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seek4science / seek

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
http://www.seek4science.org
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Biologist friendly Batch upload for sample, studies, ... #98

Closed cpommier closed 3 years ago

cpommier commented 5 years ago

This issue address the needs of the plant phenoytping community (Elixir & Emphasis).

API loading. To batch submit from an internal system (isa-tab compatible tool =pISA-tree app). Documentation, possibly some API level improvement needed. Some issues possibly fixed already. Work in progress handled in another issue by Alan & Andrej

The main purpose of this issue is user interface loading using an Excel Spreedsheet following MIAPPE templates. Reusing the API batch upload ie a buton in the Investigation to upload a list ?

Sample batch upload

Sample (Biological Material) batch loading: Users have list (named panel or collections) of hundreds of Biological Material that they share through excel. We would need to be able to upload those list hand have the possibility to link them as a whole to a study or an assay. It would also be necessary to have the possibility to add each Biological material independently.

Studies Batch Upload

We can have a whole plant phenotyping network with tens of studies that we need to upload in a single investigation. This upload need to be done through a web interface to remain biologist friendly. Ideally, this upload process would check that the Biological material list is consistent, but that might be too much for the current project.

cpommier commented 4 years ago

DOI to be added soon.

MIAPPEv1.1_popyomics.xlsx

cpommier commented 4 years ago

Create a separate page for Plant Biological Material/Sample submission, with the relevant documentation and instructions. Already merged in master branch: https://github.com/seek4science/seek/commit/7b332fe16c8ca7e8ba0acb15549f21f65c6a2c34 https://github.com/seek4science/seek/commit/6a2a1088627eed8d8bd13651e34a4408c6618612 https://github.com/seek4science/seek/commit/28466f483c3e36bece26bd816dd70d66a1aad97e

Plant How To in Seek gh page to show how to upload the Biological Material template: https://github.com/seek4science/seek/tree/gh-pages

cpommier commented 4 years ago

Studies: See https://github.com/seek4science/seek/tree/add-study-batch