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ucsd-ccbb / qiimp

Web application to collect metadata specifications from an experimenter and produce metadata input files with appropriate constraints
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Update packages to use MiMARKS standard field names #125

Closed AmandaBirmingham closed 6 years ago

AmandaBirmingham commented 6 years ago

From @ackermag via email:

At the request of EBI, we are going to adopt the use of the host-associated terms from the MiMARKS standard and rename all the existing fields in Qiita accordingly. This is the list and our consensus: All hosts: host_subject_id [unchanged] - we use this host_common_name [unchanged]- we use this host_taxid [unchanged]- we use this life_stage [change] host_life_stage

Plants and animals height [change] host_height - when provided

All animals: age - [change] host_age body_site - [change] host_body_site body_product - [change] host_body_product body_habitat - [change] host_body_habitat height - [change] host_height weight - [change] host_weight

Humans: BMI->host_body_mass_index

When the following are provided make sure they are prefixed with "host_":

host_growth_conditions host_substrate host_occupation host_total_mass host_dry_mass host_phenotype host_genotype host_infra_specific_name host_infra_specific_rank host_body_temperature host_color host_shape

I believe Stephanie can assist with implementing this in the metadata Wizard. Please let me know if you need additional information.

AmandaBirmingham commented 6 years ago

This should not require any code changes, just changes to the package definitions--hopefully only in the four files for the four packages Gail has called out above.

AmandaBirmingham commented 6 years ago

@adswafford Given that this requires (only) changes to package files, I'm guessing you want @stephanieorch to handle it. Can you confirm or deny? :)

adswafford commented 6 years ago

Confirm, @stephanieorch do you know what changes to make or do you need instructions from Amanda?

-- Austin D. Swafford, PhD Director of Research, Center for Microbiome Innovation Jacobs School of Engineering | UC San Diego O: 858-246-2906

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On Wed, Apr 4, 2018 at 4:09 PM, Amanda Birmingham notifications@github.com wrote:

@adswafford https://github.com/adswafford Given that this requires (only) changes to package files, I'm guessing you want @stephanieorch https://github.com/stephanieorch to handle it. Can you confirm or deny? :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ucsd-ccbb/cmi_metadata_wizard/issues/125#issuecomment-378773091, or mute the thread https://github.com/notifications/unsubscribe-auth/AZxBhrg-GLKixUonx6lrUDp18PrKWbGDks5tlVKfgaJpZM4SlDC_ .

stephanieorch commented 6 years ago

I can make these changes I just need the old package files from @AmandaBirmingham

AmandaBirmingham commented 6 years ago

@stephanieorch The best place to get the most current package files is the github repository. Go to https://github.com/ucsd-ccbb/cmi_metadata_wizard/tree/master/metadata_wizard/settings/packages to see all the package files in the current master branch, and click on the one you want to work on. The page that opens will have a "Download" button--click it to download the package file to your machine so you can work on it.

Once you're done with them, you can send them to me to commit back to the GitHub repo (or you can commit them yourself, or I can teach you to if you don't know how but want to :) ).

AmandaBirmingham commented 6 years ago

Fixed by PRs 130 and 132