def open_repo(self, name, root=None):
self.active = True
super(WorkspaceManager, self).open_repo(name, root)
e = Manifest.exists(self.path)
# init manifest object
self._manifest = Manifest(self.path)
if not e:
self.add(self._manifest.path, msg='Added manifest file')
self.update_gitignore('.index.db')
self.index_db = IndexAdapter(path=os.path.join(self.path, '.index.db'))
self.index_db.connect()
self.index_db.create_all(Base.metadata)
self.create_branch('develop')
self.checkout_branch('develop')
def open_repo(self, name, root=None):
self.active = True
super(WorkspaceManager, self).open_repo(name, root)
e = Manifest.exists(self.path)
# init manifest object
self._manifest = Manifest(self.path)
if not e:
self.add(self._manifest.path, msg='Added manifest file')
self.update_gitignore('.index.db')
self.index_db = IndexAdapter(path=os.path.join(self.path, '.index.db'))
self.index_db.connect()
self.index_db.create_all(Base.metadata)
self.create_branch('develop')
self.checkout_branch('develop')
class WorkspaceManager(GitRepoManager):
index_db = Instance(IndexAdapter)
# test = Button
# selected = Any
dclicked = Event
repo_updated = Event
branches = List
commits = List
selected_text = Str
# selected_commits = List
active = False
def make_analyses(self, ans):
self.debug('make analyses')
def func(ai):
p = os.path.join(self.path, '{}.yaml'.format(ai.record_id))
w = WorkspaceAnalysis()
w.sync(p)
return w
return [func(ai) for ai in ans]
def _open_directory_dialog(self, **kw):
dialog = DirectoryDialog(action='open', **kw)
if dialog.open() == OK:
r = dialog.path
return r
def open_workspace(self):
self.debug('open workspace')
p = os.path.join(paths.workspace_root_dir, 'test')
if not os.path.isdir(p):
p = self._open_directory_dialog(default_directory=paths.workspace_root_dir)
if p:
self.open_repo(p)
def _validate_diff(self):
return self.selected.endswith('.yaml')
def _diff_view_factory(self, l, r):
dd = self._calculate_diff_dict(l, r)
dv = DiffView(l.summary, r.summary, dd)
return dv
def open_repo(self, name, root=None):
self.active = True
super(WorkspaceManager, self).open_repo(name, root)
e = Manifest.exists(self.path)
# init manifest object
self._manifest = Manifest(self.path)
if not e:
self.add(self._manifest.path, msg='Added manifest file')
self.update_gitignore('.index.db')
self.index_db = IndexAdapter(path=os.path.join(self.path, '.index.db'))
self.index_db.connect()
self.index_db.create_all(Base.metadata)
self.create_branch('develop')
self.checkout_branch('develop')
def load_branches(self):
self.branches = [bi.name for bi in self._repo.branches]
def create_branch(self, name):
super(WorkspaceManager, self).create_branch(name)
self.load_branches()
def find_existing(self, names):
return [os.path.splitext(ni)[0] for ni in self._manifest.names if ni in names]
def add_to_manifest(self, path):
self._manifest.add(os.path.basename(path))
def add_manifest_to_index(self):
p = self._manifest.path
index = self.index
index.add([p])
def commit_manifest(self):
p = self._manifest.path
self._add_to_repo(p, msg='Updated manifest')
def add_analysis(self, path, commit=True, message=None, **kw):
"""
path: absolute path to flat file
commit: commit changes
message: message to use for commit
1. copy file at path to the repository
2. add record to index
"""
repo = self._repo
# copy file to repo
dest = os.path.join(repo.working_dir, os.path.basename(path))
if not os.path.isfile(dest):
shutil.copyfile(path, dest)
# add to master changeset
index = repo.index
index.add([dest])
if commit:
if message is None:
message = 'added record {}'.format(path)
index.commit(message)
self.repo_updated = True
def add_analysis_to_index(self, ai):
# add to sqlite index
im = self.index_db
im.add(repo=self._repo.working_dir,
identifier=ai.identifier,
aliquot=ai.aliquot,
increment=ai.increment,
cleanup=ai.cleanup,
duration=ai.duration,
extract_value=ai.extract_value,
uuid=ai.uuid,
measurement_script=ai.measurement_script_name,
extraction_script=ai.extraction_script_name,
mass_spectrometer=ai.mass_spectrometer,
extract_device=ai.extract_device,
material=ai.material,
sample=ai.sample,
project=ai.project,
irradiation=ai.irradiation,
irradiation_level=ai.irradiation_level,
irradiation_position=ai.irradiation_pos,
tag = ai.tag,
position = ai.position,
analysis_timestamp = ai.analysis_timestamp,
analysis_type = ai.analysis_type)
def modify_analysis(self, path, message=None, branch='develop'):
"""
commit the modification to path to the working branch
"""
self.checkout_branch(branch)
index = self.index
index.add([path])
if message is None:
message = 'modified record {}'.format(os.path.relpath(path, self.path))
index.commit(message)
def _load_file_text(self, new):
with open(new, 'r') as fp:
self.selected_text = fp.read()
def _calculate_diff_dict(self, left, right):
left = self.get_commit(left.hexsha)
right = self.get_commit(right.hexsha)
ds = left.diff(right, create_patch=True)
attrs = ['age', 'age_err',
'age_err_wo_j', 'age_err_wo_j_irrad',
'ar39decayfactor',
'ar37decayfactor',
'j', 'j_err',
'tag',
'material', 'sample',
('constants', 'abundance_sensitivity', 'atm4036', 'lambda_k'),
('production_ratios', 'Ca_K', 'Cl_K'),
('interference_corrections', 'ca3637', 'ca3637_err', 'ca3837', 'ca3837_err', 'ca3937', 'ca3937_err',
'cl3638', 'cl3638_err',
'k3739', 'k3739_err', 'k3839', 'k3839_err', 'k4039', 'k4039_err')]
if not isinstance(attrs, (tuple, list)):
attrs = (attrs, )
attr_diff = []
for ci in ds.iter_change_type('M'):
try:
a = ci.a_blob.data_stream
except Exception, e:
print 'a', e
continue
try:
b = ci.b_blob.data_stream
except Exception, e:
print 'b', e
continue
ayd = yaml.load(a)
byd = yaml.load(b)
# use the first analysis only
ayd = ayd[ayd.keys()[0]]
byd = byd[byd.keys()[0]]
def func(ad, bd, attr):
try:
av = ad[attr]
except KeyError:
av = None
try:
bv = bd[attr]
except KeyError:
bv = None
attr_diff.append((attr, av, bv))
for attr in attrs:
if isinstance(attr, (list, tuple)):
subdict = attr[0]
sa, sb = ayd[subdict], byd[subdict]
for ai in attr[1:]:
func(sa, sb, ai)
else:
func(ayd, byd, attr)
aisos = ayd['isotopes']
bisos = byd['isotopes']
for aisod in aisos:
name = aisod['name']
bisod = next((b for b in bisos if b['name'] == name), None)
av = aisod['value']
bv = bisod['value'] if bisod else 0
attr_diff.append((name, av, bv))
for a in ('baseline', 'baseline_err', 'blank',
'blank_err', 'ic_factor', 'ic_factor_err', 'fit'):
av, bv = aisod[a], bisod[a]
attr_diff.append(('{} {}'.format(name, a), av, bv))
class WorkspaceManager(GitRepoManager):
index_db = Instance(IndexAdapter)
# test = Button
# selected = Any
dclicked = Event
repo_updated = Event
branches = List
commits = List
selected_text = Str
# selected_commits = List
active = False
def make_analyses(self, ans):
self.debug('make analyses')
def func(ai):
p = os.path.join(self.path, '{}.yaml'.format(ai.record_id))
w = WorkspaceAnalysis()
w.sync(p)
return w
return [func(ai) for ai in ans]
def _open_directory_dialog(self, **kw):
dialog = DirectoryDialog(action='open', **kw)
if dialog.open() == OK:
r = dialog.path
return r
def open_workspace(self):
self.debug('open workspace')
p = os.path.join(paths.workspace_root_dir, 'test')
if not os.path.isdir(p):
p = self._open_directory_dialog(
default_directory=paths.workspace_root_dir)
if p:
self.open_repo(p)
def _validate_diff(self):
return self.selected.endswith('.yaml')
def _diff_view_factory(self, l, r):
dd = self._calculate_diff_dict(l, r)
dv = DiffView(l.summary, r.summary, dd)
return dv
def open_repo(self, name, root=None):
self.active = True
super(WorkspaceManager, self).open_repo(name, root)
e = Manifest.exists(self.path)
# init manifest object
self._manifest = Manifest(self.path)
if not e:
self.add(self._manifest.path, msg='Added manifest file')
self.update_gitignore('.index.db')
self.index_db = IndexAdapter(path=os.path.join(self.path, '.index.db'))
self.index_db.connect()
self.index_db.create_all(Base.metadata)
self.create_branch('develop')
self.checkout_branch('develop')
def load_branches(self):
self.branches = [bi.name for bi in self._repo.branches]
def create_branch(self, name):
super(WorkspaceManager, self).create_branch(name)
self.load_branches()
def find_existing(self, names):
return [
os.path.splitext(ni)[0] for ni in self._manifest.names
if ni in names
]
def add_to_manifest(self, path):
self._manifest.add(os.path.basename(path))
def add_manifest_to_index(self):
p = self._manifest.path
index = self.index
index.add([p])
def commit_manifest(self):
p = self._manifest.path
self._add_to_repo(p, msg='Updated manifest')
def add_analysis(self, path, commit=True, message=None, **kw):
"""
path: absolute path to flat file
commit: commit changes
message: message to use for commit
1. copy file at path to the repository
2. add record to index
"""
repo = self._repo
# copy file to repo
dest = os.path.join(repo.working_dir, os.path.basename(path))
if not os.path.isfile(dest):
shutil.copyfile(path, dest)
# add to master changeset
index = repo.index
index.add([dest])
if commit:
if message is None:
message = 'added record {}'.format(path)
index.commit(message)
self.repo_updated = True
def add_analysis_to_index(self, ai):
# add to sqlite index
im = self.index_db
im.add(repo=self._repo.working_dir,
identifier=ai.identifier,
aliquot=ai.aliquot,
increment=ai.increment,
cleanup=ai.cleanup,
duration=ai.duration,
extract_value=ai.extract_value,
uuid=ai.uuid,
measurement_script=ai.measurement_script_name,
extraction_script=ai.extraction_script_name,
mass_spectrometer=ai.mass_spectrometer,
extract_device=ai.extract_device,
material=ai.material,
sample=ai.sample,
project=ai.project,
irradiation=ai.irradiation,
irradiation_level=ai.irradiation_level,
irradiation_position=ai.irradiation_pos,
tag=ai.tag,
position=ai.position,
analysis_timestamp=ai.analysis_timestamp,
analysis_type=ai.analysis_type)
def modify_analysis(self, path, message=None, branch='develop'):
"""
commit the modification to path to the working branch
"""
self.checkout_branch(branch)
index = self.index
index.add([path])
if message is None:
message = 'modified record {}'.format(
os.path.relpath(path, self.path))
index.commit(message)
def _load_file_text(self, new):
with open(new, 'r') as rfile:
self.selected_text = rfile.read()
def _calculate_diff_dict(self, left, right):
left = self.get_commit(left.hexsha)
right = self.get_commit(right.hexsha)
ds = left.diff(right, create_patch=True)
attrs = [
'age', 'age_err', 'age_err_wo_j', 'age_err_wo_j_irrad',
'ar39decayfactor', 'ar37decayfactor', 'j', 'j_err', 'tag',
'material', 'sample',
('constants', 'abundance_sensitivity', 'atm4036', 'lambda_k'),
('production_ratios', 'Ca_K', 'Cl_K'),
('interference_corrections', 'ca3637', 'ca3637_err', 'ca3837',
'ca3837_err', 'ca3937', 'ca3937_err', 'cl3638', 'cl3638_err',
'k3739', 'k3739_err', 'k3839', 'k3839_err', 'k4039', 'k4039_err')
]
if not isinstance(attrs, (tuple, list)):
attrs = (attrs, )
attr_diff = []
for ci in ds.iter_change_type('M'):
try:
a = ci.a_blob.data_stream
except Exception, e:
print 'a', e
continue
try:
b = ci.b_blob.data_stream
except Exception, e:
print 'b', e
continue
ayd = yaml.load(a)
byd = yaml.load(b)
# use the first analysis only
ayd = ayd[ayd.keys()[0]]
byd = byd[byd.keys()[0]]
def func(ad, bd, attr):
try:
av = ad[attr]
except KeyError:
av = None
try:
bv = bd[attr]
except KeyError:
bv = None
attr_diff.append((attr, av, bv))
for attr in attrs:
if isinstance(attr, (list, tuple)):
subdict = attr[0]
sa, sb = ayd[subdict], byd[subdict]
for ai in attr[1:]:
func(sa, sb, ai)
else:
func(ayd, byd, attr)
aisos = ayd['isotopes']
bisos = byd['isotopes']
for aisod in aisos:
name = aisod['name']
bisod = next((b for b in bisos if b['name'] == name), None)
av = aisod['value']
bv = bisod['value'] if bisod else 0
attr_diff.append((name, av, bv))
for a in ('baseline', 'baseline_err', 'blank', 'blank_err',
'ic_factor', 'ic_factor_err', 'fit'):
av, bv = aisod[a], bisod[a]
attr_diff.append(('{} {}'.format(name, a), av, bv))
