From 1890c40c29c521c4901221820ad1e8cb9e2b0846 Mon Sep 17 00:00:00 2001
From: Damion Dooley <damion_dooley@sfu.ca>
Date: Fri, 6 Sep 2024 10:27:56 -0700
Subject: [PATCH] Update dh-validate.py

---
 script/dh-validate.py | 52 +++++++++++++++++++++----------------------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/script/dh-validate.py b/script/dh-validate.py
index c732d04b..33d8d5b3 100644
--- a/script/dh-validate.py
+++ b/script/dh-validate.py
@@ -52,17 +52,6 @@
 from linkml_runtime.dumpers.yaml_dumper import YAMLDumper
 import subprocess
 
-# ISSUE TRYING TO IMPORT linkml, getting "error: no such option: --schema" when --schema provided to argparse; and "Input LinkML schema file not given" when not given that parameter!
-"""
-try:
-	from linkml.validator import validate
-except Exception as inst:
-	print(type(inst))    # the exception type
-	print(inst.args)     # arguments stored in .args
-	print(inst)          # __str__ allows args to be printed directly,
-	                     # but may be overridden in exception subclasses
-"""
-
 def init_parser():
 
 	parser = argparse.ArgumentParser(
@@ -530,15 +519,33 @@ def isInteger(x):
 if len(warnings):
 	print ("\nWARNING: \n", "\n ".join(warnings));
 
-
+"""
 # SNIPETS:
-#
-#stderr=None;
-#try:
+# A challenge trying to get linkml-validate working via python module.
+
+report = validate(data_handle, args.schema_path, "Person") # , "Person"
+if not report.results:
+  print('The instance is valid!')
+else:
+  for result in report.results:
+      print(result.message)
+
+# ISSUE TRYING TO IMPORT linkml, getting "error: no such option: --schema" when --schema provided to argparse; and "Input LinkML schema file not given" when not given that parameter!
+try:
+	from linkml.validator import validate
+except Exception as inst:
+	print(type(inst))    # the exception type
+	print(inst.args)     # arguments stored in .args
+	print(inst)          # __str__ allows args to be printed directly,
+	                     # but may be overridden in exception subclasses
+
+	
+stderr=None;
+try:
 # e.g. > linkml-convert -s schema.yaml -C CanCOGeNCovid19 --index-slot specimen_collector_sample_id -o validTestData_2-1-2.tmp.tsv.json validTestData_2-1-2.tmp.tsv
 # ISSUE IS range="ANY_OF" slots may have content but if REQUIRED=True, ARE THROWING ERROR.
-#run_state = subprocess.check_output(["linkml-convert", "-s", args.schema_path, "-C", target_class, "--index-slot", slot_key, "-o", temp_file + '.json', temp_file]) #, stderr=subprocess.STDOUT
-"""
+	run_state = subprocess.check_output(["linkml-convert", "-s", args.schema_path, "-C", target_class, "--index-slot", slot_key, "-o", temp_file + '.json', temp_file]) #, stderr=subprocess.STDOUT
+
 except BaseException as inst:
 
 	print(type(inst))		# the exception type
@@ -547,15 +554,6 @@ def isInteger(x):
 												# but may be overridden in exception subclasses
 
 finally:
-"""
+...
 
 """
-# A challenge trying to get linkml-validate working via python module.
-
-report = validate(data_handle, args.schema_path, "Person") # , "Person"
-if not report.results:
-  print('The instance is valid!')
-else:
-  for result in report.results:
-      print(result.message)
-"""
\ No newline at end of file