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Error appears while opening SMARTS file with query which contains comma #1310

Closed
urszula-gawlowska opened this issue Oct 9, 2023 · 0 comments · Fixed by #1327
Closed

Error appears while opening SMARTS file with query which contains comma #1310

urszula-gawlowska opened this issue Oct 9, 2023 · 0 comments · Fixed by #1327
Assignees
@AliaksandrDziarkach
Labels
Bug epic: smarts
Projects
Indigo
Milestone
Indigo-1.15.0-rc.1

Comments

@urszula-gawlowska
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urszula-gawlowska commented Oct 9, 2023 •
edited

Steps to Reproduce

  1. Launch "Ketcher"
  2. Draw a Benzene
  3. Double click on the Benzene to open 'Atom properties' menu
  4. Open 'Query properties' submenu
  5. Set up values for few properties
  6. Scroll down and mark 'Custom query' option
  7. Replace any semicolon with a comma
  8. Click 'Apply' button
  9. Click 'Save as' button
  10. Set file format to 'Daylight SMARTS'
  11. Click 'Save' button
  12. Click 'Open' button
  13. Click 'Open from file' button
  14. Choose smarts file with comma which was created at step 11.
  15. Click 'Add to canvas' button

Expected behavior
File open properly without errors

Actual behavior
File is not open and error message appears:
Convert error! Unexpected token '<', "<!DOCTYPE "... is not valid JSON
Request with 502 status code appears:
Payload:

{
  "struct": "[#6]1-[#6]=[#6]-[#6]=[#6]-[b;r;3;s&2,X3]=1",
  "output_format": "chemical/x-indigo-ket",
  "options": {
    "smart-layout": true,
    "ignore-stereochemistry-errors": true,
    "mass-skip-error-on-pseudoatoms": false,
    "gross-formula-add-rsites": true,
    "aromatize-skip-superatoms": true,
    "dearomatize-on-load": false,
    "ignore-no-chiral-flag": false
  }
}

Response:

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">

<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
    <head>
        <title>The page is temporarily unavailable</title>
        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
        <style type="text/css">
            /*<![CDATA[*/
            body {
                background-color: #fff;
                color: #000;
                font-size: 0.9em;
                font-family: sans-serif,helvetica;
                margin: 0;
                padding: 0;
            }
            :link {
                color: #c00;
            }
            :visited {
                color: #c00;
            }
            a:hover {
                color: #f50;
            }
            h1 {
                text-align: center;
                margin: 0;
                padding: 0.6em 2em 0.4em;
                background-color: #294172;
                color: #fff;
                font-weight: normal;
                font-size: 1.75em;
                border-bottom: 2px solid #000;
            }
            h1 strong {
                font-weight: bold;
                font-size: 1.5em;
            }
            h2 {
                text-align: center;
                background-color: #3C6EB4;
                font-size: 1.1em;
                font-weight: bold;
                color: #fff;
                margin: 0;
                padding: 0.5em;
                border-bottom: 2px solid #294172;
            }
            h3 {
                text-align: center;
                background-color: #ff0000;
                padding: 0.5em;
                color: #fff;
            }
            hr {
                display: none;
            }
            .content {
                padding: 1em 5em;
            }
            .alert {
                border: 2px solid #000;
            }

            img {
                border: 2px solid #fff;
                padding: 2px;
                margin: 2px;
            }
            a:hover img {
                border: 2px solid #294172;
            }
            .logos {
                margin: 1em;
                text-align: center;
            }
            /*]]>*/
        </style>
    </head>

    <body>
        <h1><strong>nginx error!</strong></h1>

        <div class="content">

            <h3>The page you are looking for is temporarily unavailable.  Please try again later.</h3>

            <div class="alert">
                <h2>Website Administrator</h2>
                <div class="content">
                    <p>Something has triggered an error on your
                    website.  This is the default error page for
                    <strong>nginx</strong> that is distributed with
                    Amazon Linux 2.  It is located
                    <tt>/usr/share/nginx/html/50x.html</tt></p>

                    <p>You should customize this error page for your own
                    site or edit the <tt>error_page</tt> directive in
                    the <strong>nginx</strong> configuration file
                    <tt>/etc/nginx/nginx.conf</tt>.</p>

                </div>
            </div>

            <div class="logos">
                <a href="http://nginx.net/"><img
                    src="/nginx-logo.png"
                    alt="[ Powered by nginx ]"
                    width="121" height="32" /></a>

                <a href="https://amazonlinux.com/"><img 
                    src="/poweredby.png"
                    alt="[ Powered by Amazon Linux 2 ]" 
                    width="88" height="31" /></a>
            </div>
        </div>
    </body>
</html>

Attachments
Example of smarts file:
smarts_with_comma.zip

smarts_with_comma_error

Indigo/Bingo version
Version 1.11.0-rc.1.72-g5c14b0708-x86_64-linux-gnu-11.4.0

Additional context
@urszula-gawlowska urszula-gawlowska added this to the Indigo-1.14.0-rc.3 milestone Oct 9, 2023
@urszula-gawlowska urszula-gawlowska added this to Product Backlog in Indigo via automation Oct 9, 2023
@AliaksandrDziarkach AliaksandrDziarkach moved this from Product Backlog to In review in Indigo Oct 13, 2023
@AliaksandrDziarkach AliaksandrDziarkach linked a pull request Oct 13, 2023 that will close this issue
#1310 Error while opening SMARTS contains comma #1327
Merged
Indigo automation moved this from In review to Done Oct 13, 2023
AliaksandrDziarkach added a commit that referenced this issue Oct 13, 2023
@AliaksandrDziarkach
#1310 Error while opening SMARTS contains comma (#1327)
e82c9eb
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Assignees

@AliaksandrDziarkach AliaksandrDziarkach

Labels
Bug epic: smarts
Projects
Indigo
  
Done
Milestone
Indigo-1.15.0-rc.1
Development

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#1310 Error while opening SMARTS contains comma
4 participants
@AlexanderSavelyev @even1024 @AliaksandrDziarkach @urszula-gawlowska