From 16c5f4883c7a84d459c35fc0a096426d9e1ae346 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 30 Aug 2023 20:24:44 -0700
Subject: [PATCH 01/13] feat: add ConsistencyChecks schemas

---
 .../has_consistency_checks.json               | 13 +++++++
 schema/system/consistency_checks.json         | 39 +++++++++++++++++++
 2 files changed, 52 insertions(+)
 create mode 100644 schema/in_memory_entity/has_consistency_checks.json
 create mode 100644 schema/system/consistency_checks.json

diff --git a/schema/in_memory_entity/has_consistency_checks.json b/schema/in_memory_entity/has_consistency_checks.json
new file mode 100644
index 000000000..507cd4a2c
--- /dev/null
+++ b/schema/in_memory_entity/has_consistency_checks.json
@@ -0,0 +1,13 @@
+{
+  "$id": "in-memory-entity/has-consistency-checks",
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "title": "Has consistency checks",
+  "allOf": [
+    {
+      "$ref": "base.json"
+    },
+    {
+      "$ref": "../system/consistency_checks.json"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
new file mode 100644
index 000000000..5b5860ea6
--- /dev/null
+++ b/schema/system/consistency_checks.json
@@ -0,0 +1,39 @@
+{
+  "$id": "system/consistency-checks",
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "title": "consistency checks schema",
+  "properties": {
+    "consistency_checks": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "name": {
+            "type": "string"
+          },
+          "description": {
+            "type": "string"
+          },
+          "severity": {
+            "enum": ["info", "warning", "error"]
+          },
+          "arguments": {
+            "type": "object"
+          },
+          "message": {
+            "type": "string"
+          },
+          "enabled": {
+            "type": "boolean"
+          }
+        },
+        "required": [
+          "name",
+          "severity",
+          "arguments",
+          "message"
+        ]
+      }
+    }
+  }
+}
\ No newline at end of file

From af2beec1249e566eaae98302d098977686a62d7b Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 31 Aug 2023 17:27:05 -0700
Subject: [PATCH 02/13] update: refine checks schema

---
 schema/system/consistency_checks.json | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index 5b5860ea6..b915754a3 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -9,28 +9,36 @@
         "type": "object",
         "properties": {
           "name": {
-            "type": "string"
+            "type": "string",
+            "description": "Name of the consistency check which comes from an exported enum."
           },
           "description": {
-            "type": "string"
+            "type": "string",
+            "description": "Description of the consistency check provided for developers."
           },
-          "severity": {
-            "enum": ["info", "warning", "error"]
+          "keys": {
+            "type": "array",
+            "items": {}
           },
           "arguments": {
-            "type": "object"
+            "type": "array",
+            "items": {
+              "type": "object"
+            },
+            "description": "Arguments provided by consistency check function for message construction, specific to each check."
+          },
+          "severity": {
+            "enum": ["info", "warning", "error"]
           },
           "message": {
             "type": "string"
-          },
-          "enabled": {
-            "type": "boolean"
           }
         },
         "required": [
           "name",
-          "severity",
+          "keys",
           "arguments",
+          "severity",
           "message"
         ]
       }

From 2b3357cebe897169f91b023570fb7ec9f190237f Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 31 Aug 2023 17:34:01 -0700
Subject: [PATCH 03/13] update: fix small issue

---
 schema/in_memory_entity/has_consistency_checks.json | 2 +-
 schema/system/consistency_checks.json               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/schema/in_memory_entity/has_consistency_checks.json b/schema/in_memory_entity/has_consistency_checks.json
index 507cd4a2c..f141a3160 100644
--- a/schema/in_memory_entity/has_consistency_checks.json
+++ b/schema/in_memory_entity/has_consistency_checks.json
@@ -10,4 +10,4 @@
       "$ref": "../system/consistency_checks.json"
     }
   ]
-}
\ No newline at end of file
+}
diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index b915754a3..6d7a26aa9 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -44,4 +44,4 @@
       }
     }
   }
-}
\ No newline at end of file
+}

From ec448b0a57f0a47bb51d3a277a328bff68fbecb3 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 31 Aug 2023 20:10:11 -0700
Subject: [PATCH 04/13] update: change schema as per discussion with TB

---
 schema/system/consistency_checks.json | 45 +++++++++++++--------------
 1 file changed, 22 insertions(+), 23 deletions(-)

diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index 6d7a26aa9..97cc02cf4 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -8,38 +8,37 @@
       "items": {
         "type": "object",
         "properties": {
-          "name": {
-            "type": "string",
-            "description": "Name of the consistency check which comes from an exported enum."
-          },
-          "description": {
-            "type": "string",
-            "description": "Description of the consistency check provided for developers."
-          },
           "keys": {
             "type": "array",
-            "items": {}
+            "items": {
+              "type": "string"
+            }
           },
-          "arguments": {
+          "messages": {
             "type": "array",
             "items": {
-              "type": "object"
-            },
-            "description": "Arguments provided by consistency check function for message construction, specific to each check."
-          },
-          "severity": {
-            "enum": ["info", "warning", "error"]
-          },
-          "message": {
-            "type": "string"
+              "type": "object",
+              "properties": {
+                "key": {
+                  "type": "string"
+                },
+                "checkName": {
+                  "type": "string",
+                  "description": "Name of the consistency check which comes from an exported enum."
+                },
+                "severity": {
+                  "enum": ["info", "warning", "error"]
+                },
+                "message": {
+                  "type": "string"
+                }
+              }
+            }
           }
         },
         "required": [
-          "name",
           "keys",
-          "arguments",
-          "severity",
-          "message"
+          "messages"
         ]
       }
     }

From 9224c05609c00c5dd243ccdd028c3ab3eae2d1c3 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 31 Aug 2023 20:58:44 -0700
Subject: [PATCH 05/13] update: make all properties required

---
 schema/system/consistency_checks.json | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index 97cc02cf4..2c4582d1b 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -33,7 +33,13 @@
                   "type": "string"
                 }
               }
-            }
+            },
+            "required": [
+              "key",
+              "checkName",
+              "severity",
+              "message"
+            ]
           }
         },
         "required": [

From e3f8f6cdd71c08c7a3c2e700b6d41a29329005b4 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 5 Sep 2023 15:16:38 -0700
Subject: [PATCH 06/13] update: redefine CChecks as one object

---
 schema/system/consistency_checks.json | 36 +++++++++++----------------
 1 file changed, 14 insertions(+), 22 deletions(-)

diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index 2c4582d1b..ee1ae2e85 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -1,13 +1,8 @@
 {
   "$id": "system/consistency-checks",
   "$schema": "http://json-schema.org/draft-04/schema#",
-  "title": "consistency checks schema",
-  "properties": {
-    "consistency_checks": {
-      "type": "array",
-      "items": {
-        "type": "object",
-        "properties": {
+  "title": "consistency checks",
+      "properties": {
           "keys": {
             "type": "array",
             "items": {
@@ -32,21 +27,18 @@
                 "message": {
                   "type": "string"
                 }
-              }
-            },
-            "required": [
-              "key",
-              "checkName",
-              "severity",
-              "message"
-            ]
+              },
+              "required": [
+                "key",
+                "checkName",
+                "severity",
+                "message"
+              ]
+            }
           }
         },
-        "required": [
-          "keys",
-          "messages"
-        ]
-      }
+      "required": [
+        "keys",
+        "messages"
+      ]
     }
-  }
-}

From 5c98cd1a80022693f893950e6d1dc8d4895d0c73 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 5 Sep 2023 19:30:52 -0700
Subject: [PATCH 07/13] update: perform lint:fix and change check names type to
 enum

---
 .../has_consistency_checks.json               | 22 +++---
 schema/system/consistency_checks.json         | 74 ++++++++++---------
 2 files changed, 51 insertions(+), 45 deletions(-)

diff --git a/schema/in_memory_entity/has_consistency_checks.json b/schema/in_memory_entity/has_consistency_checks.json
index f141a3160..257c694e5 100644
--- a/schema/in_memory_entity/has_consistency_checks.json
+++ b/schema/in_memory_entity/has_consistency_checks.json
@@ -1,13 +1,13 @@
 {
-  "$id": "in-memory-entity/has-consistency-checks",
-  "$schema": "http://json-schema.org/draft-04/schema#",
-  "title": "Has consistency checks",
-  "allOf": [
-    {
-      "$ref": "base.json"
-    },
-    {
-      "$ref": "../system/consistency_checks.json"
-    }
-  ]
+    "$id": "in-memory-entity/has-consistency-checks",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Has consistency checks",
+    "allOf": [
+        {
+            "$ref": "base.json"
+        },
+        {
+            "$ref": "../system/consistency_checks.json"
+        }
+    ]
 }
diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index ee1ae2e85..acf5517e6 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -1,44 +1,50 @@
 {
-  "$id": "system/consistency-checks",
-  "$schema": "http://json-schema.org/draft-04/schema#",
-  "title": "consistency checks",
-      "properties": {
-          "keys": {
+    "$id": "system/consistency-checks",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "consistency checks",
+    "properties": {
+        "keys": {
             "type": "array",
             "items": {
-              "type": "string"
+                "type": "string"
             }
-          },
-          "messages": {
+        },
+        "messages": {
             "type": "array",
             "items": {
-              "type": "object",
-              "properties": {
-                "key": {
-                  "type": "string"
-                },
-                "checkName": {
-                  "type": "string",
-                  "description": "Name of the consistency check which comes from an exported enum."
+                "type": "object",
+                "properties": {
+                    "key": {
+                        "type": "string"
+                    },
+                    "checkName": {
+                        "enum": [
+                            "atomsTooClose"
+                        ],
+                        "description": "Name of the consistency check which is exported as an enum"
+                    },
+                    "severity": {
+                        "enum": [
+                            "info",
+                            "warning",
+                            "error"
+                        ]
+                    },
+                    "message": {
+                        "type": "string"
+                    }
                 },
-                "severity": {
-                  "enum": ["info", "warning", "error"]
-                },
-                "message": {
-                  "type": "string"
-                }
-              },
-              "required": [
-                "key",
-                "checkName",
-                "severity",
-                "message"
-              ]
+                "required": [
+                    "key",
+                    "checkName",
+                    "severity",
+                    "message"
+                ]
             }
-          }
-        },
-      "required": [
+        }
+    },
+    "required": [
         "keys",
         "messages"
-      ]
-    }
+    ]
+}

From c9a389e30e43adb19c9e5e95e3bc5e7766a47639 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 5 Sep 2023 20:00:45 -0700
Subject: [PATCH 08/13] update: add default to enum

---
 schema/system/consistency_checks.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
index acf5517e6..5831425b1 100644
--- a/schema/system/consistency_checks.json
+++ b/schema/system/consistency_checks.json
@@ -19,6 +19,7 @@
                     },
                     "checkName": {
                         "enum": [
+                            "default",
                             "atomsTooClose"
                         ],
                         "description": "Name of the consistency check which is exported as an enum"

From 0ae1c426c405d312a879919ffb8889cf68fce975 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 20 Oct 2023 21:37:14 -0700
Subject: [PATCH 09/13] update: isolate singular CCheck definition and ref in
 in_memory_entity

---
 schema/in_memory_entity/base.json             |  7 +++
 .../has_consistency_checks.json               | 13 -----
 schema/system/consistency_check.json          |  0
 schema/system/consistency_checks.json         | 51 -------------------
 4 files changed, 7 insertions(+), 64 deletions(-)
 delete mode 100644 schema/in_memory_entity/has_consistency_checks.json
 create mode 100644 schema/system/consistency_check.json
 delete mode 100644 schema/system/consistency_checks.json

diff --git a/schema/in_memory_entity/base.json b/schema/in_memory_entity/base.json
index 05d890942..6f7f0c7ac 100644
--- a/schema/in_memory_entity/base.json
+++ b/schema/in_memory_entity/base.json
@@ -19,6 +19,13 @@
         },
         "systemName": {
             "type": "string"
+        },
+        "consistency_checks": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "$ref": "../system/consistency_check.json"
+            }
         }
     }
 }
diff --git a/schema/in_memory_entity/has_consistency_checks.json b/schema/in_memory_entity/has_consistency_checks.json
deleted file mode 100644
index 257c694e5..000000000
--- a/schema/in_memory_entity/has_consistency_checks.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
-    "$id": "in-memory-entity/has-consistency-checks",
-    "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "Has consistency checks",
-    "allOf": [
-        {
-            "$ref": "base.json"
-        },
-        {
-            "$ref": "../system/consistency_checks.json"
-        }
-    ]
-}
diff --git a/schema/system/consistency_check.json b/schema/system/consistency_check.json
new file mode 100644
index 000000000..e69de29bb
diff --git a/schema/system/consistency_checks.json b/schema/system/consistency_checks.json
deleted file mode 100644
index 5831425b1..000000000
--- a/schema/system/consistency_checks.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
-    "$id": "system/consistency-checks",
-    "$schema": "http://json-schema.org/draft-04/schema#",
-    "title": "consistency checks",
-    "properties": {
-        "keys": {
-            "type": "array",
-            "items": {
-                "type": "string"
-            }
-        },
-        "messages": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "properties": {
-                    "key": {
-                        "type": "string"
-                    },
-                    "checkName": {
-                        "enum": [
-                            "default",
-                            "atomsTooClose"
-                        ],
-                        "description": "Name of the consistency check which is exported as an enum"
-                    },
-                    "severity": {
-                        "enum": [
-                            "info",
-                            "warning",
-                            "error"
-                        ]
-                    },
-                    "message": {
-                        "type": "string"
-                    }
-                },
-                "required": [
-                    "key",
-                    "checkName",
-                    "severity",
-                    "message"
-                ]
-            }
-        }
-    },
-    "required": [
-        "keys",
-        "messages"
-    ]
-}

From 21fc9b7290801e643b55a3f6ec0f5623a11a25fc Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 20 Oct 2023 21:46:30 -0700
Subject: [PATCH 10/13] update: add consistecny check schema

---
 schema/system/consistency_check.json | 37 ++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/schema/system/consistency_check.json b/schema/system/consistency_check.json
index e69de29bb..3c191a5ba 100644
--- a/schema/system/consistency_check.json
+++ b/schema/system/consistency_check.json
@@ -0,0 +1,37 @@
+{
+    "$id": "system/consistency-check",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "consistency check",
+    "consistency_check": {
+        "type": "object",
+        "properties": {
+            "key": {
+                "type": "string",
+                "description": "Key of the property of the entity on which the consistency check is performed, e.g. 'basis.coordinates.1'"
+            },
+            "name": {
+                "enum": [
+                    "default",
+                    "atomsTooClose"
+                ],
+                "description": "Name of the consistency check which is exported as an enum"
+            },
+            "severity": {
+                "enum": [
+                    "info",
+                    "warning",
+                    "error"
+                ]
+            },
+            "message": {
+                "type": "string"
+            }
+        },
+        "required": [
+            "key",
+            "name",
+            "severity",
+            "message"
+        ]
+    }
+}

From 0ff6045abf495344a92bbb97214230147aadb6fb Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 20 Oct 2023 22:40:41 -0700
Subject: [PATCH 11/13] fix: error with reference

---
 schema/in_memory_entity/base.json    |  1 -
 schema/system/consistency_check.json | 60 ++++++++++++++--------------
 2 files changed, 29 insertions(+), 32 deletions(-)

diff --git a/schema/in_memory_entity/base.json b/schema/in_memory_entity/base.json
index 6f7f0c7ac..d33e7dd7c 100644
--- a/schema/in_memory_entity/base.json
+++ b/schema/in_memory_entity/base.json
@@ -23,7 +23,6 @@
         "consistency_checks": {
             "type": "array",
             "items": {
-                "type": "object",
                 "$ref": "../system/consistency_check.json"
             }
         }
diff --git a/schema/system/consistency_check.json b/schema/system/consistency_check.json
index 3c191a5ba..e314823aa 100644
--- a/schema/system/consistency_check.json
+++ b/schema/system/consistency_check.json
@@ -2,36 +2,34 @@
     "$id": "system/consistency-check",
     "$schema": "http://json-schema.org/draft-04/schema#",
     "title": "consistency check",
-    "consistency_check": {
-        "type": "object",
-        "properties": {
-            "key": {
-                "type": "string",
-                "description": "Key of the property of the entity on which the consistency check is performed, e.g. 'basis.coordinates.1'"
-            },
-            "name": {
-                "enum": [
-                    "default",
-                    "atomsTooClose"
-                ],
-                "description": "Name of the consistency check which is exported as an enum"
-            },
-            "severity": {
-                "enum": [
-                    "info",
-                    "warning",
-                    "error"
-                ]
-            },
-            "message": {
-                "type": "string"
-            }
+    "type": "object",
+    "properties": {
+        "key": {
+            "type": "string",
+            "description": "Key of the property of the entity on which the consistency check is performed, e.g. 'basis.coordinates.1'"
         },
-        "required": [
-            "key",
-            "name",
-            "severity",
-            "message"
-        ]
-    }
+        "name": {
+            "enum": [
+                "default",
+                "atomsTooClose"
+            ],
+            "description": "Name of the consistency check which is exported as an enum"
+        },
+        "severity": {
+            "enum": [
+                "info",
+                "warning",
+                "error"
+            ]
+        },
+        "message": {
+            "type": "string"
+        }
+    },
+    "required": [
+        "key",
+        "name",
+        "severity",
+        "message"
+    ]
 }

From 19d14ec8240fb7a9ef31cb6a460bbcc3bcda09d4 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Thu, 26 Oct 2023 12:51:53 -0700
Subject: [PATCH 12/13] update: add description

---
 schema/in_memory_entity/base.json    |  2 +-
 schema/system/consistency_check.json | 11 +++++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/schema/in_memory_entity/base.json b/schema/in_memory_entity/base.json
index d33e7dd7c..9de7a7a8c 100644
--- a/schema/in_memory_entity/base.json
+++ b/schema/in_memory_entity/base.json
@@ -20,7 +20,7 @@
         "systemName": {
             "type": "string"
         },
-        "consistency_checks": {
+        "consistencyChecks": {
             "type": "array",
             "items": {
                 "$ref": "../system/consistency_check.json"
diff --git a/schema/system/consistency_check.json b/schema/system/consistency_check.json
index e314823aa..7792aaedc 100644
--- a/schema/system/consistency_check.json
+++ b/schema/system/consistency_check.json
@@ -3,27 +3,30 @@
     "$schema": "http://json-schema.org/draft-04/schema#",
     "title": "consistency check",
     "type": "object",
+    "description": "The output of consistency checks performed on data adhering to JSON schema, but inconsistent with scientific or logical rules, to show problems in UI.",
     "properties": {
         "key": {
             "type": "string",
-            "description": "Key of the property of the entity on which the consistency check is performed, e.g. 'basis.coordinates.1'"
+            "description": "Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'"
         },
         "name": {
             "enum": [
                 "default",
                 "atomsTooClose"
             ],
-            "description": "Name of the consistency check which is exported as an enum"
+            "description": "Name of the consistency check that is performed, which is listed in an enum."
         },
         "severity": {
             "enum": [
                 "info",
                 "warning",
                 "error"
-            ]
+            ],
+            "description": "Severity level of the problem, which is used in UI to differentiate."
         },
         "message": {
-            "type": "string"
+            "type": "string",
+            "description": "Message generated by the consistency check describing the problem."
         }
     },
     "required": [

From 3e7805a3707b9d1c9670c4d6573048ac403235fa Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 27 Oct 2023 13:41:06 -0700
Subject: [PATCH 13/13] update: add example for CCheck

---
 example/system/consistency_check.json | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 example/system/consistency_check.json

diff --git a/example/system/consistency_check.json b/example/system/consistency_check.json
new file mode 100644
index 000000000..78632ba17
--- /dev/null
+++ b/example/system/consistency_check.json
@@ -0,0 +1,6 @@
+{
+    "key": "basis.coordinates.0",
+    "name": "atomsTooClose",
+    "severity": "warning",
+    "message": "Atom 0 is too close to atom X"
+}