metadatacenter / cedar-project Goto Github PK

Build project for all CEDAR Java repositories

Home Page: https://github.com/metadatacenter/cedar-docs/wiki

License: Other

metadata fair fairness ontologies interoperability semantics bioportal java knowledge-management knowledge-representation

cedar-project's Introduction

CEDAR Project

This repository contains a Maven POM for building all CEDAR Java-based components. The repository can also be used to report CEDAR issues. To access the CEDAR application, visit the production web site. You will be prompted to log in, and can create an account if you do not have one.

For general documentation about CEDAR see our project web site. A complete list of CEDAR references can be found at our references page.

Developer-focused documentation can be found on the CEDAR technical wiki.

Before building CEDAR, note that Maven must first be executed on the POM in the CEDAR parent repository to generate appropriate configuration information and version dependencies for the build.

Notes for CEDAR releases can be found in the Release section of this repo.

Questions

If you have questions about this repository, please subscribe to the CEDAR Developer Support mailing list. After subscribing, send messages to cedar-developers at lists.stanford.edu.

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cedar-project's Issues

Develop prototype CEDAR to BioSample translator

See here for XSD and sample XML files:

https://github.com/metadatacenter/cedar-docs/tree/develop/BioSample

Create sub-domains for staging server

Need standard subdomains from staging.metadatacenter.net.

As per:

https://github.com/metadatacenter/cedar-docs/wiki/Configure-host-names-on-RHEL-6.6

Develop caDSR template

Develop template to represent caDSR CDE.

See caDSR DTD here:

https://github.com/metadatacenter/cedar-docs/tree/develop/ISO11179/caDSR

PICK FROM A LIST field requires options even if values coming from ontology

Even when an ontology reference is specified for values, it requires adding non-empty options

ISWC Submission

http://iswc2016.semanticweb.org/pages/calls/applications.html

Clean up POM files

Document Let's Encrypt Installation

No current documentation for Let's Encrypt on CEDAR Red Hat servers.

Documentation should explain generation of PEM files (e.g., /etc/letsencrypt/live/auth.staging.metadatacenter.net/privkey.pem;) and explain how these files are related to the host name. On the two current CEDAR servers (staging.metadatacenter.net and metadatacenter.net) the files are called:

staging.metadatacenter.net
auth.metadatacenter.net

which does not seem to be consistent.

Server documentation here:

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

Set up a monitoring service from outside

We should monitor the frontend and the rest endpoints

Add clone templates/elements ability

In order to create a new template/element based on an existing template/element, support cloning an element

Update documentation to reflect the two new servers: resource, valuerecommender

demo example for intelligent authoring

Develop demo scenario intelligent authoring service

Set up external HTTP monitoring service

https://www.statuscake.com/

Set up local Nexus Repository Manager

Also needs to be externally accessible so that a Travis CI server can access it.

AMIA Demo Sumission

https://www.amia.org/amia2016/call-participation

test

Consolidate documentation links

Remove documentation from the README.md files in the following repos:
cedar-template-server
cedar-template-editor
cedar-terminology-server

Just point to the main documentation page:
https://github.com/metadatacenter/cedar-docs/wiki
If relevant information is present on the mentioned pages, integrate those into the main documentation

Review CEDAR template model document and finalize

Review John's comments and put into releasable form.

Review ImmPort auto-generated CEDAR templates

The JSON for the templates can be found here:

https://github.com/metadatacenter/cedar-templates/tree/master/immport_template/template/generated

Current live templates and titles:

Title: ImmPort basic_study_design
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/a70835f7-7c7a-44b0-a1cd-10669545a770

Title: ImmPort experimentSamples.ELISA
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/a954dfdf-d050-4877-ae9f-1af560077999

Title: Immport elisa_results template schema
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/422023fb-9856-44d8-b7c1-63fc82175167

Title: ImmPort bioSamples
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/1b85143f-4050-4ba8-b02d-442418968143

Title: ImmPort adverseEvents
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/eea73436-dd4d-408f-8ac1-0f68d0eeef19

Title: ImmPort assessments
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/5a17bdbc-2479-497b-ba92-ca4a5b1fa1ff

Title: ImmPort controlSamples
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/0ef64540-8077-45f4-87f2-442ddd024673

Title: ImmPort labTests
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/ce8126a0-14a7-4290-a273-030005c931ac

Title: ImmPort subjectsHuman
https://cedar.metadatacenter.net/templates/edit/https://repo.metadatacenter.org/templates/b94f53af-18f9-44d6-9cd8-36c313a2e848

Support searching for ontologies, in addition to search for classes

Determine if private Nexus server works with paid Travis

CEDAR services architecture diagram

Prepare architecture diagram(s) describing the current CEDAR system architecture.

Find solution for backing up MongoDB database

Fins generic solution for backing up MongoDB database on CEDAR servers.

User Login

Implement single sign-on with Keycloak

Set up staging server

Set up staging.metadatacenter.net

Search by field/value

Search template/instance for field (demo scenario number 20)
Search instances for value (demo scenario number 21)

not clear how to close a field

After opening a field, it isn't clear how to make it close (so one can save the form).

Continuous Integration

Need Travis-based continuous integration environment for CEDAR services.

Update ImmPort Basic Study Design Template

Customize Keycloak Login Screen

We do have the built-in login screen from Keycloak, but we need to align it with our design.

Deleting fields from the template gui does not remove them from the template json

keyboard shortcuts

add keyboard shortcuts for selection, menu, action, etc.

Document SSL certificate process

Document how a vendor SSL certificate is generated and applied to a specific CEDAR server. Currently we have the installation process for a CEDAR machine documented but it is missing details on this step.

Current documentation here:

https://github.com/metadatacenter/cedar-docs/wiki/Install-guide

Reorganize Maven repos

cedar-auth - multi-module
cedar-auth-operations
cedar-auth-operations-keycloak - 2 files
* cedar-auth-operations-play - 2 file

cedar-server-utils
cedar-server-utils-core - this is the new name for ....-core
cedar-template-operations
* cedar-server-utils-play - the common code from current ...-play

auto-save edits

Hide 'Children' option in controlled term modal for childless terms

'Children' option should not be available for terms with no children.

Example childless term:

http://purl.obolibrary.org/obo/OBI_0000052

CREATE NEW does not work from the Elements List page

Clicking the CREATE NEW button on the 'All Elements list' page (https://cedar.metadatacenter.net/elements/list) does not do anything.

Undo and redo analysis

Initial task here is to figure out what all the actions are that can support undo and redo (may be different list for each). Then we can prioritize which ones to implement based on each action's cost/value.

Docker deployment

Need to configure an automated deployment environment. Docker?

Update Git version on CEDAR servers

logout error saving template

I'm getting logged out and not automatically logged in again.

Travis and private Nexus server

Can the free version of Travis work with a private Nexus server.

If not, does the commercial version support it?

Centralized configuration service for CEDAR services

Revisit Dependency Injection framework

Guice probably

Backup MongoDB and Neo4J on CEDAR machines

As discussed, hourly backup for 2 weeks on current CEDAR machines (dev1 and dev2).

Pre-populate form from another instance

Indicate whether field entry is complete

The field or element should have a clear indication that it is done or not done. A red circled x or a green circled check tells the user whether it is done.

Deploying ImmPort-generated CEDAR Templates

Define process for using ImmPort-generated CEDAR templates to feed metadata into ImmPort.

Can't edit page break

I want to be able to edit an existing page break, to add title or description. (Note re #119: not sure what difference between section and page breaks are conceptually (one's bigger, I know). They are much more useful if one can associate display text with them.