Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

first-any_of-range #10

Merged
merged 1 commit into from
Sep 13, 2024
Merged

first-any_of-range #10

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions assets/MimsSoil-collection_date-absent-report.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
[ERROR] [src/data/examples/invalid/MimsSoil-collection_date-absent.yaml/0] 'collection_date' is a required property in /
1 change: 1 addition & 0 deletions assets/MimsSoil-collection_date-from_enum-report.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
No issues found
1 change: 1 addition & 0 deletions assets/MixsCompliantData-001-report.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
No issues found
18 changes: 16 additions & 2 deletions project.Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,27 @@
RUN=poetry run

src/data/valid/MixsCompliantData-001-report.txt: src/data/examples/valid \
assets/MixsCompliantData-001-report.txt: src/data/examples/valid/MixsCompliantData-001.yaml \
src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
$(RUN) linkml-validate \
--schema $(word 2,$^) \
--target-class $(shell echo $(basename $(notdir $(word 1,$^))) | cut -d'-' -f1) \
$(word 1,$^) > $@

src/data/valid/MixsCompliantData-001.tsv: src/data/examples/valid \
assets/MimsSoil-collection_date-absent-report.txt: src/data/examples/invalid/MimsSoil-collection_date-absent.yaml \
src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
$(RUN) linkml-validate \
--schema $(word 2,$^) \
--target-class $(shell echo $(basename $(notdir $(word 1,$^))) | cut -d'-' -f1) \
$(word 1,$^) > $@

assets/MimsSoil-collection_date-from_enum-report.txt: src/data/examples/valid/MimsSoil-collection_date-from_enum.yaml \
src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
$(RUN) linkml-validate \
--schema $(word 2,$^) \
--target-class $(shell echo $(basename $(notdir $(word 1,$^))) | cut -d'-' -f1) \
$(word 1,$^) > $@

assets/MixsCompliantData-001.tsv: src/data/examples/valid/MixsCompliantData-001.yaml \
src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
$(RUN) linkml-convert --schema $(word 2,$^) \
--output $@ \
Expand Down
12 changes: 12 additions & 0 deletions src/data/examples/invalid/MimsSoil-collection_date-absent.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
depth: "123"
elev: "123"
project_name: abc
samp_name: abc

env_broad_scale: unicorn [example:999]
env_local_scale: unicorn [example:999]
env_medium: unicorn [example:999]
geo_loc_name: "unicorn: unicorn, unicorn"
lat_lon: 45.67 45.67
samp_taxon_id: unicorn [NCBITaxon:999]
seq_meth: xxx
0 ...les/invalid/Soil-missing_sample_name.yaml → ...ples/invalid/Soil-sample_name-absent.yaml
View file
Open in desktop
File renamed without changes.
13 changes: 13 additions & 0 deletions src/data/examples/valid/MimsSoil-collection_date-from_enum.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
depth: "123"
elev: "123"
project_name: abc
samp_name: abc

collection_date: '2013-03-25T12:42:31+01:00'
env_broad_scale: unicorn [example:999]
env_local_scale: unicorn [example:999]
env_medium: unicorn [example:999]
geo_loc_name: "unicorn: unicorn, unicorn"
lat_lon: 45.67 45.67
samp_taxon_id: unicorn [NCBITaxon:999]
seq_meth: xxx
11 changes: 11 additions & 0 deletions src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,11 @@ classes:
mixins:
- Mims
class_uri: MIXS:0010007_0016012
slot_usage:
collection_date:
any_of:
- range: datetime
- range: MixsMissingValueEnum
Mims:
description: Metagenome or Environmental
title: MIMS
Expand Down Expand Up @@ -1882,6 +1887,12 @@ slots:
partial_match: true

enums:
MixsMissingValueEnum:
permissible_values:
missing1: { }
missing2: { }
missing3: { }

DrainageClassEnum:
permissible_values:
excessively drained:
Expand Down
Loading