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bib-lookup-0.0.9
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مشاهده بیشترتوضیحات
A useful tool for looking up Bib entries using DOI, or pubmed ID (or URL), or arXiv ID (or URL).
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bib-lookup-0.0.9 |
| نام | bib-lookup |
| نسخه کتابخانه | 0.0.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | DeepPSP |
| ایمیل نویسنده | wenh06@gmail.com |
| آدرس صفحه اصلی | https://github.com/DeepPSP/bib_lookup |
| آدرس اینترنتی | https://pypi.org/project/bib-lookup/ |
| مجوز | MIT |
# bib_lookup
[](https://codecov.io/github/DeepPSP/bib_lookup)
[](https://zenodo.org/badge/latestdoi/476130336)
A useful tool for looking up Bib entries using DOI, or pubmed ID (or URL), or arXiv ID (or URL).
It is an updated version of
<https://github.com/wenh06/utils/blob/master/utils_universal/utils_bib.py>
**NOTE** that you should have internet connection to use `bib_lookup`.
<!-- toc -->
- [Installation](#installation)
- [Dependencies](#dependencies)
- [Basic Usage Examples](#basic-usage-examples)
- [Command-line Usage](#command-line-usage)
- [Output (Append) to a `.bib` File](#append-to-file)
- [arXiv to DOI](#arxiv-to-doi)
- [Bib Items Checking](#bib-items-checking)
- [Simplify a `.bib` File](#simplify-file)
- [`CitationMixin` class](#citation-mixin)
- [TODO](#todo)
- [WARNING](#warning)
- [Biblatex Cheetsheet](#biblatex-cheetsheet)
- [Citation](#citation)
- [References](#references)
<!-- tocstop -->
## Installation
Run
```bash
python -m pip install bib-lookup
```
or install the latest version in [GitHub](https://github.com/DeepPSP/bib_lookup/) using
```bash
python -m pip install git+https://github.com/DeepPSP/bib_lookup.git
```
or git clone this repository and install locally via
```bash
cd bib_lookup
python -m pip install .
```
:point_right: [Back to TOC](#bib_lookup)
## Dependencies
- requests
- feedparser
- pandas
:point_right: [Back to TOC](#bib_lookup)
## Basic Usage Examples
<details>
<summary>Click to expand!</summary>
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup(align="middle")
>>> print(bl("1707.07183"))
@article{wen2017_1707.07183v2,
author = {Hao Wen and Chunhui Liu},
title = {Counting Multiplicities in a Hypersurface over a Number Field},
journal = {arXiv preprint arXiv:1707.07183v2},
year = {2017},
month = {7},
}
>>> print(bl("10.1109/CVPR.2016.90"))
@inproceedings{He_2016,
author = {Kaiming He and Xiangyu Zhang and Shaoqing Ren and Jian Sun},
title = {Deep Residual Learning for Image Recognition},
booktitle = {2016 {IEEE} Conference on Computer Vision and Pattern Recognition ({CVPR})},
doi = {10.1109/cvpr.2016.90},
year = {2016},
month = {6},
publisher = {{IEEE}},
}
>>> print(bl("10.23919/cinc53138.2021.9662801", align="left-middle"))
@inproceedings{Wen_2021,
author = {Hao Wen and Jingsu Kang},
title = {Hybrid Arrhythmia Detection on Varying-Dimensional Electrocardiography: Combining Deep Neural Networks and Clinical Rules},
booktitle = {2021 Computing in Cardiology ({CinC})},
doi = {10.23919/cinc53138.2021.9662801},
year = {2021},
month = {9},
publisher = {{IEEE}},
}
```
:point_right: [Back to TOC](#bib_lookup)
</details>
## Command-line Usage
<details>
<summary>Click to expand!</summary>
After installation, one can use `bib-lookup` in the command line:
```bash
bib-lookup 10.1109/CVPR.2016.90 10.23919/cinc53138.2021.9662801 --ignore-fields url doi -i path/to/input.txt -o path/to/output.bib
```
View current version:
```bash
bib-lookup --version
```
View current configuration:
```bash
bib-lookup --config show
```
Remove current configuration:
```bash
bib-lookup --config reset
```
Set specific configuration:
```bash
bib-lookup --config "timeout=2.0;print_result=true;ignore_fields=['url','pdf']"
```
or from a `json` file or `yaml` file:
```bash
bib-lookup --config /path/to/config.json
bib-lookup --config /path/to/config.yaml
```
Note that unrecognized fields will be ignored and warning messages will be printed. The following table lists all the available configuration options:
| Option | Type | Default | Description |
|-----------------|---------|-----------------------------------------------|-----------------------------------------------------|
| `align` | `str` | `middle` | Alignment of the bib item. |
| `email` | `str` | `None` | Email address to be used in the request. |
| `ignore_fields` | `list` | `['url', 'pdf']` | Fields to be ignored in the output. |
| `ignore_errors` | `bool` | `False` | Whether to ignore errors. |
| `timeout` | `float` | `6.0` | Timeout in seconds for each request. |
| `arxiv2doi` | `bool` | `True` | Whether to convert arXiv ID to DOI. |
| `format` | `str` | `bibtex` | Output format. |
| `style` | `str` | `apa` | Citation style. Valid only when `format` is `text`. |
| `verbose` | `int` | `0` | Verbosity level. |
| `print_result` | `bool` | `False` | Whether to print the result. |
| `ordering` | `list` | `['title', 'author', 'journal', 'booktitle']` | Ordering of the fields. |
:point_right: [Back to TOC](#bib_lookup)
</details>
## <a name="append-to-file"></a> Output (Append) to a `.bib` File
<details>
<summary>Click to expand!</summary>
Each time a bib item is successfully found, it will be cached. One can call the `save` function to write the cached bib items to a `.bib` file, in the append mode.
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup()
>>> bl(["10.1109/CVPR.2016.90", "10.23919/cinc53138.2021.9662801", "DOI: 10.1142/S1005386718000305"]);
>>> len(bl)
3
>>> bl[0]
'10.1109/CVPR.2016.90'
>>> bl.save([0, 2], "path/to/some/file.bib") # save bib item corr. to "10.1109/CVPR.2016.90" and "DOI: 10.1142/S1005386718000305"
>>> len(bl)
1
>>> bl.pop(0) # remove the bib item corr. "10.23919/cinc53138.2021.9662801", equivalent to `bl.pop("10.23919/cinc53138.2021.9662801")`
>>> len(bl)
0
```
:point_right: [Back to TOC](#bib_lookup)
</details>
## arXiv to DOI
<details>
<summary>Click to expand!</summary>
From 2022.2.17, new arXiv articles are automatically assigned DOIs (old ones in progress). If one prefers DOI citation to arXiv citation then
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup(arxiv2doi=True) # the default for `arxiv2doi` is False
>>> print(bl("https://arxiv.org/abs/2204.04420"))
@misc{https://doi.org/10.48550/arxiv.2204.04420,
author = {Hao, Wen and Jingsu, Kang},
title = {Investigating Deep Learning Benchmarks for Electrocardiography Signal Processing},
doi = {10.48550/ARXIV.2204.04420},
keywords = {Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences},
publisher = {arXiv},
year = {2022},
copyright = {Creative Commons Attribution 4.0 International}
}
```
while with `bl = BibLookup()`, one would get
```latex
@article{hao2022_2204.04420v1,
author = {Wen Hao and Kang Jingsu},
title = {Investigating Deep Learning Benchmarks for Electrocardiography Signal Processing},
journal = {arXiv preprint arXiv:2204.04420v1},
year = {2022},
month = {4}
}
```
:point_right: [Back to TOC](#bib_lookup)
</details>
## Bib Items Checking
<details>
<summary>Click to expand!</summary>
One can use `BibLookup` to check the validity (**required fields, duplicate labels**, etc) of bib items in a Bib file. The following is an example with a [Bib file](/test/invalid_items.bib) with incorrect and duplicate bib items.
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup()
>>> bl.check_bib_file("./test/invalid_items.bib")
Bib item "He_2016"
starting from line 3 is not valid.
Bib item of entry type "inproceedings" should have the following fields:
['author', 'title', 'booktitle', 'year']
Bib item "Wen_2018"
starting from line 16 is not valid.
Bib item of entry type "article" should have the following fields:
['author', 'title', 'journal', 'year']
Bib items "He_2016" starting from line 3
and "He_2016" starting from line 45 is duplicate.
[3, 16, 45]
```
or from command line
```bash
bib-lookup -c ./test/invalid_items.bib
bib-lookup --ignore-fields url doi -i ./test/sample_input.txt -o ./tmp/a.bib -c true
```
:point_right: [Back to TOC](#bib_lookup)
</details>
## <a name="simplify-file"></a> Simplify a `.bib` File
<details>
<summary>Click to expand!</summary>
Sometimes one wants a clean bib without bib items that are not cited, then one can use the static method `simplify_bib_file` to generate a new `.bib` File that contains only the cited bib items from an old `.bib` File.
```python
>>> from bib_lookup import BibLookup
>>> new_bib_file_path = BibLookup.simplify_bib_file("path/to/tex/source/file", "path/to/old/bib/file")
>>> # or use the following if one has multiple source files
>>> new_bib_file_path = BibLookup.simplify_bib_file(list_of_tex_source_files_or_folders, "path/to/old/bib/file")
```
:point_right: [Back to TOC](#bib_lookup)
</details>
## <a name="citation-mixin"></a> `CitationMixin` class
<details>
<summary>Click to expand!</summary>
One can inherit the `CitationMixin` class to have the method `get_citation` for any class,
in which case one only needs to provide a `self.doi`. For example:
```python
from bib_lookup import CitationMixin
class SomeClass(CitationMixin):
doi = "10.23919/cinc53138.2021.9662801" # can also be a list
```
</details>
## TODO
<details>
<summary>Click to expand!</summary>
1. ([:heavy_check_mark:](#command-line-usage)) ~~add CLI support~~;
2. use eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi for PubMed, as in \[[3](#ref3)\];
3. try using google scholar api described in \[[4](#ref4)\] (unfortunately \[[4](#ref4)\] is charged);
4. use `Flask` to write a simple browser-based UI;
5. (:heavy_check_mark:) ~~check if the bib item is already existed in the output file, and skip saving it if so~~;
6. since arXiv articles are now automatically assigned DOIs (ref. [this blog](https://blog.arxiv.org/2022/02/17/new-arxiv-articles-are-now-automatically-assigned-dois/)), consider converting arXiv identifiers to DOI indentifiers, and requesting from DOI. Currently, the request results are different, at least the entry type is change from `article` to `misc`;
7. make `__call__` method asynchronised using `asyncio` and `aiohttp` or `httpx`.
:point_right: [Back to TOC](#bib_lookup)
</details>
## WARNING
<details>
<summary>Click to expand!</summary>
Many journals have specific requirements for the Bib entries,
for example, the title and/or journal (and/or booktitle), etc. should be **capitalized**,
which could not be done automatically since
- some abbreviations in title should have characters all in the upper case, for example
> ALBERT: A Lite BERT for Self-supervised Learning of Language Representations
- some should have characters all in in the lower case,
> mixup: Beyond Empirical Risk Minimization
- and some others should have mixed cases,
> KeMRE: Knowledge-enhanced Medical Relation Extraction for Chinese Medicine Instructions
This should be corrected by the user himself **if necessary** (which although is rare),
and remember to enclose such fields with **double curly braces**.
For example, the lookup result for the `AlexNet` paper is
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup()
>>> print(bl("https://doi.org/10.1145/3065386"))
@article{Krizhevsky_2017,
author = {Alex Krizhevsky and Ilya Sutskever and Geoffrey E. Hinton},
title = {{ImageNet} classification with deep convolutional neural networks},
journal = {Communications of the {ACM}},
doi = {10.1145/3065386},
year = {2017},
month = {5},
publisher = {Association for Computing Machinery ({ACM})},
volume = {60},
number = {6},
pages = {84--90}
}
```
This result (the title) should be adjusted to
```latex
@article{Krizhevsky_2017,
author = {Alex Krizhevsky and Ilya Sutskever and Geoffrey E. Hinton},
title = {{ImageNet Classification with Deep Convolutional Neural Networks}},
journal = {Communications of the {ACM}},
doi = {10.1145/3065386},
year = {2017},
month = {5},
publisher = {Association for Computing Machinery ({ACM})},
volume = {60},
number = {6},
pages = {84--90}
}
```
A more severe example that need manual correction is as follows
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup()
>>> print(bl("10.1093/acprof:oso/9780195058239.001.0001"))
@book{Malmivuo_1995,
author = {Jaakko Malmivuo and Robert Plonsey},
title = {{BioelectromagnetismPrinciples} and Applications of Bioelectric and Biomagnetic Fields},
doi = {10.1093/acprof:oso/9780195058239.001.0001},
year = {1995},
month = {10},
publisher = {Oxford University Press}
}
```
Adjust it to
```latex
@book{Malmivuo_1995,
author = {Jaakko Malmivuo and Robert Plonsey},
title = {{Bioelectromagnetism: Principles and Applications of Bioelectric and Biomagnetic Fields}},
doi = {10.1093/acprof:oso/9780195058239.001.0001},
year = {1995},
month = {10},
publisher = {Oxford University Press}
}
```
This shows that the data in the DOI database is **NOT** always correct.
:point_right: [Back to TOC](#bib_lookup)
</details>
## Biblatex Cheetsheet
[This file](/biblatex-cheatsheet.pdf) downloaded from \[[6](#ref6)\] gives full knowledge about `bib` entries.
:point_right: [Back to TOC](#bib_lookup)
## Citation
```latex
@misc{https://doi.org/10.5281/zenodo.6435017,
author = {WEN, Hao},
title = {bib\_lookup: A Useful Tool for Uooking Up Bib Entries},
doi = {10.5281/ZENODO.6435017},
url = {https://zenodo.org/record/6435017},
publisher = {Zenodo},
year = {2022},
copyright = {MIT License}
}
```
The above citation can be get via
```python
>>> from bib_lookup import BibLookup
>>> bl = BibLookup()
>>> print(bl("DOI: 10.5281/zenodo.6435017"))
```
:point_right: [Back to TOC](#bib_lookup)
## References
1. <a name="ref1"></a> https://github.com/davidagraf/doi2bib2
2. <a name="ref2"></a> https://arxiv.org/help/api
3. <a name="ref3"></a> https://github.com/mfcovington/pubmed-lookup/
4. <a name="ref4"></a> https://serpapi.com/google-scholar-cite-api
5. <a name="ref5"></a> https://www.bibtex.com/
6. <a name="ref6"></a> http://tug.ctan.org/info/biblatex-cheatsheet/biblatex-cheatsheet.pdf
:point_right: [Back to TOC](#bib_lookup)
نیازمندی
| مقدار | نام |
|---|---|
| - | requests |
| - | feedparser |
| - | pandas |
| - | PyYAML |
| ==22.3.0 | black |
| - | flake8 |
| - | pytest |
| - | pytest-xdist |
| - | pytest-cov |
| - | IPython |
| ==22.3.0 | black |
| - | flake8 |
| - | pytest |
| - | pytest-xdist |
| - | pytest-cov |
| - | IPython |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl bib-lookup-0.0.9:
pip install bib-lookup-0.0.9.whl
نصب پکیج tar.gz bib-lookup-0.0.9:
pip install bib-lookup-0.0.9.tar.gz