def update_w3d(branch="master"):
target_ref = 'refs/heads/{}'.format(branch).encode()
w3d_repo = dulwich.repo.Repo(W3D_PATH)
porcelain.reset(w3d_repo, "hard")
porcelain.pull(W3D_PATH, REMOTE_PATH, target_ref)
w3d_repo.refs.set_symbolic_ref('HEAD'.encode(), target_ref)
porcelain.reset(w3d_repo, "hard")
def test_hard_head(self):
f = open(os.path.join(self.repo.path, 'foo'), 'w')
try:
f.write("BAR")
finally:
f.close()
porcelain.add(self.repo.path, paths=["foo"])
porcelain.commit(self.repo.path,
message="Some message",
committer="Jane <*****@*****.**>",
author="John <*****@*****.**>")
f = open(os.path.join(self.repo.path, 'foo'), 'w')
try:
f.write("OOH")
finally:
f.close()
porcelain.reset(self.repo, "hard", "HEAD")
index = self.repo.open_index()
changes = list(
tree_changes(self.repo, index.commit(self.repo.object_store),
self.repo['HEAD'].tree))
self.assertEquals([], changes)
def test_hard_commit(self):
with open(os.path.join(self.repo.path, "foo"), "w") as f:
f.write("BAR")
porcelain.add(self.repo.path, paths=["foo"])
sha = porcelain.commit(
self.repo.path,
message=b"Some message",
committer=b"Jane <*****@*****.**>",
author=b"John <*****@*****.**>",
)
with open(os.path.join(self.repo.path, "foo"), "wb") as f:
f.write(b"BAZ")
porcelain.add(self.repo.path, paths=["foo"])
porcelain.commit(
self.repo.path,
message=b"Some other message",
committer=b"Jane <*****@*****.**>",
author=b"John <*****@*****.**>",
)
porcelain.reset(self.repo, "hard", sha)
index = self.repo.open_index()
changes = list(tree_changes(self.repo, index.commit(self.repo.object_store), self.repo[sha].tree))
self.assertEqual([], changes)
def test_hard_commit(self):
fullpath = os.path.join(self.repo.path, 'foo')
with open(fullpath, 'w') as f:
f.write("BAR")
porcelain.add(self.repo.path, paths=[fullpath])
sha = porcelain.commit(self.repo.path,
message=b"Some message",
committer=b"Jane <*****@*****.**>",
author=b"John <*****@*****.**>")
with open(fullpath, 'wb') as f:
f.write(b"BAZ")
porcelain.add(self.repo.path, paths=[fullpath])
porcelain.commit(self.repo.path,
message=b"Some other message",
committer=b"Jane <*****@*****.**>",
author=b"John <*****@*****.**>")
porcelain.reset(self.repo, "hard", sha)
index = self.repo.open_index()
changes = list(
tree_changes(self.repo, index.commit(self.repo.object_store),
self.repo[sha].tree))
self.assertEqual([], changes)
def test_hard_head(self):
f = open(os.path.join(self.repo.path, 'foo'), 'w')
try:
f.write("BAR")
finally:
f.close()
porcelain.add(self.repo.path, paths=["foo"])
porcelain.commit(self.repo.path, message="Some message",
committer="Jane <*****@*****.**>",
author="John <*****@*****.**>")
f = open(os.path.join(self.repo.path, 'foo'), 'w')
try:
f.write("OOH")
finally:
f.close()
porcelain.reset(self.repo, "hard", "HEAD")
index = self.repo.open_index()
changes = list(tree_changes(self.repo,
index.commit(self.repo.object_store),
self.repo['HEAD'].tree))
self.assertEqual([], changes)
def restore(self, commit):
"""
does a hard reset to a given commit
:param commit: list-of-dulwich.objects.Commit; commit to reset to
"""
porcelain.reset(self.repo, 'hard',
str.encode(commit.sha().hexdigest()))
self.commit("Restored setting and data.")
Config.read_config()
def __exit__(self, exc_type, value, tb):
if value is None:
self.repo.refs.set_symbolic_ref('HEAD', self.start)
# lol, only reset --hard is supported
if self.delete:
self.repo.refs.remove_if_equals(self.branch, None)
else:
six.reraise(exc_type, value, tb)
git.reset(self.repo, "hard")
def __exit__(self, exc_type, value, tb):
if value is None:
self.repo.refs.set_symbolic_ref('HEAD', self.start)
# lol, only reset --hard is supported
if self.delete:
self.repo.refs.remove_if_equals(self.branch, None)
else:
six.reraise(exc_type, value, tb)
git.reset(self.repo, "hard")
def reset_to_remote(self, workspace, branch=None):
outstream = BytesIO()
errstream = BytesIO()
# XXX not actually resetting to remote
# XXX assuming 'master' is the current branch
if branch is None:
branch = 'master'
porcelain.reset(workspace.working_dir, 'hard', committish=b'HEAD')
return outstream.getvalue().decode(), errstream.getvalue().decode()
def reset_to_remote(self, workspace, branch=None):
outstream = BytesIO()
errstream = BytesIO()
# XXX not actually resetting to remote
# XXX assuming 'master' is the current branch
if branch is None:
branch = 'master'
porcelain.reset(workspace.working_dir, 'hard', committish=b'HEAD')
return outstream.getvalue().decode(), errstream.getvalue().decode()
def run(self, args):
opts, args = getopt(args, "", ["hard", "soft", "mixed"])
opts = dict(opts)
mode = ""
if "--hard" in opts:
mode = "hard"
elif "--soft" in opts:
mode = "soft"
elif "--mixed" in opts:
mode = "mixed"
porcelain.reset('.', mode=mode, *args)
def git_reset_repo_to_origin():
try:
repo = porcelain.Repo(database)
porcelain.fetch(repo)
tree_head_id = repo[repo[b'refs/heads/master'].tree].id
tree_origin_master_id = repo[
repo[b'refs/remotes/origin/master'].tree].id
store = repo.object_store
list_all_files_head = list_all_files(store, tree_head_id)
list_all_files_origin_master = list_all_files(store,
tree_origin_master_id)
deleted_files = list(
set(list_all_files_head) - set(list_all_files_origin_master))
# print(deleted_files)
if deleted_files != []:
for all in deleted_files:
file_path = os.path.join(database, all.decode('utf-8'))
os.remove(file_path)
status = porcelain.status(repo)
repo.stage(status.unstaged)
porcelain.commit(repo, message="delete files")
###working###
porcelain.reset(repo, "hard", treeish=b"refs/remotes/origin/master")
porcelain.clean(repo=repo, target_dir=database)
resolve_divergence()
########
return True
except MaxRetryError:
print('MaxRetryError')
return False
except ProtocolError:
print('ProtocolError')
return False
def test_hard_head(self):
with open(os.path.join(self.repo.path, 'foo'), 'w') as f:
f.write("BAR")
porcelain.add(self.repo.path, paths=["foo"])
porcelain.commit(self.repo.path, message=b"Some message",
committer=b"Jane <*****@*****.**>",
author=b"John <*****@*****.**>")
with open(os.path.join(self.repo.path, 'foo'), 'wb') as f:
f.write(b"OOH")
porcelain.reset(self.repo, "hard", b"HEAD")
index = self.repo.open_index()
changes = list(tree_changes(self.repo,
index.commit(self.repo.object_store),
self.repo[b'HEAD'].tree))
self.assertEqual([], changes)
def test_hard_head(self):
fullpath = os.path.join(self.repo.path, 'foo')
with open(fullpath, 'w') as f:
f.write("BAR")
porcelain.add(self.repo.path, paths=[fullpath])
porcelain.commit(self.repo.path, message=b"Some message",
committer=b"Jane <*****@*****.**>",
author=b"John <*****@*****.**>")
with open(os.path.join(self.repo.path, 'foo'), 'wb') as f:
f.write(b"OOH")
porcelain.reset(self.repo, "hard", b"HEAD")
index = self.repo.open_index()
changes = list(tree_changes(self.repo,
index.commit(self.repo.object_store),
self.repo[b'HEAD'].tree))
self.assertEqual([], changes)
def update_dulwich():
try:
import dulwich.repo
from dulwich import porcelain
except ImportError:
install_dulwich()
return
try:
dulwich_repo = dulwich.repo.Repo(os.path.join(INSTALL_PATH, "dulwich"))
except dulwich.errors.NotGitRepository:
try:
shutil.rmtree(os.path.join(INSTALL_PATH, "dulwich"))
except FileNotFoundError:
pass # Directory already gone
dulwich_repo = porcelain.clone("https://github.com/jelmer/dulwich.git",
os.path.join(INSTALL_PATH, "dulwich"))
porcelain.reset(dulwich_repo, "hard")
porcelain.pull(dulwich_repo,
remote_location="https://github.com/jelmer/dulwich.git")
install_dulwich()
def push(name, api, domain):
repo = git.Repo(os.getcwd())
branch = "temp-{}".format(str(uuid.uuid4())[:8])
set_deploy_branch(name, branch, api, domain)
remote = git_url(name, api, domain)
if is_dirty():
print("Nuking changes.")
git.reset(repo, "hard")
with TempBranch(branch, repo, delete=True):
for fname, file_info in openshift_files.items():
with open(fname, 'w') as f:
f.write(file_info.get("contents", ""))
repo.stage(fname)
repo.do_commit("Commit openshift files")
push_out = StringIO()
push_err = StringIO()
print("Pushing to openshift (may take a few minutes)")
git.push(repo,
remote,
"refs/heads/{}".format(branch),
outstream=push_out,
errstream=push_err)
push_out.seek(0)
out = push_out.read()
if not re.match(r'^Push to .* successful.', out):
print("There was a failure while pushing")
print("---BEGIN STDERR---")
push_err.seek(0)
print(push_err.read())
print("---BEGIN STDOUT---")
print(out)
print("There was a failure while pushing")
git.rm(repo, openshift_files.keys())
map(os.remove, openshift_files.keys())
return get_app(name, api, domain)['app_url']
def run_nextflow(run, params, rundir, gitwfdir, profiles, nf_version=False):
"""Fairly generalized code for kantele celery task to run a WF in NXF"""
print('Starting nextflow workflow {}'.format(run['nxf_wf_fn']))
outdir = os.path.join(rundir, 'output')
try:
clone(run['repo'], gitwfdir, checkout=run['wf_commit'])
except FileExistsError:
pull(gitwfdir, run['repo'])
reset(gitwfdir, 'hard', run['wf_commit'])
# FIXME dulwich does not seem to checkout anything, use this until it does
subprocess.run(['git', 'checkout', run['wf_commit']], check=True, cwd=gitwfdir)
print('Checked out repo {} at commit {}'.format(run['repo'], run['wf_commit']))
# There will be files inside data dir of WF repo so we must be in
# that dir for WF to find them
cmd = ['nextflow', 'run', run['nxf_wf_fn'], *params, '--outdir', outdir, '-profile', profiles, '-with-trace', '-resume']
print(cmd)
env = os.environ
if nf_version:
env['NXF_VER'] = nf_version
log_analysis(run['analysis_id'], 'Running command {}, nextflow version {}'.format(' '.join(cmd), env.get('NXF_VER', 'default')))
subprocess.run(cmd, check=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE, cwd=gitwfdir, env=env)
return rundir
def push(name, api, domain):
repo = git.Repo(os.getcwd())
branch = "temp-{}".format(str(uuid.uuid4())[:8])
set_deploy_branch(name, branch, api, domain)
remote = git_url(name, api, domain)
if is_dirty():
print("Nuking changes.")
git.reset(repo, "hard")
with TempBranch(branch, repo, delete=True):
for fname, file_info in openshift_files.items():
with open(fname, 'w') as f:
f.write(file_info.get("contents", ""))
repo.stage(fname)
repo.do_commit("Commit openshift files")
push_out = StringIO()
push_err = StringIO()
print("Pushing to openshift (may take a few minutes)")
git.push(repo, remote, "refs/heads/{}".format(branch),
outstream=push_out, errstream=push_err)
push_out.seek(0)
out = push_out.read()
if not re.match(r'^Push to .* successful.', out):
print("There was a failure while pushing")
print("---BEGIN STDERR---")
push_err.seek(0)
print(push_err.read())
print("---BEGIN STDOUT---")
print(out)
print("There was a failure while pushing")
git.rm(repo, openshift_files.keys())
map(os.remove, openshift_files.keys())
return get_app(name, api, domain)['app_url']
def reset(self, sender):
porcelain.reset(self.g.path, mode="hard", committish="HEAD")
self.refresh()
def reset(self,sender):
porcelain.reset(self.g.path,mode='hard',committish='HEAD')
self.refresh()
def git_reset(args):
if len(args) == 0:
repo = _get_repo()
porcelain.reset(repo.repo, 'hard')
else:
print command_help['reset']
def reset(self, sender):
porcelain.reset(self.g.path, mode='hard', committish='HEAD')
self.refresh()
