Closed AlexanderGetka-cbica closed 3 years ago
Hi Alexander. Thank you for trying ePad. We are using nginx so the addresses can be different then the documentation that you read online. To access the keycloak management interface via browser. You will need to use http://getka-pc/keycloak/auth/ . You can edit keycloak's redirecting browser address. To change the redirection address please follow ; Select ePad realm From the left menu, select clients From the right side select epad-auth Under the settings tab you will see 4 input boxes to edit. (Root URL, Valid Redirect URIs, Admin URL, Web Origins)
One important note here you shouldn't use localhost nor the 127.0.0.1 . Please use computer real ip or hostname which is mapped to a real ip other than 127.0.0.1. I will add this in the documentation.Let me know if you have further questions, issues. Thanks
On Thu, Feb 18, 2021 at 11:47 AM Alexander Getka notifications@github.com wrote:
I've recently installed ePADlite from the instructions/download available at https://epad.stanford.edu/epad-agreement.
Setup through docker-compose works for me. However, when I connect (via localhost or my hostname in the browser), I briefly see the ePAD UI before being redirected to a page with only the following contents:
ePad We are sorry... Invalid parameter: redirect_uri
I believe this error originates from Keycloak. Some brief searching yielded this ge https://stackoverflow.com/questions/45352880/keycloak-invalid-parameter-redirect-uri which suggests that this is some sort of Keycloak redirect setting that should be editable from the admin console. However, going to the keycloak admin console (via http://getka-pc/keycloak/ in my case) fails and yields a page that says "Loading..." but never actually loads. According to answers here https://stackoverflow.com/questions/59361923/keycloak-admin-console-not-accessible this has something to do with settings in Keycloak's standalone.xml causing some URLs to not be prepended with "/auth/". I looked at the Dockerfile under the Keycloak subdirectory of my "epad_lite_dist" folder and noticed that it seems to be directly manipulating the same fields in standalone.xml as mentioned in the above SO page.
I would like to try out ePADlite but I really have no idea what to do from here. Are there any tweaks I can make from the user-side to try and fix this?
Thank you!
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Hi @acavit, thank you for the quick response!
In my epad configuration file I set the hostname to be "Getka-PC". Is it possible that it's case-sensitive somehow? If so, I can try to re-configure and try again.
Also, when I use the link you provided and select the Administration console, I get auto-redirected to the page http://getka-pc/keycloak/auth/admin/master/console/ , which displays the following: This page never actually loads. Looking at the dev tools on Firefox/Chrome reveals that the page tries to load several scripts, and they fail with code 500 (log is attached). epadHTTPlogs.txt
Please let me know if there are any additional diagnostic steps I can take.
Hi Alexander you are welcome. Definitely you shouldn't use capital letters.Please use all lowercase. Please edit your hostname and let me know. I want to remind that whenever you edit your configuration you will need to edit your epad.yml again and you will need to rebuild your epad_lite_dist folder by using the ./configure_epad.sh ../epad_lite_dist ./epad.yml command. Let me know if this doesn't solve the problem we can set up a zoom call.
On Thu, Feb 18, 2021 at 12:49 PM Alexander Getka notifications@github.com wrote:
Hi @acavit https://github.com/acavit, thank you for the quick response!
In my epad configuration file I set the hostname to be "Getka-PC". Is it possible that it's case-sensitive somehow? If so, I can try to re-configure and try again.
Also, when I use the link you provided and select the Administration console, I get auto-redirected to the page http://getka-pc/keycloak/auth/admin/master/console/ , which displays the following: [image: image] https://user-images.githubusercontent.com/59709326/108418300-0a662e80-71ff-11eb-95f1-795862c87e42.png This page never actually loads. Looking at the dev tools on Firefox/Chrome reveals that the page tries to load several scripts, and they fail with code 500 (log is attached). epadHTTPlogs.txt https://github.com/RubinLab/epadlite/files/6005772/epadHTTPlogs.txt
Please let me know if there are any additional diagnostic steps I can take.
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OK, this fixed the issue with ePAD redirecting me, I can now access the application at a basic level. Thanks!
However, I suspect a few things are still wrong -- please let me know if I should open another issue for this.
First, the keycloak admin console is still inaccessible, same page/error.
Second, the UI appears to be missing some components, and uploading DICOMs via the upload dialog doesn't seem to cause any change. The page looks like the following screenshot, and nothing I do seems to add information. (I only included the top, the rest of the view is just gray.) Clicking Display doesn't make any change and using the upload button succeeds/throws no error, but nothing appears afterwards in any menu I can find... am I missing something?
Let's coordinate for a call whenever you have time in the next few days.
Hi Alexander please delete all containers and all epad images before this fresh start. For the configuration please edit mode and set it to thick instead of lite. Let me know if the issue persists so we can set a zoom call. I will suggest using the installation script. It will make all these steps easier since it deletes the images and containers for you automatically.
On Thu, Feb 18, 2021 at 2:12 PM Alexander Getka notifications@github.com wrote:
OK, this fixed the issue with ePAD redirecting me, I can now access the application at a basic level. Thanks!
However, I suspect a few things are still wrong -- please let me know if I should open another issue for this.
First, the keycloak admin console is still inaccessible, same page/error.
Second, the UI appears to be missing some components, and uploading DICOMs via the upload dialog doesn't seem to cause any change. The page looks like the following screenshot, and nothing I do seems to add information. (I only included the top, the rest of the view is just gray.) [image: image] https://user-images.githubusercontent.com/59709326/108427877-cd546900-720b-11eb-8c61-4f5461bfaa23.png Clicking Display doesn't make any change and using the upload button succeeds/throws no error, but nothing appears afterwards in any menu I can find... am I missing something?
Let's coordinate for a call whenever you have time in the next few days.
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OK, setting the mode to thick made some further progress.
Now I see more of the UI (with Reports, Flex and Projects), but now it wants me to create a project before I can upload anything. Based on the documentation, this makes sense. But when I try to create a project (or add a user, or anything...) I get the following text: "Verifying token and getting userinfo: getaddrinfo ENOTFOUND getka-pc".
Would you send me the error messages by checking the log files? ( Docker logs epad_lite ) Thanks
On Thu, Feb 18, 2021 at 2:45 PM Alexander Getka notifications@github.com wrote:
OK, setting the mode to thick made some further progress.
Now I see more of the UI (with Reports, Flex and Projects), but now it wants me to create a project before I can upload anything. Based on the documentation, this makes sense. But when I try to create a project (or add a user, or anything...) I get the following text: [image: image] https://user-images.githubusercontent.com/59709326/108431252-9c2a6780-7210-11eb-9b0b-4dcbdd8e947c.png "Verifying token and getting userinfo: getaddrinfo ENOTFOUND getka-pc".
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Oddly, when I redirect this to my log file I get the following:
You have triggered an unhandledRejection, you may have forgotten to catch a Promise rejection: TypeError: Cannot read property 'define' of undefined at module.exports (/home/node/app/models/annotations.js:4:20) at Object.initOntologyModels (/home/node/app/plugins/Ontology.js:20:9) at /home/node/app/plugins/Ontology.js:476:15 at manageErr (/home/node/app/node_modules/fastify/fastify.js:436:11) at exit (/home/node/app/node_modules/fastify/lib/hooks.js:90:5) at manageTimeout (/home/node/app/node_modules/fastify/lib/hooks.js:107:11) at _encapsulateThreeParam (/home/node/app/node_modules/avvio/boot.js:545:7) at Boot.timeoutCall (/home/node/app/node_modules/avvio/boot.js:447:5) at Boot.callWithCbOrNextTick (/home/node/app/node_modules/avvio/boot.js:428:19) at Task.release (/home/node/app/node_modules/fastq/queue.js:143:16)
But anyway the log is attached. epad_lite.log
ddi you change the mysql password and user in between the installation ? Looks like it does not connect to your epad_mysql.
On Thu, Feb 18, 2021 at 2:59 PM Alexander Getka notifications@github.com wrote:
Oddly, when I redirect this to my log file I get the following:
You have triggered an unhandledRejection, you may have forgotten to catch a Promise rejection: TypeError: Cannot read property 'define' of undefined at module.exports (/home/node/app/models/annotations.js:4:20) at Object.initOntologyModels (/home/node/app/plugins/Ontology.js:20:9) at /home/node/app/plugins/Ontology.js:476:15 at manageErr (/home/node/app/node_modules/fastify/fastify.js:436:11) at exit (/home/node/app/node_modules/fastify/lib/hooks.js:90:5) at manageTimeout (/home/node/app/node_modules/fastify/lib/hooks.js:107:11) at _encapsulateThreeParam (/home/node/app/node_modules/avvio/boot.js:545:7) at Boot.timeoutCall (/home/node/app/node_modules/avvio/boot.js:447:5) at Boot.callWithCbOrNextTick (/home/node/app/node_modules/avvio/boot.js:428:19) at Task.release (/home/node/app/node_modules/fastq/queue.js:143:16)
But anyway the log is attached. epad_lite.log https://github.com/RubinLab/epadlite/files/6006422/epad_lite.log
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I didn't change anything from between these installations. The first time before I ran the installation I changed everything in epad.yml to have admin/admin as the credentials for everything I could (keycloak, couchdb, and mariadb) as mentioned in the installation guide. Is that what you're talking about? Is there a specific location to control the mysql user/password?
I see. I was mentioning the same location epad.yml. This is the only location that we set/edit passwords and users. Would you try to login to your mysql in epad_mariadb container to see if it is working? To login :
Does it login to your mysql ?
On Thu, Feb 18, 2021, 3:20 PM Alexander Getka notifications@github.com wrote:
I didn't change anything from between these installations. The first time before I ran the installation I changed everything in epad.yml to have admin/admin as the credentials for everything I could (keycloak, couchdb, and mariadb) as mentioned in the installation guide. Is that what you're talking about? Is there a specific location to control the mysql user/password?
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docker exec -it epad_mariadb sh
mysql -uroot -p
Enter password: ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)
Hmm, seems like it's not allowing this. I do have the password and root password set to the same in this instance if that matters.
I see. looks like the script didn't complete the installation yet or encountered some issues . Would you go to your epad_lite_dist folder and do docker-compose down and after use docker-compose up -d to restart all ? Please check that all the containers are healthy (we are expecting to see 4 healthy containers ) (to list containers: docker ps -a) What is your operating system ? Thanks
On Thu, Feb 18, 2021, 3:39 PM Alexander Getka notifications@github.com wrote:
docker exec -it epad_mariadb sh
mysql -uroot -p
Enter password: ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES)
Hmm, seems like it's not allowing this. I do have the password and root password set to the same in this instance if that matters.
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All containers were/are healthy both before and after a restart. I see: epad_mariadb, epad_couchdb, epad_keycloak, epad_dicomweb, epad_lite, epad_js all running.
I'm on Windows using MobaXTerm for the Linux utilities. Every script so far has run without any sort of error message. I'm also going to try on an Ubuntu 18.04 workstation later tonight, I'll let you know how that goes.
We didn't test ePad on windows before. Thank you very much for your feedback.
On Thu, Feb 18, 2021 at 4:11 PM Alexander Getka notifications@github.com wrote:
All containers were/are healthy both before and after a restart. I see: epad_mariadb, epad_couchdb, epad_keycloak, epad_dicomweb, epad_lite, epad_js all running.
I'm on Windows using MobaXTerm for the Linux utilities. Every script so far has run without any sort of error message. I'm also going to try on an Ubuntu 18.04 workstation later tonight, I'll let you know how that goes.
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I will suggest you to use centos7 for now. We encountered a couple issues with Ubuntu and we are working to make ePad stable on Ubuntu. Thanks
On Thu, Feb 18, 2021 at 4:31 PM cavit altindag cavitaltindag@gmail.com wrote:
We didn't test ePad on windows before. Thank you very much for your feedback.
On Thu, Feb 18, 2021 at 4:11 PM Alexander Getka notifications@github.com wrote:
All containers were/are healthy both before and after a restart. I see: epad_mariadb, epad_couchdb, epad_keycloak, epad_dicomweb, epad_lite, epad_js all running.
I'm on Windows using MobaXTerm for the Linux utilities. Every script so far has run without any sort of error message. I'm also going to try on an Ubuntu 18.04 workstation later tonight, I'll let you know how that goes.
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Hi Alexander. Just finished testing on Ubuntu 20.04.2.0 LTS. So it is safe to use this version. By default the server has the hostname ubuntu and the name is mapped to 127.0.0.1. If you want to use the default server hostname you will need to remap its ip to a real ip. To do : edit the ip in /etc/hosts
To find the server real ip : use the command ifconfig
Thanks
On Thu, Feb 18, 2021 at 4:41 PM cavit altindag cavitaltindag@gmail.com wrote:
I will suggest you to use centos7 for now. We encountered a couple issues with Ubuntu and we are working to make ePad stable on Ubuntu. Thanks
On Thu, Feb 18, 2021 at 4:31 PM cavit altindag cavitaltindag@gmail.com wrote:
We didn't test ePad on windows before. Thank you very much for your feedback.
On Thu, Feb 18, 2021 at 4:11 PM Alexander Getka notifications@github.com wrote:
All containers were/are healthy both before and after a restart. I see: epad_mariadb, epad_couchdb, epad_keycloak, epad_dicomweb, epad_lite, epad_js all running.
I'm on Windows using MobaXTerm for the Linux utilities. Every script so far has run without any sort of error message. I'm also going to try on an Ubuntu 18.04 workstation later tonight, I'll let you know how that goes.
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Thanks so much again for the detailed support. I'll give this a try!
Hi Alexander,
I've encountered the same issues as you on keycloak. I switched back to keycloak 11.0.0 and it seems to solve the problem. I've also encountered another issue related to missing the _users database in CouchDB. I've created one and the problem disappeared.
Now it couldn't start the ReactJS's epadlite server. I've encountered the following
{"level":40,"time":1613730165830,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_user"} {"level":40,"time":1613730165831,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist"} {"level":40,"time":1613730165876,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_study"} {"level":40,"time":1613730165983,"pid":17,"hostname":"fc996b546722","msg":"worklist_id column is added to project_subject_study_series_user_status"} {"level":40,"time":1613730165990,"pid":17,"hostname":"fc996b546722","msg":"We need to migrate the db for lite project"} {"level":40,"time":1613730166012,"pid":17,"hostname":"fc996b546722","msg":"Lite project is created"} {"level":50,"time":1613730166021,"pid":17,"hostname":"fc996b546722","msg":"Cannot connect to mariadb (err:afterDBReady. Error: Lite2thick data migration. Error: Cannot read property 'filter' of undefined), shutting down the server"} {"level":30,"time":1613730166393,"pid":17,"hostname":"fc996b546722","msg":"Server listening at http://0.0.0.0:8080"}
Any advice on this would be appreciated.
Hi Are you using sudo during the installation process? Did you make your couchdb data folder public (777) ? What is your operating system? Wkuld you try mode:thick instead of mode: lite Thanks Cavit
On Sun, Feb 21, 2021, 5:18 AM yonefx notifications@github.com wrote:
Hi Alexander,
I've encountered the same issues as you on keycloak. I switched back to keycloak 11.0.0 and it seems to solve the problem. I've also encountered another issue related to missing the _users database in CouchDB. I've created one and the problem disappeared.
Now it couldn't start the ReactJS's epadlite server. I've encountered the following
{"level":40,"time":1613730165830,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_user"} {"level":40,"time":1613730165831,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist"} {"level":40,"time":1613730165876,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_study"} {"level":40,"time":1613730165983,"pid":17,"hostname":"fc996b546722","msg":"worklist_id column is added to project_subject_study_series_user_status"} {"level":40,"time":1613730165990,"pid":17,"hostname":"fc996b546722","msg":"We need to migrate the db for lite project"} {"level":40,"time":1613730166012,"pid":17,"hostname":"fc996b546722","msg":"Lite project is created"} {"level":50,"time":1613730166021,"pid":17,"hostname":"fc996b546722","msg":"Cannot connect to mariadb (err:afterDBReady. Error: Lite2thick data migration. Error: Cannot read property 'filter' of undefined), shutting down the server"} {"level":30,"time":1613730166393,"pid":17,"hostname":"fc996b546722","msg":"Server listening at http://0.0.0.0:8080"}
Any advice on this would be appreciated.
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Hi Are you using sudo during the installation process? Did you make your couchdb data folder public (777) ? What is your operating system? Wkuld you try mode:thick instead of mode: lite Thanks Cavit … On Sun, Feb 21, 2021, 5:18 AM yonefx @.***> wrote: Hi Alexander, I've encountered the same issues as you on keycloak. I switched back to keycloak 11.0.0 and it seems to solve the problem. I've also encountered another issue related to missing the _users database in CouchDB. I've created one and the problem disappeared. Now it couldn't start the ReactJS's epadlite server. I've encountered the following {"level":40,"time":1613730165830,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_user"} {"level":40,"time":1613730165831,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist"} {"level":40,"time":1613730165876,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_study"} {"level":40,"time":1613730165983,"pid":17,"hostname":"fc996b546722","msg":"worklist_id column is added to project_subject_study_series_user_status"} {"level":40,"time":1613730165990,"pid":17,"hostname":"fc996b546722","msg":"We need to migrate the db for lite project"} {"level":40,"time":1613730166012,"pid":17,"hostname":"fc996b546722","msg":"Lite project is created"} {"level":50,"time":1613730166021,"pid":17,"hostname":"fc996b546722","msg":"Cannot connect to mariadb (err:afterDBReady. Error: Lite2thick data migration. Error: Cannot read property 'filter' of undefined), shutting down the server"} {"level":30,"time":1613730166393,"pid":17,"hostname":"fc996b546722","msg":"Server listening at http://0.0.0.0:8080"} Any advice on this would be appreciated. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#219 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFUAUTBUSCL637PJVDQLRLTAEB4DANCNFSM4X25HSAA .
Solved by using v0.5 for both epadlite and epadjs and changed to the think mode Works like a charm.
Hi. I am not sure about your setup so if you could provide me some info about your setup I can guide you better. Log files also would be good for epad_lite and epad_mariadb. 401 code by itself it doesn't explain much. It says you need to login. Thanks
On Sun, Feb 21, 2021 at 7:25 PM yonefx notifications@github.com wrote:
Hi Are you using sudo during the installation process? Did you make your couchdb data folder public (777) ? What is your operating system? Wkuld you try mode:thick instead of mode: lite Thanks Cavit … <#m536305855235776090> On Sun, Feb 21, 2021, 5:18 AM yonefx @.***> wrote: Hi Alexander, I've encountered the same issues as you on keycloak. I switched back to keycloak 11.0.0 and it seems to solve the problem. I've also encountered another issue related to missing the _users database in CouchDB. I've created one and the problem disappeared. Now it couldn't start the ReactJS's epadlite server. I've encountered the following {"level":40,"time":1613730165830,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_user"} {"level":40,"time":1613730165831,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist"} {"level":40,"time":1613730165876,"pid":17,"hostname":"fc996b546722","msg":"Migrated worklist_study"} {"level":40,"time":1613730165983,"pid":17,"hostname":"fc996b546722","msg":"worklist_id column is added to project_subject_study_series_user_status"} {"level":40,"time":1613730165990,"pid":17,"hostname":"fc996b546722","msg":"We need to migrate the db for lite project"} {"level":40,"time":1613730166012,"pid":17,"hostname":"fc996b546722","msg":"Lite project is created"} {"level":50,"time":1613730166021,"pid":17,"hostname":"fc996b546722","msg":"Cannot connect to mariadb (err:afterDBReady. Error: Lite2thick data migration. Error: Cannot read property 'filter' of undefined), shutting down the server"} {"level":30,"time":1613730166393,"pid":17,"hostname":"fc996b546722","msg":"Server listening at http://0.0.0.0:8080"} Any advice on this would be appreciated. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#219 (comment) https://github.com/RubinLab/epadlite/issues/219#issuecomment-782856944>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFUAUTBUSCL637PJVDQLRLTAEB4DANCNFSM4X25HSAA .
Solved by using v0.5 for both epadlite and epadjs. I've got the following: {"statusCode":401,"error":"Unauthorized","message":"Authentication info does not exist or conform with the server"} after calling /api
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Great to hear that it solved the issue. Thanks for your feedback during the installation process.
I've recently installed ePADlite from the instructions/download available at https://epad.stanford.edu/epad-agreement.
Setup through docker-compose works for me. However, when I connect (via localhost or my hostname in the browser), I briefly see the ePAD UI before being redirected to a page with only the following contents:
ePad We are sorry... Invalid parameter: redirect_uri
I believe this error originates from Keycloak. Some brief searching yielded this page which suggests that this is some sort of Keycloak redirect setting that should be editable from the admin console.
However, going to the keycloak admin console (via http://getka-pc/keycloak/ in my case) fails and yields a page that says "Loading..." but never actually loads. According to answers here this has something to do with settings in Keycloak's standalone.xml causing some URLs to not be prepended with "/auth/". I looked at the Dockerfile under the Keycloak subdirectory of my "epad_lite_dist" folder and noticed that it seems to be directly manipulating the same fields in standalone.xml as mentioned in the above SO page.
I would like to try out ePADlite but I really have no idea what to do from here. Are there any tweaks I can make from the user-side to try and fix this?
Thank you!