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NCBI-Hackathons / Metadata_categorization

A crowdsourcing/expert curation platform for metadata categorization.
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Add a Harvest Site field #26

Closed FullyWashable closed 8 years ago

FullyWashable commented 8 years ago

This is a field where the curators will add an anatomical location from which the cells were harvested if it is different from the anatomy of the cells (like in the case of secondary tumors or blood harvested peripheral to a body area). For SOLR, please add field; it doesn't require any population. For UI, please add to the individual record view. This is a project critical addition.

lepons commented 8 years ago

I created entries for this in the Solr schema for both annotation and AnnotationsDev. Since these do not contain source data, I am not planning at this time to re-index to generate the default entries. @eweitz let me know if this poses a problem for you and I can re-rerun the populations jobs, so that default values are set. But with the field in the schema, these values can be stored from user input.

FullyWashable commented 8 years ago

Thank you!

On Thu, Mar 3, 2016 at 1:39 PM, lepons notifications@github.com wrote:

I created entries for this in the Solr schema for both annotation and AnnotationsDev. Since these do not contain source data, I am not planning at this time to re-index to generate the default entries. @eweitz https://github.com/eweitz let me know if this poses a problem for you and I can re-rerun the populations jobs, so that default values are set. But with the field in the schema, these values can be stored from user input.

— Reply to this email directly or view it on GitHub https://github.com/NCBI-Hackathons/Metadata_categorization/issues/26#issuecomment-191906346 .

eweitz commented 8 years ago

@eweitz let me know if this poses a problem for you and I can re-rerun the populations jobs, so that default values are set.

@lepons, to wire this into the UI and web backend, I will need harvestSite pre-populated with "0" in Solr, like the other fields. ("0" represents "empty" per our hackathon work.) Let's hold off on that quasi-pre-population until after today's demo, which ends around 4:00 PM today. This will be trivial to implement on my end once harvestSite is 0-filled.

eweitz commented 8 years ago

With indexers starting work tomorrow, pre-populating harvestSite with "0" seems like it might be time-sensitive. If we can add "harvestSite": "0" for all records without wiping out existing annot values, then it's somewhat less urgent.

If not, then I think we would need this part done today. Otherwise I suspect that adding "harvestSite": "0" while preserving indexers' work will be complex.

lepons commented 8 years ago

I should be able to do this tonight. If I recall correctly, I wrote it so I can add a new field by essentially copying the existing data, so if there are stored annotations that aren't in the source data, I will capture them too (I will confirm this before I run the job and run it in Dev first as a test). Should be able to complete this easily, but can't do it until after I put my kids to bed. I'll send around a notice when it's done. If I can't do it tonight, I should be able to do it first thing tomorrow morning, barring anything happening, both jobs should run in about 10 min total. Should I restrict this to Drosophila samples or go ahead and populate harvestSite for everything?

eweitz commented 8 years ago

If I recall correctly, I wrote it so I can add a new field by essentially copying the existing data, so if there are stored annotations that aren't in the source data, I will capture them too (I will confirm this before I run the job and run it in Dev first as a test).

Fantastic!

Should I restrict this to Drosophila samples or go ahead and populate harvestSite for everything?

Let's populate harvestSite for everything, i.e. human and Drosophila.

lepons commented 8 years ago

These are fully populated in annotation, I didn't fully populate them for AnnotationsDev, which doesn't have reliable data on a number of fronts, so I didn't think it would be useful. Let me know if you want me to run the job for AnnotationsDev too.

On Thu, Mar 3, 2016 at 5:45 PM, Eric Weitz notifications@github.com wrote:

If I recall correctly, I wrote it so I can add a new field by essentially copying the existing data, so if there are stored annotations that aren't in the source data, I will capture them too (I will confirm this before I run the job and run it in Dev first as a test).

Fantastic!

Should I restrict this to Drosophila samples or go ahead and populate harvestSite for everything?

Let's populate harvestSite for everything, i.e. human and Drosophila.

— Reply to this email directly or view it on GitHub https://github.com/NCBI-Hackathons/Metadata_categorization/issues/26#issuecomment-192002521 .

eweitz commented 8 years ago

@FullyWashable, done. @lepons and I have added a "Harvest Site" field to the app. As the field is not pulling source values from BioSample, it is simply white and does not use the pink/green convention for source and annotated fields.