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correct misspelling word botte to bottle :-) #28

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correct misspelling word botte to bottle :-) #28

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299f4d1
correct misspelling word `botte` to `bottle` :-)
def-fun Apr 15, 2020
cce8c5e
旧版Dockerfile无法构建，升级debian
def-fun Apr 9, 2024
e6b6649
update readme
def-fun Apr 9, 2024
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8 changes: 2 additions & 6 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
FROM debian:jessie-slim
FROM debian:bookworm-slim

ENV PYTHONUNBUFFERED 1

# install required ubuntu packages
RUN apt-get update --fix-missing && \
apt-get install -y --no-install-recommends ca-certificates libxrender1 libxext6 wget bzip2 libgraphicsmagick++3 libopenbabel4 libpotrace0 && \
apt-get install -y --no-install-recommends ca-certificates libxrender1 libxext6 wget bzip2 osra libopenbabel7 libpotrace0 && \
apt-get -qq -y autoremove && \
apt-get autoclean && \
rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
Expand All @@ -27,10 +27,6 @@ RUN conda env create -n chembl-beaker -f /tmp/environment.yml
# activate env (add conda env bin to path)
ENV PATH /opt/conda/envs/chembl-beaker/bin:$PATH

# osra needs both files in the same bin dir
RUN cp /opt/conda/pkgs/osra-2.0.1-0/share/spelling.txt /opt/conda/envs/chembl-beaker/bin/spelling.txt && \
cp /opt/conda/pkgs/osra-2.0.1-0/share/superatom.txt /opt/conda/envs/chembl-beaker/bin/superatom.txt

# copy beaker and config file
COPY src/chembl_beaker chembl_beaker
COPY beaker.conf beaker.conf
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241 changes: 241 additions & 0 deletions README.md
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@@ -0,0 +1,241 @@
# chembl_beaker

这个是[molOCR化学结构式识别](https://github.com/def-fun/molOCR)
的后端，在[chembl_beaker](https://github.com/chembl/chembl_beaker)的基础上修改

部署方式如下：

```shell
# install docker on your linux machine
sudo snap install docker

# download
wget https://github.com/def-fun/chembl_beaker/archive/refs/heads/master.zip
unzip chembl_beaker-master.zip

# build and run
cd chembl_beaker-master
sudo docker build -f Dockerfile -t my_chembl_beaker:v1.2 .
sudo docker run -p 5000:5000 my_chembl_beaker:v1.2

# backup
#sudo docker save -o my_chembl_beaker-v1.2.tar my_chembl_beaker:v1.2
sudo docker save 722c1891ce36 > my_chembl_beaker-v1.2.tar
7z a -mx9 my_chembl_beaker-v1.2.tar.7z my_chembl_beaker-v1.2.tar

# check size and sha1sum
# my_chembl_beaker-v1.2.tar.7z 922M de78350d2db6c7a2a1f3f9a4b86195466a3437ef
# my_chembl_beaker-v1.2.tar 3.1G 338d26ab0ccee04e661d74c9975641e5adbaa592

# restore
sudo docker load -i my_chembl_beaker-v1.2.tar
```

在Ubuntu 22.04.3 LTS上测试通过

```shell
curl -v -X POST --data-binary @test/5.png http://127.0.0.1:5000/image2ctab
```

输出结果如下

```text
* Trying 127.0.0.1:5000...
* Connected to 127.0.0.1 (127.0.0.1) port 5000 (#0)
> POST /image2ctab HTTP/1.1
> Host: 127.0.0.1:5000
> User-Agent: curl/8.1.2
> Accept: */*
> Content-Length: 18716
> Content-Type: application/x-www-form-urlencoded
>
< HTTP/1.1 200 OK
< Server: gunicorn/20.0.0
< Date: Tue, 09 Apr 2024 06:51:27 GMT
< Connection: close
< Access-Control-Allow-Origin: *
< Access-Control-Allow-Methods: GET, POST, PUT, OPTIONS
< Access-Control-Allow-Headers: Origin, Accept, Content-Type, X-Requested-With, X-CSRF-Token
< X-Chembl-In-Cache: False
< X-Chembl-Retrieval-Time: 0.5003535747528076
< Content-Length: 6474
< Content-Type: text/html; charset=UTF-8
<

OpenBabel04092406512D

11 11 0 0 0 0 0 0 0 0999 V2000
2.0160 -3.0171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4095 -3.8122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4013 -3.9398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2209 -2.4106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9388 -2.6317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9731 -1.0923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2040 -0.4284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4751 -1.1245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7645 -0.4218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2211 -3.3535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4656 -2.6188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
10 11 2 0 0 0 0
11 8 1 0 0 0 0
M END
> <Surrounding_box>
42x13-139x64

$$$$

OpenBabel04092406512D

8 8 0 0 0 0 0 0 0 0999 V2000
1.6719 -7.1503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6742 -8.6782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9791 -6.3822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2481 -7.1202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5246 -6.4152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0302 -9.3472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3258 -9.4518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2275 -8.6211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
2 6 1 0 0 0 0
2 7 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
6 8 2 0 0 0 0
8 4 1 0 0 0 0
M END
> <Surrounding_box>
41x104-120x151

$$$$

OpenBabel04092406512D

13 15 0 0 0 0 0 0 0 0999 V2000
0.4236 -13.7979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3447 -12.7275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0315 -12.1205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8915 -13.1916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2364 -12.9836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6691 -12.6501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7117 -13.7852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2770 -14.4402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8242 -14.4049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3141 -15.6207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9035 -15.3204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1576 -15.1932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7654 -15.5325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 11 1 0 0 0 0
2 4 1 0 0 0 0
3 4 1 0 0 0 0
4 8 2 0 0 0 0
5 3 1 0 0 0 0
5 6 1 0 0 0 0
6 7 2 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
9 5 2 0 0 0 0
9 13 1 0 0 0 0
11 10 2 0 0 0 0
12 7 1 0 0 0 0
13 12 2 0 0 0 0
M END
> <Surrounding_box>
42x193-153x245

$$$$

OpenBabel04092406512D

10 11 0 0 0 0 0 0 0 0999 V2000
1.6178 -19.3401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9426 -20.0320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2246 -19.3403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5461 -20.0617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5608 -21.5790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3129 -22.2478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9618 -21.5744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6980 -22.2497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3691 -21.5768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3981 -20.0590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
5 6 1 0 0 0 0
5 4 1 0 0 0 0
7 6 1 0 0 0 0
7 2 1 0 0 0 0
8 7 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
10 1 1 0 0 0 0
M END
> <Surrounding_box>
40x303-121x348

$$$$

OpenBabel04092406512D

21 23 0 0 0 0 0 0 0 0999 V2000
2.1113 -33.6262 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9409 -34.6115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0499 -33.2811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0859 -31.7463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3295 -31.0534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5904 -31.7770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8705 -31.0132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8677 -29.5344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6449 -28.8224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6222 -27.2593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9136 -26.5218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1333 -27.2780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1496 -28.7533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2062 -31.7853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4346 -34.0029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.7113 -33.2725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1704 -33.2844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2807 -33.9680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5347 -33.3323 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.6800 -31.7831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4253 -31.0646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
3 4 2 0 0 0 0
3 18 1 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 7 1 0 0 0 0
6 19 1 0 0 0 0
7 8 1 0 0 0 0
8 13 2 0 0 0 0
9 8 1 0 0 0 0
10 9 2 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
13 12 1 0 0 0 0
14 7 1 0 0 0 0
14 21 1 0 0 0 0
15 16 2 0 0 0 0
15 17 1 0 0 0 0
17 14 2 0 0 0 0
18 19 2 0 0 0 0
20 16 1 0 0 0 0
21 20 2 0 0 0 0
M END
> <Surrounding_box>
40x414-199x534

$$$$
* Closing connection 0
```
2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -85,4 +85,4 @@ Like every good software written in Python, beaker is self-documented. When you

Development - writing your own extentions
--------
Developing new app should be easy. The only required file is ``views.py`` where you should define your botte ``routes``.
Developing new app should be easy. The only required file is ``views.py`` where you should define your bottle ``routes``.
2 changes: 1 addition & 1 deletion beaker.conf
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Expand Up @@ -4,4 +4,4 @@ BOTTLE_PORT = 5000
BOTTLE_HOST = 0.0.0.0
SERVER_MIDDLEWARE = gunicorn
WORKERS = 4
OSRA_BINARIES_LOCATION = /opt/conda/envs/chembl-beaker/bin/osra
OSRA_BINARIES_LOCATION = /usr/bin/osra
1 change: 0 additions & 1 deletion environment.yml
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Expand Up @@ -10,7 +10,6 @@ dependencies:
- lxml==4.4.1
- matplotlib==3.1.1
- pycairo==1.18.1
- osra==2.0.1
- chembl_structure_pipeline==1.0.0
- pip:
- bottle==0.12.18
Expand Down
1 change: 1 addition & 0 deletions src/chembl_beaker/beaker/core_apps/osra/impl.py
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Expand Up @@ -22,6 +22,7 @@ def _recogniseImage(img, osra, frmt=None, jaggy=False, adaptive=False, unpaper=0
arguments.extend(['-u', str(unpaper)])
if frmt and frmt in ('can', 'smi', 'sdf'):
arguments.extend(['-f', frmt])
arguments.append('-c') # add surrounding box coordinates
arguments.append(fpath)
p = Popen(arguments, stdin=PIPE, stdout=PIPE, stderr=PIPE)
result, err = p.communicate(input=img)
Expand Down
4 changes: 1 addition & 3 deletions src/chembl_beaker/beaker/core_apps/osra/views.py
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Expand Up @@ -18,9 +18,7 @@ def image2ctabView(img, params):
kwargs['adaptive'] = _parseFlag(params.get('adaptive', False))
kwargs['unpaper'] = int(params.get('unpaper', 0))

known_location = '/usr/local/bin/osra'
if not os.path.exists(known_location):
known_location = '/usr/bin/osra'
known_location = '/usr/bin/osra'
return _image2ctab(img, config.get('osra_binaries_location', known_location), **kwargs)


Expand Down
Binary file added test/5.png
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