Add visual indicator of samples [ACAD #2]

[Li-ReDBox]

Add visual indicator of whether a sample has been:

1. extracted
2. had a library made (Amplification?)
3. Enrichment
4. been sequenced

[Li-ReDBox]

Currently,

1. red start is used for "has been extracted"
2. blue start is used for "is_carbondated"

@sgoodswen, could you please:

1. verify if the above four items to be included in displaying indicators;
2. clarify the question mark;
3. confirm if red and blue starts should be used as current and
4. pick what symbols to use. The symbols can be choose from here, currently used or any other sets you can find.

[sgoodswen]

1. extracted <- this is currently a red star
2. had a library made (Amplification?) <- Yes, for Amplification: symbol = glyphicon glyphicon-plus (green)
3. has Enrichment (?) <- Yes, for Enrichment : symbol = glyphicon glyphicon-play-circle (magenta)
4. been sequenced <- Yes, for sequencing: symbol = glyphicon glyphicon-ok (black)

Yes, please continue to use red and blue stars as is current

Is it possible to have a legend on the Samples selection page please?

[Li-ReDBox]

Thanks @sgoodswen.

Could you please clarify "Is it possible to have a legend on the Samples selection page please?"

Thanks

[sgoodswen]

On the Samples page (https://upload-fix.oagr.org.au/sample/) in the blank space on the right hand side, please have the following:

(Red star) Extraction (Green plus) Amplification (Magenta circle) Enrichment (Black ok symbol) Sequencing (Blue star) Carbon dated

Within the brackets you would place the actual coloured symbol

[Li-ReDBox]

@sgoodswen, could you please create some testing dataset which has all these linked data?

[sgoodswen]

Sample 2 now has an extraction, amplification, Enrichment, Sequencing and Carbon dating (we should see 5 coloured symbols) Sample 7 has extraction, amplification, Enrichment (we should see 3 coloured symbols)

[Li-ReDBox]

Thanks @sgoodswen

[Li-ReDBox]

@sgoodswen , could you please help me to understand sequence model? It seems to me is a method description: what amplification and enrichment methods are used. I have not found links to any results.

[sgoodswen]

Sorry Li, not sure what you mean by “sequence model”.

Sample ID 2 is linked to Extractions, Amplifications, Enrichments and Sequences

To find the links to the results for Sample 2 select ‘Extraction 2016-01-22 steve”. You will see extraction result 2A.

Select “Amplification 2016-01-29 stephen” and you will see Amplification results for 2A_2, 2A_1, 7A_1.

Select “Enrichment 2016-01-29 harry” and you will see Enrichment results for 2A_1a and 2A_2a

Hopefully the following will help explain how the IDs link together.

There is a hierarchical relationship between the Sample ID and the Lab options:

Extractions -> New extraction (no ID is given)

Extraction results -> [+]
    Add a result … enter a Sample ID e.g. 444

Note: 1 extraction can have 0 to 1 extraction results (linked to sample IDs). Extraction result ID uses the sample ID + an incremental uppercase letter commencing from A e.g. Sample ID = 444 -> Extraction result ID = 444A

Amplifications -> New amplification (no ID is given) [Mandatory: Date, Prepared by, Method]

Amplification results -> [+]

Add a result … enter a Extraction result ID e.g. 444A

Note: Amplification result ID uses the Extraction result ID + an incremental number commencing from 1 e.g. Extraction result ID = 444A -> Amplification result ID = 444A_1

Enrichments -> New enrichment (no ID is given) [Mandatory: Date, Prepared by]

Enrichment results -> [+]

Add a result … enter an Amplification result ID = 444A_1

Note: 1Enrichment can have 0 to 1 Enrichment results. Enrichment result ID uses the Amplification result ID + an incremental lowercase letter commencing from a e.g. Amplification result ID = 444A_1 -> Enrichment result ID = 444A_1a

Sequencing -> New sequencing

Select Amplification and Enrichment from drop down boxes

[Li-ReDBox]

I think I was on the correct direction: Sequencing does not link to Amplification results or Enrichment results. If you could confirm, or clarify more in case you cannot confirm, will be good.

[sgoodswen]

Yes you are correct ,it does not link to the Amplification "results" or Enrichment "results" but is linked to either an Amplification or Enrichment title e.g. a path name to a sequence file is linked to "Sequence for Amplification 2016-01-29 Stephen" in the test database

[sgoodswen]

Sample 2 has both Amplification and Enrichment and 7 only has Amplification as you said.

We need to show sequencing symbol if a sample is associated with an Amplification OR an Enrichment OR both

[Li-ReDBox]

I have made it as OR and now 7 has OK label shown.

[sgoodswen]

I agree, everything is now displayed as expected.

[sgoodswen]

We still need a legend for the symbols please

[Li-ReDBox]

Could you please let me know if I have it is as you wanted? See it on the dev site.

[sgoodswen]

If you could please remove the words "Red star, Green plus etc.. " and only have the symbol

[Li-ReDBox]

I have removed my debug strings to make it more production like. I have check in Firefox and Chromium on a high def screen. Hopefully it looks ok in others.

[sgoodswen]

It looks good.

I think this issue can now be closed ... thanks