Hello
When running worker micro-service it shows an exception "Error while looking up admin user"

Abstracted paper comments:

------------- Model --------- Martin
- can templates be combined
- predefined sub-forms
- 11179 / ISO/NP TS 21526
- explicit Provenance Model
                In 2.1 we should talk about composability somehow.
 
 
------------- Atti
- how many templates, metadata, users, groups
                We should look this up.
- Take a look at swagger . Could it be upgraded
 
 
------------- BioPortal --------- Martin
- FAIR, seems buzzwordy for the sake of a buzzword
- Mention that you can upload an ontology to BioPortal, and it will be immmediately available.
- BioPortal is just one external source. We could use others as well.
- Terminology server has the role of a mediator.
- What about if a user who is filling out a template decides an appropriate term does not exist?
 
 
------ ask Marcos
- Figure 4 - make it a recommendation / ontology example
 
 
------ ValueRecommender -------- Marcos
- What about if a user who is filling out a template decides an appropriate term does not exist?
- Do the authors have any thoughts on creating suggestions for ontologies to use for common terms
- Have the authors also thought about a Value "Constraint System"

Hello,
Could you please provide us with an updated working link to Install instructions documentation ?

Thank you

https://github.com/metadatacenter/cedar-docs/wiki/CEDAR-Template,-Element,-and-Field-Instances

here is an example curl invocation of the validation endpoint to validate that instance:

curl -H "Content-Type: application/json" -H "Authorization: apiKey <KEY>" -H "Accept: application/json" -X POST --data-binary @instance.json "https://resource.staging.metadatacenter.org/command/validate?resource_type=instance"

URL https://resource.staging.metadatacenter.org/command/validate is invalid - it doesn't accept user API keys.

Update architecture diagram to reflect removal of workspace server and renaming of template server to artifact server.

Hello CEDAR team,

I'm trying to access the gene expression template at the CEDAR workbench at
https://cedar.metadatacenter.org

because I want to go through this tutorial here:
https://docs.google.com/document/d/1kmRs3oubY2OCtH-IwIndcPbaW484Cv6lJHN8bmoXnMI/

This however results in a 500 server error. Is it possible to:

• Fix the problem with this CEDAR deployment?
• Download the gene expression template from somewhere else such that I can upload it to our local CEDAR deployment?

Thanks in advance

Update model document to reflect 1.3 model updates.

https://waffle.io/metadatacenter/cedar-project?label=Model&milestone=1.5

https://github.com/search?q=user:metadatacenter+label:Model+milestone:1.5&type=Issues

Documentation needs to be updated in several places.

Some notes from Alex:

CEDAR Documentation instructs to start frontend service with “gulp” or “starteditor” command; however that is not necessary since nginx can serve frontend content directly as long as  etc/nginx/cedar/frontend-cedar.inc.conf configured something like this:
 

server {

    listen          80;

    server_name     cedar.metadatacenter.orgx;

    return          301 https://cedar.metadatacenter.orgx$request_uri;

}

 

server {

    listen          443 ssl;

    server_name     cedar.metadatacenter.orgx;

    include         cedar/include-ssl.conf;

    root              /home/cedar/CEAR/cedar-template-editor/app/;

    try_files       $uri /index.html;

    error_log       /home/cedar/CEDAR/log/cedar-frontend-editor/nginx-error.log warn;

    access_log      /home/cedar/CEDAR/log/cedar-frontend-editor/nginx-access.log combined if=$loggable;

}

 

When changing CEDAR_BIOPORTAL_REST_BASE it is a good idea to do the following in order to avoid odd inconsistencies:
clear browser cache
clear terminology server cache.  Terminology service caches the full list of ontologies and value sets (just their general description). It’s regenerated every 2 hours I believe. To force regeneration do: stopterminology, delete the {$CEDAR_HOME}/cache/terminology folder, startterminology, and wait for the cache to be regenerated (it will take around 5 minutes). The console output will tell you once it’s done
 
My previous recommendation to add  CEDAR_BIOPORTAL_API_KEY and CEDAR_BIOPORTAL_REST_BASE environmental variables to  ~/.bash_profile turned out to be counterproductive and it is better to set them only in one place (set-env-external.sh)

I'm checking the unit representation in the InvestigationSchema.json and it contains some enums, e.g.

"enum": [
"http://purl.obolibrary.org/obo/UO_0000003"
]

This seems a mistake as it prevents to include other values for the units. Or am I missing something?

Thanks!

What does API expects as a value for idRequest in an API call such as:
https://resource.metadatacenter.org/api/#!/OpenView/post_command_make_artifact_open

I tried putting ID of an template instance such as:
https://repo.metadatacenter.org/template-instances/f15e7ef3-83b4-4577-8f22-d0ef574bab32

but I've got:

{
  "error": "no response from server"
}

Dear CEDAR team,

I am currently trying to install the CEDAR server ecosystem locally for development purposes. Now I am stuck at this step here:

git clone https://github.com/metadatacenter/cedar-conf.git
The repository cannot be cloned, as it is private and I do not have permission to access it. However, the install guide for CEDAR implies that cloning this repository is a necessary step for installing CEDAR:

https://github.com/metadatacenter/cedar-docs/wiki/Clone-the-projects-from-Github-on-OS-X

Can you perhaps provide me with some instruction on how to proceed here?

Best wishes
Lukas

https://github.com/metadatacenter/cedar-docs/wiki/CEDAR-Server-Install-Guide

"Docker based install process" link is a 404

Cheers!

M

Page: https://more.metadatacenter.org/tools-training/cedar-api

contains incorrect URLs for Swagger UI:

http://resource.metadatacenter.net/api

should be:

http://resource.metadatacenter.org/api

https://github.com/metadatacenter/cedar-docs/wiki/CEDAR-REST-APIs,

To find all instances of a particular template use the derived_from_id field to identify the template:

According to https://resource.metadatacenter.org/api/#!/Template32Instances/get_search, the command should be is_based_on

Hi,

We are working on setting up HTTPS/SSL for Keycloak server.
We are facing an issue while doing so. We followed below documentation:
http://blog.keycloak.org/2015/06/openshift-ui-console-authentication.html
We are not getting errors while starting the server.
After configuration, when we are opening the server, we are getting below error in browser.
This site can’t be reached

Please help us resolving this

Based on model defined in metadatacenter/cedar-model-validation-library#54 update document to reflect.

Why are some fields in the CEDAR templates named with an '_'? For example the '_ui' and '_valueConstraints'? Was wondering why it is named differently from the other fields?

Hi CEDAR team,

I have three questions concerning one request of your API:

1. 404 for indexed value_set

I am trying to get used to the way your API works (based on https://terminology.metadatacenter.org/api/). More precisely, I try to get the "/vs-collections/{vs_collection}/values/{id}/value-set" work. I send a request with:

• vs_collection = "CEDARVS"
• vs_id = "803d8340-6a1e-0138-64d8-005056010073"

from my R session (see my work at: https://github.com/earnaud/cedarr/tree/master) and it returns me 404. When I try this same query on the swagger UI, I get:

{
  "status": "INTERNAL_SERVER_ERROR",
  "errorType": null,
  "errorKey": null,
  "errorReasonKey": null,
  "message": null,
  "parameters": {},
  "entities": {},
  "suggestedAction": "none",
  "originalException": {
    "cause": null,
    "stackTrace": [
       /* truncated */
    ],
    "message": null,
    "localizedMessage": null,
    "causes": []
  },
  "operation": null
}

2. Some IDs don't seem to be recognized

The value_set ID I am using originates from a request to retrieve the value_sets contained in the VS_collection "CEDARVS", and there I rely on the "id" items. Among those items, only the ones that are not user-legible (e.g. "803d8340-6a1e-0138-64d8-005056010073") seem to work. Another question would be: how could I get the value_set for id "Study_File_Type" ?

Please find attached a screenshot from my R session for the table I retrieve when querying for CEDARVS content.

3. The provided example is not listed in the VS_collection

The swagger UI for the API provides " af033050-b04b-0133-981f-005056010074" as an example with the CEDARVS collection, which returns an empty body. Also, this VS id does not appear among the ones listed in the CEDARVS. This is more a little notification more than an actual question but it seemed important to me to get consistent examples to learn to use the API.

Thanks a lot for your amazing work !

Add appendix describing REST calls for artifact manipulation and validation