From 30042f060ac386f08bdd282f5a01269f8321b9f7 Mon Sep 17 00:00:00 2001
From: Nico Trummer <nictru32@gmail.com>
Date: Thu, 17 Oct 2024 10:59:01 +0200
Subject: [PATCH] Update schema regexes

---
 assets/schema_counts_design.json | 29 +++++++++++++--------
 assets/schema_input.json         | 43 ++++++++++++++++++++++----------
 assets/schema_input_bam.json     | 32 ++++++++++++++++--------
 3 files changed, 71 insertions(+), 33 deletions(-)

diff --git a/assets/schema_counts_design.json b/assets/schema_counts_design.json
index 081b6d7..2caca7b 100644
--- a/assets/schema_counts_design.json
+++ b/assets/schema_counts_design.json
@@ -9,21 +9,27 @@
         "properties": {
             "sample": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Sample name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "id"
+                ]
             },
             "condition": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Condition name must be provided and cannot contain spaces",
-                "meta": ["condition"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Condition name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "condition"
+                ]
             },
             "batch": {
-                "type": "string",
-                "pattern": "^\\S+$",
+                "type": ["string", "integer"],
+                "pattern": "^[a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
                 "errorMessage": "Batch identifier cannot contain spaces",
-                "meta": ["batch"]
+                "meta": [
+                    "batch"
+                ]
             },
             "counts_file": {
                 "type": "string",
@@ -33,6 +39,9 @@
                 "errorMessage": "Counts file must be a .csv or .txt file"
             }
         },
-        "required": ["sample", "condition"]
+        "required": [
+            "sample",
+            "condition"
+        ]
     }
 }
diff --git a/assets/schema_input.json b/assets/schema_input.json
index b5ff417..da4782a 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -9,21 +9,27 @@
         "properties": {
             "sample": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Sample name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "id"
+                ]
             },
             "condition": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Condition name must be provided and cannot contain spaces",
-                "meta": ["condition"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Condition name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "condition"
+                ]
             },
             "assay": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Assay name must be provided and cannot contain spaces",
-                "meta": ["assay"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Assay name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "assay"
+                ]
             },
             "peak_file": {
                 "type": "string",
@@ -36,22 +42,33 @@
                 "type": "boolean",
                 "default": true,
                 "errorMessage": "footprinting must be a boolean value",
-                "meta": ["footprinting"]
+                "meta": [
+                    "footprinting"
+                ]
             },
             "include_original": {
                 "type": "boolean",
                 "default": true,
                 "errorMessage": "include_original must be a boolean value",
-                "meta": ["include_original"]
+                "meta": [
+                    "include_original"
+                ]
             },
             "max_peak_gap": {
                 "type": "integer",
                 "default": 500,
                 "minimum": 0,
                 "errorMessage": "max_peak_gap must be a positive integer",
-                "meta": ["max_peak_gap"]
+                "meta": [
+                    "max_peak_gap"
+                ]
             }
         },
-        "required": ["sample", "condition", "assay", "peak_file"]
+        "required": [
+            "sample",
+            "condition",
+            "assay",
+            "peak_file"
+        ]
     }
 }
diff --git a/assets/schema_input_bam.json b/assets/schema_input_bam.json
index 9b0f569..cf44fd0 100644
--- a/assets/schema_input_bam.json
+++ b/assets/schema_input_bam.json
@@ -9,21 +9,27 @@
         "properties": {
             "sample": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Sample name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "id"
+                ]
             },
             "condition": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Condition name must be provided and cannot contain spaces",
-                "meta": ["condition"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Condition name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "condition"
+                ]
             },
             "assay": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Assay name must be provided and cannot contain spaces",
-                "meta": ["assay"]
+                "pattern": "^[a-zA-Z][a-zA-Z0-9]*(?:[-_][a-zA-Z0-9]+)*$",
+                "errorMessage": "Assay name must be provided, has to start with a letter, and cannot contain spaces",
+                "meta": [
+                    "assay"
+                ]
             },
             "signal": {
                 "type": "string",
@@ -40,6 +46,12 @@
                 "errorMessage": "Control file must be provided and must be a .bam file"
             }
         },
-        "required": ["sample", "condition", "assay", "signal", "control"]
+        "required": [
+            "sample",
+            "condition",
+            "assay",
+            "signal",
+            "control"
+        ]
     }
 }