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  1. IGB
  2. IGBF-2494

Fix [Fatal Error] :1:50: White spaces are required between publicId and systemId occurring in Update plugin

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      0.25
    • Sprint:
      Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep

      Description

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            ann.loraine Ann Loraine added a comment - - edited

            Moving forward, IGB code that accesses BioViz.org needs to use https instead of http as the protocol.

            However, older version of IGB do not do this. So I am concerned that if we continue to redirect http to https on the Web server, we might end up blocking the ability of old versions of IGB to access the Web site.

            So I wonder: should I modify the bioviz site to stop redirecting client requests to https?

            attn: Philip Badzuh and Prutha Kulkarni

            Relevant code is in:

            Code is:

            - name: httpd.conf
              become: yes
              blockinfile:
                dest: /etc/httpd/conf/httpd.conf
                insertafter: EOF
                state: present
                block: |
                  Alias "/public" "/var/www/genome-dashboard/public"
                  Redirect /igb/news.html https://{{ server_name }}/news.html
                  Redirect /igb/help.html https://{{ server_name }}/help.html
                  <VirtualHost *:80>
                     ServerName {{ server_name }}
                     Redirect / https://{{ server_name }}/
                  </VirtualHost>
            
            Show
            ann.loraine Ann Loraine added a comment - - edited Moving forward, IGB code that accesses BioViz.org needs to use https instead of http as the protocol. However, older version of IGB do not do this. So I am concerned that if we continue to redirect http to https on the Web server, we might end up blocking the ability of old versions of IGB to access the Web site. So I wonder: should I modify the bioviz site to stop redirecting client requests to https? attn: Philip Badzuh and Prutha Kulkarni Relevant code is in: https://bitbucket.org/lorainelab/bioviz-playbooks/src/master/roles/apache/tasks/main.yml Code is: - name: httpd.conf become: yes blockinfile: dest: /etc/httpd/conf/httpd.conf insertafter: EOF state: present block: | Alias "/ public " "/ var /www/genome-dashboard/ public " Redirect /igb/news.html https: //{{ server_name }}/news.html Redirect /igb/help.html https: //{{ server_name }}/help.html <VirtualHost *:80> ServerName {{ server_name }} Redirect / https: //{{ server_name }}/ </VirtualHost>
            Hide
            prutha Prutha Kulkarni (Inactive) added a comment -

            I think there shouldn't be a problem if we change all the "bioviz.org" links that pare present in all the IGB modules to "https".
            Currently when I searched "bioviz.org" link all over IGB codebase, I found that of all the links which are pointing to "bioviz.org", there are some links which has "https". Whereas, a few of them still have "http". In order to address the issues that might occur in future, even if we point the site to "http" again, we will have to make a few uniform changes in IGB codebase to make each link consistent or we could just change all the links in IGB codebase to "https" instead of changing the bioviz server back to "http".

            cc: [~aloraine]

            Show
            prutha Prutha Kulkarni (Inactive) added a comment - I think there shouldn't be a problem if we change all the "bioviz.org" links that pare present in all the IGB modules to "https". Currently when I searched "bioviz.org" link all over IGB codebase, I found that of all the links which are pointing to "bioviz.org", there are some links which has "https". Whereas, a few of them still have "http". In order to address the issues that might occur in future, even if we point the site to "http" again, we will have to make a few uniform changes in IGB codebase to make each link consistent or we could just change all the links in IGB codebase to "https" instead of changing the bioviz server back to "http". cc: [~aloraine]
            Hide
            ann.loraine Ann Loraine added a comment -

            I agree. If there are "http" links going to BioViz.org, let's change them to "https".

            Show
            ann.loraine Ann Loraine added a comment - I agree. If there are "http" links going to BioViz.org, let's change them to "https".
            Hide
            shamika Shamika Gajanan Kulkarni (Inactive) added a comment -

            Please find the code changes here:
            https://bitbucket.org/skulka2710/shamika_igb/branch/IGBF-2494#diff

            Moving the ticket to First Level Review.

            Show
            shamika Shamika Gajanan Kulkarni (Inactive) added a comment - Please find the code changes here: https://bitbucket.org/skulka2710/shamika_igb/branch/IGBF-2494#diff Moving the ticket to First Level Review.
            Hide
            pbadzuh Philip Badzuh (Inactive) added a comment -

            I have tested the branch, and the error is no longer being thrown with the new changes. Please submit a pull request at your convenience.

            Show
            pbadzuh Philip Badzuh (Inactive) added a comment - I have tested the branch, and the error is no longer being thrown with the new changes. Please submit a pull request at your convenience.
            Show
            shamika Shamika Gajanan Kulkarni (Inactive) added a comment - PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/823/igbf-2494-change-http-links-to-biovizorg/diff
            Hide
            ann.loraine Ann Loraine added a comment -

            Merged and built master branch installers. Ready for testing.

            Show
            ann.loraine Ann Loraine added a comment - Merged and built master branch installers. Ready for testing.
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -

            Working as expected.

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - Working as expected.

              People

              • Assignee:
                shamika Shamika Gajanan Kulkarni (Inactive)
                Reporter:
                prutha Prutha Kulkarni (Inactive)
              • Votes:
                0 Vote for this issue
                Watchers:
                5 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: