germinateplatform / germinate-vue Goto Github PK

Thank you in advance for your time.

I'm trying out your application to integrate into a biology project that I have.
I've already managed locally using your tutorial to get the application running, but I didn't understand how I input my data into the platform.

Can you help me?

Look into loading the locale .json externally

I setup your germinate server and gatekeeper via your docker sample implementation. The server will need to be a public facing website so the academics can collaborate. Our IT security team scanned the site to check for issues before allowing it to be public. One issue that they said needed to be fixed to allow it to be public facing was,

Stack Trace Disclosure (Java) tomcat. An attacker can obtain information such as: Tomcat version. Physical file path of Tomcat files. Information about the generated exception.
This information might help an attacker gain more information and potentially focus on the development of further attacks to the target system. Research indicated that the following needed to be done on the app,

1. Open the server.xml file in your Tomcat installation directory.
2. Locate the <Host> section and add the following line inside it:
   <Valve className="org.apache.catalina.valves.ErrorReportValve" showReport="false" showServerInfo="false" />
3. Save the file and restart Tomcat.

Could this change be made so the tomcat app on both germinate and gatekeeper does not reveal errors and reports? You may want to check if that's the best option to address the Stack Trace Disclosure issue in tomcat-java.

the scan was created with 23.12.0.43017-release_is-23.12.0-2427fdc https://www.invicti.com

Hello Germinate Team,

I've translated the en_GB.json file into Chinese, mainly using OpenAI's translation. Some parts have been manually checked, but due to time constraints, I wasn't able to review everything.

I hope this translation can help make Germinate more accessible to Chinese speakers.

zh_CN.json

Whenever I press the 'Submit' button on the Germinate Settings page, I am automatically logged out. However, the changes I made are saved.

If a user requests a specific page from Germinate, but is redirected to the login page, Germinate should redirect the user to the requested page after the login procedure.

The Issue

When importing data from a Germinate upload template, traits that share the same name do not auto merge with the existing traits in the database, causing a user to have to run trait unification for each trait they uploaded.

Additional Quirks

• Using BrAPI import in Gridscore to import traits works fine. When exporting data from Gridscore, the Germinate upload template only includes the name and the data type of the trait, none of the trait metadata
• When defining a new trait in Gridscore with categorical data, the trait exports with the discrete categories in a comma separated format like hi,med,lo instead of the correct format required by Germinate uploads, ["hi","med","lo"].

Proposed Solution

Can Germinate have a name checking feature during upload which checks to see if the name, data type, and categories (if applicable) of traits match and then auto merge them? And if no matches are found, it would then upload it as a new trait.

Good morning,

I'm trying Germinate to integrate it with a project from my university I would like to ask if there are other ways to upload data to the Germinate database in addition to uploading an excel file.

Thank you in advance,
Foglia Fabrizio

good evening,

I saw the BrAPI documentation and wanted to ask for some information.

First, I would like to know how I can connect to my server and then make the calls.
I saw that API requests are structured as
https: // / brapi / v2 /
but i can't figure out what to put in the server.

Subsequently, I read that one of the possible calls concerns Crossing Projects; I wanted to know if they are present in Germinate and, therefore, are usable.

If there are no Crossing Projects, would it be possible to modify the database locally?

For example, would it be possible to add a column to one of the tables on Germinate?

Finally, I would like to ask for some clarification on BrAPI calls:

• among all the possible calls, how can I know which ones can be performed on Germinate?
• why (taking as an example the call to create a new Germplasm) is there a difference between the fields required by the Excel templates and the fields required by the BrAPI call?

Thank you in advance and wish you a good day.

Foglia Fabrizio

The Issue:

I recently added 10 new traits to our ontology and uploaded them to our Germinate instance. However, I forgot to upload the short_name and description along with the traits. When I edit them in the GUI, adding a the short name and description completely removes all of the trait units and constraints.

Sebastian,

This has been an issue for some time, but I'm just getting around to submitting an issue. If you are uploading new germplasm via the template, you have to include at least three new lines (accnumbs) in the template otherwise you get the following log errors.

Is there a specific reason that the data validator doesn't like uploads of less than 3 varieties?

Bo