From aec89e94c9087c71dffc66fd811a6042b58ebde9 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Thu, 16 Apr 2026 17:30:49 -0700 Subject: [PATCH 1/4] add new data types to experiment and aligned tables --- GREGoR_data_model.json | 6 +++--- sheets_to_JSON.R | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 376d282..245f5c3 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -1,7 +1,7 @@ { "name": "GREGoR Data Model", "description": "Data model for the GREGoR consortium", - "version": "1.11", + "version": "1.11.1", "tables": [ { "table": "participant", @@ -743,7 +743,7 @@ "column": "table_name", "required": true, "data_type": "enumeration", - "enumerations": ["experiment_dna_short_read", "experiment_rna_short_read", "experiment_nanopore", "experiment_pac_bio", "experiment_atac_short_read"], + "enumerations": ["experiment_dna_short_read", "experiment_rna_short_read", "experiment_nanopore", "experiment_pac_bio", "experiment_atac_short_read", "experiment_optical_mapping", "experiment_iclr"], "examples": "experiment_dna_short_read" }, { @@ -776,7 +776,7 @@ "column": "table_name", "required": true, "data_type": "enumeration", - "enumerations": ["aligned_dna_short_read", "aligned_rna_short_read", "aligned_nanopore", "aligned_pac_bio", "aligned_atac_short_read"], + "enumerations": ["aligned_dna_short_read", "aligned_rna_short_read", "aligned_nanopore", "aligned_pac_bio", "aligned_atac_short_read", "aligned_iclr"], "examples": "aligned_dna_short_read" }, { diff --git a/sheets_to_JSON.R b/sheets_to_JSON.R index a0b9049..d433e14 100644 --- a/sheets_to_JSON.R +++ b/sheets_to_JSON.R @@ -7,7 +7,7 @@ library(jsonlite) url <- "https://docs.google.com/spreadsheets/d/1p_0nhKMvKBueSrUAQMCe9cHv16WyhKSX_jnxNCuGFWg" model_name = "GREGoR Data Model" model_description = "Data model for the GREGoR consortium" -model_version = "1.11" +model_version = "1.11.1" # table metadata meta <- read_sheet(url, sheet="Table overview/status", skip=1) From 2c873c4697b88dc10c4f1cc99acb6106674ca3c2 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Mon, 27 Apr 2026 11:13:15 -0700 Subject: [PATCH 2/4] add optical mapping to aligned table --- GREGoR_data_model.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 245f5c3..73df8b0 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -776,7 +776,7 @@ "column": "table_name", "required": true, "data_type": "enumeration", - "enumerations": ["aligned_dna_short_read", "aligned_rna_short_read", "aligned_nanopore", "aligned_pac_bio", "aligned_atac_short_read", "aligned_iclr"], + "enumerations": ["aligned_dna_short_read", "aligned_rna_short_read", "aligned_nanopore", "aligned_pac_bio", "aligned_atac_short_read", "aligned_optical_mapping", "aligned_iclr"], "examples": "aligned_dna_short_read" }, { From 0f54a116845d51ec19c501dcb4e93b002abee152 Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Mon, 27 Apr 2026 11:19:07 -0700 Subject: [PATCH 3/4] update changelog --- CHANGELOG.md | 10 ++++++++++ change_log.R | 1 + 2 files changed, 11 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe573d2..0977b57 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,15 @@ # Change log +## 1.11.1 + +|Table |Field |Change notes | +|:----------|:----------|:-------------------------------------------------| +|experiment |table_name |add enumerated value 'experiment_optical_mapping' | +|experiment |table_name |add enumerated value 'experiment_iclr' | +|aligned |table_name |add enumerated value 'aligned_optical_mapping' | +|aligned |table_name |add enumerated value 'aligned_iclr' | + + ## 1.11 |Table |Field |Change notes | diff --git a/change_log.R b/change_log.R index baf5ee9..60e9420 100644 --- a/change_log.R +++ b/change_log.R @@ -1,6 +1,7 @@ library(googlesheets4) library(dplyr) library(readr) +library(tidyr) url <- "https://docs.google.com/spreadsheets/d/1p_0nhKMvKBueSrUAQMCe9cHv16WyhKSX_jnxNCuGFWg" From fab5beb29b9f789bd9399c363fc9d880b002a35e Mon Sep 17 00:00:00 2001 From: "Stephanie M. Gogarten" Date: Mon, 27 Apr 2026 11:57:59 -0700 Subject: [PATCH 4/4] fix optical mapping enumeration --- CHANGELOG.md | 12 ++++++------ GREGoR_data_model.json | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0977b57..d041630 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,12 +2,12 @@ ## 1.11.1 -|Table |Field |Change notes | -|:----------|:----------|:-------------------------------------------------| -|experiment |table_name |add enumerated value 'experiment_optical_mapping' | -|experiment |table_name |add enumerated value 'experiment_iclr' | -|aligned |table_name |add enumerated value 'aligned_optical_mapping' | -|aligned |table_name |add enumerated value 'aligned_iclr' | +|Table |Field |Change notes | +|:----------|:----------|:--------------------------------------------------------| +|experiment |table_name |add enumerated value 'experiment_optical_mapping' | +|experiment |table_name |add enumerated value 'experiment_iclr' | +|aligned |table_name |add enumerated value 'aligned_molecules_optical_mapping' | +|aligned |table_name |add enumerated value 'aligned_iclr' | ## 1.11 diff --git a/GREGoR_data_model.json b/GREGoR_data_model.json index 73df8b0..a267580 100644 --- a/GREGoR_data_model.json +++ b/GREGoR_data_model.json @@ -776,7 +776,7 @@ "column": "table_name", "required": true, "data_type": "enumeration", - "enumerations": ["aligned_dna_short_read", "aligned_rna_short_read", "aligned_nanopore", "aligned_pac_bio", "aligned_atac_short_read", "aligned_optical_mapping", "aligned_iclr"], + "enumerations": ["aligned_dna_short_read", "aligned_rna_short_read", "aligned_nanopore", "aligned_pac_bio", "aligned_atac_short_read", "aligned_molecules_optical_mapping", "aligned_iclr"], "examples": "aligned_dna_short_read" }, {