def test_static_isinstance(self):
self.assertTrue(
static_isinstance(obj=list(),
obj_type=["builtins.list", "__builtin__.list"]))
self.assertTrue(
any([
static_isinstance(obj=list(), obj_type="builtins.list"),
static_isinstance(obj=list(), obj_type="__builtin__.list"),
]))
self.assertRaises(TypeError, static_isinstance, list(), 1)
def _kill_child(job):
"""
Internal helper function to kill a child process.
Args:
job (JobCore): job object to decompress
"""
if (
static_isinstance(
obj=job.__class__, obj_type="pyiron_base.master.GenericMaster"
)
and not job.server.run_mode.queue
and (job.status.running or job.status.submitted)
):
for proc in psutil.process_iter():
try:
pinfo = proc.as_dict(attrs=["pid", "cwd"])
except psutil.NoSuchProcess:
pass
else:
if pinfo["cwd"] is not None and pinfo["cwd"].startswith(
job.working_directory
):
job_process = psutil.Process(pinfo["pid"])
job_process.kill()
def validate_que_request(item):
"""
Internal function to convert the job_ID or hamiltonian to the queuing system ID.
Args:
item (int, pyiron_base.job.generic.GenericJob): Provide either the job_ID or the full hamiltonian
Returns:
int: queuing system ID
"""
if isinstance(item, int):
que_id = item
elif static_isinstance(item.__class__,
"pyiron_base.master.generic.GenericMaster"):
if item.server.queue_id:
que_id = item.server.queue_id
else:
queue_id_lst = [
item.project.load(child_id).server.queue_id
for child_id in item.child_ids
]
que_id = [
queue_id for queue_id in queue_id_lst if queue_id is not None
]
if len(que_id) == 0:
raise ValueError("This job does not have a queue ID.")
elif static_isinstance(item.__class__,
"pyiron_base.job.generic.GenericJob"):
if item.server.queue_id:
que_id = item.server.queue_id
else:
raise ValueError("This job does not have a queue ID.")
elif static_isinstance(item.__class__, "pyiron_base.job.core.JobCore"):
if "server" in item.project_hdf5.list_nodes():
server_hdf_dict = item.project_hdf5["server"]
if "qid" in server_hdf_dict.keys():
que_id = server_hdf_dict["qid"]
else:
raise ValueError("This job does not have a queue ID.")
else:
raise ValueError("This job does not have a queue ID.")
else:
raise TypeError(
"The queue can either query for IDs or for pyiron GenericJobObjects."
)
return que_id
def export_database(project_instance, directory_to_transfer,
archive_directory):
# here we first check wether the archive directory is a path
# or a project object
if isinstance(archive_directory, str):
if archive_directory[-7:] == ".tar.gz":
archive_directory = archive_directory[:-7]
archive_directory = os.path.basename(archive_directory)
# if the archive_directory is a project
elif static_isinstance(
obj=archive_directory.__class__,
obj_type=[
"pyiron_base.project.generic.Project",
],
):
archive_directory = archive_directory.path
else:
raise RuntimeError("""the given path for exporting to,
does not have the correct format paths as string
or pyiron Project objects are expected""")
directory_to_transfer = os.path.basename(directory_to_transfer)
pr = project_instance.open(os.curdir)
df = pr.job_table()
job_ids_sorted = sorted(df.id.values)
new_job_ids = list(range(len(job_ids_sorted)))
job_translate_dict = {j: n for j, n in zip(job_ids_sorted, new_job_ids)}
df["id"] = [
new_job_id(job_id=job_id, job_translate_dict=job_translate_dict)
for job_id in df.id
]
df["masterid"] = [
new_job_id(job_id=job_id, job_translate_dict=job_translate_dict)
for job_id in df.masterid
]
df["parentid"] = [
new_job_id(job_id=job_id, job_translate_dict=job_translate_dict)
for job_id in df.parentid
]
df["project"] = update_project(
project_instance,
directory_to_transfer=directory_to_transfer,
archive_directory=archive_directory,
df=df,
)
del df["projectpath"]
return df
def _get_project_for_copy(job, project, new_job_name):
"""
Internal helper function to generate a project and hdf5 project for copying
Args:
job (JobCore): Job object used for comparison
project (JobCore/ProjectHDFio/Project/None): The project to copy the job to.
(Default is None, use the same project.)
new_job_name (str): The new name to assign the duplicate job. Required if the
project is `None` or the same project as the copied job. (Default is None,
try to keep the same name.)
Returns:
Project, ProjectHDFio
"""
if static_isinstance(
obj=project.__class__,
obj_type="pyiron_base.job.core.JobCore"
):
file_project = project.project
hdf5_project = project.project_hdf5.open(new_job_name)
elif isinstance(project, job.project.__class__):
file_project = project
hdf5_project = job.project_hdf5.__class__(
project=project,
file_name=new_job_name,
h5_path="/" + new_job_name
)
elif isinstance(project, job.project_hdf5.__class__):
file_project = project.project
hdf5_project = project.open(new_job_name)
elif project is None:
file_project = job.project
hdf5_project = job.project_hdf5.__class__(
project=file_project,
file_name=new_job_name,
h5_path="/" + new_job_name
)
else:
raise ValueError("Project should be JobCore/ProjectHDFio/Project/None")
return file_project, hdf5_project
def import_jobs(project_instance,
directory_to_import_to,
archive_directory,
df,
compressed=True):
# Copy HDF5 files
# if the archive_directory is a path(string)/name of the compressed file
if isinstance(archive_directory, str):
archive_directory = os.path.basename(archive_directory)
# if the archive_directory is a project
elif static_isinstance(obj=archive_directory.__class__,
obj_type=[
"pyiron_base.project.generic.Project",
]):
archive_directory = archive_directory.path
else:
raise RuntimeError("""the given path for importing from,
does not have the correct format paths
as string or pyiron Project objects are expected""")
if compressed:
extract_archive(archive_directory)
archive_name = getdir(path=archive_directory)
if directory_to_import_to[-1] != '/':
directory_to_import_to = os.path.basename(directory_to_import_to)
else:
directory_to_import_to = os.path.basename(directory_to_import_to[:-1])
# destination folder
des = os.path.abspath(os.path.join(os.curdir, directory_to_import_to))
# source folder; archive folder
src = os.path.abspath(os.path.join(os.curdir, archive_directory))
copy_tree(src, des)
if compressed:
rmtree(archive_directory)
# Update Database
pr_import = project_instance.open(os.curdir)
df["project"] = [
os.path.join(pr_import.project_path, os.path.relpath(p, archive_name))
+ "/" for p in df["project"].values
]
df['projectpath'] = len(df) * [pr_import.root_path]
# Add jobs to database
job_id_lst = []
for entry in df.dropna(axis=1).to_dict(orient="records"):
if 'id' in entry:
del entry['id']
if 'parentid' in entry:
del entry['parentid']
if 'masterid' in entry:
del entry['masterid']
if 'timestart' in entry:
entry["timestart"] = pandas.to_datetime(entry["timestart"])
if 'timestop' in entry:
entry["timestop"] = pandas.to_datetime(entry["timestop"])
if 'username' not in entry:
entry["username"] = s.login_user
job_id = pr_import.db.add_item_dict(par_dict=entry)
job_id_lst.append(job_id)
# Update parent and master ids
for job_id, masterid, parentid in zip(
job_id_lst,
update_id_lst(record_lst=df["masterid"].values,
job_id_lst=job_id_lst),
update_id_lst(record_lst=df["parentid"].values,
job_id_lst=job_id_lst),
):
if masterid is not None or parentid is not None:
pr_import.db.item_update(item_id=job_id,
par_dict={
"parentid": parentid,
"masterid": masterid
})