How to query the API ?

With cURL

The REST API is queryable in command line by using cURL

Command :

$  curl --url 'https://metabocloud.mesocentre.uca.fr/index/compounds/HVYWMOMLDIMFJA-DPAQBDIFSA-N.png?community=chebi&size=medium&outputType=resource' \
        --output <path/to/output/file>

Output :

The PNG image is saved according to the path defined in the --output option.

Command :

$ curl -i --url 'https://metabocloud.mesocentre.uca.fr/index/compounds/HVYWMOMLDIMFJA-DPAQBDIFSA-N.mol?community=chebi&outputType=resource'

Output :

HTTP/2 200
accept-ranges: bytes
access-control-allow-headers: X-Metadata-Chebi-Id,X-Metadata-Creation-Date,X-Metadata-Data-License,X-Metadata-Data-Source
access-control-allow-origin: *
access-control-expose-headers: *
content-disposition: inline;filename=f.txt
content-type: text/plain
date: Fri, 20 Sep 2024 07:49:50 GMT
vary: Origin
vary: Access-Control-Request-Method
vary: Access-Control-Request-Headers
x-metadata-chebi-id: CHEBI:16113
x-metadata-creation-date: 2024-08-12
x-metadata-data-license: Creative Commons License (CC BY 4.0)
x-metadata-data-source: Chemical Entities of Biological Interest (ChEBI) Database
content-length: 3175

2024-08-12  CHEBI:16113
Chemical Entities of Biological Interest (ChEBI) Database
Creative Commons License (CC BY 4.0)
 32 35  0     1  0            999 V2000
   -2.6376   -0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5146   -0.9853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5146   -2.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6376   -2.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -2.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208   -2.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -0.9853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208    0.4770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339    0.9867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8154    0.4770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8154   -0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7677   -0.8155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3337   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7677    0.7881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8154    1.5055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -0.0040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8154   -1.5134    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6954    0.6279    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4046   -2.5266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208   -0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208   -1.5056    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9007    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339   -0.9853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339    0.0162    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339   -2.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5020    1.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3691    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2363    1.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2363    0.8154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6349    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7677    1.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1035    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0     0  0
 14 10  1  0     0  0
  9 10  1  0     0  0
 10 15  1  1     0  0
 23 11  1  0     0  0
 12 11  1  0     0  0
 11 17  1  6     0  0
  8 20  1  0     0  0
  7 20  1  0     0  0
 23 20  1  0     0  0
 25 23  1  0     0  0
  5  7  1  0     0  0
  7 16  1  1     0  0
  1  7  1  0     0  0
 13 14  1  0     0  0
 31 14  1  0     0  0
 14 18  1  6     0  0
  8  9  1  0     0  0
 13 12  1  0     0  0
  6 25  1  0     0  0
  4  5  1  0     0  0
  6  5  2  0     0  0
  2  1  1  0     0  0
  3  4  1  0     0  0
  3  2  1  0     0  0
  3 19  1  1     0  0
 20 21  1  6     0  0
 31 22  1  6     0  0
 23 24  1  1     0  0
 30 26  1  0     0  0
 27 26  1  0     0  0
 28 27  1  0     0  0
 29 28  1  0     0  0
 32 28  1  0     0  0
 30 31  1  0     0  0
M  END

Command :

$ curl -i --url 'https://metabocloud.mesocentre.uca.fr/index/compounds/HVYWMOMLDIMFJA-DPAQBDIFSA-N.png?community=chebi&size=medium&outputType=url'

Output :

HTTP/2 200
accept-ranges: bytes
access-control-allow-headers: X-Metadata-Image-Size,X-Metadata-Chebi-Id,X-Metadata-Creation-Date,X-Metadata-Data-License,X-Metadata-Data-Source
access-control-allow-origin: *
access-control-expose-headers: *
content-type: text/plain
date: Fri, 20 Sep 2024 08:48:01 GMT
vary: Origin
vary: Access-Control-Request-Method
vary: Access-Control-Request-Headers
x-metadata-chebi-id: 16113
x-metadata-creation-date: 2024-08-26
x-metadata-data-license: Creative Commons License (CC BY 4.0)
x-metadata-data-source: Chemical Entities of Biological Interest (ChEBI) Database
x-metadata-image-size: 350 x 350 px
content-length: 107

https://unh-metabocloud-resources.s3.mesocentre.uca.fr/png/chebi/medium/HVYWMOMLDIMFJA-DPAQBDIFSA-N_350.png

Command :

$ curl -i --url 'https://metabocloud.mesocentre.uca.fr/index/compounds/HVYWMOMLDIMFJA-DPAQBDIFSA-N.mol?community=chebi&outputType=url'

Output :

HTTP/2 200
accept-ranges: bytes
access-control-allow-headers: X-Metadata-Chebi-Id,X-Metadata-Creation-Date,X-Metadata-Data-License,X-Metadata-Data-Source
access-control-allow-origin: *
access-control-expose-headers: *
content-disposition: inline;filename=f.txt
content-type: text/plain
date: Fri, 20 Sep 2024 08:53:14 GMT
vary: Origin
vary: Access-Control-Request-Method
vary: Access-Control-Request-Headers
x-metadata-chebi-id: CHEBI:16113
x-metadata-creation-date: 2024-08-12
x-metadata-data-license: Creative Commons License (CC BY 4.0)
x-metadata-data-source: Chemical Entities of Biological Interest (ChEBI) Database
content-length: 96

https://unh-metabocloud-resources.s3.mesocentre.uca.fr/mol/chebi/HVYWMOMLDIMFJA-DPAQBDIFSA-N.mol

Command :

$ curl --head --url 'https://metabocloud.mesocentre.uca.fr/index/compounds/HVYWMOMLDIMFJA-DPAQBDIFSA-N.png?community=chebi&size=small&outputType=url'

Output :

HTTP/2 200
accept-ranges: bytes
access-control-allow-headers: X-Metadata-Image-Size,X-Metadata-Chebi-Id,X-Metadata-Creation-Date,X-Metadata-Data-License,X-Metadata-Data-Source
access-control-allow-origin: *
access-control-expose-headers: *
content-type: text/plain
date: Fri, 20 Sep 2024 08:10:28 GMT
vary: Origin
vary: Access-Control-Request-Method
vary: Access-Control-Request-Headers
x-metadata-chebi-id: 16113
x-metadata-creation-date: 2024-08-26
x-metadata-data-license: Creative Commons License (CC BY 4.0)
x-metadata-data-source: Chemical Entities of Biological Interest (ChEBI) Database
x-metadata-image-size: 50 x 50 px
content-length: 105

Command :

$ curl --head --url 'https://metabocloud.mesocentre.uca.fr/index/compounds/HVYWMOMLDIMFJA-DPAQBDIFSA-N.mol?community=chebi&outputType=url'

Output :

HTTP/2 200
accept-ranges: bytes
access-control-allow-headers: X-Metadata-Chebi-Id,X-Metadata-Creation-Date,X-Metadata-Data-License,X-Metadata-Data-Source
access-control-allow-origin: *
access-control-expose-headers: *
content-disposition: inline;filename=f.txt
content-type: text/plain
date: Fri, 20 Sep 2024 08:13:02 GMT
vary: Origin
vary: Access-Control-Request-Method
vary: Access-Control-Request-Headers
x-metadata-chebi-id: CHEBI:16113
x-metadata-creation-date: 2024-08-12
x-metadata-data-license: Creative Commons License (CC BY 4.0)
x-metadata-data-source: Chemical Entities of Biological Interest (ChEBI) Database
content-length: 96

With Python

One of the ways to query a REST-API with Python is to use the requests library.

After installing the requests library, you can query the REST API :

import requests

# Variables
file_format = "png"
output_type = "resource"
inchi_key = "Compound's InChI Key"
community = "Community from which the file must be retrieved"
size = "Image size wanted ('small', 'medium' or 'large')"

# Request
result = requests.get(f"https://metabocloud.mesocentre.uca.fr/index/compounds/{inchi_key}.{file_format}?community={community}&size={size}&outputType={output_type}")

# Metadata
headers = result.headers
metadata = dict(filter(lambda x: x[0].startswith("X-Metadata"), headers.items()))

# Output
with open("image.png", "wb") as file:
    file.write(result.content)

print("Metadata : ", metadata)

Output :

The PNG image is saved and the metadata are displayed.

Metadata :  {'X-Metadata-Chebi-Id': '16113', 'X-Metadata-Creation-Date': '2024-08-26', 'X-Metadata-Data-License': 'Creative Commons License (CC BY 4.0)', 'X-Metadata-Data-Source': 'Chemical Entities of Biological Interest (ChEBI) Database', 'X-Metadata-Image-Size': '350 x 350 px'}

import requests

# Variables
file_format = "mol"
output_type = "resource"
inchi_key = "Compound's InChI Key"
community = "Community from which the file must be retrieved"

# Request
result = requests.get(f"https://metabocloud.mesocentre.uca.fr/index/compounds/{inchi_key}.{file_format}?community={community}&outputType={output_type}")

# Metadata
headers = result.headers
metadata = dict(filter(lambda x: x[0].startswith("X-Metadata"), headers.items()))

# Output
output = result.text

print("Metadata : ", metadata)
print("Resource :\n", output)

Output :

Metadata :  {'X-Metadata-Chebi-Id': 'CHEBI:16113', 'X-Metadata-Creation-Date': '2024-08-12', 'X-Metadata-Data-License': 'Creative Commons License (CC BY 4.0)', 'X-Metadata-Data-Source': 'Chemical Entities of Biological Interest (ChEBI) Database'}
Resource :
2024-08-12     CHEBI:16113
Chemical Entities of Biological Interest (ChEBI) Database
Creative Commons License (CC BY 4.0)
35  0     1  0            999 V2000
   -2.6376   -0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5146   -0.9853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5146   -2.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6376   -2.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -2.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208   -2.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -0.9853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208    0.4770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339    0.9867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
8154    0.4770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
8154   -0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
7677   -0.8155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
3337   -0.0228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
7677    0.7881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
8154    1.5055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -0.0040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
8154   -1.5134    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
6954    0.6279    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4046   -2.5266    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208   -0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9208   -1.5056    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
9007    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339   -0.9853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339    0.0162    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0339   -2.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
5020    1.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
3691    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
2363    1.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
2363    0.8154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
6349    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
7677    1.8166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
1035    2.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10  1  0     0  0
10  1  0     0  0
10  1  0     0  0
15  1  1     0  0
11  1  0     0  0
11  1  0     0  0
17  1  6     0  0
20  1  0     0  0
20  1  0     0  0
20  1  0     0  0
23  1  0     0  0
7  1  0     0  0
16  1  1     0  0
7  1  0     0  0
14  1  0     0  0
14  1  0     0  0
18  1  6     0  0
9  1  0     0  0
12  1  0     0  0
25  1  0     0  0
5  1  0     0  0
5  2  0     0  0
1  1  0     0  0
4  1  0     0  0
2  1  0     0  0
19  1  1     0  0
21  1  6     0  0
22  1  6     0  0
24  1  1     0  0
26  1  0     0  0
26  1  0     0  0
27  1  0     0  0
28  1  0     0  0
28  1  0     0  0
31  1  0     0  0
M  END

import requests

# Variables
file_format = "png"
output_type = "url"
inchi_key = "Compound's InChI Key"
community = "Community from which the file must be retrieved"
size = "Image size wanted ('small', 'medium' or 'large')"

# Request
result = requests.get(f"https://metabocloud.mesocentre.uca.fr/index/compounds/{inchi_key}.{file_format}?community={community}&size={size}&outputType={output_type}")

# Metadata
headers = result.headers
metadata = dict(filter(lambda x: x[0].startswith("X-Metadata"), headers.items()))

# Output
output = result.text

print("Metadata : ", metadata)
print("URL : ", output)

Output :

Metadata :  {'X-Metadata-Chebi-Id': '16113', 'X-Metadata-Creation-Date': '2024-08-26', 'X-Metadata-Data-License': 'Creative Commons License (CC BY 4.0)', 'X-Metadata-Data-Source': 'Chemical Entities of Biological Interest (ChEBI) Database', 'X-Metadata-Image-Size': '350 x 350 px'}
Output :  https://unh-metabocloud-resources.s3.mesocentre.uca.fr/png/chebi/medium/HVYWMOMLDIMFJA-DPAQBDIFSA-N_350.png

import requests

# Variables
file_format = "mol"
output_type = "url"
inchi_key = "Compound's InChI Key"
community = "Community from which the file must be retrieved"

# Request
result = requests.get(f"https://metabocloud.mesocentre.uca.fr/index/compounds/{inchi_key}.{file_format}?community={community}&outputType={output_type}")

# Metadata
headers = result.headers
metadata = dict(filter(lambda x: x[0].startswith("X-Metadata"), headers.items()))

# Output
output = result.text

print("Metadata : ", metadata)
print("URL : ", output)

Output :

Metadata :  {'X-Metadata-Chebi-Id': '16113', 'X-Metadata-Creation-Date': '2024-08-26', 'X-Metadata-Data-License': 'Creative Commons License (CC BY 4.0)', 'X-Metadata-Data-Source': 'Chemical Entities of Biological Interest (ChEBI) Database'}
Output :  https://unh-metabocloud-resources.s3.mesocentre.uca.fr/mol/chebi/HVYWMOMLDIMFJA-DPAQBDIFSA-N.mol

import requests

# Variables
file_format = "png"
output_type = "resource"
inchi_key = "Compound's InChI Key"
community = "Community from which the file must be retrieved"
size = "Image size wanted ('small', 'medium' or 'large')"

# Request
result = requests.head(f"https://metabocloud.mesocentre.uca.fr/index/compounds/{inchi_key}.{file_format}?community={community}&size={size}&outputType={output_type}")

# Metadata
headers = result.headers
metadata = dict(filter(lambda x: x[0].startswith("X-Metadata"), headers.items()))

print("Metadata : ", metadata)

Output :

Metadata :  {'X-Metadata-Chebi-Id': '16113', 'X-Metadata-Creation-Date': '2024-08-26', 'X-Metadata-Data-License': 'Creative Commons License (CC BY 4.0)', 'X-Metadata-Data-Source': 'Chemical Entities of Biological Interest (ChEBI) Database', 'X-Metadata-Image-Size': '350 x 350 px'}

import requests

# Variables
file_format = "mol"
output_type = "resource"
inchi_key = "Compound's InChI Key"
community = "Community from which the file must be retrieved"

# Request
result = requests.head(f"https://metabocloud.mesocentre.uca.fr/index/compounds/{inchi_key}.{file_format}?community={community}&outputType={output_type}")

# Metadata
headers = result.headers
metadata = dict(filter(lambda x: x[0].startswith("X-Metadata"), headers.items()))

print("Metadata : ", metadata)

Output :

Metadata :  {'X-Metadata-Chebi-Id': '16113', 'X-Metadata-Creation-Date': '2024-08-26', 'X-Metadata-Data-License': 'Creative Commons License (CC BY 4.0)', 'X-Metadata-Data-Source': 'Chemical Entities of Biological Interest (ChEBI) Database'}

Note

If you ran the application locally on your machine from a virtual environment or via Docker, you need to change the URL you send the request to. This means that https://metabocloud.mesocentre.uca.fr/index/compounds/ will become http://localhost:8084/compounds/ if you launched the application with the default parameters.

If you choose another port to run the application then you need to change the URL accordingly.

With a client generated by Swagger

From the OpenAPI specification file describing this REST API, you can auto-generated a client in the language you want thanks to Swagger using the option Generate Client in the menu.

The OpenAPI specification file is downloadable here : https://metabocloud.mesocentre.uca.fr/index/metabocloud-index.yaml