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elixir-europe / plant-brapi-to-isa

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Assay file improvements #34

Closed bedroesb closed 5 years ago

bedroesb commented 5 years ago

Current state:

Examples:

a_RIGW1_BLOCK>PLOT.txt:

Sample Name Protocol REF Assay Name Derived Data File
26212 phenotyping 2990931-2008 d_RIGW1_BLOCK>PLOT.txt
26212 phenotyping 2990931-2007 d_RIGW1_BLOCK>PLOT.txt
26212 phenotyping 2990931-2009 d_RIGW1_BLOCK>PLOT.txt
26212 phenotyping 2990931-2006 d_RIGW1_BLOCK>PLOT.txt

a_POPYOMICS-POP2-F_VIRTUAL_TRIAL.txt:

Sample Name Protocol REF Assay Name Derived Data File
101-74 phenotyping 2889403-2004 d_POPYOMICS-POP2-F_VIRTUAL_TRIAL.txt
101-74 phenotyping 2889403-2005 d_POPYOMICS-POP2-F_VIRTUAL_TRIAL.txt
661300224 phenotyping 2889073-2005 d_POPYOMICS-POP2-F_VIRTUAL_TRIAL.txt
661300224 phenotyping 2889073-2004 d_POPYOMICS-POP2-F_VIRTUAL_TRIAL.txt

a_VIB_study___40_plant.txt:

Sample Name Protocol REF Assay Name Derived Data File
pot_1 phenotyping P_6583 d_VIB_study___40_plant.txt
pot_10 phenotyping P_6592 d_VIB_study___40_plant.txt
pot_100 phenotyping P_6463 d_VIB_study___40_plant.txt
pot_101 phenotyping P_6464 d_VIB_study___40_plant.txt

a_BTH_Clermont-Ferrand_2000_SetB1_REPLICATION.txt:

Sample Name Protocol REF Assay Name Derived Data File
1 phenotyping 2763979-2000 d_BTH_Clermont-Ferrand_2000_SetB1_REPLICATION.txt
2 phenotyping 2763968-2000 d_BTH_Clermont-Ferrand_2000_SetB1_REPLICATION.txt
CF00188itkt phenotyping 2763922-2000 d_BTH_Clermont-Ferrand_2000_SetB1_REPLICATION.txt
CF00188itkt phenotyping 2763977-2000 d_BTH_Clermont-Ferrand_2000_SetB1_REPLICATION.txt
cpommier commented 5 years ago

@bedroesb I am generating my datafiles with that

bedroesb commented 5 years ago

I am still trying to figure out the material - protocol - source - sample - assay object hierarchy in ISA to generate the assay files how it should be

proccaserra commented 5 years ago

@bedroesb what is wrong with the current one as available in the original code (I mean besides the new request that came up to break down by observational units as we went along) ?

bedroesb commented 5 years ago

@cpommier what do you mean ?

bedroesb commented 5 years ago

Missing columns at the moment based on isa validator:

To be fixed in configuration files see:

https://github.com/MIAPPE/ISA-Tab-for-plant-phenotyping/issues/12

bedroesb commented 5 years ago

Issues that still need to be solved based on isa validator:

"message": "Missing Protocol declaration",
            "supplemental": "Protocol(s) of type ['Phenotyping', 'Sampling'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Assay Name' but has not been found, in the file 'a_VIB_study___55_plant.txt'",
            "code": 1007
"message": "Missing Protocol declaration",
            "supplemental": "Protocol(s) of type ['Data Transformation'] defined in the ISA-configuration expected as a between 'Assay Name' and 'Derived Data File' but has not been found, in the file 'a_VIB_study___55_plant.txt'",
            "code": 1007
bedroesb commented 5 years ago

Will open new pull request/issue with final to do list with things that need to be done, and were I will need assistance with.