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I have the following URL which I want to post the form:

https://cluspro.bu.edu/home.php

This script does the job (thanks to DPH):

library(RSelenium) # Follow instruction here # https://rpubs.com/grahamplace/rseleniumonmac # Step 1: cd /path_to_r_code/ # Step 2: ./geckodriver #downloadable here: https://github.com/mozilla/geckodriver/releases/tag/v0.30.0 # Step 3: java -jar selenium-server-standalone.jar -port 5556 # Step 4: run this script webpage <- 'https://cluspro.bu.edu/home.php' my_jobname <- "test" receptor_pdb <- "/path/to/my_file/2fyl.pdb" ligand_pdb <- "/path/to/my_file/144_from_2yrq.pdb" # tried with double slash but don't work browser <- remoteDriver(port = 5556) browser$open() browser$navigate(webpage) # This works clk <- browser$findElement(using = "link text", "Use the server without the benefits of your own account") clk$clickElement() # This works jbn <- browser$findElement(using = "name", "jobname") jbn$sendKeysToElement(list(my_jobname)) # This works svr <- browser$findElement(using = "name", "server") svr$sendKeysToElement(list("gpu")) # This doesn't work receptor <- browser$findElement(using = "id", "showrecfile") receptor$clickElement() receptor$sendKeysToElement(list(receptor_pdb)) # # This doesn't work as well # ligand <- browser$findElement(using = "id", "showligfile") # ligand$sendKeysToElement(list(ligand_pdb)) # # This works agree <- browser$findElement(using = "name", "noncommercial") agree$clickElement() # # This works # dock <- browser$findElement(using = "name", "action") # dock$clickElement()

Except on the page where it ask for browser upload to receptor:

enter image description here

The corresponding HTML is this:

 <div> <span id="showrecpdb" class="link">Use PDB ID</span><span id="showrecfile" class="link">Upload PDB</span> </div>

This part of the code above:

receptor <- browser$findElement(using = "id", "showrecfile") receptor$clickElement() receptor$sendKeysToElement(list(receptor_pdb))

only activated the browser button like below but no file uploaded or selected.

enter image description here

If it works, it'll look something like this:

enter image description here

How can I enable it?

I'm using MacOS.X

The PDB file can be downloaded here (receptor) and here (ligand).

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2 Answers 2

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2
+150

Is this what you are after:

# This for upload 1 link receptor <- browser$findElement(using = "id", "showrecfile") receptor$clickElement() # This is the upload 1 file element rec <- browser$findElement(using = "id", "rec") rec$sendKeysToElement(list(receptor_pdb)) # This for upload 2 ligand <- browser$findElement(using = "id", "showligfile") ligand$clickElement() #This is the upload 2 file element lig <- browser$findElement(using = "id", "lig") lig$sendKeysToElement(list(ligand_pdb))
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2 Comments

upvote, though I did not test it (no dropbox), anyhow this should be the solution - no way arround clicking the button I guess!
@djmonki you saved my life!
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The RSelenium package enables to remote control the comon web browsers from R. The following code opens a remote browser session in mozilla firefox(chrome should work as well) and works the login screen - with the correct usr and pw the next page will open. As I do not have access to the closed part I can not try nor debug my code after the login screen click so I just showed one upload:

library(RSelenium) webpage <- 'https://cluspro.bu.edu/home.php' # set up and start remote controlle browser driver <- RSelenium::rsDriver(browser = 'firefox', port = 4818L) remDr <- driver[['client']] # navigate to the page remDr$navigate(webpage) # find elements by id and populate/click them usr <- remDr$findElement(using = "id", "username") usr$sendKeysToElement(list("your user name")) psw <- remDr$findElement(using = "id", "password") psw$sendKeysToElement(list("your password")) clk <- remDr$findElement(using = "id", "submit") clk$clickElement() # next page will open (you already know how to fill out the textboxes so here goes one upload upl <- remDr$findElement(using = "id", "showrecpdb") # you need a path with these double backslashes upl$sendKeysToElement(list("C:\\...\\...\\your_file.something")) # session end remDr$close()
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6 Comments

DPH thanks. I'm almost there. Everything works except the uploading of the file part. Note that the web page has a dropodown browse file for receptor and ligand upload procedure. Please see my update in my OP.
@scamander have you tried to write de file path with double backslashes not an object... on win maschines it does not work with simple slash or backslash as far as I am aware? (I can not see the content of "ligand_pdb")
I tried double slash, but still won't work. I'm using MacOS.X.
I updated my post with the link where you can download the ligand_pdb file to test for uploading.
@scamander unfortunately I do not have any MAC PC also I do not have access to the closed area - I have tried the shown combination of function calls to make an upload from Win10pro PC to this public Website maxlaumeister.com/pagecrypt and it works
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