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OHDSI / Atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
http://atlas-demo.ohdsi.org/
Apache License 2.0
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Atlas never loads and struck in the same state (attached screenshot) forever #2932

Closed hkamineni closed 6 months ago

hkamineni commented 6 months ago

Hello All, Please help to resolve the following issue. Thanks for your help. Hari

Expected behavior

I expect Atlas to load. But it struck forever to load.

Actual behavior

Atlas_screenshot

The following is the result of http://localhost:8080/WebAPI/source/sources [{"sourceId":1,"sourceName":"My Cdm","sourceDialect":"sql server","sourceKey":"MY_CDM","daimons":[{"sourceDaimonId":1,"daimonType":"CDM","tableQualifier":"cdm","priority":0},{"sourceDaimonId":2,"daimonType":"Vocabulary","tableQualifier":"cdm","priority":1},{"sourceDaimonId":3,"daimonType":"Results","tableQualifier":"results","priority":1},{"sourceDaimonId":4,"daimonType":"Temp","tableQualifier":"temp","priority":0}]}]

I have sql server for CDM/Vocabulary and postgres for WebAPI.

I used the following sql statements to populate source and souce_daimon tables.

INSERT INTO webapi.source (source_id, source_name, source_key, source_connection, source_dialect,username,password) VALUES(1, 'My Cdm', 'MY_CDM', 'jdbc:sqlserver://localhost:1433;encrypt=false;integratedSecurity=false,trustServerCertificate=true','sql server','ohdsi_app_user','app1');

INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) SELECT 1, source_id, 0, 'cdm', 0 FROM webapi.source WHERE source_key = 'MY_CDM' ;

INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) SELECT 2, source_id, 1, 'cdm', 1 FROM webapi.source WHERE source_key = 'MY_CDM' ;

INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) SELECT 3, source_id, 2, 'results', 1 FROM webapi.source WHERE source_key = 'MY_CDM' ; INSERT INTO webapi.source_daimon (source_daimon_id, source_id, daimon_type, table_qualifier, priority) SELECT 4, source_id, 5, 'temp', 0 FROM webapi.source WHERE source_key = 'MY_CDM' ;

Steps to reproduce behavior

hkamineni commented 6 months ago

webapi log attached. webapi.log

chrisknoll commented 6 months ago

It looks like it didn't find one of the external libraries (d3.js) when it started up the app.

Did you follow the Atlas Setup Instructions?

To download the dependencies, you run:

npm run build

This requires you have node.js installed, which is indicated in the Prerequisites section.

hkamineni commented 6 months ago

Chris: Thanks for your quick response. Yes, I did follow the installation instructions for Atlas. I did install nodejs and ran npm build command. After npm run build and few iterations of npm audit fix i got the following. Is there anything else I should be doing to fix these errors? Thank you. Hari c:\Git\OHDSI\Atlas>npm audit fix

up to date, audited 412 packages in 2s

26 packages are looking for funding run npm fund for details

npm audit report

moment-timezone 0.1.0 - 0.5.34 Severity: moderate Command Injection in moment-timezone - https://github.com/advisories/GHSA-56x4-j7p9-fcf9 Cleartext Transmission of Sensitive Information in moment-timezone - https://github.com/advisories/GHSA-v78c-4p63-2j6c fix available via npm audit fix node_modules/moment-timezone eonasdan-bootstrap-datetimepicker >=4.17.42 Depends on vulnerable versions of moment-timezone node_modules/eonasdan-bootstrap-datetimepicker

2 vulnerabilities (1 low, 1 moderate)

To address all issues, run: npm audit fix

On Fri, May 3, 2024 at 6:36 AM Chris Knoll @.***> wrote:

It looks like it didn't find one of the external libraries (d3.js) when it started up the app.

Did you follow the Atlas Setup Instructions https://github.com/OHDSI/Atlas/wiki/Atlas-Setup-Guide#atlas-installation ?

To download the dependencies, you run:

npm run build

This requires you have node.js installed, which is indicated in the Prerequisites section.

— Reply to this email directly, view it on GitHub https://github.com/OHDSI/Atlas/issues/2932#issuecomment-2093038161, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHOF47TOLWOP5NAU4NWHGHLZAOHFLAVCNFSM6AAAAABHFQWRV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJTGAZTQMJWGE . You are receiving this because you authored the thread.Message ID: @.***>

chrisknoll commented 6 months ago

After you confirmed npm run build ran, can you check if there's a folder in your atlas root: node_modules/d3/build which should contain d3.js. After all that is there, you should be able to reload atlas and check for errors again. If it says it can't find the d3.js file, there's some local problem with your environment that's preventing it from downloading.

You don't need to run npm audit fix. When we address node library versions, we'll issue PRs and instructions on updating. I would not just update any of those dependencies because it may not work with the current version of Atlas (it would require testing before you update anything).

hkamineni commented 6 months ago

I have C:\Git\OHDSI\Atlas\node_modules\d3 folder., but there is no build directory under it. I have dist, node_modules, src directories and LICENCE, package.json and README files. Thats all i have under d3 folder.

hkamineni commented 6 months ago

ATLAS v2.14.1 is the version I have installed.

chrisknoll commented 6 months ago

The problem is the modules aren't being instaled in an expected way.

This is what is on my filesystem under node_modules/d3: image

When you do an npm build, it should also produce a package-lock.json indicating the specific version of d3 installed like this:

        "d3": "4.13.0",
        "d3-scale-chromatic": "1.5.0",
        "d3-tip": "0.9.1",

Can you check that as well?

hkamineni commented 6 months ago

[image: node_modules_d3- folder.PNG]

On Fri, May 3, 2024 at 10:45 AM Chris Knoll @.***> wrote:

The problem is the modules aren't being instaled in an expected way.

This is what is on my filesystem under node_modules/d3: image.png (view on web) https://github.com/OHDSI/Atlas/assets/6818777/96aeb7d5-07d4-4e31-8e48-bf2a5f7b0294

When you do an npm build, it should also produce a package-lock.json indicating the specific version of d3 installed like this:

    "d3": "4.13.0",
    "d3-scale-chromatic": "1.5.0",
    "d3-tip": "0.9.1",

Can you check that as well?

— Reply to this email directly, view it on GitHub https://github.com/OHDSI/Atlas/issues/2932#issuecomment-2093486384, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHOF47UCRC6XTIXQ7B45633ZAPEKBAVCNFSM6AAAAABHFQWRV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJTGQ4DMMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>

hkamineni commented 6 months ago

Chris: I don't see what you see. build directory is missing..

On Fri, May 3, 2024 at 11:48 AM Sreehari Kamineni < @.***> wrote:

[image: node_modules_d3- folder.PNG]

On Fri, May 3, 2024 at 10:45 AM Chris Knoll @.***> wrote:

The problem is the modules aren't being instaled in an expected way.

This is what is on my filesystem under node_modules/d3: image.png (view on web) https://github.com/OHDSI/Atlas/assets/6818777/96aeb7d5-07d4-4e31-8e48-bf2a5f7b0294

When you do an npm build, it should also produce a package-lock.json indicating the specific version of d3 installed like this:

    "d3": "4.13.0",
    "d3-scale-chromatic": "1.5.0",
    "d3-tip": "0.9.1",

Can you check that as well?

— Reply to this email directly, view it on GitHub https://github.com/OHDSI/Atlas/issues/2932#issuecomment-2093486384, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHOF47UCRC6XTIXQ7B45633ZAPEKBAVCNFSM6AAAAABHFQWRV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJTGQ4DMMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>

hkamineni commented 6 months ago

Chris: Can you suggest ATLAS and nodejs version combinations that worked for you? I will try that to make sure there are no other issues in my environment. Thanks for your help.

On Fri, May 3, 2024 at 11:48 AM Sreehari Kamineni < @.***> wrote:

Chris: I don't see what you see. build directory is missing..

On Fri, May 3, 2024 at 11:48 AM Sreehari Kamineni < @.***> wrote:

[image: node_modules_d3- folder.PNG]

On Fri, May 3, 2024 at 10:45 AM Chris Knoll @.***> wrote:

The problem is the modules aren't being instaled in an expected way.

This is what is on my filesystem under node_modules/d3: image.png (view on web) https://github.com/OHDSI/Atlas/assets/6818777/96aeb7d5-07d4-4e31-8e48-bf2a5f7b0294

When you do an npm build, it should also produce a package-lock.json indicating the specific version of d3 installed like this:

    "d3": "4.13.0",
    "d3-scale-chromatic": "1.5.0",
    "d3-tip": "0.9.1",

Can you check that as well?

— Reply to this email directly, view it on GitHub https://github.com/OHDSI/Atlas/issues/2932#issuecomment-2093486384, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHOF47UCRC6XTIXQ7B45633ZAPEKBAVCNFSM6AAAAABHFQWRV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJTGQ4DMMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>

hkamineni commented 6 months ago

Chris: It looks like we simply need to download and unzip the atlas.zip https://github.com/OHDSI/Atlas/releases/download/v2.14.1/atlas.zip into C:\tomcat\webapps. npm can't be run on this because package.json does not exist. I have been trying to use Source code https://github.com/OHDSI/Atlas/archive/refs/tags/v2.14.1.tar.gz (tar.gz) https://github.com/OHDSI/Atlas/archive/refs/tags/v2.14.1.tar.gz to run npm run build and it's been failing. With simply unzipping atlas.zip in webapps folder, the atlas screen came up fine. I am trying to install Atlas first time and has been following the installation instructions. Let me know if my observation here is right. Thanks for your help. Hari

On Fri, May 3, 2024 at 11:56 AM Sreehari Kamineni < @.***> wrote:

Chris: Can you suggest ATLAS and nodejs version combinations that worked for you? I will try that to make sure there are no other issues in my environment. Thanks for your help.

On Fri, May 3, 2024 at 11:48 AM Sreehari Kamineni < @.***> wrote:

Chris: I don't see what you see. build directory is missing..

On Fri, May 3, 2024 at 11:48 AM Sreehari Kamineni < @.***> wrote:

[image: node_modules_d3- folder.PNG]

On Fri, May 3, 2024 at 10:45 AM Chris Knoll @.***> wrote:

The problem is the modules aren't being instaled in an expected way.

This is what is on my filesystem under node_modules/d3: image.png (view on web) https://github.com/OHDSI/Atlas/assets/6818777/96aeb7d5-07d4-4e31-8e48-bf2a5f7b0294

When you do an npm build, it should also produce a package-lock.json indicating the specific version of d3 installed like this:

    "d3": "4.13.0",
    "d3-scale-chromatic": "1.5.0",
    "d3-tip": "0.9.1",

Can you check that as well?

— Reply to this email directly, view it on GitHub https://github.com/OHDSI/Atlas/issues/2932#issuecomment-2093486384, or unsubscribe https://github.com/notifications/unsubscribe-auth/BHOF47UCRC6XTIXQ7B45633ZAPEKBAVCNFSM6AAAAABHFQWRV2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJTGQ4DMMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>