Generic info fields input into 'custom'.
This commit is contained in:
lwark
429
src/submissions/resources/viral_culture.json
Normal file
429
src/submissions/resources/viral_culture.json
Normal file
@@ -0,0 +1,429 @@
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||||
{
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||||
"name": "Viral Culture",
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||||
"defaults": {
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||||
"abbreviation": "VE",
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"details_ignore": [
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||||
],
|
||||
"form_ignore": [
|
||||
"cost_centre"
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],
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"regex": "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)",
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"sample_type": "Basic Sample"
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},
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"info": {
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||||
"comment": {
|
||||
"read": [
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||||
{
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||||
"column": 2,
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"row": 34,
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"sheet": "Sample List"
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||||
}
|
||||
],
|
||||
"write": []
|
||||
},
|
||||
"contact": {
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||||
"read": [
|
||||
{
|
||||
"column": 2,
|
||||
"row": 4,
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||||
"sheet": "Sample List"
|
||||
}
|
||||
],
|
||||
"write": []
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||||
},
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||||
"contact_phone": {
|
||||
"read": [],
|
||||
"write": [
|
||||
{
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||||
"column": 2,
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||||
"row": 5,
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"sheet": "Sample List"
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||||
}
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]
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||||
},
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||||
"cost_centre": {
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||||
"read": [
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||||
{
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||||
"column": 2,
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||||
"row": 6,
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||||
"sheet": "Sample List"
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||||
}
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],
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"write": []
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||||
},
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||||
"custom": {},
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||||
"extraction_kit": {
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||||
"read": [
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||||
{
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||||
"column": 4,
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||||
"row": 5,
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"sheet": "Sample List"
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}
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||||
],
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||||
"write": []
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||||
},
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"rsl_plate_num": {
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||||
"read": [
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||||
{
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||||
"column": 2,
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"row": 13,
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"sheet": "Sample List"
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}
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||||
],
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||||
"write": []
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},
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"sample_count": {
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||||
"read": [
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||||
{
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"column": 4,
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"row": 4,
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"sheet": "Sample List"
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}
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],
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||||
"write": []
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||||
},
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"signed_by": {
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||||
"read": [],
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||||
"write": [
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||||
{
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"column": 2,
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"row": 15,
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"sheet": "Sample List"
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}
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]
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},
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"submission_category": {
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"read": [
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{
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"column": 4,
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"row": 6,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submission_type": {
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||||
"read": [
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{
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"column": 4,
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"row": 3,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submitted_date": {
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"read": [
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{
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"column": 2,
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"row": 3,
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||||
"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submitter_plate_num": {
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"read": [
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{
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"column": 2,
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"row": 2,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"submitting_lab": {
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"read": [
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{
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"column": 4,
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"row": 2,
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"sheet": "Sample List"
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}
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],
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"write": []
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},
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"technician": {
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"read": [
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{
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"column": 2,
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"row": 14,
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"sheet": "Sample List"
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}
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],
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"write": []
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}
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},
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"samples": {
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"lookup_table": {
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"end_row": 132,
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"merge_on_id": "submitter_id",
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"sample_columns": {
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||||
"column": 6,
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"concentration": 4,
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"organism": 3,
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"row": 5,
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"submitter_id": 2
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},
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"sheet": "Sample List",
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"start_row": 37
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||||
},
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"plate_map": {
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||||
"end_column": 13,
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"end_row": 14,
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"sheet": "Plate Map",
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"start_column": 2,
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"start_row": 7
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}
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},
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"kits": [
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{
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"constant_cost": 0.00,
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"mutable_cost_column": 0.00,
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"mutable_cost_sample": 0.00,
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"kit_type": {
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"name": "MagMAX-96 Viral RNA Isolation Kit",
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"reagent roles": [
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{
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"expiry": {
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"column": 4,
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"row": 19
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||||
},
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"lot": {
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||||
"column": 3,
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"row": 19
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||||
},
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"name": {
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"column": 2,
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"row": 19
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},
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"sheet": "Sample List",
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"required": 1,
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"role": "Wash Solution 1 (MagMAX-96 Viral)",
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"extension_of_life": 0
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||||
},
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{
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"expiry": {
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||||
"column": 4,
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"row": 20
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||||
},
|
||||
"lot": {
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||||
"column": 3,
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||||
"row": 20
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||||
},
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||||
"name": {
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||||
"column": 2,
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||||
"row": 20
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||||
},
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||||
"sheet": "Sample List",
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||||
"required": 1,
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||||
"role": "Wash Solution 2 (MagMAX-96 Viral)",
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||||
"extension_of_life": 0
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||||
},
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||||
{
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||||
"expiry": {
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||||
"column": 4,
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||||
"row": 21
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||||
},
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||||
"lot": {
|
||||
"column": 3,
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||||
"row": 21
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||||
},
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||||
"name": {
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||||
"column": 2,
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||||
"row": 21
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||||
},
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||||
"sheet": "Sample List",
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||||
"required": 1,
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||||
"role": "Lysis/Binding Solution (MagMAX-96 Viral)",
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||||
"extension_of_life": 0
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||||
},
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||||
{
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||||
"expiry": {
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||||
"column": 4,
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||||
"row": 22
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||||
},
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||||
"lot": {
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||||
"column": 3,
|
||||
"row": 22
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||||
},
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||||
"name": {
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||||
"column": 2,
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||||
"row": 22
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||||
},
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||||
"sheet": "Sample List",
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||||
"required": 1,
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||||
"role": "RNA Binding Beads (MagMAX-96 Viral)",
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||||
"extension_of_life": 0
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||||
},
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||||
{
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||||
"expiry": {
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||||
"column": 4,
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"row": 23
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||||
},
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||||
"lot": {
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||||
"column": 3,
|
||||
"row": 23
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||||
},
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||||
"name": {
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||||
"column": 2,
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||||
"row": 23
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||||
},
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||||
"sheet": "Sample List",
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||||
"required": 1,
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||||
"role": "Lysis/Binding Enhancer (MagMAX-96 Viral)",
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||||
"extension_of_life": 0
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||||
},
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||||
{
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||||
"expiry": {
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||||
"column": 4,
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||||
"row": 24
|
||||
},
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||||
"lot": {
|
||||
"column": 3,
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||||
"row": 24
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||||
},
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||||
"name": {
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||||
"column": 2,
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||||
"row": 24
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||||
},
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||||
"sheet": "Sample List",
|
||||
"required": 0,
|
||||
"role": "Bacterial-Lysis Buffer",
|
||||
"extension_of_life": 0
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||||
},
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||||
{
|
||||
"expiry": {
|
||||
"column": 4,
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||||
"row": 25
|
||||
},
|
||||
"lot": {
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||||
"column": 3,
|
||||
"row": 25
|
||||
},
|
||||
"name": {
|
||||
"column": 2,
|
||||
"row": 25
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||||
},
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||||
"sheet": "Sample List",
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||||
"required": 1,
|
||||
"role": "Elution Buffer (MagMAX-96 Viral)",
|
||||
"extension_of_life": 0
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||||
},
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||||
{
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||||
"expiry": {
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||||
"column": 4,
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||||
"row": 30
|
||||
},
|
||||
"lot": {
|
||||
"column": 3,
|
||||
"row": 30
|
||||
},
|
||||
"name": {
|
||||
"column": 2,
|
||||
"row": 30
|
||||
},
|
||||
"sheet": "Sample List",
|
||||
"required": 0,
|
||||
"role": "Bacterial-Positive Control",
|
||||
"extension_of_life": 0
|
||||
},
|
||||
{
|
||||
"expiry": {
|
||||
"column": 4,
|
||||
"row": 31
|
||||
},
|
||||
"lot": {
|
||||
"column": 3,
|
||||
"row": 31
|
||||
},
|
||||
"name": {
|
||||
"column": 2,
|
||||
"row": 31
|
||||
},
|
||||
"sheet": "Sample List",
|
||||
"required": 1,
|
||||
"role": "Bead Plate",
|
||||
"extension_of_life": 0
|
||||
},
|
||||
{
|
||||
"expiry": {
|
||||
"column": 4,
|
||||
"row": 28
|
||||
},
|
||||
"lot": {
|
||||
"column": 3,
|
||||
"row": 28
|
||||
},
|
||||
"name": {
|
||||
"column": 2,
|
||||
"row": 28
|
||||
},
|
||||
"sheet": "Sample List",
|
||||
"required": 1,
|
||||
"role": "Isopropanol",
|
||||
"extension_of_life": 0
|
||||
},
|
||||
{
|
||||
"expiry": {
|
||||
"column": 4,
|
||||
"row": 29
|
||||
},
|
||||
"lot": {
|
||||
"column": 3,
|
||||
"row": 29
|
||||
},
|
||||
"name": {
|
||||
"column": 2,
|
||||
"row": 29
|
||||
},
|
||||
"sheet": "Sample List",
|
||||
"required": 1,
|
||||
"role": "Ethanol",
|
||||
"extension_of_life": 0
|
||||
},
|
||||
{
|
||||
"expiry": {
|
||||
"column": 4,
|
||||
"row": 32
|
||||
},
|
||||
"lot": {
|
||||
"column": 3,
|
||||
"row": 32
|
||||
},
|
||||
"name": {
|
||||
"column": 2,
|
||||
"row": 32
|
||||
},
|
||||
"sheet": "Sample List",
|
||||
"required": 1,
|
||||
"role": "Carrier RNA",
|
||||
"extension_of_life": 0
|
||||
}
|
||||
],
|
||||
"equipment roles": [
|
||||
{
|
||||
"static": 0,
|
||||
"role": "Extractor",
|
||||
"processes": [
|
||||
"OBT_M4029_KFF_v1.0"
|
||||
]
|
||||
},
|
||||
{
|
||||
"static": 1,
|
||||
"role": "Momentum - Extraction",
|
||||
"processes": [
|
||||
"Omega_MagBind_Universal_VarCol"
|
||||
]
|
||||
},
|
||||
{
|
||||
"static": 1,
|
||||
"role": "Liquid Handler",
|
||||
"processes": [
|
||||
"Bacterial_Core_Submission"
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
310
src/submissions/resources/viral_culture.yml
Normal file
310
src/submissions/resources/viral_culture.yml
Normal file
@@ -0,0 +1,310 @@
|
||||
name: &NAME Viral Culture
|
||||
# The defaults section helps us with some parsing and writing functions
|
||||
defaults:
|
||||
# The abbreviation gets put in the RSL-{abbreviation}-20XXXXXX-1 plate name
|
||||
abbreviation: &ABBREV VE
|
||||
# Details ignore tells us what to leave out of the details view.
|
||||
# For basic submissions this is typically and empty list or '[]'
|
||||
# To add entries, remove [] and add list entries preceded by dashes (see 'form_ignore' as an example)
|
||||
details_ignore: []
|
||||
# Form ignore tells us what to leave out of the form created when importing the submission.
|
||||
# It is in list format. Each entry is preceded by a dash.
|
||||
form_ignore:
|
||||
- cost_centre
|
||||
sample_type: Basic Sample
|
||||
# The regex is used to identify a submission type by its file name, example: RSL-WW-20240924-1R1
|
||||
# By default the regex will be programmatically constructed using the submission type name and abbreviation
|
||||
# https://stackoverflow.com/a/23212501
|
||||
regex: !regex [*NAME, *ABBREV]
|
||||
# The info section holds a map of where submission info can be located in the submission form.
|
||||
# For example, below the 'comment' field is found on the 'Sample List' tab in column 2 of tow 34.
|
||||
# 'read' is a list of where the info can be parsed from, write is a list of where it will be written to.
|
||||
# By default, items in the 'read' list will be appended to the 'write' list.
|
||||
# These fields are common to all submissions. Without programming changes, at present no new fields can be added.
|
||||
info:
|
||||
comment:
|
||||
read:
|
||||
- column: 2
|
||||
row: 34
|
||||
sheet: Sample List
|
||||
write: []
|
||||
contact:
|
||||
read:
|
||||
- column: 2
|
||||
row: 4
|
||||
sheet: Sample List
|
||||
write: []
|
||||
contact_phone:
|
||||
read: []
|
||||
write:
|
||||
- column: 2
|
||||
row: 5
|
||||
sheet: Sample List
|
||||
cost_centre:
|
||||
read:
|
||||
- column: 2
|
||||
row: 6
|
||||
sheet: Sample List
|
||||
write: []
|
||||
custom: {}
|
||||
extraction_kit:
|
||||
read:
|
||||
- column: 4
|
||||
row: 5
|
||||
sheet: Sample List
|
||||
write: []
|
||||
rsl_plate_num:
|
||||
read:
|
||||
- column: 2
|
||||
row: 13
|
||||
sheet: Sample List
|
||||
write: []
|
||||
sample_count:
|
||||
read:
|
||||
- column: 4
|
||||
row: 4
|
||||
sheet: Sample List
|
||||
write: []
|
||||
signed_by:
|
||||
read: []
|
||||
write:
|
||||
- column: 2
|
||||
row: 15
|
||||
sheet: Sample List
|
||||
submission_category:
|
||||
read:
|
||||
- column: 4
|
||||
row: 6
|
||||
sheet: Sample List
|
||||
write: []
|
||||
submission_type:
|
||||
read:
|
||||
- column: 4
|
||||
row: 3
|
||||
sheet: Sample List
|
||||
write: []
|
||||
submitted_date:
|
||||
read:
|
||||
- column: 2
|
||||
row: 3
|
||||
sheet: Sample List
|
||||
write: []
|
||||
submitter_plate_num:
|
||||
read:
|
||||
- column: 2
|
||||
row: 2
|
||||
sheet: Sample List
|
||||
write: []
|
||||
submitting_lab:
|
||||
read:
|
||||
- column: 4
|
||||
row: 2
|
||||
sheet: Sample List
|
||||
write: []
|
||||
technician:
|
||||
read:
|
||||
- column: 2
|
||||
row: 14
|
||||
sheet: Sample List
|
||||
write: []
|
||||
kits:
|
||||
- constant_cost: 0.0
|
||||
kit_type:
|
||||
name: MagMAX-96 Viral RNA Isolation Kit
|
||||
equipment roles:
|
||||
- role: Extractor
|
||||
processes:
|
||||
- OBT_M4029_KFF_v1.0
|
||||
static: 0
|
||||
- processes:
|
||||
- Omega_MagBind_Universal_VarCol
|
||||
role: Momentum - Extraction
|
||||
static: 1
|
||||
- processes:
|
||||
- Bacterial_Core_Submission
|
||||
role: Liquid Handler
|
||||
static: 1
|
||||
reagent roles:
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 19
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 19
|
||||
name:
|
||||
column: 2
|
||||
row: 19
|
||||
required: 1
|
||||
role: Wash Solution 1 (MagMAX-96 Viral)
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 20
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 20
|
||||
name:
|
||||
column: 2
|
||||
row: 20
|
||||
required: 1
|
||||
role: Wash Solution 2 (MagMAX-96 Viral)
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 21
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 21
|
||||
name:
|
||||
column: 2
|
||||
row: 21
|
||||
required: 1
|
||||
role: Lysis/Binding Solution (MagMAX-96 Viral)
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 22
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 22
|
||||
name:
|
||||
column: 2
|
||||
row: 22
|
||||
required: 1
|
||||
role: RNA Binding Beads (MagMAX-96 Viral)
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 23
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 23
|
||||
name:
|
||||
column: 2
|
||||
row: 23
|
||||
required: 1
|
||||
role: Lysis/Binding Enhancer (MagMAX-96 Viral)
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 24
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 24
|
||||
name:
|
||||
column: 2
|
||||
row: 24
|
||||
required: 0
|
||||
role: Bacterial-Lysis Buffer
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 25
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 25
|
||||
name:
|
||||
column: 2
|
||||
row: 25
|
||||
required: 1
|
||||
role: Elution Buffer (MagMAX-96 Viral)
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 30
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 30
|
||||
name:
|
||||
column: 2
|
||||
row: 30
|
||||
required: 0
|
||||
role: Bacterial-Positive Control
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 31
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 31
|
||||
name:
|
||||
column: 2
|
||||
row: 31
|
||||
required: 0
|
||||
role: Bead Plate
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 28
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 28
|
||||
name:
|
||||
column: 2
|
||||
row: 28
|
||||
required: 1
|
||||
role: Isopropanol
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 29
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 29
|
||||
name:
|
||||
column: 2
|
||||
row: 29
|
||||
required: 1
|
||||
role: Ethanol
|
||||
sheet: Sample List
|
||||
- expiry:
|
||||
column: 4
|
||||
row: 32
|
||||
extension_of_life: 0
|
||||
lot:
|
||||
column: 3
|
||||
row: 32
|
||||
name:
|
||||
column: 2
|
||||
row: 32
|
||||
required: 1
|
||||
role: Carrier RNA
|
||||
sheet: Sample List
|
||||
mutable_cost_column: 0.0
|
||||
mutable_cost_sample: 0.0
|
||||
samples:
|
||||
lookup_table:
|
||||
end_row: 132
|
||||
merge_on_id: submitter_id
|
||||
sample_columns:
|
||||
column: 6
|
||||
concentration: 4
|
||||
organism: 3
|
||||
row: 5
|
||||
submitter_id: 2
|
||||
sheet: Sample List
|
||||
start_row: 37
|
||||
plate_map:
|
||||
end_column: 13
|
||||
end_row: 14
|
||||
sheet: Plate Map
|
||||
start_column: 2
|
||||
start_row: 7
|
||||
orgs:
|
||||
- name: IRVC-Genomics
|
||||
cost_centre: xxx
|
||||
contacts:
|
||||
- name: Ruimin Gao
|
||||
phone: (204) 789-5078
|
||||
email: Ruimin.Gao@phac-aspc.gc.ca
|
||||
Reference in New Issue
Block a user