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Add excel_worksheet_name annotations to DhInterface subclasses #215

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Jul 23, 2024
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Add excel_worksheet_name annotations to DhInterface subclasses #215

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42 changes: 21 additions & 21 deletions schemasheets/tsv_in/classes.tsv
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Original file line number Diff line number Diff line change
@@ -1,24 +1,24 @@
>key class = one DH interface title Desc tree_root parent term yes, I am a mixin mixins non-imported slots
>class title description tree_root is_a mixin mixins slots
> "internal_separator: ""|""" "internal_separator: ""|"""
AirInterface Air air dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
BiofilmInterface Biofilm biofilm dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
BuiltEnvInterface Built Env built_env dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
EmslInterface Emsl emsl dh_interface DhInterface DhMultiviewCommonColumnsMixin emsl_store_temp|project_id|replicate_number|sample_shipped|sample_type|technical_reps
HcrCoresInterface Hcr Cores hcr_cores dh_interface DhInterface DhMultiviewCommonColumnsMixin
HcrFluidsSwabsInterface Hcr Fluids Swabs hcr_fluids_swabs dh_interface DhInterface DhMultiviewCommonColumnsMixin
HostAssociatedInterface Host Associated host_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
JgiMgInterface JGI MG Metadata for samples sent to JGI for standard metagenome sequencing DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
JgiMgLrInterface JGI MG (Long Read) Metadata for samples sent to JGI for long read metagenome sequecning DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
JgiMtInterface JGI MT jgi_mt dh_interface DhInterface DhMultiviewCommonColumnsMixin dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume
MiscEnvsInterface Misc Envs misc_envs dh_interface DhInterface DhMultiviewCommonColumnsMixin
PlantAssociatedInterface Plant Associated plant_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
SedimentInterface Sediment sediment dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
SoilInterface Soil soil dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin|SoilMixsInspiredMixin
WastewaterSludgeInterface Wastewater Sludge wastewater_sludge dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
WaterInterface Water water dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin
DhMultiviewCommonColumnsMixin Dh Mutliview Common Columns Mixin with DhMutliviewCommon Columns TRUE
>key class = one DH interface title Desc tree_root parent term yes, I am a mixin mixins non-imported slots excel sheet name
>class title description tree_root is_a mixin mixins slots annotations
> "internal_separator: ""|""" "internal_separator: ""|""" "inner_key: ""excel_worksheet_name"""
AirInterface Air air dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin air
BiofilmInterface Biofilm biofilm dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin microbial mat_biofilm
BuiltEnvInterface Built Env built_env dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin built environment
EmslInterface Emsl emsl dh_interface DhInterface DhMultiviewCommonColumnsMixin emsl_store_temp|project_id|replicate_number|sample_shipped|sample_type|technical_reps EMSL
HcrCoresInterface Hcr Cores hcr_cores dh_interface DhInterface DhMultiviewCommonColumnsMixin hcr core
HcrFluidsSwabsInterface Hcr Fluids Swabs hcr_fluids_swabs dh_interface DhInterface DhMultiviewCommonColumnsMixin hcr fluids swab
HostAssociatedInterface Host Associated host_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin host-associated
JgiMgInterface JGI MG Metadata for samples sent to JGI for standard metagenome sequencing DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna JGI MG
JgiMgLrInterface JGI MG (Long Read) Metadata for samples sent to JGI for long read metagenome sequecning DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna JGI MG (Long Read)
JgiMtInterface JGI MT jgi_mt dh_interface DhInterface DhMultiviewCommonColumnsMixin dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume JGI MT
MiscEnvsInterface Misc Envs misc_envs dh_interface DhInterface DhMultiviewCommonColumnsMixin misc natural or artificial
PlantAssociatedInterface Plant Associated plant_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin plant-associated
SedimentInterface Sediment sediment dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin sediment
SoilInterface Soil soil dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin|SoilMixsInspiredMixin soil
WastewaterSludgeInterface Wastewater Sludge wastewater_sludge dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin wastewater sludge
WaterInterface Water water dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin water
DhMultiviewCommonColumnsMixin Dh Mutliview Common Columns Mixin with DhMutliviewCommon Columns TRUE
SampIdNewTermsMixin SampId New Terms Mixin with SampIdNew Terms TRUE sample_link
SoilMixsInspiredMixin Soil MIxS Inspired Mixin Mixin with SoilMixsInspired Terms TRUE collection_date_inc|collection_time|collection_time_inc|experimental_factor_other|filter_method|isotope_exposure|micro_biomass_c_meth|micro_biomass_n_meth|microbial_biomass_c|microbial_biomass_n|non_microb_biomass|non_microb_biomass_method|org_nitro_method|other_treatment|start_date_inc|start_time_inc
DhInterface Dh Root Interface One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types
DhInterface Dh Root Interface One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types
SampleData SampleData represents data produced by the DataHarmonizer tabs of the submission portal TRUE air_data|biofilm_data|built_env_data|host_associated_data|plant_associated_data|sediment_data|soil_data|wastewater_sludge_data|water_data|emsl_data|jgi_mg_lr_data|jgi_mg_data|jgi_mt_data
32 changes: 32 additions & 0 deletions tests/test_schema.py
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import unittest
from pathlib import Path

from linkml_runtime import SchemaView

SCHEMA_YAML_PATH = Path(__file__).parent / "../src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml"


class TestSchema(unittest.TestCase):
"""Tests that the schema itself is well-formed, outside any specific data instances"""

def test_excel_worksheet_name_annotations(self):
"""Test that all DhInterface subclasses have an excel_worksheet_name annotation and that its
value is not longer than 31 characters, which is the maximum length of a worksheet name in
Excel.
"""

schema_view = SchemaView(SCHEMA_YAML_PATH)
for class_name, class_def in schema_view.all_classes().items():
if class_def.is_a != "DhInterface":
continue

excel_worksheet_name_annotation = class_def.annotations.get("excel_worksheet_name")
self.assertIsNotNone(
excel_worksheet_name_annotation,
f"Missing excel_worksheet_name annotation for {class_name}"
)
self.assertLessEqual(
len(excel_worksheet_name_annotation.value),
31,
f"excel_worksheet_name \"{excel_worksheet_name_annotation.value}\" is too long"
)
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