.cache.s3:
self._do_gc('s3', self.cache.s3.gc, clist)
if self.cache.gs:
self._do_gc('gs', self.cache.gs.gc, clist)
if self.cache.ssh:
self._do_gc('ssh', self.cache.ssh.gc, clist)
if self.cache.hdfs:
self._do_gc('hdfs', self.cache.hdfs.gc, clist)
if self.cache.azure:
self._do_gc('azure', self.cache.azure.gc, clist)
if cloud:
self._do_gc('remote',
self.cloud._get_cloud(remote, 'gc -c').gc, clist)
def push(self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False):
self.cloud.push(self._used_cache(target, all_branches)['local'],
jobs,
remote=remote,
show_checksums=show_checksums)
def fetch(self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False):
self.cloud.pull(self._used_cache(target, all_branches)['local'],
jobs,
remote=remote,
show_checksums=show_checksums)
def pull(self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False):
self.fetch(target,
jobs,
remote=remote,
all_branches=all_branches,
show_checksums=show_checksums)
self.checkout(target=target)
def _local_status(self, target=None):
status = {}
if target:
stages = [Stage.load(self, target)]
else:
stages = self.active_stages()
for stage in stages:
if stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependecies are not ' \
'going to be shown in status output.'
self.logger.warn(msg.format(stage.relpath))
status.update(stage.status())
return status
def _cloud_status(self,
target=None,
jobs=1,
remote=None,
show_checksums=False):
import dvc.remote.base as cloud
status = {}
for md5, ret in self.cloud.status(self._used_cache(target)['local'],
jobs,
remote=remote,
show_checksums=show_checksums):
if ret == cloud.STATUS_OK:
continue
prefix_map = {
cloud.STATUS_DELETED: 'deleted',
cloud.STATUS_NEW: 'new',
}
status[md5] = prefix_map[ret]
return status
def status(self,
target=None,
jobs=1,
cloud=False,
remote=None,
show_checksums=False):
if cloud:
return self._cloud_status(target,
jobs,
remote=remote,
show_checksums=show_checksums)
return self._local_status(target)
def _read_metric_json(self, fd, json_path):
import json
from jsonpath_rw import parse
parser = parse(json_path)
return [x.value for x in parser.find(json.load(fd))]
def _do_read_metric_xsv(self, reader, row, col):
if col is not None and row is not None:
return [reader[row][col]]
elif col is not None:
return [r[col] for r in reader]
elif row is not None:
return reader[row]
return None
def _read_metric_hxsv(self, fd, hxsv_path, delimiter):
import csv
col, row = hxsv_path.split(',')
row = int(row)
reader = list(csv.DictReader(fd, delimiter=delimiter))
return self._do_read_metric_xsv(reader, row, col)
def _read_metric_xsv(self, fd, xsv_path, delimiter):
import csv
col, row = xsv_path.split(',')
row = int(row)
col = int(col)
reader = list(csv.reader(fd, delimiter=delimiter))
return self._do_read_metric_xsv(reader, row, col)
def _read_metric(self, path, typ=None, xpath=None):
ret = None
if not os.path.exists(path):
return ret
try:
with open(path, 'r') as fd:
if typ == 'json':
ret = self._read_metric_json(fd, xpath)
elif typ == 'csv':
ret = self._read_metric_xsv(fd, xpath, ',')
elif typ == 'tsv':
ret = self._read_metric_xsv(fd, xpath, '\t')
elif typ == 'hcsv':
ret = self._read_metric_hxsv(fd, xpath, ',')
elif typ == 'htsv':
ret = self._read_metric_hxsv(fd, xpath, '\t')
else:
ret = fd.read()
except Exception as exc:
self.logger.error('Unable to read metric in \'{}\''.format(path),
exc)
return ret
def _find_output_by_path(self, path, outs=None):
from dvc.exceptions import OutputDuplicationError
if not outs:
astages = self.active_stages()
outs = [out for stage in astages for out in stage.outs]
abs_path = os.path.abspath(path)
matched = [out for out in outs if out.path == abs_path]
stages = [out.stage.relpath for out in matched]
if len(stages) > 1:
raise OutputDuplicationError(path, stages)
return matched[0] if matched else None
def metrics_show(self,
path=None,
typ=None,
xpath=None,
all_branches=False):
res = {}
for branch in self.scm.brancher(all_branches=all_branches):
astages = self.active_stages()
outs = [out for stage in astages for out in stage.outs]
if path:
out = self._find_output_by_path(path, outs=outs)
stage = out.stage.path if out else None
if out and all(
[out.metric, not typ,
isinstance(out.metric, dict)]):
entries = [(path,
out.metric.get(out.PARAM_METRIC_TYPE, None),
out.metric.get(out.PARAM_METRIC_XPATH, None))]
else:
entries = [(path, typ, xpath)]
else:
metrics = filter(lambda o: o.metric, outs)
stage = None
entries = []
for o in metrics:
if not typ and isinstance(o.metric, dict):
t = o.metric.get(o.PARAM_METRIC_TYPE, typ)
x = o.metric.get(o.PARAM_METRIC_XPATH, xpath)
else:
t = typ
x = xpath
entries.append((o.path, t, x))
for fname, t, x in entries:
if stage:
self.checkout(stage)
rel = os.path.relpath(fname)
metric = self._read_metric(fname, typ=t, xpath=x)
if not metric:
continue
if branch not in res:
res[branch] = {}
res[branch][rel] = metric
for branch, val in res.items():
if all_branches:
self.logger.info('{}:'.format(branch))
for fname, metric in val.items():
self.logger.info('\t{}: {}'.format(fname, metric))
if res:
return res
if path:
msg = 'File \'{}\' does not exist'.format(path)
else:
msg = 'No metric files in this repository. ' \
'Use \'dvc metrics add\' to add a metric file to track.'
raise DvcException(msg)
def _metrics_modify(self, path, typ=None, xpath=None, delete=False):
out = self._find_output_by_path(path)
if not out:
msg = 'Unable to find file \'{}\' in the pipeline'.format(path)
raise DvcException(msg)
if out.path_info['scheme'] != 'local':
msg = 'Output \'{}\' scheme \'{}\' is not supported for metrics'
raise DvcException(msg.format(out.path, out.path_info['scheme']))
if out.use_cache:
msg = 'Cached output \'{}\' is not supported for metrics'
raise DvcException(msg.format(out.rel_path))
if typ:
if not isinstance(out.metric, dict):
out.metric = {}
out.metric[out.PARAM_METRIC_TYPE] = typ
if xpath:
if not isinstance(out.metric, dict):
out.metric = {}
out.metric[out.PARAM_METRIC_XPATH] = xpath
if delete:
out.metric = None
out._verify_metric()
out.stage.dump()
def metrics_modify(self, path=None, typ=None, xpath=None):
self._metrics_modify(path, typ, xpath)
def metrics_add(self, path, typ=None, xpath=None):
if not typ:
typ = 'raw'
self._metrics_modify(path, typ, xpath)
def metrics_remove(self, path):
self._metrics_modify(path, delete=True)
def graph(self):
import networkx as nx
from dvc.exceptions import OutputDuplicationError
G = nx.DiGraph()
G_active = nx.DiGraph()
stages = self.stages()
outs = []
outs_by_path = {}
for stage in stages:
for o in stage.outs:
existing = outs_by_path.get(o.path, None)
if existing is not None:
stages = [o.stage.relpath, existing.stage.relpath]
raise OutputDuplicationError(o.path, stages)
outs.append(o)
outs_by_path[o.path] = o
# collect the whole DAG
for stage in stages:
node = os.path.relpath(stage.path, self.root_dir)
G.add_node(node, stage=stage)
G_active.add_node(node, stage=stage)
for dep in stage.deps:
for out in outs:
if out.path != dep.path \
and not dep.path.startswith(out.path + out.sep):
continue
dep_stage = out.stage
dep_node = os.path.relpath(dep_stage.path, self.root_dir)
G.add_node(dep_node, stage=dep_stage)
G.add_edge(node, dep_node)
if not stage.locked:
G_active.add_node(dep_node, stage=dep_stage)
G_active.add_edge(node, dep_node)
return G, G_active
def pipelines(self):
import networkx as nx
G, G_active = self.graph()
if len(G.nodes()) == 0:
return []
# find pipeline ends aka "output stages"
ends = [node for node, in_degree in G.in_degree() if in_degree == 0]
# filter out subgraphs that didn't exist in original G
pipelines = []
for c in nx.weakly_connected_components(G_active):
H = G_active.subgraph(c)
found = False
for node in ends:
if node in H:
found = True
break
if found:
pipelines.append(H)
return pipelines
def stages(self):
stages = []
outs = []
for root, dirs, files in os.walk(self.root_dir):
for fname in files:
path = os.path.join(root, fname)
if not Stage.is_stage_file(path):
continue
stage = Stage.load(self, path)
for out in stage.outs:
outs.append(out.path + out.sep)
stages.append(stage)
def filter_dirs(dname):
path = os.path.join(root, dname)
if path == self.dvc_dir or path == self.scm.dir:
return False
for out in outs:
if path == os.path.normpath(out) or path.startswith(out):
return False
return True
dirs[:] = list(filter(filter_dirs, dirs))
return stages
def active_stages(self):
import networkx as nx
stages = []
for G in self.pipelines():
stages.extend(list(nx.get_node_attributes(G, 'stage').values()))
return stages
class Project(object):
DVC_DIR = '.dvc'
def __init__(self, root_dir):
self.root_dir = os.path.abspath(os.path.realpath(root_dir))
self.dvc_dir = os.path.join(self.root_dir, self.DVC_DIR)
self.config = Config(self.dvc_dir)
self.scm = SCM(self.root_dir)
self.lock = Lock(self.dvc_dir)
# NOTE: storing state and link_state in the repository itself to avoid
# any possible state corruption in 'shared cache dir' scenario.
self.state = State(self)
self.link_state = LinkState(self)
self.logger = Logger(self.config._config[Config.SECTION_CORE].get(
Config.SECTION_CORE_LOGLEVEL, None))
self.cache = Cache(self)
self.cloud = DataCloud(self, config=self.config._config)
self.updater = Updater(self.dvc_dir)
self._ignore()
self.updater.check()
@staticmethod
def init(root_dir=os.curdir, no_scm=False):
"""
Initiate dvc project in directory.
Args:
root_dir: Path to project's root directory.
Returns:
Project instance.
Raises:
KeyError: Raises an exception.
"""
root_dir = os.path.abspath(root_dir)
dvc_dir = os.path.join(root_dir, Project.DVC_DIR)
scm = SCM(root_dir)
if type(scm) == Base and not no_scm:
msg = "{} is not tracked by any supported scm tool(e.g. git).".format(
root_dir)
raise InitError(msg)
os.mkdir(dvc_dir)
config = Config.init(dvc_dir)
proj = Project(root_dir)
scm.add([config.config_file])
if scm.ignore_file():
scm.add([os.path.join(dvc_dir, scm.ignore_file())])
return proj
def _ignore(self):
l = [
self.link_state.state_file, self.link_state._lock_file.lock_file,
self.lock.lock_file, self.config.config_local_file,
self.updater.updater_file
]
if self.cache.local.cache_dir.startswith(self.root_dir):
l += [self.cache.local.cache_dir]
self.scm.ignore_list(l)
def install(self):
self.scm.install()
def to_dvc_path(self, path):
return os.path.relpath(path, self.root_dir)
def add(self, fname):
out = os.path.basename(os.path.normpath(fname))
stage_fname = out + Stage.STAGE_FILE_SUFFIX
cwd = os.path.dirname(os.path.abspath(fname))
stage = Stage.loads(project=self,
cmd=None,
deps=[],
outs=[out],
fname=stage_fname,
cwd=cwd)
stage.save()
stage.dump()
return stage
def remove(self, target, outs_only=False):
if not Stage.is_stage_file(target):
raise NotDvcFileError(target)
stage = Stage.load(self, target)
if outs_only:
stage.remove_outs()
else:
stage.remove()
return stage
def lock_stage(self, target, unlock=False):
if not Stage.is_stage_file(target):
raise NotDvcFileError(target)
stage = Stage.load(self, target)
stage.locked = False if unlock else True
stage.dump()
return stage
def move(self, from_path, to_path):
from_out = Output.loads_from(Stage(self, cwd=os.curdir),
[from_path])[0]
found = False
for stage in self.stages():
for out in stage.outs:
if out.path != from_out.path:
continue
if not stage.is_data_source:
raise DvcException(
'Dvcfile \'{}\' is not a data source.'.format(
stage.rel_path))
found = True
to_out = Output.loads_from(out.stage, [to_path], out.cache,
out.metric)[0]
out.move(to_out)
stage_base = os.path.basename(stage.path).rstrip(
Stage.STAGE_FILE_SUFFIX)
stage_dir = os.path.dirname(stage.path)
from_base = os.path.basename(from_path)
to_base = os.path.basename(to_path)
if stage_base == from_base:
os.unlink(stage.path)
stage.path = os.path.join(
stage_dir, to_base + Stage.STAGE_FILE_SUFFIX)
stage.dump()
if not found:
raise DvcException(
'Unable to find dvcfile with output \'{}\''.format(from_path))
def run(self,
cmd=None,
deps=[],
outs=[],
outs_no_cache=[],
metrics_no_cache=[],
fname=Stage.STAGE_FILE,
cwd=os.curdir,
no_exec=False):
stage = Stage.loads(project=self,
fname=fname,
cmd=cmd,
cwd=cwd,
outs=outs,
outs_no_cache=outs_no_cache,
metrics_no_cache=metrics_no_cache,
deps=deps)
if not no_exec:
stage.run()
stage.dump()
return stage
def imp(self, url, out):
stage_fname = out + Stage.STAGE_FILE_SUFFIX
cwd = os.path.dirname(os.path.abspath(out))
stage = Stage.loads(project=self,
cmd=None,
deps=[url],
outs=[out],
fname=stage_fname,
cwd=cwd)
stage.run()
stage.dump()
return stage
def _reproduce_stage(self, stages, node, force):
stage = stages[node].reproduce(force=force)
if not stage:
return []
stage.dump()
return [stage]
def reproduce(self, target, recursive=True, force=False):
stages = nx.get_node_attributes(self.graph(), 'stage')
node = os.path.relpath(os.path.abspath(target), self.root_dir)
if node not in stages:
raise NotDvcFileError(target)
if recursive:
return self._reproduce_stages(stages, node, force)
return self._reproduce_stage(stages, node, force)
def _reproduce_stages(self, stages, node, force):
result = []
for n in nx.dfs_postorder_nodes(self.graph(), node):
try:
result += self._reproduce_stage(stages, n, force)
except Exception as ex:
raise ReproductionError(stages[n].relpath, ex)
return result
def _cleanup_unused_links(self, all_stages):
used = []
for stage in all_stages:
for out in stage.outs:
used.append(out.path)
self.link_state.remove_unused(used)
def checkout(self, target=None):
all_stages = self.stages()
if target:
if not Stage.is_stage_file(target):
raise NotDvcFileError(target)
stages = [Stage.load(self, target)]
else:
stages = all_stages
self._cleanup_unused_links(all_stages)
for stage in stages:
stage.checkout()
def _used_cache(self, target=None, all_branches=False):
cache = {}
cache['local'] = []
cache['s3'] = []
cache['gs'] = []
cache['hdfs'] = []
cache['ssh'] = []
for branch in self.scm.brancher(all_branches=all_branches):
if target:
stages = [Stage.load(self, target)]
else:
stages = self.stages()
for stage in stages:
for out in stage.outs:
if not out.use_cache or not out.info:
continue
cache[out.path_info['scheme']] += [out.info]
return cache
def gc(self, all_branches=False):
clist = self._used_cache(target=None, all_branches=all_branches)
self.cache.local.gc(clist['local'])
if self.cache.s3:
self.cache.s3.gc(clist['s3'])
if self.cache.gs:
self.cache.gs.gc(clist['gs'])
if self.cache.ssh:
self.cache.ssh.gc(clist['ssh'])
if self.cache.hdfs:
self.cache.hdfs.gc(clist['hdfs'])
def push(self, target=None, jobs=1, remote=None, all_branches=False):
self.cloud.push(self._used_cache(target, all_branches)['local'],
jobs,
remote=remote)
def fetch(self, target=None, jobs=1, remote=None, all_branches=False):
self.cloud.pull(self._used_cache(target, all_branches)['local'],
jobs,
remote=remote)
def pull(self, target=None, jobs=1, remote=None, all_branches=False):
self.fetch(target, jobs, remote=remote, all_branches=all_branches)
self.checkout(target=target)
def _local_status(self, target=None):
status = {}
if target:
stages = [Stage.load(self, target)]
else:
stages = self.stages()
for stage in stages:
status.update(stage.status())
return status
def _cloud_status(self, target=None, jobs=1, remote=None):
import dvc.remote.base as cloud
status = {}
for md5, ret in self.cloud.status(self._used_cache(target)['local'],
jobs,
remote=remote):
if ret == cloud.STATUS_OK:
continue
prefix_map = {
cloud.STATUS_DELETED: 'deleted',
cloud.STATUS_NEW: 'new',
}
status[md5] = prefix_map[ret]
return status
def status(self, target=None, jobs=1, cloud=False, remote=None):
if cloud:
return self._cloud_status(target, jobs, remote=remote)
return self._local_status(target)
def _read_metric_json(self, fd, json_path):
parser = parse(json_path)
return [x.value for x in parser.find(json.load(fd))]
def _do_read_metric_tsv(self, reader, row, col):
if col != None and row != None:
return [reader[row][col]]
elif col != None:
return [r[col] for r in reader]
elif row != None:
return reader[row]
return None
def _read_metric_htsv(self, fd, htsv_path):
col, row = htsv_path.split(',')
row = int(row)
reader = list(csv.DictReader(fd, delimiter='\t'))
return self._do_read_metric_tsv(reader, row, col)
def _read_metric_tsv(self, fd, tsv_path):
col, row = tsv_path.split(',')
row = int(row)
col = int(col)
reader = list(csv.reader(fd, delimiter='\t'))
return self._do_read_metric_tsv(reader, row, col)
def _read_metric(self,
path,
json_path=None,
tsv_path=None,
htsv_path=None):
ret = None
if not os.path.exists(path):
return ret
try:
with open(path, 'r') as fd:
if json_path:
ret = self._read_metric_json(fd, json_path)
elif tsv_path:
ret = self._read_metric_tsv(fd, tsv_path)
elif htsv_path:
ret = self._read_metric_htsv(fd, htsv_path)
else:
ret = fd.read()
except Exception as exc:
self.logger.debug('Unable to read metric in \'{}\''.format(path),
exc)
return ret
def metrics_show(self,
path=None,
json_path=None,
tsv_path=None,
htsv_path=None,
all_branches=False):
res = {}
for branch in self.scm.brancher(all_branches=all_branches):
metrics = filter(lambda o: o.metric, self.outs())
fnames = [path] if path else map(lambda o: o.path, metrics)
for fname in fnames:
rel = os.path.relpath(fname)
metric = self._read_metric(fname,
json_path=json_path,
tsv_path=tsv_path,
htsv_path=htsv_path)
if not metric:
continue
if branch not in res:
res[branch] = {}
res[branch][rel] = metric
for branch, val in res.items():
self.logger.info('{}:'.format(branch))
for fname, metric in val.items():
self.logger.info('\t{}: {}'.format(fname, metric))
return res
def _metrics_modify(self, path, val):
apath = os.path.abspath(path)
for stage in self.stages():
for out in stage.outs:
if apath != out.path:
continue
if out.path_info['scheme'] != 'local':
msg = 'Output \'{}\' scheme \'{}\' is not supported for metrics'
raise DvcException(
msg.format(out.path, out.path_info['scheme']))
if out.use_cache:
msg = 'Cached output \'{}\' is not supported for metrics'
raise DvcException(msg.format(out.rel_path))
out.metric = val
stage.dump()
def metrics_add(self, path):
self._metrics_modify(path, True)
def metrics_remove(self, path):
self._metrics_modify(path, False)
def graph(self):
G = nx.DiGraph()
stages = self.stages()
outs = self.outs()
for stage in stages:
node = os.path.relpath(stage.path, self.root_dir)
G.add_node(node, stage=stage)
if stage.locked:
continue
for dep in stage.deps:
for out in outs:
if out.path != dep.path and not dep.path.startswith(
out.path + out.sep):
continue
dep_stage = out.stage
dep_node = os.path.relpath(dep_stage.path, self.root_dir)
G.add_node(dep_node, stage=dep_stage)
G.add_edge(node, dep_node)
return G
def stages(self):
stages = []
for root, dirs, files in os.walk(self.root_dir):
for fname in files:
path = os.path.join(root, fname)
if not Stage.is_stage_file(path):
continue
stages.append(Stage.load(self, path))
return stages
def outs(self):
outs = []
for stage in self.stages():
outs += stage.outs
return outs
class Project(object):
DVC_DIR = '.dvc'
def __init__(self, root_dir=None):
from dvc.logger import logger
from dvc.config import Config
from dvc.state import State
from dvc.lock import Lock
from dvc.scm import SCM
from dvc.cache import Cache
from dvc.data_cloud import DataCloud
from dvc.updater import Updater
from dvc.prompt import Prompt
root_dir = self._find_root(root_dir)
self.root_dir = os.path.abspath(os.path.realpath(root_dir))
self.dvc_dir = os.path.join(self.root_dir, self.DVC_DIR)
self.config = Config(self.dvc_dir)
self.scm = SCM(self.root_dir, project=self)
self.lock = Lock(self.dvc_dir)
# NOTE: storing state and link_state in the repository itself to avoid
# any possible state corruption in 'shared cache dir' scenario.
self.state = State(self, self.config._config)
core = self.config._config[Config.SECTION_CORE]
self.logger = logger
self.logger.set_level(core.get(Config.SECTION_CORE_LOGLEVEL, None))
self.cache = Cache(self)
self.cloud = DataCloud(self, config=self.config._config)
self.updater = Updater(self.dvc_dir)
self.prompt = Prompt()
self._files_to_git_add = []
self._ignore()
self.updater.check()
@staticmethod
def _find_root(root=None):
if root is None:
root = os.getcwd()
else:
root = os.path.abspath(os.path.realpath(root))
while True:
dvc_dir = os.path.join(root, Project.DVC_DIR)
if os.path.isdir(dvc_dir):
return root
if os.path.ismount(root):
break
root = os.path.dirname(root)
raise NotDvcProjectError(root)
@staticmethod
def _find_dvc_dir(root=None):
root_dir = Project._find_root(root)
return os.path.join(root_dir, Project.DVC_DIR)
def _remind_to_git_add(self):
if len(self._files_to_git_add) == 0:
return
msg = '\nTo track the changes with git run:\n\n'
msg += '\tgit add ' + " ".join(self._files_to_git_add)
self.logger.info(msg)
@staticmethod
def init(root_dir=os.curdir, no_scm=False, force=False):
"""
Initiate dvc project in directory.
Args:
root_dir: Path to project's root directory.
Returns:
Project instance.
Raises:
KeyError: Raises an exception.
"""
import colorama
import shutil
from dvc.scm import SCM, Base
from dvc.config import Config
from dvc.logger import logger
root_dir = os.path.abspath(root_dir)
dvc_dir = os.path.join(root_dir, Project.DVC_DIR)
scm = SCM(root_dir)
if type(scm) == Base and not no_scm:
msg = "{} is not tracked by any supported scm tool(e.g. git)."
raise InitError(msg.format(root_dir))
if os.path.isdir(dvc_dir):
if not force:
msg = "'{}' exists. Use '-f' to force."
raise InitError(msg.format(os.path.relpath(dvc_dir)))
shutil.rmtree(dvc_dir)
os.mkdir(dvc_dir)
config = Config.init(dvc_dir)
proj = Project(root_dir)
scm.add([config.config_file])
if scm.ignore_file():
scm.add([os.path.join(dvc_dir, scm.ignore_file())])
logger.info('\nYou can now commit the changes to git.')
logger.info(
"\n"
"{yellow}What's next?{nc}\n"
"{yellow}------------{nc}\n"
"- Check out the documentation: {blue}https://dvc.org/doc{nc}\n"
"- Get help and share ideas: {blue}https://dvc.org/chat{nc}\n"
"- Star us on GitHub: {blue}https://github.com/iterative/dvc{nc}"
.format(yellow=colorama.Fore.YELLOW,
blue=colorama.Fore.BLUE,
green=colorama.Fore.GREEN,
nc=colorama.Fore.RESET)
)
return proj
@staticmethod
def load_all(projects_paths):
"""
Instantiate all projects in the given list of paths.
Args:
projects_paths: List of paths to projects.
Returns:
List of Project instances in the same order of the given paths.
"""
return [Project(path) for path in projects_paths]
def destroy(self):
import shutil
for stage in self.stages():
stage.remove()
shutil.rmtree(self.dvc_dir)
def _ignore(self):
flist = [
self.state.state_file,
self.lock.lock_file,
self.config.config_local_file,
self.updater.updater_file,
self.updater.lock.lock_file,
] + self.state.temp_files
if self.cache.local.cache_dir.startswith(self.root_dir):
flist += [self.cache.local.cache_dir]
self.scm.ignore_list(flist)
def install(self):
self.scm.install()
def to_dvc_path(self, path):
return os.path.relpath(path, self.root_dir)
def _check_cwd_specified_as_output(self, cwd, stages):
from dvc.exceptions import WorkingDirectoryAsOutputError
cwd_path = os.path.abspath(os.path.normpath(cwd))
for stage in stages:
for output in stage.outs:
if os.path.isdir(output.path) and output.path == cwd_path:
raise WorkingDirectoryAsOutputError(cwd, stage.relpath)
def _check_output_duplication(self, outs, stages):
from dvc.exceptions import OutputDuplicationError
for stage in stages:
for o in stage.outs:
for out in outs:
if o.path == out.path and o.stage.path != out.stage.path:
stages = [o.stage.relpath, out.stage.relpath]
raise OutputDuplicationError(o.path, stages)
def _check_circular_dependency(self, deps, outs):
from dvc.exceptions import CircularDependencyError
circular_dependencies = (
set(file.path for file in deps) &
set(file.path for file in outs)
)
if circular_dependencies:
raise CircularDependencyError(circular_dependencies.pop())
def add(self, fname, recursive=False):
from dvc.stage import Stage
fnames = []
if recursive and os.path.isdir(fname):
fnames = []
for root, dirs, files in os.walk(fname):
for f in files:
path = os.path.join(root, f)
if Stage.is_stage_file(path):
continue
if os.path.basename(path) == self.scm.ignore_file():
continue
if self.scm.is_tracked(path):
continue
fnames.append(path)
else:
fnames = [fname]
all_stages = self.stages()
stages = []
self._files_to_git_add = []
with self.state:
for f in fnames:
stage = Stage.loads(project=self,
outs=[f],
add=True)
if stage is None:
stages.append(stage)
continue
self._check_output_duplication(stage.outs, all_stages)
stage.save()
stage.dump()
stages.append(stage)
self._remind_to_git_add()
return stages
def remove(self, target, outs_only=False):
from dvc.stage import Stage
stage = Stage.load(self, target)
if outs_only:
stage.remove_outs()
else:
stage.remove()
return stage
def lock_stage(self, target, unlock=False):
from dvc.stage import Stage
stage = Stage.load(self, target)
stage.locked = False if unlock else True
stage.dump()
return stage
def move(self, from_path, to_path):
import dvc.output as Output
from dvc.stage import Stage
from_out = Output.loads_from(Stage(self, cwd=os.curdir),
[from_path])[0]
found = False
self._files_to_git_add = []
with self.state:
for stage in self.stages():
for out in stage.outs:
if out.path != from_out.path:
continue
if not stage.is_data_source:
raise MoveNotDataSourceError(stage.relpath)
found = True
to_out = Output.loads_from(out.stage,
[to_path],
out.cache,
out.metric)[0]
out.move(to_out)
stage_base = os.path.basename(stage.path)
stage_base = stage_base.rstrip(Stage.STAGE_FILE_SUFFIX)
stage_dir = os.path.dirname(stage.path)
from_base = os.path.basename(from_path)
to_base = os.path.basename(to_path)
if stage_base == from_base:
os.unlink(stage.path)
path = to_base + Stage.STAGE_FILE_SUFFIX
stage.path = os.path.join(stage_dir, path)
stage.dump()
self._remind_to_git_add()
if not found:
msg = 'Unable to find dvcfile with output \'{}\''
raise DvcException(msg.format(from_path))
def _unprotect_file(self, path):
import stat
import uuid
from dvc.system import System
from dvc.utils import copyfile, move, remove
if System.is_symlink(path) or System.is_hardlink(path):
self.logger.debug("Unprotecting '{}'".format(path))
tmp = os.path.join(os.path.dirname(path), '.' + str(uuid.uuid4()))
move(path, tmp)
copyfile(tmp, path)
remove(tmp)
else:
self.logger.debug("Skipping copying for '{}', since it is not "
"a symlink or a hardlink.".format(path))
os.chmod(path, os.stat(path).st_mode | stat.S_IWRITE)
def _unprotect_dir(self, path):
for root, dirs, files in os.walk(path):
for f in files:
path = os.path.join(root, f)
self._unprotect_file(path)
def unprotect(self, path):
if not os.path.exists(path):
raise DvcException("Can't unprotect non-existing "
"data '{}'".format(path))
if os.path.isdir(path):
self._unprotect_dir(path)
else:
self._unprotect_file(path)
def run(self,
cmd=None,
deps=[],
outs=[],
outs_no_cache=[],
metrics_no_cache=[],
fname=None,
cwd=os.curdir,
no_exec=False,
overwrite=False,
ignore_build_cache=False,
remove_outs=False):
from dvc.stage import Stage
with self.state:
stage = Stage.loads(project=self,
fname=fname,
cmd=cmd,
cwd=cwd,
outs=outs,
outs_no_cache=outs_no_cache,
metrics_no_cache=metrics_no_cache,
deps=deps,
overwrite=overwrite,
ignore_build_cache=ignore_build_cache,
remove_outs=remove_outs)
if stage is None:
return None
all_stages = self.stages()
self._check_cwd_specified_as_output(cwd, all_stages)
self._check_output_duplication(stage.outs, all_stages)
self._check_circular_dependency(stage.deps, stage.outs)
self._files_to_git_add = []
with self.state:
if not no_exec:
stage.run()
stage.dump()
self._remind_to_git_add()
return stage
def imp(self, url, out):
from dvc.stage import Stage
stage = Stage.loads(project=self,
cmd=None,
deps=[url],
outs=[out])
if stage is None:
return None
self._check_output_duplication(stage.outs, self.stages())
self._check_circular_dependency(stage.deps, stage.outs)
self._files_to_git_add = []
with self.state:
stage.run()
stage.dump()
self._remind_to_git_add()
return stage
def _reproduce_stage(self, stages, node, force, dry, interactive):
stage = stages[node]
if stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependencies are not ' \
'going to be reproduced.'
self.logger.warn(msg.format(stage.relpath))
stage = stage.reproduce(force=force, dry=dry, interactive=interactive)
if not stage:
return []
if not dry:
stage.dump()
return [stage]
def reproduce(self,
target=None,
recursive=True,
force=False,
dry=False,
interactive=False,
pipeline=False,
all_pipelines=False):
from dvc.stage import Stage
if target is None and not all_pipelines:
raise ValueError()
if not interactive:
config = self.config
core = config._config[config.SECTION_CORE]
interactive = core.get(config.SECTION_CORE_INTERACTIVE, False)
targets = []
if pipeline or all_pipelines:
if pipeline:
stage = Stage.load(self, target)
node = os.path.relpath(stage.path, self.root_dir)
pipelines = [self._get_pipeline(node)]
else:
pipelines = self.pipelines()
for G in pipelines:
for node in G.nodes():
if G.in_degree(node) == 0:
targets.append(os.path.join(self.root_dir, node))
else:
targets.append(target)
self._files_to_git_add = []
ret = []
with self.state:
for target in targets:
stages = self._reproduce(target,
recursive=recursive,
force=force,
dry=dry,
interactive=interactive)
ret.extend(stages)
self._remind_to_git_add()
return ret
def _reproduce(self,
target,
recursive=True,
force=False,
dry=False,
interactive=False):
import networkx as nx
from dvc.stage import Stage
stage = Stage.load(self, target)
G = self.graph()[1]
stages = nx.get_node_attributes(G, 'stage')
node = os.path.relpath(stage.path, self.root_dir)
if recursive:
ret = self._reproduce_stages(G,
stages,
node,
force,
dry,
interactive)
else:
ret = self._reproduce_stage(stages,
node,
force,
dry,
interactive)
return ret
def _reproduce_stages(self, G, stages, node, force, dry, interactive):
import networkx as nx
result = []
for n in nx.dfs_postorder_nodes(G, node):
try:
result += self._reproduce_stage(stages,
n,
force,
dry,
interactive)
except Exception as ex:
raise ReproductionError(stages[n].relpath, ex)
return result
def _cleanup_unused_links(self, all_stages):
used = []
for stage in all_stages:
for out in stage.outs:
used.append(out.path)
self.state.remove_unused_links(used)
def checkout(self, target=None, with_deps=False, force=False):
all_stages = self.active_stages()
stages = all_stages
if target:
stages = self._collect(target, with_deps=with_deps)
with self.state:
self._cleanup_unused_links(all_stages)
for stage in stages:
if stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependencies are ' \
'not going to be checked out.'
self.logger.warn(msg.format(stage.relpath))
stage.checkout(force=force)
def _get_pipeline(self, node):
pipelines = list(filter(lambda g: node in g.nodes(),
self.pipelines()))
assert len(pipelines) == 1
return pipelines[0]
def _collect(self, target, with_deps=False):
import networkx as nx
from dvc.stage import Stage
stage = Stage.load(self, target)
if not with_deps:
return [stage]
node = os.path.relpath(stage.path, self.root_dir)
G = self._get_pipeline(node)
stages = nx.get_node_attributes(G, 'stage')
ret = [stage]
for n in nx.dfs_postorder_nodes(G, node):
ret.append(stages[n])
return ret
def _collect_dir_cache(self,
out,
branch=None,
remote=None,
force=False,
jobs=None):
info = out.dumpd()
ret = [info]
r = out.remote
md5 = info[r.PARAM_MD5]
if self.cache.local.changed_cache_file(md5):
try:
self.cloud.pull(ret,
jobs=jobs,
remote=remote,
show_checksums=False)
except DvcException as exc:
msg = "Failed to pull cache for '{}': {}"
self.logger.debug(msg.format(out, exc))
if self.cache.local.changed_cache_file(md5):
msg = "Missing cache for directory '{}'. " \
"Cache for files inside will be lost. " \
"Would you like to continue? Use '-f' to force. "
if not (force or self.prompt.prompt(msg, False)):
raise DvcException("Unable to fully collect "
"used cache without cache "
"for directory '{}'".format(out))
else:
return ret
for i in self.cache.local.load_dir_cache(md5):
i['branch'] = branch
i[r.PARAM_PATH] = os.path.join(info[r.PARAM_PATH],
i[r.PARAM_RELPATH])
ret.append(i)
return ret
def _collect_used_cache(self,
out,
branch=None,
remote=None,
force=False,
jobs=None):
if not out.use_cache or not out.info:
return []
info = out.dumpd()
info['branch'] = branch
ret = [info]
if out.path_info['scheme'] != 'local':
return ret
md5 = info[out.remote.PARAM_MD5]
cache = self.cache.local.get(md5)
if not out.remote.is_dir_cache(cache):
return ret
return self._collect_dir_cache(out,
branch=branch,
remote=remote,
force=force,
jobs=jobs)
def _used_cache(self,
target=None,
all_branches=False,
active=True,
with_deps=False,
all_tags=False,
remote=None,
force=False,
jobs=None):
cache = {}
cache['local'] = []
cache['s3'] = []
cache['gs'] = []
cache['hdfs'] = []
cache['ssh'] = []
cache['azure'] = []
for branch in self.scm.brancher(all_branches=all_branches,
all_tags=all_tags):
if target:
stages = self._collect(target,
with_deps=with_deps)
elif active:
stages = self.active_stages()
else:
stages = self.stages()
for stage in stages:
if active and not target and stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependencies are ' \
'not going to be pushed/pulled/fetched.'
self.logger.warn(msg.format(stage.relpath))
for out in stage.outs:
scheme = out.path_info['scheme']
cache[scheme] += self._collect_used_cache(out,
branch=branch,
remote=remote,
force=force,
jobs=jobs)
return cache
@staticmethod
def merge_cache_lists(clists):
merged_cache = collections.defaultdict(list)
for cache_list in clists:
for scheme, cache in cache_list.items():
for item in cache:
if item not in merged_cache[scheme]:
merged_cache[scheme].append(item)
return merged_cache
@staticmethod
def load_all_used_cache(projects,
target=None,
all_branches=False,
active=True,
with_deps=False,
all_tags=False,
remote=None,
force=False,
jobs=None):
clists = []
for project in projects:
with project.state:
project_clist = project._used_cache(target=None,
all_branches=all_branches,
active=False,
with_deps=with_deps,
all_tags=all_tags,
remote=remote,
force=force,
jobs=jobs)
clists.append(project_clist)
return clists
def _do_gc(self, typ, func, clist):
removed = func(clist)
if not removed:
self.logger.info("No unused {} cache to remove.".format(typ))
def gc(self,
all_branches=False,
cloud=False,
remote=None,
with_deps=False,
all_tags=False,
force=False,
jobs=None,
projects=None):
all_projects = [self]
if projects is not None and len(projects) > 0:
all_projects.extend(Project.load_all(projects))
all_clists = Project.load_all_used_cache(all_projects,
target=None,
all_branches=all_branches,
active=False,
with_deps=with_deps,
all_tags=all_tags,
remote=remote,
force=force,
jobs=jobs)
if len(all_clists) > 1:
clist = Project.merge_cache_lists(all_clists)
else:
clist = all_clists[0]
with self.state:
self._do_gc('local', self.cache.local.gc, clist)
if self.cache.s3:
self._do_gc('s3', self.cache.s3.gc, clist)
if self.cache.gs:
self._do_gc('gs', self.cache.gs.gc, clist)
if self.cache.ssh:
self._do_gc('ssh', self.cache.ssh.gc, clist)
if self.cache.hdfs:
self._do_gc('hdfs', self.cache.hdfs.gc, clist)
if self.cache.azure:
self._do_gc('azure', self.cache.azure.gc, clist)
if cloud:
self._do_gc('remote', self.cloud._get_cloud(remote,
'gc -c').gc, clist)
def push(self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False,
with_deps=False,
all_tags=False):
with self.state:
used = self._used_cache(target,
all_branches=all_branches,
all_tags=all_tags,
with_deps=with_deps,
force=True,
remote=remote,
jobs=jobs)['local']
self.cloud.push(used,
jobs,
remote=remote,
show_checksums=show_checksums)
def fetch(self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False,
with_deps=False,
all_tags=False):
with self.state:
used = self._used_cache(target,
all_branches=all_branches,
all_tags=all_tags,
with_deps=with_deps,
force=True,
remote=remote,
jobs=jobs)['local']
self.cloud.pull(used,
jobs,
remote=remote,
show_checksums=show_checksums)
def pull(self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False,
with_deps=False,
all_tags=False,
force=False):
self.fetch(target,
jobs,
remote=remote,
all_branches=all_branches,
all_tags=all_tags,
show_checksums=show_checksums,
with_deps=with_deps)
self.checkout(target=target, with_deps=with_deps, force=force)
def _local_status(self, target=None, with_deps=False):
status = {}
if target:
stages = self._collect(target,
with_deps=with_deps)
else:
stages = self.active_stages()
for stage in stages:
if stage.locked:
msg = 'DVC file \'{}\' is locked. Its dependencies are not ' \
'going to be shown in the status output.'
self.logger.warn(msg.format(stage.relpath))
status.update(stage.status())
return status
def _cloud_status(self,
target=None,
jobs=1,
remote=None,
show_checksums=False,
all_branches=False,
with_deps=False,
all_tags=False):
import dvc.remote.base as cloud
used = self._used_cache(target,
all_branches=all_branches,
all_tags=all_tags,
with_deps=with_deps,
force=True,
remote=remote,
jobs=jobs)['local']
status = {}
for md5, ret in self.cloud.status(used,
jobs,
remote=remote,
show_checksums=show_checksums):
if ret == cloud.STATUS_OK:
continue
prefix_map = {
cloud.STATUS_DELETED: 'deleted',
cloud.STATUS_NEW: 'new',
}
status[md5] = prefix_map[ret]
return status
def status(self,
target=None,
jobs=1,
cloud=False,
remote=None,
show_checksums=False,
all_branches=False,
with_deps=False,
all_tags=False):
with self.state:
if cloud:
return self._cloud_status(target,
jobs,
remote=remote,
show_checksums=show_checksums,
all_branches=all_branches,
with_deps=with_deps,
all_tags=all_tags)
return self._local_status(target,
with_deps=with_deps)
def _read_metric_json(self, fd, json_path):
import json
from jsonpath_rw import parse
parser = parse(json_path)
return [x.value for x in parser.find(json.load(fd))]
def _do_read_metric_xsv(self, reader, row, col):
if col is not None and row is not None:
return [reader[row][col]]
elif col is not None:
return [r[col] for r in reader]
elif row is not None:
return reader[row]
return None
def _read_metric_hxsv(self, fd, hxsv_path, delimiter):
import csv
col, row = hxsv_path.split(',')
row = int(row)
reader = list(csv.DictReader(fd, delimiter=delimiter))
return self._do_read_metric_xsv(reader, row, col)
def _read_metric_xsv(self, fd, xsv_path, delimiter):
import csv
col, row = xsv_path.split(',')
row = int(row)
col = int(col)
reader = list(csv.reader(fd, delimiter=delimiter))
return self._do_read_metric_xsv(reader, row, col)
def _read_metric(self, path, typ=None, xpath=None):
ret = None
if not os.path.exists(path):
return ret
try:
with open(path, 'r') as fd:
if typ == 'json':
ret = self._read_metric_json(fd, xpath)
elif typ == 'csv':
ret = self._read_metric_xsv(fd, xpath, ',')
elif typ == 'tsv':
ret = self._read_metric_xsv(fd, xpath, '\t')
elif typ == 'hcsv':
ret = self._read_metric_hxsv(fd, xpath, ',')
elif typ == 'htsv':
ret = self._read_metric_hxsv(fd, xpath, '\t')
else:
ret = fd.read()
except Exception as exc:
self.logger.error('Unable to read metric in \'{}\''.format(path),
exc)
return ret
def _find_output_by_path(self, path, outs=None):
from dvc.exceptions import OutputDuplicationError
if not outs:
astages = self.active_stages()
outs = [out for stage in astages for out in stage.outs]
abs_path = os.path.abspath(path)
matched = [out for out in outs if out.path == abs_path]
stages = [out.stage.relpath for out in matched]
if len(stages) > 1:
raise OutputDuplicationError(path, stages)
return matched[0] if matched else None
def metrics_show(self,
path=None,
typ=None,
xpath=None,
all_branches=False,
all_tags=False):
res = {}
for branch in self.scm.brancher(all_branches=all_branches,
all_tags=all_tags):
astages = self.active_stages()
outs = [out for stage in astages for out in stage.outs]
if path:
out = self._find_output_by_path(path, outs=outs)
stage = out.stage.path if out else None
if out and all([out.metric,
not typ,
isinstance(out.metric, dict)]):
entries = [(path,
out.metric.get(out.PARAM_METRIC_TYPE, None),
out.metric.get(out.PARAM_METRIC_XPATH, None))]
else:
entries = [(path, typ, xpath)]
else:
metrics = filter(lambda o: o.metric, outs)
stage = None
entries = []
for o in metrics:
if not typ and isinstance(o.metric, dict):
t = o.metric.get(o.PARAM_METRIC_TYPE, typ)
x = o.metric.get(o.PARAM_METRIC_XPATH, xpath)
else:
t = typ
x = xpath
entries.append((o.path, t, x))
for fname, t, x in entries:
if stage:
self.checkout(stage, force=True)
rel = os.path.relpath(fname)
metric = self._read_metric(fname,
typ=t,
xpath=x)
if not metric:
continue
if branch not in res:
res[branch] = {}
res[branch][rel] = metric
for branch, val in res.items():
if all_branches or all_tags:
self.logger.info('{}:'.format(branch))
for fname, metric in val.items():
self.logger.info('\t{}: {}'.format(fname, metric))
if res:
return res
if path:
msg = 'File \'{}\' does not exist'.format(path)
else:
msg = 'No metric files in this repository. ' \
'Use \'dvc metrics add\' to add a metric file to track.'
raise DvcException(msg)
def _metrics_modify(self, path, typ=None, xpath=None, delete=False):
out = self._find_output_by_path(path)
if not out:
msg = 'Unable to find file \'{}\' in the pipeline'.format(path)
raise DvcException(msg)
if out.path_info['scheme'] != 'local':
msg = 'Output \'{}\' scheme \'{}\' is not supported for metrics'
raise DvcException(msg.format(out.path, out.path_info['scheme']))
if out.use_cache:
msg = 'Cached output \'{}\' is not supported for metrics'
raise DvcException(msg.format(out.rel_path))
if typ:
if not isinstance(out.metric, dict):
out.metric = {}
out.metric[out.PARAM_METRIC_TYPE] = typ
if xpath:
if not isinstance(out.metric, dict):
out.metric = {}
out.metric[out.PARAM_METRIC_XPATH] = xpath
if delete:
out.metric = None
out._verify_metric()
out.stage.dump()
def metrics_modify(self, path=None, typ=None, xpath=None):
self._metrics_modify(path, typ, xpath)
def metrics_add(self, path, typ=None, xpath=None):
if not typ:
typ = 'raw'
self._metrics_modify(path, typ, xpath)
def metrics_remove(self, path):
self._metrics_modify(path, delete=True)
def graph(self):
import networkx as nx
from dvc.exceptions import OutputDuplicationError
G = nx.DiGraph()
G_active = nx.DiGraph()
stages = self.stages()
outs = []
outs_by_path = {}
for stage in stages:
for o in stage.outs:
existing = outs_by_path.get(o.path, None)
if existing is not None:
stages = [o.stage.relpath, existing.stage.relpath]
raise OutputDuplicationError(o.path, stages)
outs.append(o)
outs_by_path[o.path] = o
# collect the whole DAG
for stage in stages:
node = os.path.relpath(stage.path, self.root_dir)
G.add_node(node, stage=stage)
G_active.add_node(node, stage=stage)
for dep in stage.deps:
for out in outs:
if out.path != dep.path \
and not dep.path.startswith(out.path + out.sep) \
and not out.path.startswith(dep.path + dep.sep):
continue
dep_stage = out.stage
dep_node = os.path.relpath(dep_stage.path, self.root_dir)
G.add_node(dep_node, stage=dep_stage)
G.add_edge(node, dep_node)
if not stage.locked:
G_active.add_node(dep_node, stage=dep_stage)
G_active.add_edge(node, dep_node)
return G, G_active
def pipelines(self):
import networkx as nx
G, G_active = self.graph()
if len(G.nodes()) == 0:
return []
# find pipeline ends aka "output stages"
ends = [node for node, in_degree in G.in_degree() if in_degree == 0]
# filter out subgraphs that didn't exist in original G
pipelines = []
for c in nx.weakly_connected_components(G_active):
H = G_active.subgraph(c)
found = False
for node in ends:
if node in H:
found = True
break
if found:
pipelines.append(H)
return pipelines
def stages(self):
"""
Walks down the root directory looking for Dvcfiles,
skipping the directories that are related with
any SCM (e.g. `.git`) or DVC itself (`.dvc`).
NOTE: For large projects, this could be an expensive
operation. Consider using some memorization.
"""
from dvc.stage import Stage
stages = []
outs = []
for root, dirs, files in os.walk(self.root_dir):
for fname in files:
path = os.path.join(root, fname)
if not Stage.is_stage_file(path):
continue
stage = Stage.load(self, path)
for out in stage.outs:
outs.append(out.path + out.sep)
stages.append(stage)
def filter_dirs(dname):
path = os.path.join(root, dname)
if path == self.dvc_dir or path == self.scm.dir:
return False
for out in outs:
if path == os.path.normpath(out) or path.startswith(out):
return False
return True
dirs[:] = list(filter(filter_dirs, dirs))
return stages
def active_stages(self):
import networkx as nx
stages = []
for G in self.pipelines():
stages.extend(list(nx.get_node_attributes(G, 'stage').values()))
return stages
class Project(object):
DVC_DIR = ".dvc"
def __init__(self, root_dir=None):
from dvc.config import Config
from dvc.state import State
from dvc.lock import Lock
from dvc.scm import SCM
from dvc.cache import Cache
from dvc.data_cloud import DataCloud
from dvc.updater import Updater
root_dir = self.find_root(root_dir)
self.root_dir = os.path.abspath(os.path.realpath(root_dir))
self.dvc_dir = os.path.join(self.root_dir, self.DVC_DIR)
self.config = Config(self.dvc_dir)
self.scm = SCM(self.root_dir, project=self)
self.lock = Lock(self.dvc_dir)
# NOTE: storing state and link_state in the repository itself to avoid
# any possible state corruption in 'shared cache dir' scenario.
self.state = State(self, self.config.config)
core = self.config.config[Config.SECTION_CORE]
logger.set_level(core.get(Config.SECTION_CORE_LOGLEVEL))
self.cache = Cache(self)
self.cloud = DataCloud(self, config=self.config.config)
self.updater = Updater(self.dvc_dir)
self.files_to_git_add = []
self._ignore()
self.updater.check()
def __repr__(self):
return "Project: '{root_dir}'".format(root_dir=self.root_dir)
@staticmethod
def find_root(root=None):
if root is None:
root = os.getcwd()
else:
root = os.path.abspath(os.path.realpath(root))
while True:
dvc_dir = os.path.join(root, Project.DVC_DIR)
if os.path.isdir(dvc_dir):
return root
if os.path.ismount(root):
break
root = os.path.dirname(root)
raise NotDvcProjectError(root)
@staticmethod
def find_dvc_dir(root=None):
root_dir = Project.find_root(root)
return os.path.join(root_dir, Project.DVC_DIR)
def _remind_to_git_add(self):
if not self.files_to_git_add:
return
logger.info(
"\n"
"To track the changes with git run:\n"
"\n"
"\tgit add {files}".format(files=" ".join(self.files_to_git_add)))
@staticmethod
def init(root_dir=os.curdir, no_scm=False, force=False):
"""
Creates an empty project on the given directory -- basically a
`.dvc` directory with subdirectories for configuration and cache.
It should be tracked by a SCM or use the `--no-scm` flag.
If the given directory is not empty, you must use the `--force`
flag to override it.
Args:
root_dir: Path to project's root directory.
Returns:
Project instance.
Raises:
KeyError: Raises an exception.
"""
import shutil
from dvc.scm import SCM, Base
from dvc.config import Config
root_dir = os.path.abspath(root_dir)
dvc_dir = os.path.join(root_dir, Project.DVC_DIR)
scm = SCM(root_dir)
if type(scm) == Base and not no_scm:
raise InitError(
"{project} is not tracked by any supported scm tool"
" (e.g. git). Use '--no-scm' if you don't want to use any scm."
.format(project=root_dir))
if os.path.isdir(dvc_dir):
if not force:
raise InitError(
"'{project}' exists. Use '-f' to force.".format(
project=os.path.relpath(dvc_dir)))
shutil.rmtree(dvc_dir)
os.mkdir(dvc_dir)
config = Config.init(dvc_dir)
proj = Project(root_dir)
scm.add([config.config_file])
if scm.ignore_file:
scm.add([os.path.join(dvc_dir, scm.ignore_file)])
logger.info("\nYou can now commit the changes to git.\n")
proj._welcome_message()
return proj
def destroy(self):
import shutil
for stage in self.stages():
stage.remove()
shutil.rmtree(self.dvc_dir)
def _ignore(self):
flist = [
self.state.state_file,
self.lock.lock_file,
self.config.config_local_file,
self.updater.updater_file,
self.updater.lock.lock_file,
] + self.state.temp_files
if self.cache.local.cache_dir.startswith(self.root_dir):
flist += [self.cache.local.cache_dir]
self.scm.ignore_list(flist)
def install(self):
self.scm.install()
@staticmethod
def _check_cyclic_graph(graph):
import networkx as nx
from dvc.exceptions import CyclicGraphError
cycles = list(nx.simple_cycles(graph))
if cycles:
raise CyclicGraphError(cycles[0])
def add(self, fname, recursive=False):
from dvc.stage import Stage
fnames = []
if recursive and os.path.isdir(fname):
for root, dirs, files in os.walk(str(fname)):
for f in files:
path = os.path.join(root, f)
if Stage.is_stage_file(path):
continue
if os.path.basename(path) == self.scm.ignore_file:
continue
if self.scm.is_tracked(path):
continue
fnames.append(path)
else:
fnames = [fname]
stages = []
self.files_to_git_add = []
with self.state:
for f in fnames:
stage = Stage.create(project=self, outs=[f], add=True)
if stage is None:
stages.append(stage)
continue
stage.save()
stages.append(stage)
self._check_dag(self.stages() + stages)
for stage in stages:
if stage is not None:
stage.dump()
self._remind_to_git_add()
return stages
def _check_dag(self, stages):
"""Generate graph including the new stage to check for errors"""
self.graph(stages=stages)
def remove(self, target, outs_only=False):
from dvc.stage import Stage
stage = Stage.load(self, target)
if outs_only:
stage.remove_outs()
else:
stage.remove()
return stage
def lock_stage(self, target, unlock=False):
from dvc.stage import Stage
stage = Stage.load(self, target)
stage.locked = False if unlock else True
stage.dump()
return stage
def move(self, from_path, to_path):
"""
Renames an output file and modifies the stage associated
to reflect the change on the pipeline.
If the output has the same name as its stage, it would
also rename the corresponding stage file.
E.g.
Having: (hello, hello.dvc)
$ dvc move hello greetings
Result: (greeting, greeting.dvc)
It only works with outputs generated by `add` or `import`,
also known as data sources.
"""
import dvc.output as Output
from dvc.stage import Stage
from_out = Output.loads_from(Stage(self, cwd=os.curdir),
[from_path])[0]
to_path = self._expand_target_path(from_path, to_path)
try:
stage, out = next((stage, out) for stage in self.stages()
for out in stage.outs
if from_out.path == out.path)
except StopIteration:
raise DvcException(
"unable to find stage file with output '{path}'".format(
path=from_path))
if not stage.is_data_source:
raise MoveNotDataSourceError(stage.relpath)
stage_name = os.path.splitext(os.path.basename(stage.path))[0]
from_name = os.path.basename(from_out.path)
if stage_name == from_name:
os.unlink(stage.path)
stage.path = os.path.join(
os.path.dirname(to_path),
os.path.basename(to_path) + Stage.STAGE_FILE_SUFFIX,
)
stage.cwd = os.path.join(self.root_dir, os.path.dirname(to_path))
to_out = Output.loads_from(stage, [os.path.basename(to_path)],
out.cache, out.metric)[0]
with self.state:
out.move(to_out)
stage.dump()
self._remind_to_git_add()
def _unprotect_file(self, path):
import stat
import uuid
from dvc.system import System
from dvc.utils import copyfile, move, remove
if System.is_symlink(path) or System.is_hardlink(path):
logger.debug("Unprotecting '{}'".format(path))
tmp = os.path.join(os.path.dirname(path), "." + str(uuid.uuid4()))
move(path, tmp)
copyfile(tmp, path)
remove(tmp)
else:
logger.debug("Skipping copying for '{}', since it is not "
"a symlink or a hardlink.".format(path))
os.chmod(path, os.stat(path).st_mode | stat.S_IWRITE)
def _unprotect_dir(self, path):
for root, dirs, files in os.walk(str(path)):
for f in files:
path = os.path.join(root, f)
self._unprotect_file(path)
def unprotect(self, path):
if not os.path.exists(path):
raise DvcException(
"can't unprotect non-existing data '{}'".format(path))
if os.path.isdir(path):
self._unprotect_dir(path)
else:
self._unprotect_file(path)
def run(
self,
cmd=None,
deps=None,
outs=None,
outs_no_cache=None,
metrics=None,
metrics_no_cache=None,
fname=None,
cwd=os.curdir,
no_exec=False,
overwrite=False,
ignore_build_cache=False,
remove_outs=False,
):
from dvc.stage import Stage
if outs is None:
outs = []
if deps is None:
deps = []
if outs_no_cache is None:
outs_no_cache = []
if metrics is None:
metrics = []
if metrics_no_cache is None:
metrics_no_cache = []
with self.state:
stage = Stage.create(
project=self,
fname=fname,
cmd=cmd,
cwd=cwd,
outs=outs,
outs_no_cache=outs_no_cache,
metrics=metrics,
metrics_no_cache=metrics_no_cache,
deps=deps,
overwrite=overwrite,
ignore_build_cache=ignore_build_cache,
remove_outs=remove_outs,
)
if stage is None:
return None
self._check_dag(self.stages() + [stage])
self.files_to_git_add = []
with self.state:
if not no_exec:
stage.run()
stage.dump()
self._remind_to_git_add()
return stage
def imp(self, url, out, resume=False):
from dvc.stage import Stage
stage = Stage.create(project=self, cmd=None, deps=[url], outs=[out])
if stage is None:
return None
self._check_dag(self.stages() + [stage])
self.files_to_git_add = []
with self.state:
stage.run(resume=resume)
stage.dump()
self._remind_to_git_add()
return stage
def _reproduce_stage(self, stages, node, force, dry, interactive):
stage = stages[node]
if stage.locked:
logger.warning(
"DVC file '{path}' is locked. Its dependencies are"
" not going to be reproduced.".format(path=stage.relpath))
stage = stage.reproduce(force=force, dry=dry, interactive=interactive)
if not stage:
return []
if not dry:
stage.dump()
return [stage]
def reproduce(
self,
target=None,
recursive=True,
force=False,
dry=False,
interactive=False,
pipeline=False,
all_pipelines=False,
ignore_build_cache=False,
):
from dvc.stage import Stage
if not target and not all_pipelines:
raise ValueError()
if not interactive:
config = self.config
core = config.config[config.SECTION_CORE]
interactive = core.get(config.SECTION_CORE_INTERACTIVE, False)
targets = []
if pipeline or all_pipelines:
if pipeline:
stage = Stage.load(self, target)
node = os.path.relpath(stage.path, self.root_dir)
pipelines = [self._get_pipeline(node)]
else:
pipelines = self.pipelines()
for G in pipelines:
for node in G.nodes():
if G.in_degree(node) == 0:
targets.append(os.path.join(self.root_dir, node))
else:
targets.append(target)
self.files_to_git_add = []
ret = []
with self.state:
for target in targets:
stages = self._reproduce(
target,
recursive=recursive,
force=force,
dry=dry,
interactive=interactive,
ignore_build_cache=ignore_build_cache,
)
ret.extend(stages)
self._remind_to_git_add()
return ret
def _reproduce(
self,
target,
recursive=True,
force=False,
dry=False,
interactive=False,
ignore_build_cache=False,
):
import networkx as nx
from dvc.stage import Stage
stage = Stage.load(self, target)
G = self.graph()[1]
stages = nx.get_node_attributes(G, "stage")
node = os.path.relpath(stage.path, self.root_dir)
if recursive:
ret = self._reproduce_stages(G, stages, node, force, dry,
interactive, ignore_build_cache)
else:
ret = self._reproduce_stage(stages, node, force, dry, interactive)
return ret
def _reproduce_stages(self, G, stages, node, force, dry, interactive,
ignore_build_cache):
import networkx as nx
result = []
for n in nx.dfs_postorder_nodes(G, node):
try:
ret = self._reproduce_stage(stages, n, force, dry, interactive)
if len(ret) == 0 and ignore_build_cache:
# NOTE: we are walking our pipeline from the top to the
# bottom. If one stage is changed, it will be reproduced,
# which tells us that we should force reproducing all of
# the other stages down below, even if their direct
# dependencies didn't change.
force = True
result += ret
except Exception as ex:
raise ReproductionError(stages[n].relpath, ex)
return result
def _cleanup_unused_links(self, all_stages):
used = []
for stage in all_stages:
for out in stage.outs:
used.append(out.path)
self.state.remove_unused_links(used)
def checkout(self,
target=None,
with_deps=False,
force=False,
recursive=False):
if target and not recursive:
from dvc.stage import (
StageFileDoesNotExistError,
StageFileBadNameError,
)
all_stages = self.active_stages()
try:
stages = self._collect(target, with_deps=with_deps)
except (StageFileDoesNotExistError, StageFileBadNameError) as exc:
raise DvcException(
str(exc) +
" Did you mean 'git checkout {}'?".format(target))
else:
all_stages = self.active_stages(target)
stages = all_stages
with self.state:
self._cleanup_unused_links(all_stages)
for stage in stages:
if stage.locked:
logger.warning(
"DVC file '{path}' is locked. Its dependencies are"
" not going to be checked out.".format(
path=stage.relpath))
stage.checkout(force=force)
def _get_pipeline(self, node):
pipelines = list(filter(lambda g: node in g.nodes(), self.pipelines()))
assert len(pipelines) == 1
return pipelines[0]
def _collect(self, target, with_deps=False):
import networkx as nx
from dvc.stage import Stage
stage = Stage.load(self, target)
if not with_deps:
return [stage]
node = os.path.relpath(stage.path, self.root_dir)
G = self._get_pipeline(node)
stages = nx.get_node_attributes(G, "stage")
ret = [stage]
for n in nx.dfs_postorder_nodes(G, node):
ret.append(stages[n])
return ret
def _collect_dir_cache(self,
out,
branch=None,
remote=None,
force=False,
jobs=None):
info = out.dumpd()
ret = [info]
r = out.remote
md5 = info[r.PARAM_CHECKSUM]
if self.cache.local.changed_cache_file(md5):
try:
self.cloud.pull(ret,
jobs=jobs,
remote=remote,
show_checksums=False)
except DvcException as exc:
msg = "Failed to pull cache for '{}': {}"
logger.debug(msg.format(out, exc))
if self.cache.local.changed_cache_file(md5):
msg = ("Missing cache for directory '{}'. "
"Cache for files inside will be lost. "
"Would you like to continue? Use '-f' to force. ")
if not force and not prompt.confirm(msg):
raise DvcException(
"unable to fully collect used cache"
" without cache for directory '{}'".format(out))
else:
return ret
for i in self.cache.local.load_dir_cache(md5):
i["branch"] = branch
i[r.PARAM_PATH] = os.path.join(info[r.PARAM_PATH],
i[r.PARAM_RELPATH])
ret.append(i)
return ret
def _collect_used_cache(self,
out,
branch=None,
remote=None,
force=False,
jobs=None):
if not out.use_cache or not out.info:
if not out.info:
logger.warning("Output '{}'({}) is missing version "
"info. Cache for it will not be collected. "
"Use dvc repro to get your pipeline up to "
"date.".format(out, out.stage))
return []
info = out.dumpd()
info["branch"] = branch
ret = [info]
if out.scheme != "local":
return ret
md5 = info[out.remote.PARAM_CHECKSUM]
cache = self.cache.local.get(md5)
if not out.remote.is_dir_cache(cache):
return ret
return self._collect_dir_cache(out,
branch=branch,
remote=remote,
force=force,
jobs=jobs)
def _used_cache(
self,
target=None,
all_branches=False,
active=True,
with_deps=False,
all_tags=False,
remote=None,
force=False,
jobs=None,
recursive=False,
):
cache = {}
cache["local"] = []
cache["s3"] = []
cache["gs"] = []
cache["hdfs"] = []
cache["ssh"] = []
cache["azure"] = []
for branch in self.scm.brancher(all_branches=all_branches,
all_tags=all_tags):
if target:
if recursive:
stages = self.stages(target)
else:
stages = self._collect(target, with_deps=with_deps)
elif active:
stages = self.active_stages()
else:
stages = self.stages()
for stage in stages:
if active and not target and stage.locked:
logger.warning(
"DVC file '{path}' is locked. Its dependencies are"
" not going to be pushed/pulled/fetched.".format(
path=stage.relpath))
for out in stage.outs:
scheme = out.path_info["scheme"]
cache[scheme] += self._collect_used_cache(
out,
branch=branch,
remote=remote,
force=force,
jobs=jobs,
)
return cache
@staticmethod
def merge_cache_lists(clists):
merged_cache = collections.defaultdict(list)
for cache_list in clists:
for scheme, cache in cache_list.items():
for item in cache:
if item not in merged_cache[scheme]:
merged_cache[scheme].append(item)
return merged_cache
@staticmethod
def load_all_used_cache(
projects,
target=None,
all_branches=False,
active=True,
with_deps=False,
all_tags=False,
remote=None,
force=False,
jobs=None,
):
clists = []
for project in projects:
with project.state:
project_clist = project._used_cache(
target=None,
all_branches=all_branches,
active=False,
with_deps=with_deps,
all_tags=all_tags,
remote=remote,
force=force,
jobs=jobs,
)
clists.append(project_clist)
return clists
def _do_gc(self, typ, func, clist):
removed = func(clist)
if not removed:
logger.info("No unused {} cache to remove.".format(typ))
def gc(
self,
all_branches=False,
cloud=False,
remote=None,
with_deps=False,
all_tags=False,
force=False,
jobs=None,
projects=None,
):
all_projects = [self]
if projects:
all_projects.extend(Project(path) for path in projects)
all_clists = Project.load_all_used_cache(
all_projects,
target=None,
all_branches=all_branches,
active=False,
with_deps=with_deps,
all_tags=all_tags,
remote=remote,
force=force,
jobs=jobs,
)
if len(all_clists) > 1:
clist = Project.merge_cache_lists(all_clists)
else:
clist = all_clists[0]
with self.state:
self._do_gc("local", self.cache.local.gc, clist)
if self.cache.s3:
self._do_gc("s3", self.cache.s3.gc, clist)
if self.cache.gs:
self._do_gc("gs", self.cache.gs.gc, clist)
if self.cache.ssh:
self._do_gc("ssh", self.cache.ssh.gc, clist)
if self.cache.hdfs:
self._do_gc("hdfs", self.cache.hdfs.gc, clist)
if self.cache.azure:
self._do_gc("azure", self.cache.azure.gc, clist)
if cloud:
self._do_gc("remote",
self.cloud._get_cloud(remote, "gc -c").gc, clist)
def push(
self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False,
with_deps=False,
all_tags=False,
recursive=False,
):
with self.state:
used = self._used_cache(
target,
all_branches=all_branches,
all_tags=all_tags,
with_deps=with_deps,
force=True,
remote=remote,
jobs=jobs,
recursive=recursive,
)["local"]
self.cloud.push(used,
jobs,
remote=remote,
show_checksums=show_checksums)
def fetch(
self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False,
with_deps=False,
all_tags=False,
recursive=False,
):
with self.state:
used = self._used_cache(
target,
all_branches=all_branches,
all_tags=all_tags,
with_deps=with_deps,
force=True,
remote=remote,
jobs=jobs,
recursive=recursive,
)["local"]
self.cloud.pull(used,
jobs,
remote=remote,
show_checksums=show_checksums)
def pull(
self,
target=None,
jobs=1,
remote=None,
all_branches=False,
show_checksums=False,
with_deps=False,
all_tags=False,
force=False,
recursive=False,
):
self.fetch(
target,
jobs,
remote=remote,
all_branches=all_branches,
all_tags=all_tags,
show_checksums=show_checksums,
with_deps=with_deps,
recursive=recursive,
)
self.checkout(
target=target,
with_deps=with_deps,
force=force,
recursive=recursive,
)
def _local_status(self, target=None, with_deps=False):
status = {}
if target:
stages = self._collect(target, with_deps=with_deps)
else:
stages = self.active_stages()
for stage in stages:
if stage.locked:
logger.warning(
"DVC file '{path}' is locked. Its dependencies are"
" not going to be shown in the status output.".format(
path=stage.relpath))
status.update(stage.status())
return status
def _cloud_status(
self,
target=None,
jobs=1,
remote=None,
show_checksums=False,
all_branches=False,
with_deps=False,
all_tags=False,
):
import dvc.remote.base as cloud
used = self._used_cache(
target,
all_branches=all_branches,
all_tags=all_tags,
with_deps=with_deps,
force=True,
remote=remote,
jobs=jobs,
)["local"]
ret = {}
status_info = self.cloud.status(used,
jobs,
remote=remote,
show_checksums=show_checksums)
for md5, info in status_info.items():
name = info["name"]
status = info["status"]
if status == cloud.STATUS_OK:
continue
prefix_map = {
cloud.STATUS_DELETED: "deleted",
cloud.STATUS_NEW: "new",
}
ret[name] = prefix_map[status]
return ret
def status(
self,
target=None,
jobs=1,
cloud=False,
remote=None,
show_checksums=False,
all_branches=False,
with_deps=False,
all_tags=False,
):
with self.state:
if cloud:
return self._cloud_status(
target,
jobs,
remote=remote,
show_checksums=show_checksums,
all_branches=all_branches,
with_deps=with_deps,
all_tags=all_tags,
)
return self._local_status(target, with_deps=with_deps)
@staticmethod
def _read_metric_json(fd, json_path):
import json
from jsonpath_rw import parse
parser = parse(json_path)
return [x.value for x in parser.find(json.load(fd))]
@staticmethod
def _do_read_metric_xsv(reader, row, col):
if col is not None and row is not None:
return [reader[row][col]]
elif col is not None:
return [r[col] for r in reader]
elif row is not None:
return reader[row]
return None
@classmethod
def _read_metric_hxsv(cls, fd, hxsv_path, delimiter):
import csv
col, row = hxsv_path.split(",")
row = int(row)
reader = list(csv.DictReader(fd, delimiter=builtin_str(delimiter)))
return cls._do_read_metric_xsv(reader, row, col)
@classmethod
def _read_metric_xsv(cls, fd, xsv_path, delimiter):
import csv
col, row = xsv_path.split(",")
row = int(row)
col = int(col)
reader = list(csv.reader(fd, delimiter=builtin_str(delimiter)))
return cls._do_read_metric_xsv(reader, row, col)
def _read_metric(self, path, typ=None, xpath=None):
ret = None
if not os.path.exists(path):
return ret
try:
with open(path, "r") as fd:
if typ == "json":
ret = self._read_metric_json(fd, xpath)
elif typ == "csv":
ret = self._read_metric_xsv(fd, xpath, ",")
elif typ == "tsv":
ret = self._read_metric_xsv(fd, xpath, "\t")
elif typ == "hcsv":
ret = self._read_metric_hxsv(fd, xpath, ",")
elif typ == "htsv":
ret = self._read_metric_hxsv(fd, xpath, "\t")
else:
ret = fd.read().strip()
except Exception:
logger.error("unable to read metric in '{}'".format(path))
return ret
def _find_output_by_path(self, path, outs=None, recursive=False):
from dvc.exceptions import OutputDuplicationError
if not outs:
astages = self.active_stages()
outs = [out for stage in astages for out in stage.outs]
abs_path = os.path.abspath(path)
if os.path.isdir(abs_path) and recursive:
matched = [
out for out in outs
if os.path.abspath(out.path).startswith(abs_path)
]
else:
matched = [out for out in outs if out.path == abs_path]
stages = [out.stage.relpath for out in matched]
if len(stages) > 1:
raise OutputDuplicationError(path, stages)
return matched if matched else []
def metrics_show(
self,
path=None,
typ=None,
xpath=None,
all_branches=False,
all_tags=False,
recursive=False,
):
res = {}
for branch in self.scm.brancher(all_branches=all_branches,
all_tags=all_tags):
astages = self.active_stages()
outs = [out for stage in astages for out in stage.outs]
if path:
outs = self._find_output_by_path(path,
outs=outs,
recursive=recursive)
stages = [out.stage.path for out in outs]
entries = []
for out in outs:
if all([out.metric, not typ,
isinstance(out.metric, dict)]):
entries += [(
out.path,
out.metric.get(out.PARAM_METRIC_TYPE, None),
out.metric.get(out.PARAM_METRIC_XPATH, None),
)]
else:
entries += [(out.path, typ, xpath)]
if not entries:
if os.path.isdir(path):
logger.warning(
"Path '{path}' is a directory. "
"Consider running with '-R'.".format(path=path))
return {}
else:
entries += [(path, typ, xpath)]
else:
metrics = filter(lambda o: o.metric, outs)
stages = None
entries = []
for o in metrics:
if not typ and isinstance(o.metric, dict):
t = o.metric.get(o.PARAM_METRIC_TYPE, typ)
x = o.metric.get(o.PARAM_METRIC_XPATH, xpath)
else:
t = typ
x = xpath
entries.append((o.path, t, x))
for fname, t, x in entries:
if stages:
for stage in stages:
self.checkout(stage, force=True)
rel = os.path.relpath(fname)
metric = self._read_metric(fname, typ=t, xpath=x)
if not metric:
continue
if branch not in res:
res[branch] = {}
res[branch][rel] = metric
for branch, val in res.items():
if all_branches or all_tags:
logger.info("{}:".format(branch))
for fname, metric in val.items():
logger.info("\t{}: {}".format(fname, metric))
if res:
return res
if path and os.path.isdir(path):
return res
if path:
msg = "file '{}' does not exist or malformed".format(path)
else:
msg = ("no metric files in this repository."
" use 'dvc metrics add' to add a metric file to track.")
raise DvcException(msg)
def _metrics_modify(self, path, typ=None, xpath=None, delete=False):
outs = self._find_output_by_path(path)
if not outs:
msg = "unable to find file '{}' in the pipeline".format(path)
raise DvcException(msg)
if len(outs) != 1:
msg = ("-R not yet supported for metrics modify. "
"Make sure only one metric is referred to by '{}'".format(
path))
raise DvcException(msg)
out = outs[0]
if out.scheme != "local":
msg = "output '{}' scheme '{}' is not supported for metrics"
raise DvcException(msg.format(out.path, out.path_info["scheme"]))
if typ:
if not isinstance(out.metric, dict):
out.metric = {}
out.metric[out.PARAM_METRIC_TYPE] = typ
if xpath:
if not isinstance(out.metric, dict):
out.metric = {}
out.metric[out.PARAM_METRIC_XPATH] = xpath
if delete:
out.metric = None
out._verify_metric()
out.stage.dump()
def metrics_modify(self, path=None, typ=None, xpath=None):
self._metrics_modify(path, typ, xpath)
def metrics_add(self, path, typ=None, xpath=None):
if not typ:
typ = "raw"
self._metrics_modify(path, typ, xpath)
def metrics_remove(self, path):
self._metrics_modify(path, delete=True)
def graph(self, stages=None, from_directory=None):
import networkx as nx
from dvc.exceptions import (
OutputDuplicationError,
WorkingDirectoryAsOutputError,
)
G = nx.DiGraph()
G_active = nx.DiGraph()
stages = stages or self.stages(from_directory)
stages = [stage for stage in stages if stage]
outs = []
for stage in stages:
for out in stage.outs:
existing = [o.stage for o in outs if o.path == out.path]
if existing:
stages = [stage.relpath, existing[0].relpath]
raise OutputDuplicationError(out.path, stages)
outs.append(out)
for stage in stages:
for out in outs:
overlaps = stage.cwd == out.path or stage.cwd.startswith(
out.path + os.sep)
if overlaps:
raise WorkingDirectoryAsOutputError(
stage.cwd, stage.relpath)
# collect the whole DAG
for stage in stages:
node = os.path.relpath(stage.path, self.root_dir)
G.add_node(node, stage=stage)
G_active.add_node(node, stage=stage)
for dep in stage.deps:
for out in outs:
if (out.path != dep.path
and not dep.path.startswith(out.path + out.sep)
and not out.path.startswith(dep.path + dep.sep)):
continue
dep_stage = out.stage
dep_node = os.path.relpath(dep_stage.path, self.root_dir)
G.add_node(dep_node, stage=dep_stage)
G.add_edge(node, dep_node)
if not stage.locked:
G_active.add_node(dep_node, stage=dep_stage)
G_active.add_edge(node, dep_node)
self._check_cyclic_graph(G)
return G, G_active
def pipelines(self, from_directory=None):
import networkx as nx
G, G_active = self.graph(from_directory=from_directory)
return [
G.subgraph(c).copy() for c in nx.weakly_connected_components(G)
]
def stages(self, from_directory=None):
"""
Walks down the root directory looking for Dvcfiles,
skipping the directories that are related with
any SCM (e.g. `.git`), DVC itself (`.dvc`), or directories
tracked by DVC (e.g. `dvc add data` would skip `data/`)
NOTE: For large projects, this could be an expensive
operation. Consider using some memoization.
"""
from dvc.stage import Stage
if not from_directory:
from_directory = self.root_dir
stages = []
outs = []
for root, dirs, files in os.walk(str(from_directory)):
for fname in files:
path = os.path.join(root, fname)
if not Stage.is_stage_file(path):
continue
stage = Stage.load(self, path)
for out in stage.outs:
outs.append(out.path + out.sep)
stages.append(stage)
def filter_dirs(dname, root=root):
path = os.path.join(root, dname)
if path in (self.dvc_dir, self.scm.dir):
return False
for out in outs:
if path == os.path.normpath(out) or path.startswith(out):
return False
return True
dirs[:] = list(filter(filter_dirs, dirs))
return stages
def active_stages(self, from_directory=None):
import networkx as nx
stages = []
for G in self.pipelines(from_directory):
stages.extend(list(nx.get_node_attributes(G, "stage").values()))
return stages
@staticmethod
def _welcome_message():
import colorama
logger.box(
"DVC has enabled anonymous aggregate usage analytics.\n"
"Read the analytics documentation (and how to opt-out) here:\n"
"{blue}https://dvc.org/doc/user-guide/analytics{nc}".format(
blue=colorama.Fore.BLUE, nc=colorama.Fore.RESET),
border_color="red",
)
logger.info(
"{yellow}What's next?{nc}\n"
"{yellow}------------{nc}\n"
"- Check out the documentation: {blue}https://dvc.org/doc{nc}\n"
"- Get help and share ideas: {blue}https://dvc.org/chat{nc}\n"
"- Star us on GitHub: {blue}https://github.com/iterative/dvc{nc}".
format(
yellow=colorama.Fore.YELLOW,
blue=colorama.Fore.BLUE,
nc=colorama.Fore.RESET,
))
@staticmethod
def _expand_target_path(from_path, to_path):
if os.path.isdir(to_path) and not os.path.isdir(from_path):
return os.path.join(to_path, os.path.basename(from_path))
return to_path
class Project(object):
DVC_DIR = '.dvc'
def __init__(self, root_dir):
self.root_dir = os.path.abspath(os.path.realpath(root_dir))
self.dvc_dir = os.path.join(self.root_dir, self.DVC_DIR)
self.config = Config(self.dvc_dir)
self.scm = SCM(self.root_dir)
self.lock = Lock(self.dvc_dir)
self.link_state = LinkState(self.root_dir, self.dvc_dir)
self.logger = Logger(self.config._config[Config.SECTION_CORE].get(
Config.SECTION_CORE_LOGLEVEL, None))
self.cache = Cache(self)
self.cloud = DataCloud(cache=self.cache, config=self.config._config)
self.updater = Updater(self.dvc_dir)
self._ignore()
self.updater.check()
@staticmethod
def init(root_dir=os.curdir, no_scm=False):
"""
Initiate dvc project in directory.
Args:
root_dir: Path to project's root directory.
Returns:
Project instance.
Raises:
KeyError: Raises an exception.
"""
root_dir = os.path.abspath(root_dir)
dvc_dir = os.path.join(root_dir, Project.DVC_DIR)
scm = SCM(root_dir)
if type(scm) == Base and not no_scm:
msg = "{} is not tracked by any supported scm tool(e.g. git).".format(
root_dir)
raise InitError(msg)
os.mkdir(dvc_dir)
config = Config.init(dvc_dir)
proj = Project(root_dir)
scm.add([config.config_file])
if scm.ignore_file():
scm.add([os.path.join(dvc_dir, scm.ignore_file())])
return proj
def _ignore(self):
l = [
self.link_state.state_file, self.link_state._lock_file.lock_file,
self.lock.lock_file, self.config.config_local_file,
self.updater.updater_file
]
if self.cache.local.cache_dir.startswith(self.root_dir):
l += [self.cache.local.cache_dir]
self.scm.ignore_list(l)
def install(self):
self.scm.install()
def to_dvc_path(self, path):
return os.path.relpath(path, self.root_dir)
def add(self, fname):
out = os.path.basename(os.path.normpath(fname))
stage_fname = out + Stage.STAGE_FILE_SUFFIX
cwd = os.path.dirname(os.path.abspath(fname))
stage = Stage.loads(project=self,
cmd=None,
deps=[],
outs=[out],
fname=stage_fname,
cwd=cwd)
stage.save()
stage.dump()
return stage
def remove(self, target):
if not Stage.is_stage_file(target):
raise StageNotFoundError(target)
stage = Stage.load(self, target)
for out in stage.outs:
out.remove()
return stage
def run(self,
cmd=None,
deps=[],
outs=[],
outs_no_cache=[],
fname=Stage.STAGE_FILE,
cwd=os.curdir,
no_exec=False):
stage = Stage.loads(project=self,
fname=fname,
cmd=cmd,
cwd=cwd,
outs=outs,
outs_no_cache=outs_no_cache,
deps=deps)
if not no_exec:
stage.run()
stage.dump()
return stage
def _reproduce_stage(self, stages, node, force):
stage = stages[node].reproduce(force=force)
if not stage:
return []
stage.dump()
return [stage]
def reproduce(self, target, recursive=True, force=False):
stages = nx.get_node_attributes(self.graph(), 'stage')
node = os.path.relpath(os.path.abspath(target), self.root_dir)
if node not in stages:
raise StageNotFoundError(target)
if recursive:
return self._reproduce_stages(stages, node, force)
return self._reproduce_stage(stages, node, force)
def _reproduce_stages(self, stages, node, force):
result = []
for n in nx.dfs_postorder_nodes(self.graph(), node):
try:
result += self._reproduce_stage(stages, n, force)
except Exception as ex:
raise ReproductionError(stages[n].relpath, ex)
return result
def checkout(self, target=None):
if target:
if not Stage.is_stage_file(target):
raise StageNotFoundError(target)
stages = [Stage.load(self, target)]
else:
self.link_state.remove_all()
stages = self.stages()
for stage in stages:
stage.checkout()
def _used_cache(self, target=None):
cache_set = set()
if target:
stages = [Stage.load(self, target)]
else:
stages = self.stages()
for stage in stages:
for out in stage.outs:
if out.path_info['scheme'] != 'local':
continue
if not out.use_cache or not out.cache:
continue
cache_set |= set([out.cache])
if self.cache.local.is_dir_cache(out.cache) and os.path.isfile(
out.cache):
dir_cache = self.cache.local.dir_cache(out.cache)
cache_set |= set(dir_cache.values())
return list(cache_set)
def gc(self):
clist = self._used_cache()
for cache in self.cache.local.all():
if cache in clist:
continue
os.unlink(cache)
self.logger.info(u'\'{}\' was removed'.format(
self.to_dvc_path(cache)))
def push(self, target=None, jobs=1, remote=None):
return self.cloud.push(self._used_cache(target), jobs, remote=remote)
def fetch(self, target=None, jobs=1, remote=None):
return self.cloud.pull(self._used_cache(target), jobs, remote=remote)
def pull(self, target=None, jobs=1, remote=None):
ret = self.fetch(target, jobs, remote=remote)
self.checkout()
return ret
def _local_status(self, target=None):
status = {}
if target:
stages = [Stage.load(self, target)]
else:
stages = self.stages()
for stage in stages:
status.update(stage.status())
return status
def _cloud_status(self, target=None, jobs=1, remote=None):
status = {}
for target, ret in self.cloud.status(self._used_cache(target),
jobs,
remote=remote):
if ret == cloud.STATUS_UNKNOWN or ret == cloud.STATUS_OK:
continue
prefix_map = {
cloud.STATUS_DELETED: 'deleted',
cloud.STATUS_MODIFIED: 'modified',
cloud.STATUS_NEW: 'new',
}
path = os.path.relpath(target, self.cache.local.cache_dir)
status[path] = prefix_map[ret]
return status
def status(self, target=None, jobs=1, cloud=False, remote=None):
if cloud:
return self._cloud_status(target, jobs, remote=remote)
return self._local_status(target)
def _read_metric_json(self, fd, json_path):
parser = parse(json_path)
return [x.value for x in parser.find(json.load(fd))]
def _do_read_metric_tsv(self, reader, row, col):
if col != None and row != None:
return [reader[row][col]]
elif col != None:
return [r[col] for r in reader]
elif row != None:
return reader[row]
return None
def _read_metric_htsv(self, fd, htsv_path):
col, row = htsv_path.split(',')
row = int(row)
reader = list(csv.DictReader(fd, delimiter='\t'))
return self._do_read_metric_tsv(reader, row, col)
def _read_metric_tsv(self, fd, tsv_path):
col, row = tsv_path.split(',')
row = int(row)
col = int(col)
reader = list(csv.reader(fd, delimiter='\t'))
return self._do_read_metric_tsv(reader, row, col)
def _read_metric(self,
path,
json_path=None,
tsv_path=None,
htsv_path=None):
ret = None
try:
with open(path, 'r') as fd:
if json_path:
ret = self._read_metric_json(fd, json_path)
elif tsv_path:
ret = self._read_metric_tsv(fd, tsv_path)
elif htsv_path:
ret = self._read_metric_htsv(fd, htsv_path)
else:
ret = fd.read()
except Exception as exc:
self.logger.error('Unable to read metric in \'{}\''.format(path),
exc)
return ret
def metrics(self, path, json_path=None, tsv_path=None, htsv_path=None):
res = {}
saved = self.scm.active_branch()
for branch in self.scm.list_branches():
self.scm.checkout(branch)
self.checkout()
res[branch] = self._read_metric(path,
json_path=json_path,
tsv_path=tsv_path,
htsv_path=htsv_path)
self.scm.checkout(saved)
self.checkout()
return res
def graph(self):
G = nx.DiGraph()
stages = self.stages()
outs_map = {}
for stage in stages:
for o in stage.outs:
outs_map[o.path] = stage
for stage in stages:
node = os.path.relpath(stage.path, self.root_dir)
G.add_node(node, stage=stage)
for dep in stage.deps:
dep_stage = outs_map.get(dep.path, None)
if not dep_stage:
continue
dep_node = os.path.relpath(dep_stage.path, self.root_dir)
G.add_node(dep_node, stage=dep_stage)
G.add_edge(node, dep_node)
return G
def stages(self):
stages = []
for root, dirs, files in os.walk(self.root_dir):
for fname in files:
path = os.path.join(root, fname)
if not Stage.is_stage_file(path):
continue
stages.append(Stage.load(self, path))
return stages
def outs(self):
outs = []
for stage in self.stages():
outs += stage.outs
return outs
