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sidora-tools / sidora.cli

A CLI for terminal based data extraction and summary for the MPI-SHH Department of Archaeogenetics PANDORA Database
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Batch views should also list all entries associated with a given batch #23

Open jfy133 opened 4 years ago

jfy133 commented 4 years ago 
fellows@shh.mpg.de@dat4903339:~/bin/sidora.cli$ sidora-cli view -t extract -i 'EXB034.A27'

|Field                          |Value                           |
|:------------------------------|:-------------------------------|
|Sample                         |4916                            |
|Extract_Id                     |27                              |
|Full_Extract_Id                |EXB034.A27                      |
|Protocol                       |calculus DNA only protocol 2017 |
|Worker                         |Raphaela Stahl                  |
|Creation_Date                  |2019-10-28 13:07:38             |
|Experiment_Date                |2019-10-28 13:07:00             |
|Batch                          |Ex26_RS_2019-10-28_CalculusLena |
|Robot                          |FALSE                           |
|Quantity_Sample                |0                               |
|Quantity_Lysate                |0                               |
|External_Extract_Id            |                                |
|Position_on_Plate              |                                |
|Location_Room                  |Ancient Lab/204d (Extraction 3) |
|Location                       |1/5                             |
|Ethically_culturally_sensitive |FALSE                           |
|Files                          |0                               |
|Notes                          |                                |
|Tags                           |                                |
|Projects                       |                                |

fellows@shh.mpg.de@dat4903339:~/bin/sidora.cli$ sidora-cli view -t batch -i 'Ex26_RS_2019-10-28_CalculusLena'

|Field         |Value                                                   |
|:-------------|:-------------------------------------------------------|
|Type          |NA                                                      |
|Name          |Ex26_RS_2019-10-28_CalculusLena                         |
|Worker        |Raphaela Stahl                                          |
|Creation_Date |2019-10-28 13:07:38                                     |
|Notes         |Extraction performed by Lena Semerau and Raphaela Stahl |
|Tags          |Tina Warinner                                           |
|Projects      |                                                        |
|Files         |0                                                       |

But there is no way of me knowing what other samples are associated in that batch.

jfy133 commented 4 years ago

Batch view on the right from the pandora web page

image

(Note different search term to published data for privacy)

nevrome commented 4 years ago

I guess that would be a job for summarise? Or maybe an integration of view and summarise to have one module to show meaningful, human readable information about individual entities.

jfy133 commented 4 years ago

Yes, good point. I guess it depends if summarise will actually list all the IDs or not or just the 'number'. I've not played around with summarise much I have to admit ;)