microbiomedata / sheets_and_friends

Enhance a LinkML model with imported and optionally modified slots
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examples from new_terms tab failing in do_shuttle #31

Closed turbomam closed 2 years ago

turbomam commented 2 years ago

TypeError: linkml_runtime.linkml_model.meta.Example() argument after ** must be a mapping, not extended_str

turbomam commented 2 years ago
slot examples
analysis_type metagenomics; metabolomics; proteomics
collection_date_inc 2021-04-15, 2021-04 and 2021 are all acceptable.
collection_time 13:33 or 13:33:55
collection_time_inc 13:33 or 13:33:55
dna_absorb1 2.02
dna_absorb2 2.02
dna_collect_site untreated pond water
dna_concentration 100
dna_cont_type plate
dna_cont_well B2
dna_container_ID Pond_MT_041618
dna_dnase no
dna_isolate_meth phenol/chloroform extraction
dna_organisms expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)
dna_project_contact John Jones
dna_samp_ID 187654
dna_sample_format Water
dna_sample_name JGI_pond_041618
dna_seq_project 1191234
dna_seq_project_name JGI Pond metagenomics
dna_seq_project_PI Jane Johnson
dna_volume 25
dnase_rna no
EMSL_store_temp -80
env_package soil
proposal_dna 504000
proposal_rna 504000
rna_absorb1 2.02
rna_absorb2 2.02
rna_collect_site untreated pond water
rna_concentration 100
rna_cont_type plate
rna_cont_well B2
rna_container_ID Pond_MT_041618
rna_isolate_meth phenol/chloroform extraction
rna_organisms expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)
rna_project_contact John Jones
rna_samp_ID 187654
rna_sample_format Water
rna_sample_name JGI_pond_041618
rna_seq_project 1191234
rna_seq_project_name JGI Pond metatranscriptomics
rna_seq_project_PI Jane Johnson
rna_volume 25
sample_link IGSN:DSJ0284
sample_type water extracted soil
start_date_inc 2021-04-15, 2021-04 and 2021 are all acceptable.
start_time_inc 13:33 or 13:33:55
turbomam commented 2 years ago

temporarily moved to modification tab

turbomam commented 2 years ago

I guess do_shuttle is complaining when opening a SchemaView of artifacts/from_sheets2linkml.yaml, containing malformed examples:

        examples:
        - IGSN:DSJ0284

as opposed to

        examples:
        - value: IGSN:AU1243