In [1]:

from linkml_runtime.utils.schemaview import SchemaView

In [2]:

view = SchemaView("../tests/test_utils/input/mixs/mixs.yaml")

In [4]:

len(view.all_slots())

Loading schema water from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema terms from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema ranges from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema https://w3id.org/linkml/types from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema wastewater_sludge from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema soil from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema sediment from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema plant_associated from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema miscellaneous_natural_or_artificial_environment from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema microbial_mat_biofilm from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema hydrocarbon_resources_fluids_swabs from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema hydrocarbon_resources_cores from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema human_vaginal from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema human_skin from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema human_oral from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema human_gut from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema human_associated from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema host_associated from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema built_environment from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema air from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema core from ../tests/test_utils/input/mixs/mixs.yaml
Loading schema checklists from ../tests/test_utils/input/mixs/mixs.yaml

Out[4]:

In [10]:

list(view.all_classes().keys())[0:10]

Out[10]:

['water',
 'quantity value',
 'wastewater_sludge',
 'soil',
 'sediment',
 'plant-associated',
 'miscellaneous natural or artificial environment',
 'microbial mat_biofilm',
 'hydrocarbon resources-fluids_swabs',
 'hydrocarbon resources-cores']

In [19]:

view.get_slot('elev').required is True

Out[19]:

False

In [20]:

view.induced_slot('elev', 'soil').required is True

Out[20]:

True

In [21]:

view.induced_slot('elev', 'human-gut').required is True

Out[21]:

False

In [23]:

view.get_class('MIUVIG').description

Out[23]:

'Minimum Information About an Uncultivated Virus Genome'

In [25]:

view.class_descendants('MIUVIG')

Out[25]:

['MIUVIG',
 'air MIUVIG',
 'built environment MIUVIG',
 'host-associated MIUVIG',
 'human-associated MIUVIG',
 'human-gut MIUVIG',
 'human-oral MIUVIG',
 'human-skin MIUVIG',
 'human-vaginal MIUVIG',
 'hydrocarbon resources-cores MIUVIG',
 'hydrocarbon resources-fluids_swabs MIUVIG',
 'microbial mat_biofilm MIUVIG',
 'miscellaneous natural or artificial environment MIUVIG',
 'plant-associated MIUVIG',
 'sediment MIUVIG',
 'soil MIUVIG',
 'wastewater_sludge MIUVIG',
 'water MIUVIG']

In [26]:

view.induced_slot('vir_ident_software', 'MIUVIG').required is True

Out[26]:

True

In [27]:

view.induced_slot('vir_ident_software', 'soil MIUVIG').required is True

Out[27]:

True

In [28]:

view.induced_slot('vir_ident_software', 'soil').required is True

Out[28]:

False

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