Download enhacements

[omarbenites]

[NOW FIXED! 👍 ]

1. Se va exportar un sheet llamado Trait List donde

• Los labels del field operations deben estar acompañados de: Group, Subgroup, ... Label

2. Los trait con unidades deben ser exportado como Ex. harvest_cm 12

[omarbenites]

@marieALaporte here you can attach the excel file

[omarbenites]

[NOW FIXED! 👍 ]

Fix issues in metadata as follow

• experimental unit
• factor label name
• inclide expeirmwntal design and parameters

[omarbenites]

• [x] Seedbed preparation: list only the variables for the method chosen in AgroFIMS. I have selected tillage in AgroFIMS, but I also get the variables for ''puddling'', and ''land levelling'' in the fieldbook.
• [x] Planting-transplanting: list only the variables for the method selected in AgroFIMS. I have selected ''direct seeding'' but I also get the variables for ''transplanting''
• [x] Trait list : This is what I get:

• [x] Phenology: should be like ''Fieldbook'' with PLOT, ROW, COL, TREATMENT, and the variables selected
  

• [x] Weather and Soil : the column header should be the variables name, without PLOT, ROW, COL, TREATMENT.
  

• [x] What is ''Input''?

This is how is should be:

[omarbenites]

• [x] Intecrop fails with soil and fertitlity (solved 👍 )

[omarbenites]

🚫 This issues is not valid any more. Please check the next issue ⏭ https://github.com/AGROFIMS/hagrofims/issues/166#issuecomment-520443203

• [x] KDSMART RULES

We had a call with Brian and Medha this morning about the ''NumberofMeasurementperPlot''. In KDSmart, they add a # in the trait name to give the number of measurement per plot. I put an example in the attached file with 2 variables in yellow in the Trait List and in the Fieldbook tab.

HEADER RULE IN FIELDBOOK: TraitName__(NumberMeaPerSeason)#(NumberMeaPerPlot)

• Case 1

  • Number of Measurement per season = 1
  • Number of measurement per plot = 1 Outcome: The Trait name in the field book will be: TraitName__1

• Case 2

  • Number of Measurement per season = 2
  • and Number of measurement per plot = 3 Outcome: The Trait name in the fieldbook will be: TraitName1#1, TraiName1#2, TraitName1#3, TraitName2#1, TraitName2#2, TraitName2#3

• Case 3

  • Number of Measurement per season = 1
  • and Number of measurement per plot = 3 Outcome: The Trait name in the fieldbook will be: TraitName1#1 , TraitName1#2, TraitName1#3, TraitName2#1, TraitName2#2, TraitName2#3

[omarbenites]

METADATA

• [x] Treatment: should use the traitName label - should not be called ''Technique'' but ''tillage_technique''

Residue management tab

• [x] Residue_management_residue_incorporation_depthcm - should be Residue_management_residue_incorporation_depth_cm
• [x] Residue_management_description_start date - should be Residue_management_description_start_date The names are correct tin the Datadictionnary

Irrigation tab

• [x] only 1 underscore instead of the 2 required by KDSmart: Irrigation_splinkler_irrigation_system_1 should be Irrigation_splinkler_irrigation_system__1

Harvest tab

• [x] why is there a « 1 » when there is only one Harvest process? Whereas the is no « 1 » in the residue management tab, for which there is only one process too. Make it consistent.

• [x] In AgroFIMS I entered ''Harvest cut height''= 15cm, in the fieldbook the 15 is under Harvest_amount

TraitList

• [x] There are more variables in the TraitList than in the process tabs: Weeding_end_date and residue management_end_date for instance
• [x] Could you please change ''CropMeasurementPerPlot'' to ''NumberofMeasurementPerPlot''
• [x] Could you please change ''CropMeasurementPerSeason'' to ''NumberofMeasurementPerSeason''

[omarbenites]

Celine reported: checked the Excel file and it seems that they are still some little bugs:

• [x] Funding Agency name: name of the CGIAR center is missing. I enterted Bioversity International in AgroFIMS :

• [x] Experiment lead: I entered nothing in AgroFIMS, but it automatically selected CGIAR center in the fieldbook.

• [x] Factor: I have 5 factors in my experiment. Why is there only 3 of them in a single column in the fieldbook? Ans: I added an underscore for every factor that user is adding

• [x] Crop: Other I have an ''Other'' crop. In AgroFIMS, the crop measurement tab didn't appear for ''other''. In the fieldbook, the measurements selected for Maize appear also in the tab for Other

• [x] Name of weather variable: should use TraitName

• [x] Name of soil variable in labbook: should use TraitName

• [x] Variables: not the same name used in TraitList and in the tab. Ex: in Traitlist: Soil_fertility_Product_rate , in Soil fertility tab: Soil_fertility_productrate(kg/ha)__1 more variables in the TraitList than in the Soil fertility tab. I didn't find the names of the variables in the red square in the DataDictionnary in the Drive. Please use the names listed in the TraitName colunm. the variables without a VariableiD should not appear in the fieldbook (ex: Soil_fertility_biofertilizer_other)

• [x] Direct seeding variables are in the trait list, but there is no ''Direct seeding'' tab. Plus I only selected - [x] Direct seeding and there are also variables for Transplanting.

[celineaubert]

• [x] In the TraitList, add name of the Crop in the ''Crop'' column for phenology.
• [x] For intercrop, concatenate the name of the crop with the name of the variable for Phenology, planting and harvest. ex'' cassava_harvest_start_date

[celineaubert]

Better if the cells that have not been fill in AgroFIMS are blank. Don't add ''NA''

[celineaubert]

In the Excel fielbook, there is a mix between the factor -levels.

This is what I get:

It should be like this:

• [ ]

[celineaubert]

• [x] If the NumberofMeasurmentperPlot is 1, the name of the trait in the tab headers should be TraitName__1 , no "#1".

[celineaubert]

• [x] In Metadata, ''Select crop 1'' , call it ''Crop 1'' (same for crop 2,3, ...)

• [x] ''Crop variety(s) 1 '', call it ''Crop variety 1'' (same for variety 2,3, ...)

• [x] In Metadata find a better way to link Crop and Crop variety. In the example it is not possible to know which variety is maize and which on is soybean Example:

Possible solutions

1. list the varieties under the Crop

2. Add the name of the crop into the row header (Selected option)
   3. any other solution you think off

[celineaubert]

• [x] Downloaded fielbook metadata should have the AgroFIMS version - to help to find issues

[celineaubert]

• [x] Name of the Fielbook file instead of fileNameBook: Fieldbook ID-System ID

[celineaubert]

• [x] Have info about Person group per person number. All info about person 1 should be display together, all info about person 2 should be display together how it is currently (info mixed between person 1 and 2)

How it should be

[celineaubert]

Have different Ids, trait names and trait alias when a measurement is used for 2 crops in the same expriment.

• [x] How it is currently in the Excel fieldbook

• [x]

@celineaubert Thanks for reminding this issue. As we discussed in MPL, We are going to generate a random ID (for KDSMART) for all the traits in order to avoid duplications.

[celineaubert]

Hi @omarbenites

here is the last HEADER RULE IN FIELDBOOK: (NumberMeaPerSeason):TraitName__(NumberMeaPerPlot) ex: NumberMeaPerSeason =2 NumberMeaPerPlot= 3

Header in fieldbook, in the Soil tab: 1:SoilPorosity1, 1:SoilPorosity2, 1:SoilPorosity3, 2:SoilPorosity1, 2:SoilPorosity2, 2:SoilPorosity3 see Excel file

Explanation for this choice from Brian Naming of Traits using nMeasurementsPerSeason and nMeasurementsPerPlot.

It is better to use the "nPerSeason" to specify the "prefix" and the "nPerPlot" for the TraitInstance suffix. By doing it in this way it will be much easier for the user in KDSmart. When KDSmart asks the user to select the "active" Traits, it presents each of the TraitInstances grouped within the Trait. So by using the TraitInstance-number for the "nPerPlot" they will see the following for nPerSeason==3 and nPerPlot==2:

.---- nPerSeason | v ( ) 1:PH ( ) 1:PH1 <--- nPerPlot ( ) 1:PH2

() 2:PH <--- One click selects all the "children" () 2:PH1 (*) 2:PH2

( ) 3:PH ( ) 3:PH1 ( ) 3:PH2

Each "nPerSeason" Trait collects its instances below it. And you can quickly select "all of the TraitInstances for nPerSeason==2" at the same time.

Doing it the other way around the user would get:

.--- this was where you had the "nPerPlot" | v ( ) 1:PH ( ) 1:PH1 <--- you had this as nPerSeason (*) 1:PH2 ( ) 1:PH__3

( ) 2:PH ( ) 2:PH1 (*) 2:PH2 ( ) 2:PH__3

So to choose "nPerSeason==2" the user would have to expand each of the "nPerPlot" items and then choose the "__2" items individually.

As you can image it gets even worse when you have nPerSeason==12 !

[celineaubert]

@omarbenites

• [x] Add the TraitLevel colomn in the TraitList tab of the Excel file . the colunm is already in the data dictionnary

• @celineaubert The column is already there (⬇️ ), or are you requesting for other values?

[celineaubert]

@omarbenites

• [x] Info filled in the module Planting and transplanting are not exported in the Excel file.

-Solved for the next update

[celineaubert]

@omarbenites

• [x] Choice for ''other'' type of experiment are not exported in the Excel file (ex: blabla is missing in the Excel)

Fixed for the next update ✔️

@omarbenites

remove the ''other'' in the list. Keep only the value of ''other'' (here: oth type) but not the name '' other''

[celineaubert]

@omarbenites

• [ ] List the project management info about a Project entity together (like pic 2). Do the same for Funding agency

Currently

Info grouped by number

[celineaubert]

• [x] @omarbenites In the Excel file, change ''Row geometry Maize'' to '' Number of row Maize'' (same for all the crop)

AgroFIMS

Current Excel file

✅ fixed for the next update

[celineaubert]

✅ @omarbenites In Intercropp, protocol info for the second crop is not exported in the Excel file.

A: @celineaubert look that you should have not selected the check box to export the information

[celineaubert]

• [x] Did not export in the Excel file: Plant density for Maize, and all the info about Planting_Cassava

✅ Solved for the next update

[celineaubert]

Timing for Crop Measurement:

• The value is missing for other

• [ ] Days after planting: I did not choose it, it was automatically added. Make sure it's not automatically added to the fieldbook.

• @celineaubert that is because in the interface, we pre-filled with one value (in one call we agreed on it should have at least one value to know how they are measuring)

@omarbenites it is better to not have any prefilled value.

[celineaubert]

Crop Phenology

Column alignement issue in the Traitlist

• ✅ fixed for the next update

[celineaubert]

@omarbenites

• [x] Nomenclature is: (NumberMeaPerSeason):TraitName__(NumberMeaPerPlot)

Change the # for :

✅ Solved next update

[celineaubert]

@omarbenites I have highlighted in yellow the tabs where the issues are.

CRD_rice_issues in yellow.xlsx

The issue for missing values in Traitlist for the measurement ''Plant density'' comes from AgroFIMS as it allows to select ''grain'' for ''Plant density''.

However, in the Crop_measurement file in the Drive, '' Plant density'' is only for whole plant

• ✅ Solved for the next update

[celineaubert]

@omarbenites

• [x] CGIAR center name are missing in the list

✅ Fixed for the next update

[celineaubert]

@omarbenites

• [ ] Affilitation name is missing - and ''Organization name 1'' doesn't seems to be linked to any box in AgroFIMS

[celineaubert]

@omarbenites

• [x] Factor notes is not listed

✅ Fixed for next update

[celineaubert]

@omarbenites

• [x] factor level is written twice

✅ Ready for the next update

[celineaubert]

@omarbenites

• [x] info on Planting and Transplanting are not exported in the TraitList but some variable are missing in the Planting tab fileNameBook (3).xlsx ✅ Already fixed. Just need to select the check box to export the values

• [x] Residue info missing in trait lits (from To be collected) ⚠️ 💬 Residue incorporation depth will appear in case you select in the combo ✅ Fixed for the next update

• [x] Weeding info missing

✅ fixed for the next update

• [x] Harvest info missing

✅

[celineaubert]

• [x] Irrigation - To be collected

• [x] Remove : Surface irrigation, Localized irrigation, Irrigation sprinkler technique from the list

• [x] Add Irrigation technique (listed in Datadictionnary, in tab Irrigation line 6)

• [x] Crop Phenology - TraitLevel

Please refer to the DataDictionnary when adding TraitLevel - TraitLevel for Phenology is Subplot

Info in the DataDictionnary:

Wrong info in Excel file exported from AgroFIMS

✅

[celineaubert]

• [x] Notes-Deviations - Change the content of this tab

Delete the current content

Replace with column Header : ''Label'', ''Description''

✅

[omarbenites]

• [x] Update Tillage management data
• [x] Update soil, weather and phenology data

[celineaubert]

@omarbenites ''other'' type of experiment

• [ ] remove the ''other'' in the list. Keep only the value of ''other'' (here: oth type) but not the name '' other''

✅

[celineaubert]

@omarbenites

• [ ] review line Header in Excel file

current names --> Change to

• [ ] Project management center 1 --> Project management CGIAR center 1

• [ ] Project management contributor 1 --> Project management CRP contributor 1

• [x] Experiment, lead organization name 1 --> Experiment lead organization 1

• [x] Experiment, CGIAR center name 1 --> Experiment lead CGIAR center 1

• [x] Experiment, lead contributor crp 1 --> Experiment lead CRP contributor 1

[celineaubert]

@omarbenites

• [x] ''Other'' info for Site, Vegetation surronding the exp site not reported in Excel

✅

[celineaubert]

@omarbenites

• [x] In Design, Crop info (when in intercrop) is not exported for the factors where it's needed (harvest date, planting date, crop variety, ...)

[celineaubert]

@omarbenites

Management practices

• [x] When adding a second ''harvest'',''Irrigation'', ''weeding'', info are not reported in Excel. Be careful, when the info are reported they need to be numbered (ex: Harvest_start_date_2)

• [x] Irrigation

• [x] Weeding

• [x] Harvest

✅

@celineaubert You mean in the Protocol Sheet? @omarbenites Yes in the Protocol sheet ⚠️ I have modified some variables in the Data Dict. becuase there were not filtering correctly due to misspellings.

[celineaubert]

@omarbenites Intercrop

• [x] Some variables are not all reported in Excel.
• [x] Also, why Seeding rate for common bean is in lb/ac? put it in kg/ha

✅

[celineaubert]

@omarbenites

• [x] Info on TraitLevel missing for Phenology

✅

[celineaubert]

@omarbenites

fileNameBook (5).xlsx

• [x] Transplanting variables listed in Planting tab but not listed in TraitList

• [x] TraitAlias are missing for Phenology variables in TraitList

• [x] Irrigation technique listed in Irrigation tab but not listed in TraitList. 📑 Fixed in the data dict.

• [x] ''Amount harvested'' listed twice. Keep only Amountharvestedkg

• [x] Crop_residue_thickness_ft change to Crop_residuethicknesscm

✅

[celineaubert]

@omarbenites

• [x] In Excel tab name, remove space between Planting-Crop ✅

[celineaubert]

• [x] In Intercrop, KDSmart script doesn't work because there are similar parameter names in the Metadata sheet in Excel

Change Parameter names for the one below and remove ''Information on experimental unit'':

[celineaubert]

@omarbenites

• [x] The info from Fertilizer management (soil fertility) module in Management practices should go in the Excel sheet called ‘’Fertilizer management’’ and not ‘’soil_sheet‘’. This is the sheet name recognized by KDSMart.