Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28
Description
Note: I'm not sure if this is a problem with just my browser and not clearing the cache or memory properly.
When trying to view the table at https://bioviz.org/public-trackhubs.html, an error message appeared in the console and the table never loaded.
A screen capture showing the problem and the error message is attached.
Also, clicking the icons in the final column did not do anything, even though IGB was running on the desktop. (I'm not sure if these problems are related or not.)
Attachments
Activity
To clear application data in chrome:
Developer tools > Application > Storage > Clear site data
Please see my changes here.
Changes look good! Please submit PR.
attn: Philip Badzuh
Please see PR here.
Merged and newly deployed to BioViz main. Ready for testing.
To test:
- Open IGB
- Open the trackhubs site
- Choose any row that has at least one genome icon in the genome versions column
- Click on the Q icon to copy the quickload URL
- Paste it into IGB to add a new datasource
- Click on any genome in that row and the genome should be opened in IGB
Philip Badzuh The trackhub website doesn't show any rows. I cleared the application data but still getting the same result. Please look into it.
The error I am seeing in the console is the below:
Uncaught SyntaxError: The requested module './util.js' does not provide an export named 'BACKEND_DOMAIN'
and after inspecting util.js, in the browser, I see that the line is:
const BACKEND_DOMAIN = "translate.bioviz.org";
instead of the expected
export const BACKEND_DOMAIN = "translate.bioviz.org";
The source code on which bioviz playbook runs DOES contain the export keyword, so the issue must be with the playbook. I took a look at the playbook, and it looks correct, so I am unsure what is causing this issue during deployment.
bioviz-playbooks/roles/hub_facade/tasks/main.yml
- name: Use hub facade back end domain {{ hub_facade_domain }}
become: yes
lineinfile:
path: /var/www/bioviz/htdocs/js/trackhub/util.js
regexp: "export const BACKEND_DOMAIN"
line: 'export const BACKEND_DOMAIN = "{{ hub_facade_domain }}";'
[~aloraine], it could be useful to be able to inspect util.js on the bioviz ec2 host, but I don't have ssh permissions.
Looking into it.
cc: Philip Badzuh & Omkar Marne
The file is visible at https://bioviz.org/js/trackhub/util.js
Is this what you needed Philip Badzuh ?
Yes, I saw that file, but I'm unsure why the export keyword is missing in it. I was thinking that maybe on the server the export keyword is there, but there is an issue with the apache server serving an outdated/cached version of the file. Otherwise, I'm not sure what's going on. Could you check the file that is actually on the server, [~aloraine]?
Philip Badzuh requests to see the output of the playbook following an update.
playbook output:
local aloraine$ ansible-playbook -i inventory.ini setup.yml PLAY [targets] ************************************************************************************************** TASK [Gathering Facts] ****************************************************************************************** ok: [biovizmain] TASK [install : upgrade all packages] *************************************************************************** ok: [biovizmain] TASK [install : install software] ******************************************************************************* ok: [biovizmain] TASK [install : install] **************************************************************************************** changed: [biovizmain] TASK [pubkey : Add keys for Prod stack] ************************************************************************* ok: [biovizmain] => (item=/Users/aloraine/src/bioviz-playbooks/roles/pubkey/files/Prod/Add/nowlanfreese.pub) ok: [biovizmain] => (item=/Users/aloraine/src/bioviz-playbooks/roles/pubkey/files/Prod/Add/annloraine.pub) ok: [biovizmain] => (item=/Users/aloraine/src/bioviz-playbooks/roles/pubkey/files/Prod/Add/annloraine2.pub) TASK [pubkey : Remove keys for Prod stack] ********************************************************************** ok: [biovizmain] => (item=/Users/aloraine/src/bioviz-playbooks/roles/pubkey/files/Prod/Remove/chiragshetty.pub) ok: [biovizmain] => (item=/Users/aloraine/src/bioviz-playbooks/roles/pubkey/files/Prod/Remove/karthikraveendran.pub) TASK [lorainelab_faves : .bashrc for ec2-user] ***************************************************************** ok: [biovizmain] TASK [lorainelab_faves : root .bashrc] ************************************************************************** ok: [biovizmain] TASK [lorainelab_faves : create git alias ls for root user] ***************************************************** ok: [biovizmain] TASK [lorainelab_faves : create git alias ls for ec2-user] ****************************************************** ok: [biovizmain] TASK [lorainelab_faves : create git alias ll for root user] ***************************************************** ok: [biovizmain] TASK [lorainelab_faves : create git alias ll for ec2-user] ****************************************************** ok: [biovizmain] TASK [lorainelab_faves : create git alias alias for root user] ************************************************** ok: [biovizmain] TASK [lorainelab_faves : create git alias alias for ec2-user] *************************************************** ok: [biovizmain] TASK [clone : clone https://bitbucket.org/lorainelab/bioviz.git] ************************************************ changed: [biovizmain] TASK [clone : clone https://bitbucket.org/lorainelab/genome-dashboard.git] ************************************** changed: [biovizmain] TASK [clone : clone https://bitbucket.org/nfreese/quickload-genome-in-a-bottle.git] ***************************** ok: [biovizmain] TASK [apache : document root] *********************************************************************************** ok: [biovizmain] TASK [apache : script alias] ************************************************************************************ ok: [biovizmain] TASK [apache : server name] ************************************************************************************* ok: [biovizmain] TASK [apache : allowing .htaccess] ****************************************************************************** ok: [biovizmain] TASK [apache : httpd.conf] ************************************************************************************** ok: [biovizmain] TASK [apache : ssl.conf] **************************************************************************************** ok: [biovizmain] TASK [apache : use DigiCertCA.crt] ****************************************************************************** ok: [biovizmain] TASK [apache : server-chain.crt] ******************************************************************************** ok: [biovizmain] TASK [apache : localhost.crt] *********************************************************************************** ok: [biovizmain] TASK [apache : localhost.key] *********************************************************************************** ok: [biovizmain] TASK [apache : start httpd] ************************************************************************************* ok: [biovizmain] TASK [content : igbserver] ************************************************************************************** ok: [biovizmain] TASK [igb : make release dir] *********************************************************************************** ok: [biovizmain] TASK [igb : get installer and jar files for release] ************************************************************ ok: [biovizmain] => (item=IGB-macos-9.1.8.dmg) ok: [biovizmain] => (item=IGB-unix-9.1.8.sh) ok: [biovizmain] => (item=IGB-windows-x32-9.1.8.exe) ok: [biovizmain] => (item=IGB-windows-x64-9.1.8.exe) ok: [biovizmain] => (item=igb_exe-9.1.8.jar) TASK [igb : updates.xml] **************************************************************************************** ok: [biovizmain] TASK [igb : mac installer link] ********************************************************************************* ok: [biovizmain] TASK [igb : linux installer link] ******************************************************************************* ok: [biovizmain] TASK [igb : windows 32-bit installer link] ********************************************************************** ok: [biovizmain] TASK [igb : windows 64-bit installer link] ********************************************************************** ok: [biovizmain] TASK [igb : current link] *************************************************************************************** changed: [biovizmain] TASK [igb : early access] *************************************************************************************** changed: [biovizmain] TASK [javadoc : make dir for 1.1.9] ***************************************************************************** ok: [biovizmain] TASK [javadoc : get and unzip jar] ****************************************************************************** ok: [biovizmain] TASK [javadoc : current link] *********************************************************************************** ok: [biovizmain] TASK [node : scp setup_10.x] ************************************************************************************ ok: [biovizmain] TASK [node : run setup_10.x (prep for nodejs+np install)] ******************************************************* ok: [biovizmain] TASK [node : nodejs+np install] ********************************************************************************* ok: [biovizmain] TASK [node : pm2] *********************************************************************************************** ok: [biovizmain] TASK [node : genome-dashboard dependencies] ********************************************************************* ok: [biovizmain] TASK [node : delete existing pm2 process if running] ************************************************************ changed: [biovizmain] TASK [node : start pm2] ***************************************************************************************** changed: [biovizmain] TASK [node : add pm2 to system startup] ************************************************************************* changed: [biovizmain] TASK [menu : Copy bioviz menu content to genome dashboard] ****************************************************** changed: [biovizmain] TASK [menu : Copy bioviz menu styling to genome dashboard] ****************************************************** changed: [biovizmain] TASK [menu : Modify menu href links to specify a particular bioviz hostname] ************************************ changed: [biovizmain] TASK [replace : Specify IGB branch and repo for quickloads] ***************************************************** changed: [biovizmain] TASK [replace : Specify IGB branch and repo for synonyms.txt] *************************************************** changed: [biovizmain] TASK [replace : Specify IGB branch and repo for species.txt] **************************************************** changed: [biovizmain] TASK [hub_facade : Use hub facade back end domain translate.bioviz.org] ***************************************** changed: [biovizmain] RUNNING HANDLER [node : restart apache2] ************************************************************************ changed: [biovizmain] PLAY RECAP ****************************************************************************************************** biovizmain : ok=57 changed=16 unreachable=0 failed=0 skipped=0 rescued=0 ignored=0
inventory.ini:
[targets] biovizmain ansible_host=35.153.214.38 domain=www.bioviz.org stack=Prod igb_branch=release-9.1.8 igb_version=9.1.8 igb_repository=https://bitbucket.org/lorainelab/integrated-genome-browser bioviz_repo=https://bitbucket.org/lorainelab/bioviz.git bioviz_version=master hub_facade_domain=translate.bioviz.org [targets:vars] ansible_ssh_common_args="-o StrictHostKeyChecking=no" ansible_python_interpreter=/usr/bin/python ansible_ssh_user=ec2-user
Playbooks run were up-to-date, with last commit IGBF-3007 Insert BACKEND_DOMAIN constant.
Ready for review by Philip Badzuh.
Logged into bioviz main host and checked the file util.js:
www.bioviz.org ec2-user $ git diff trackhub/util.js diff --git a/htdocs/js/trackhub/util.js b/htdocs/js/trackhub/util.js index 31b7fb4..0b2a659 100644 --- a/htdocs/js/trackhub/util.js +++ b/htdocs/js/trackhub/util.js @@ -1,4 +1,4 @@ -export const BACKEND_DOMAIN = "http://localhost:8000"; +export const BACKEND_DOMAIN = "translate.bioviz.org"; export function convertURL(url) { return BACKEND_DOMAIN.includes("http")
Does this solve the problem?
cc: Philip Badzuh
https://www.bioviz.org/public-trackhubs.html seems to be working now...is the version of bioviz-playbooks that you just ran the same one that you ran previously, [~aloraine]? If so, I am unsure as to what could have caused this problem.
Request for Omkar Marne:
Now that the table is working, please test the table interface.
Testing results:
After opening IGB and coping quickload URL as a datasource from the trackhub site, I am able to see the genome of the respective data source in the IGB.
Closing the ticket.
Add documentation to explain how to clear application memory in chrome.