-
Notifications
You must be signed in to change notification settings - Fork 13
/
export_archive.py
159 lines (142 loc) · 5.44 KB
/
export_archive.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
import os
import numpy as np
from shutil import copyfile
from pyfileindex import PyFileIndex
import tarfile
from shutil import rmtree
from pyiron_base.project.archiving.shared import getdir
from pyiron_base.utils.instance import static_isinstance
def new_job_id(job_id, job_translate_dict):
if isinstance(job_id, float) and not np.isnan(job_id):
job_id = int(job_id)
if isinstance(job_id, int):
return job_translate_dict[job_id]
else:
return None
def update_project(project_instance, directory_to_transfer, archive_directory, df):
directory_to_transfer = os.path.basename(directory_to_transfer)
pr_transfer = project_instance.open(os.curdir)
dir_name_transfer = getdir(path=directory_to_transfer)
dir_name_archive = getdir(path=archive_directory)
path_rel_lst = [
os.path.relpath(p, pr_transfer.project_path) for p in df["project"].values
]
return [
os.path.join(dir_name_archive, dir_name_transfer, p)
if p != "."
else os.path.join(dir_name_archive, dir_name_transfer)
for p in path_rel_lst
]
def filter_function(file_name):
return ".h5" in file_name
def generate_list_of_directories(df_files, directory_to_transfer, archive_directory):
path_rel_lst = [
os.path.relpath(d, directory_to_transfer) for d in df_files.dirname.unique()
]
dir_name_transfer = getdir(path=directory_to_transfer)
return [
os.path.join(archive_directory, dir_name_transfer, p)
if p != "."
else os.path.join(archive_directory, dir_name_transfer)
for p in path_rel_lst
]
def compress_dir(archive_directory):
arch_comp_name = archive_directory + ".tar.gz"
tar = tarfile.open(arch_comp_name, "w:gz")
tar.add(os.path.relpath(archive_directory, os.getcwd()))
tar.close()
rmtree(archive_directory)
def copy_files_to_archive(
directory_to_transfer, archive_directory, compressed=True, copy_all_files=False
):
"""
Create an archive of jobs in directory_to_transfer.
Args:
directory_to_transfer (str): project directory with jobs to export
archive_directory (str): name of the final archive; if no file ending is given .tar.gz is added automatically when needed
compressed (bool): if True compress archive_directory as a tarball; default True
copy_all_files (bool): if True include job output files in archive, otherwise just include .h5 files; default False
"""
if archive_directory[-7:] == ".tar.gz":
archive_directory = archive_directory[:-7]
if not compressed:
compressed = True
if directory_to_transfer[-1] != "/":
directory_to_transfer = os.path.basename(directory_to_transfer)
else:
directory_to_transfer = os.path.basename(directory_to_transfer[:-1])
# print("directory to transfer: "+directory_to_transfer)
if not copy_all_files:
pfi = PyFileIndex(path=directory_to_transfer, filter_function=filter_function)
else:
pfi = PyFileIndex(path=directory_to_transfer)
df_files = pfi.dataframe[~pfi.dataframe.is_directory]
# Create directories
dir_lst = generate_list_of_directories(
df_files=df_files,
directory_to_transfer=directory_to_transfer,
archive_directory=archive_directory,
)
# print(dir_lst)
for d in dir_lst:
os.makedirs(d, exist_ok=True)
# Copy files
dir_name_transfer = getdir(path=directory_to_transfer)
for f in df_files.path.values:
copyfile(
f,
os.path.join(
archive_directory,
dir_name_transfer,
os.path.relpath(f, directory_to_transfer),
),
)
if compressed:
compress_dir(archive_directory)
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