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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
|
%global _empty_manifest_terminate_build 0
Name: python-bdbag
Version: 1.6.4
Release: 1
Summary: Big Data Bag Utilities
License: Apache 2.0
URL: https://github.com/fair-research/bdbag/
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/07/f0/59784061351b4f148658694c4de44ff7cd01706beaff4d4c56b05c632dc8/bdbag-1.6.4.tar.gz
BuildArch: noarch
Requires: python3-pytz
Requires: python3-tzlocal
Requires: python3-certifi
Requires: python3-requests
Requires: python3-setuptools-scm
Requires: python3-bagit
Requires: python3-bagit-profile
Requires: python3-requests
Requires: python3-boto3
Requires: python3-botocore
Requires: python3-awscli
Requires: python3-google-cloud-storage
Requires: python3-globus-sdk
%description
# bdbag
[](https://app.travis-ci.com/fair-research/bdbag)
[](https://coveralls.io/github/fair-research/bdbag?branch=master)
[](https://pypi.python.org/pypi/bdbag)
[](https://pepy.tech/project/bdbag)
[](https://pypi.python.org/pypi/bdbag)
[](https://anaconda.org/conda-forge/bdbag)
[](https://anaconda.org/conda-forge/bdbag)
[](https://pypi.python.org/pypi/bdbag)
[](http://www.apache.org/licenses/LICENSE-2.0)
## Big Data Bag Utilities
The `bdbag` utilities are a collection of software programs for working with
[BagIt](https://datatracker.ietf.org/doc/draft-kunze-bagit/) packages that conform to the BDBag and Bagit/RO profiles.
The `bdbag` [profiles](https://github.com/fair-research/bdbag/tree/master/profiles) specify the use of the `fetch.txt`
file, require serialization, and specify what manifests must be provided with a `bdbag`.
The `bdbag` utilities incorporate functions from various other Python-based `bagit` components (such as the
[Bagit-Python](https://github.com/LibraryOfCongress/bagit-python) bag creation utility and the
[Bagit-Profiles-Validator](https://github.com/ruebot/bagit-profiles)
utility) and wraps them in a single, easy to use software package with additional features.
Enhanced bag support includes:
* Update-in-place functionality for existing bags.
* Automatic archiving and extraction of bags using ZIP, TAR, and TGZ formats.
* Automatic generation of file manifest entries and `fetch.txt` for remote files via configuration file.
* Automatic file retrieval based on the contents of a bag's `fetch.txt` file with multiple protocol support. Transport
handlers for `http(s)`,`ftp`,`s3`,`gs`, and `globus` are provided, along with an extensibility mechanism for adding
externally developed transports.
* Built-in `bagit-profile` validation.
* Built-in support for creation of bags with [Bagit/RO profile](https://github.com/ResearchObject/bagit-ro) compatibility.
An experimental Graphical User Interface (GUI) for `bdbag` can be found [here](https://github.com/fair-research/bdbag_gui).
#### Technical Papers
["I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets"](https://zenodo.org/record/820878) explains the motivation for BDBags and the related Minid construct, provides details on design and implementation, and gives examples of use.
["Reproducible big data science: A case study in continuous FAIRness"](https://www.biorxiv.org/content/early/2018/02/27/268755) presents a data analysis use case in which BDBags and Minids are used to capture a transcription factor binding site analysis.
### Dependencies
* [Python 2.7](https://www.python.org/downloads/release/python-27/) is the minimum Python version required.
* The code and dependencies are also compatible with Python 3, versions 3.5 through 3.9.
### Installation
The latest `bdbag` release is available on PyPi and can be installed using `pip`:
```sh
pip install bdbag
```
Note that the above command will install `bdbag` with only the minimal dependencies required to run.
If you wish to install `bdbag` with the extra fetch transport handler support provided by `boto` (for AWS S3)
and `globus` (for Globus Transfer) packages, use the following command:
```sh
pip install bdbag[boto,globus]
```
### Installation from Source
You can use `pip` to install `bdbag` directly from GitHub:
```sh
sudo pip install git+https://github.com/fair-research/bdbag
```
or:
```sh
pip install --user git+https://github.com/fair-research/bdbag
```
You can also [download](https://github.com/fair-research/bdbag/archive/master.zip) the current `bdbag` source code from GitHub or
alternatively clone the source from GitHub if you have *git* installed:
```sh
git clone https://github.com/fair-research/bdbag
```
From the root of the `bdbag` source code directory execute the following command:
```sh
sudo pip install .
```
or:
```sh
pip install --user .
```
Note that if you want to install the extra dependencies from a local source directory you would use the following command:
```sh
pip install .[boto,globus]
```
### Testing
The unit tests can be run by invoking the following command from the root of the `bdbag` source code directory:
```sh
python setup.py test
```
### Usage
This software can be used from the command-line environment by running the `bdbag` script. For detailed usage
instructions, see the [CLI Guide](./doc/cli.md).
### Configuration
Some components of the `bdbag` software can be configured via JSON-formatted configuration files.
See the [Configuration Guide](./doc/config.md) for further details.
### Application Programming Interface
It is also possible to use `bdbag` from within other Python programs via an API.
See the [API Guide](./doc/api.md) for further details.
### Utilities
A CLI utility module is provided for various ancillary tasks commonly involved with authoring **bdbags**.
See the [Utility Guide](./doc/utils.md) for further details.
### Change Log
The change log is located [here](CHANGELOG.md).
%package -n python3-bdbag
Summary: Big Data Bag Utilities
Provides: python-bdbag
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-bdbag
# bdbag
[](https://app.travis-ci.com/fair-research/bdbag)
[](https://coveralls.io/github/fair-research/bdbag?branch=master)
[](https://pypi.python.org/pypi/bdbag)
[](https://pepy.tech/project/bdbag)
[](https://pypi.python.org/pypi/bdbag)
[](https://anaconda.org/conda-forge/bdbag)
[](https://anaconda.org/conda-forge/bdbag)
[](https://pypi.python.org/pypi/bdbag)
[](http://www.apache.org/licenses/LICENSE-2.0)
## Big Data Bag Utilities
The `bdbag` utilities are a collection of software programs for working with
[BagIt](https://datatracker.ietf.org/doc/draft-kunze-bagit/) packages that conform to the BDBag and Bagit/RO profiles.
The `bdbag` [profiles](https://github.com/fair-research/bdbag/tree/master/profiles) specify the use of the `fetch.txt`
file, require serialization, and specify what manifests must be provided with a `bdbag`.
The `bdbag` utilities incorporate functions from various other Python-based `bagit` components (such as the
[Bagit-Python](https://github.com/LibraryOfCongress/bagit-python) bag creation utility and the
[Bagit-Profiles-Validator](https://github.com/ruebot/bagit-profiles)
utility) and wraps them in a single, easy to use software package with additional features.
Enhanced bag support includes:
* Update-in-place functionality for existing bags.
* Automatic archiving and extraction of bags using ZIP, TAR, and TGZ formats.
* Automatic generation of file manifest entries and `fetch.txt` for remote files via configuration file.
* Automatic file retrieval based on the contents of a bag's `fetch.txt` file with multiple protocol support. Transport
handlers for `http(s)`,`ftp`,`s3`,`gs`, and `globus` are provided, along with an extensibility mechanism for adding
externally developed transports.
* Built-in `bagit-profile` validation.
* Built-in support for creation of bags with [Bagit/RO profile](https://github.com/ResearchObject/bagit-ro) compatibility.
An experimental Graphical User Interface (GUI) for `bdbag` can be found [here](https://github.com/fair-research/bdbag_gui).
#### Technical Papers
["I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets"](https://zenodo.org/record/820878) explains the motivation for BDBags and the related Minid construct, provides details on design and implementation, and gives examples of use.
["Reproducible big data science: A case study in continuous FAIRness"](https://www.biorxiv.org/content/early/2018/02/27/268755) presents a data analysis use case in which BDBags and Minids are used to capture a transcription factor binding site analysis.
### Dependencies
* [Python 2.7](https://www.python.org/downloads/release/python-27/) is the minimum Python version required.
* The code and dependencies are also compatible with Python 3, versions 3.5 through 3.9.
### Installation
The latest `bdbag` release is available on PyPi and can be installed using `pip`:
```sh
pip install bdbag
```
Note that the above command will install `bdbag` with only the minimal dependencies required to run.
If you wish to install `bdbag` with the extra fetch transport handler support provided by `boto` (for AWS S3)
and `globus` (for Globus Transfer) packages, use the following command:
```sh
pip install bdbag[boto,globus]
```
### Installation from Source
You can use `pip` to install `bdbag` directly from GitHub:
```sh
sudo pip install git+https://github.com/fair-research/bdbag
```
or:
```sh
pip install --user git+https://github.com/fair-research/bdbag
```
You can also [download](https://github.com/fair-research/bdbag/archive/master.zip) the current `bdbag` source code from GitHub or
alternatively clone the source from GitHub if you have *git* installed:
```sh
git clone https://github.com/fair-research/bdbag
```
From the root of the `bdbag` source code directory execute the following command:
```sh
sudo pip install .
```
or:
```sh
pip install --user .
```
Note that if you want to install the extra dependencies from a local source directory you would use the following command:
```sh
pip install .[boto,globus]
```
### Testing
The unit tests can be run by invoking the following command from the root of the `bdbag` source code directory:
```sh
python setup.py test
```
### Usage
This software can be used from the command-line environment by running the `bdbag` script. For detailed usage
instructions, see the [CLI Guide](./doc/cli.md).
### Configuration
Some components of the `bdbag` software can be configured via JSON-formatted configuration files.
See the [Configuration Guide](./doc/config.md) for further details.
### Application Programming Interface
It is also possible to use `bdbag` from within other Python programs via an API.
See the [API Guide](./doc/api.md) for further details.
### Utilities
A CLI utility module is provided for various ancillary tasks commonly involved with authoring **bdbags**.
See the [Utility Guide](./doc/utils.md) for further details.
### Change Log
The change log is located [here](CHANGELOG.md).
%package help
Summary: Development documents and examples for bdbag
Provides: python3-bdbag-doc
%description help
# bdbag
[](https://app.travis-ci.com/fair-research/bdbag)
[](https://coveralls.io/github/fair-research/bdbag?branch=master)
[](https://pypi.python.org/pypi/bdbag)
[](https://pepy.tech/project/bdbag)
[](https://pypi.python.org/pypi/bdbag)
[](https://anaconda.org/conda-forge/bdbag)
[](https://anaconda.org/conda-forge/bdbag)
[](https://pypi.python.org/pypi/bdbag)
[](http://www.apache.org/licenses/LICENSE-2.0)
## Big Data Bag Utilities
The `bdbag` utilities are a collection of software programs for working with
[BagIt](https://datatracker.ietf.org/doc/draft-kunze-bagit/) packages that conform to the BDBag and Bagit/RO profiles.
The `bdbag` [profiles](https://github.com/fair-research/bdbag/tree/master/profiles) specify the use of the `fetch.txt`
file, require serialization, and specify what manifests must be provided with a `bdbag`.
The `bdbag` utilities incorporate functions from various other Python-based `bagit` components (such as the
[Bagit-Python](https://github.com/LibraryOfCongress/bagit-python) bag creation utility and the
[Bagit-Profiles-Validator](https://github.com/ruebot/bagit-profiles)
utility) and wraps them in a single, easy to use software package with additional features.
Enhanced bag support includes:
* Update-in-place functionality for existing bags.
* Automatic archiving and extraction of bags using ZIP, TAR, and TGZ formats.
* Automatic generation of file manifest entries and `fetch.txt` for remote files via configuration file.
* Automatic file retrieval based on the contents of a bag's `fetch.txt` file with multiple protocol support. Transport
handlers for `http(s)`,`ftp`,`s3`,`gs`, and `globus` are provided, along with an extensibility mechanism for adding
externally developed transports.
* Built-in `bagit-profile` validation.
* Built-in support for creation of bags with [Bagit/RO profile](https://github.com/ResearchObject/bagit-ro) compatibility.
An experimental Graphical User Interface (GUI) for `bdbag` can be found [here](https://github.com/fair-research/bdbag_gui).
#### Technical Papers
["I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets"](https://zenodo.org/record/820878) explains the motivation for BDBags and the related Minid construct, provides details on design and implementation, and gives examples of use.
["Reproducible big data science: A case study in continuous FAIRness"](https://www.biorxiv.org/content/early/2018/02/27/268755) presents a data analysis use case in which BDBags and Minids are used to capture a transcription factor binding site analysis.
### Dependencies
* [Python 2.7](https://www.python.org/downloads/release/python-27/) is the minimum Python version required.
* The code and dependencies are also compatible with Python 3, versions 3.5 through 3.9.
### Installation
The latest `bdbag` release is available on PyPi and can be installed using `pip`:
```sh
pip install bdbag
```
Note that the above command will install `bdbag` with only the minimal dependencies required to run.
If you wish to install `bdbag` with the extra fetch transport handler support provided by `boto` (for AWS S3)
and `globus` (for Globus Transfer) packages, use the following command:
```sh
pip install bdbag[boto,globus]
```
### Installation from Source
You can use `pip` to install `bdbag` directly from GitHub:
```sh
sudo pip install git+https://github.com/fair-research/bdbag
```
or:
```sh
pip install --user git+https://github.com/fair-research/bdbag
```
You can also [download](https://github.com/fair-research/bdbag/archive/master.zip) the current `bdbag` source code from GitHub or
alternatively clone the source from GitHub if you have *git* installed:
```sh
git clone https://github.com/fair-research/bdbag
```
From the root of the `bdbag` source code directory execute the following command:
```sh
sudo pip install .
```
or:
```sh
pip install --user .
```
Note that if you want to install the extra dependencies from a local source directory you would use the following command:
```sh
pip install .[boto,globus]
```
### Testing
The unit tests can be run by invoking the following command from the root of the `bdbag` source code directory:
```sh
python setup.py test
```
### Usage
This software can be used from the command-line environment by running the `bdbag` script. For detailed usage
instructions, see the [CLI Guide](./doc/cli.md).
### Configuration
Some components of the `bdbag` software can be configured via JSON-formatted configuration files.
See the [Configuration Guide](./doc/config.md) for further details.
### Application Programming Interface
It is also possible to use `bdbag` from within other Python programs via an API.
See the [API Guide](./doc/api.md) for further details.
### Utilities
A CLI utility module is provided for various ancillary tasks commonly involved with authoring **bdbags**.
See the [Utility Guide](./doc/utils.md) for further details.
### Change Log
The change log is located [here](CHANGELOG.md).
%prep
%autosetup -n bdbag-1.6.4
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-bdbag -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Apr 25 2023 Python_Bot <Python_Bot@openeuler.org> - 1.6.4-1
- Package Spec generated
|
