[View] module notes

[jfy133]

This issue contains running notes for the development of the view module.

Remaining issue currently is that some of the fields are populated with numeric 'Ids' and not actual strings. I've added to sidora.core a function id2strings which should do this conversion.

[jfy133]

I need to make a list of columns in each table which uses the Id system. This probably would be stored in a vector in data-raw in sidora.core, that is then used as a look up table.

[jfy133]

Will need to update id2columns to include the following fields. Likely will need to put this list in a data-raw named vector map. Note the Numeric ID columns must be in hte sidora form of tab.Col_Name

Also this will go in sidora.core not sidora.cli, but will ultimately be for the purpose of view.

Table	Numeric ID Column	Comment
Site	Site_Id	Not necessary if Full_Site_Id already present
Site	Worker
Sample	Site
Individual	Individual_Id	Not necessary if Full_Individual_Id is already present
Individual	Owning_institution
Individual	Worker
Individual	Creation Date
Individual	Organism
Sample	Individual
Sample	Archaeological_ID	This is the same as Individual
Sample	Type_Group
Sample	Type
Sample	Protocol
Sample	Worker
Sample	Batch
Sample	Location_Bone_Room	contains("Location) then search location Tab
Sample	Location_Bone	^
Sample	Location_Power_Room	^
Sample	Location_Powder	^
Extract	Extract_Id	Not necessary if Full_Extract_Id
Extract	Protocol
Extract	Worker
Extract	Batch
Extract	Location_Room	^
Extract	Location Room	^
Library	Library_Id	Not necessary if Full_Library_Id
Library	Worker
Library	Batch
Library	Protocol
Library	Index_Set
Library	P7/P5_Index_Id	?? Maybe ??
Library	Location_Room
Library	Location
Capture	Capture_Id	Not necessary if Full_Library_Id
Capture	Worker
Capture	Batch
Capture	Protocol
Capture	Probe_Set
Capture	Location_Room
Capture	Location
Sequencing	Sequencing_Id	Sequencing
Sequencing	Worker
Sequencing	Batch
Sequencing	Sequencer
Sequencing	Location_Room
Sequencing	Location
Raw_Data	Protocol

Note: All dates are wierd e.g. This looks wierd, e.g. 16801, so might need additional conversion

[jfy133]

Note: view_module is broken when searching ofr for individual for some reason, the column name conversion doesn't work, get error of individualFull_Indvidual_Id, i.e. missing a .

EDIT: Fixed in: https://github.com/sidora-tools/sidora.cli/commit/2a136120444b0070c960449825307b37c5eac477

[jfy133]

If view accepts 'tags' or 'project' tables, need to be aware that format is different (e.g. Deleted doesn't exist)

[jfy133]

Remaining issues:

• • [ ] All - every table has Ids of upstream table (e.g. in Extract you see the ID for Sample.
• • [x] library - Error: external pointer is not valid
• • [x] capture - Error: external pointer is not valid
• • [x] library - 'library.P7_Index_Id was not found'
• • [x] library - P7/P5 index IDs incorrect.
• • [x] library - missing post-indexying total.
• • [x] individual - owning institution returns Id
• • [x] Type_Group - is missing for certain types (e.g. id: 46)
• • [x] Location_Powder - is returns IDs not name
• • [x] sample - Archaeological_ID returns number not actual number.

Continue checking sample to sequencing

[jfy133]

Last thing to do is to remove extra/duplicate fields (Ids mainly)