Try to call the REST APIs provided by Enrichr from Matlab, but webwrite does not work

Trying to translate a piece of Python code below to Matlab. The Python code is provided by Enrichr (see maayanlab.cloud/Enrichr/help#api) as an example for calling its REST APIs.

%{

% - this is the Python code

import json

import requests

ENRICHR_URL = 'https://maayanlab.cloud/Enrichr/addList'

genes_str = '\n'.join([

'PHF14', 'RBM3', 'MSL1', 'PHF21A', 'ARL10', 'INSR', 'JADE2', 'P2RX7',

'LINC00662', 'CCDC101', 'PPM1B', 'KANSL1L', 'CRYZL1', 'ANAPC16', 'TMCC1',

'CDH8', 'RBM11', 'CNPY2', 'HSPA1L', 'CUL2', 'PLBD2', 'LARP7', 'TECPR2',

'ZNF302', 'CUX1', 'MOB2', 'CYTH2', 'SEC22C', 'EIF4E3', 'ROBO2',

'ADAMTS9-AS2', 'CXXC1', 'LINC01314', 'ATF7', 'ATP5F1'

])

description = 'Example gene list'

payload = {

'list': (None, genes_str),

'description': (None, description)

}

response = requests.post(ENRICHR_URL, files=payload)

%}

% - this is the Matlab code

ENRICHR_URL = 'https://maayanlab.cloud/Enrichr/addList';

genes = {'PHF14', 'RBM3', 'MSL1', 'PHF21A', 'ARL10', 'INSR', 'JADE2', 'P2RX7', ...

'LINC00662', 'CCDC101', 'PPM1B', 'KANSL1L', 'CRYZL1', 'ANAPC16', 'TMCC1', ...

'CDH8', 'RBM11', 'CNPY2', 'HSPA1L', 'CUL2', 'PLBD2', 'LARP7', 'TECPR2', ...

'ZNF302', 'CUX1', 'MOB2', 'CYTH2', 'SEC22C', 'EIF4E3', 'ROBO2', ...

'ADAMTS9-AS2', 'CXXC1', 'LINC01314', 'ATF7', 'ATP5F1'};

genes_str = strjoin(genes, newline);

description = 'Example gene list';

options = weboptions('MediaType', 'application/json');

payload(1).('list') = [];

payload(2).('list') = genes_str;

payload(1).('description') = [];

payload(2).('description') = description;

%payload = struct('list', {string(missing), genes_str}, ...

% 'description', {string(missing), description});

response = webwrite(ENRICHR_URL, payload, options)

But, the translated Matlab code does not work. Any suggestions would be greatly apprecaited.

Answer 1

[Piyush Kumar]

@James Cai,

It looks like the issue might be related to how the payload is structured and sent in the MATLAB code. The webwrite function in MATLAB does not directly support the multipart/form-data content type, which is required for the Enrichr API. Instead, you can use the matlab.net.http package to create a more complex HTTP request.

The Python code provided use the files parameter in the requests.post method, which is typically used for multipart form-data.

In the context of the Enrichr API, the files parameter is used to send the gene list and description as separate parts of the request, even though they are not files. This is a common pattern for APIs that expect multipart form-data.

I tried the following code and it worked -

import matlab.net.URI
import matlab.net.http.RequestMessage
import matlab.net.http.io.MultipartProvider
import matlab.net.http.io.MultipartFormProvider

ENRICHR_URL = 'https://maayanlab.cloud/Enrichr/addList';
genes = {'PHF14', 'RBM3', 'MSL1', 'PHF21A', 'ARL10', 'INSR', 'JADE2', 'P2RX7', ...
         'LINC00662', 'CCDC101', 'PPM1B', 'KANSL1L', 'CRYZL1', 'ANAPC16', 'TMCC1', ...
         'CDH8', 'RBM11', 'CNPY2', 'HSPA1L', 'CUL2', 'PLBD2', 'LARP7', 'TECPR2', ...
         'ZNF302', 'CUX1', 'MOB2', 'CYTH2', 'SEC22C', 'EIF4E3', 'ROBO2', ...
         'ADAMTS9-AS2', 'CXXC1', 'LINC01314', 'ATF7', 'ATP5F1'};
genes_str = strjoin(genes, newline);
description = 'Example gene list';
disp(genes_str)

PHF14
RBM3
MSL1
PHF21A
ARL10
INSR
JADE2
P2RX7
LINC00662
CCDC101
PPM1B
KANSL1L
CRYZL1
ANAPC16
TMCC1
CDH8
RBM11
CNPY2
HSPA1L
CUL2
PLBD2
LARP7
TECPR2
ZNF302
CUX1
MOB2
CYTH2
SEC22C
EIF4E3
ROBO2
ADAMTS9-AS2
CXXC1
LINC01314
ATF7
ATP5F1

disp(description)

Example gene list

% Create the payload
formData = MultipartFormProvider( 'list', genes_str, 'description', description);

% Create the request
request = RequestMessage('post', [], formData);

% Send the request
uri = URI(ENRICHR_URL);
response = send(request, uri);

disp(response)

  ResponseMessage with properties:

    StatusLine: 'HTTP/1.1 200 '
    StatusCode: OK
        Header: [1x11 matlab.net.http.HeaderField]
          Body: [1x1 matlab.net.http.MessageBody]
     Completed: 0

[James Cai]

@Piyush Kumar - Awesome!