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vu-rdm-tech / yoda-pilot

A place to track issues we run into in the Yoda pilots
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Create project and category naming scheme #36

Closed peer35 closed 2 years ago

peer35 commented 4 years ago

Looking at the structure and naming in Yoda as a rodsadmin should give a good clue into who is responsible for which project.

There is no technical requirement except for unique group names, but our successors will be thankful once there are hundreds of projects.

Categories: share metadata scheme (might change in future yoda versions), basic administration level (although a good naming scheme makes this less necessary).

For example: Basic category level, disciplines and institutes: Beta: few-geosciences, few-aimms, few-informatics, ... FGB: fgb-movement-sciences, fgb-psychology (or do these need subdivisions?)

Might make sense to repeat these in the groups themselves, since it's so easy to change categories: So: few-aimms-flow_cytometry few-geosciences-nlbv

Keep in mind the VU has a tendency to change or merge faculties.

End goal should be a document the project team can use when adding new projects during the pre-production which can be handed over to the functional admin (library?) when we go in production.

peer35 commented 4 years ago

Start a wiki in this repo?

bgoli commented 4 years ago

A wiki might be useful to start some proto-documentation. For general information here is the structure of the AIMMS/Yoda which is the result of evolved guesswork.

AIMMS/Yoda is used by three departments: Chemistry and Pharmacological Sciences, Environmental Health and Toxicology and Molecular Cell Biology. The departments are split into sections so, for example, MCB is split into: Systems Bioinformatics, Molecular Microbiology and Structural Biology.

Categories (institute/section level)

There is one data manager defined for AIMMS.

Sub-categories (I tried two approaches. Either research group level, typically of professors in a department or a functional grouping per research group):

Projects in each sub category the projects where named as:

or if there are functional subgroups (msc, phd) then they are also included with a project or lastname identifier:

Examples:

The good: inserting the administrative group and functional subgroups into the project name. The bad: The sub-category should be used more effectively and for something else.

Note that AIMMS uses Yoda 1.1 so I some questions about the latest version:

peer35 commented 4 years ago

AFAIK both data manager and metadata are still defined at category level in 1.6

I will also take a look at how subcategory and category are set in the irods metadata to see how useful they are for finding and reporting.

peer35 commented 4 years ago

It looks like our first publication will be an archaelogy project. So that will also be the first project in the vault. Possibilities for categories:

peer35 commented 4 years ago

Group name: research-fgw-archaeology-<project> Maybe: research-fgw-clue-<project>

peer35 commented 4 years ago

See #23 Some more info about the project here: https://euboia.labs.vu.nl/about.html

PI is https://research.vu.nl/en/persons/jan-paul-crielaard Full Professor, Faculty of Humanities, Art and Culture, History, Antiquity Full Professor, CLUE+

peer35 commented 4 years ago

https://www.clue.vu.nl/en/projects/current-projects/sea-and-landroutes-of-southern-Euboia/index.aspx

https://fgw.vu.nl/en/about-the-faculty/index.aspx states: "Scientific research at the VU is done within two Research institutes: CLUE+ and The Netwerk Institute."

So I would suggest we go with: research-fgw-clue-seslr

bgoli commented 4 years ago

I like this approach. So the generic template would be something like:

research-<faculty_abbreviation>-<institute_or_department_abbreviation>-<projectname>

So my examples from above would be:

research-beta-cap-data-archive
research-beta-cap-<lastname>-project
research-beta-mcb-nwo-54mt5
research-beta-mcb-phd-<lastname>

or

research-beta-aimms-data-archive
research-beta-aimms-<lastname>-project
research-beta-aimms-nwo-54mt5
research-beta-aimms-phd-<lastname.

However, research groups could always define their own structure in the <projectname>:

research-beta-aimms-scb-data-archive
research-beta-tc-<lastname>-project
research-beta-aimms-sbi-nwo-54mt5
research-beta-mcb-sbi-phd-<lastname>

Is there a list of department/institute abbreviations out there or could we generate one for ourselves? The advantage of maintaining our own is it could be kept a unique set, in which case we could consider dropping the (even sometime in the future).

If we do this we can free up

peer35 commented 4 years ago

Moved the fgw projects image

peer35 commented 4 years ago

Maybe we can get a list of departments from Pure. I can ask the admin, or probably get it myself with the API.

https://research.vu.nl/ws/api/518/api-docs/index.html#!/organisational45units/listOrganisationalUnits

Needs a bit of effort to parse, I'll add the scripts to the api tools repo.

peer35 commented 4 years ago

https://github.com/vu-rdm-tech/api-scripts/blob/master/pure/pure_ou.json

Research institutes are not associated with faculties in Pure. Kind of makes sense because they could contain researchers of multiple faculties.

bgoli commented 4 years ago

Interesting. In your example with archaeology, the only issue that may be problematic is that the Data Manager Role can only be defined on the faculty level ... we should consider the implications on workflow?

What about this for a completely leftfield idea. We make departments the categories and then, if necessary, include the faculty (and department) in the project name.

peer35 commented 4 years ago

Note: Yoda stores (sub)category info in the metadata of the iRODS group. It is possible to move a group to a different category, Yoda will also fix the datamanager authorization. https://github.com/vu-rdm-tech/yoda-pilot/wiki/notes

bgoli commented 4 years ago

Good to know.

Jumping back to my previous idea it might be more interesting than I originally thought as it virtually eliminates the need for structured project names. Although, we can/should still do something purely for human readable purposes.

Given Yoda's current structure would the following work?

Category -> departments Sub-category -> research groups Category data manager group -> for Yoda workflow management priv-group-add -> users that can create projects

Department of Art & Culture, History, and Antiquity

Biological Psychology

Molecular Cell Biology

Chemistry and Pharmaceutical Sciences

The advantage of this is this gives us a flexible basis to define faculties, institutes, etc.

peer35 commented 3 years ago

I've now put the ou's in a tree for readability: https://github.com/vu-rdm-tech/api-scripts/blob/master/pure/pure_ou.json

peer35 commented 3 years ago

To summarize: Yoda constraints:

System constraints: As always with filenames:

Usability:

Long term considerations:

peer35 commented 3 years ago

I agree it does not make sense to have the faculty as category, certainly not for large and diverse faculties.

Let's keep categories relatively small. So that means the category level should be research institutes and/or departments. The actual division might differ across faculties: researcht institutes for FGW, departments for SBE.

peer35 commented 3 years ago

Started a wiki here: https://github.com/vu-rdm-tech/yoda-pilot/wiki/naming

BETA: Mix of institutes and departments?

FGW: Categories = Research institutes: CLUE+ & Network Institute

FRT: https://www.frt.vu.nl/en/research/index.aspx The research is conducted in two Research Departments: Texts and Traditions, and Beliefs and Practices, which are brought together in the inter-faculty research institute VISOR, in which theologians, philosophers, historians, anthropologists and literary and religious scholars work alongside each other. Category = VISOR

LAW: ??

SBE: Categories = Departments Are there relevant Research institutes?

FGB: Biological Psychology Clinical, Neuro- & Developmental Psychology Educational and Family Studies Experimental and Applied Psychology Human Movement Sciences ,

Institutes: LEARN! Amsterdam Movement Sciences Network Institute Amsterdam Neuroscience

which makes more sense?

FSW Departments??

bgoli commented 3 years ago

Great idea with the wiki. One question though, doesn't FGB have 5 departments https://www.fgb.vu.nl/en/departments/index.aspx ?

peer35 commented 3 years ago

Added them, still a choice to make between the research institutes and departments....

peer35 commented 3 years ago

I've now excluded the ou's that no longer exist. And created a readable list. https://github.com/vu-rdm-tech/api-scripts/blob/master/pure/pure_list.txt copied in the wiki to: https://github.com/vu-rdm-tech/yoda-pilot/wiki/VU-organisational-Units

peer35 commented 3 years ago

Conclusion: we should ask the data managers and researchers for suitable abbreviations, taking care they can be matched to Pure.

peer35 commented 3 years ago

"Orgeenlijst" on vunet: https://vunet.login.vu.nl/_layouts/SharePoint.Tridion.WebParts/download.aspx?cid=tcm%3a164-336765-16

peer35 commented 3 years ago

Talked to the Pure specialist:

So this looks like the best vetted list of departments. But should we use research institutes or just departments?

peer35 commented 3 years ago

Other potentially useful info:

bgoli commented 3 years ago

If we could get access to snapshots of the sync database we could use that. We should also check the definition of an 'institute'

Regarding departments/institutes I think that practically the way to go might be to use where the funds are going to (potentially) come from and the type of storage:

peer35 commented 3 years ago

Can now confirm it is possible and easy to create the initial categories + data manager groups + data manager accounts (if known) via the web API. See #42

peer35 commented 2 years ago

Moved to https://jira.vu.nl/browse/RDA-133, closing this one