Closed omarbenites closed 4 years ago
@marieALaporte here you can attach the excel file
[NOW FIXED! 👍 ]
Fix issues in metadata as follow
[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:
🚫 This issues is not valid any more. Please check the next issue ⏭ https://github.com/AGROFIMS/hagrofims/issues/166#issuecomment-520443203
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
Case 2
Case 3
METADATA
Residue management tab
Irrigation tab
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
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.
Better if the cells that have not been fill in AgroFIMS are blank. Don't add ''NA''
In the Excel fielbook, there is a mix between the factor -levels.
This is what I get:
It should be like this:
[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
Selected option
)
How it should be
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.
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 !
@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?
@omarbenites
-Solved for the next update
@omarbenites
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''
@omarbenites
Currently
Info grouped by number
AgroFIMS
Current Excel file
✅ fixed for the next update
✅ @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
✅ Solved for the next update
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.
@omarbenites it is better to not have any prefilled value.
Crop Phenology
Column alignement issue in the Traitlist
@omarbenites
Change the # for :
✅ Solved next update
@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
@omarbenites
✅ Fixed for the next update
@omarbenites
@omarbenites
✅ Fixed for next update
@omarbenites
✅ Ready for the next update
@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] 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)
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
✅
Delete the current content
Replace with column Header : ''Label'', ''Description''
✅
@omarbenites ''other'' type of experiment
✅
@omarbenites
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
@omarbenites
✅
@omarbenites
@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.
@omarbenites Intercrop
✅
@omarbenites
✅
@omarbenites
[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
✅
@omarbenites
Change Parameter names for the one below and remove ''Information on experimental unit'':
@omarbenites
[NOW FIXED! 👍 ]
Group
,Subgroup
, ...Label
harvest_cm
12