@morscherlab/mint-sdk 1.0.0-rc.1 → 1.0.0-rc.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (143) hide show
  1. package/README.md +9 -1
  2. package/dist/__tests__/components/LcmsSequenceTable.test.d.ts +1 -0
  3. package/dist/__tests__/components/ProgressBar.test.d.ts +1 -0
  4. package/dist/__tests__/components/RackEditor.test.d.ts +1 -0
  5. package/dist/__tests__/components/SequenceProgressBar.test.d.ts +1 -0
  6. package/dist/__tests__/composables/useExperimentSamples.test.d.ts +1 -0
  7. package/dist/__tests__/utils/instrument.test.d.ts +1 -0
  8. package/dist/__tests__/utils/lcms.test.d.ts +1 -0
  9. package/dist/__tests__/utils/permissions.test.d.ts +1 -0
  10. package/dist/__tests__/utils/rack.test.d.ts +1 -0
  11. package/dist/{auth-CBG3bWEc.js → auth-B7g4J4ZF.js} +99 -5
  12. package/dist/auth-B7g4J4ZF.js.map +1 -0
  13. package/dist/components/AutoGroupModal.vue.d.ts +1 -1
  14. package/dist/components/BaseCheckbox.vue.d.ts +1 -1
  15. package/dist/components/BaseToggle.vue.d.ts +2 -2
  16. package/dist/components/BioTemplateExperimentWorkspaceView.vue.d.ts +1 -1
  17. package/dist/components/BioTemplatePackWorkspaceView.vue.d.ts +1 -1
  18. package/dist/components/BioTemplatePresetWorkspaceView.vue.d.ts +1 -1
  19. package/dist/components/DoseDesignWorkspaceView.vue.d.ts +1 -1
  20. package/dist/components/FormulaInput.vue.d.ts +1 -1
  21. package/dist/components/InstrumentAlertLog.vue.d.ts +22 -0
  22. package/dist/components/InstrumentStateBadge.vue.d.ts +11 -0
  23. package/dist/components/InstrumentStatusCard.vue.d.ts +13 -0
  24. package/dist/components/LcmsSequenceTable.vue.d.ts +26 -0
  25. package/dist/components/ProgressBar.vue.d.ts +1 -0
  26. package/dist/components/RackEditor.vue.d.ts +41 -3
  27. package/dist/components/ReagentList.vue.d.ts +1 -1
  28. package/dist/components/SampleSelector.vue.d.ts +5 -2
  29. package/dist/components/SegmentedControl.vue.d.ts +2 -0
  30. package/dist/components/SequenceInput.vue.d.ts +1 -1
  31. package/dist/components/SequenceProgressBar.vue.d.ts +15 -0
  32. package/dist/components/SettingsModal.vue.d.ts +3 -1
  33. package/dist/components/TagsInput.vue.d.ts +1 -1
  34. package/dist/components/WellPlate.vue.d.ts +42 -3
  35. package/dist/components/index.d.ts +5 -0
  36. package/dist/components/index.js +3 -3
  37. package/dist/{components-5KSfsVqf.js → components-BhK-dW99.js} +2091 -1051
  38. package/dist/components-BhK-dW99.js.map +1 -0
  39. package/dist/composables/experimentDesignData.d.ts +17 -0
  40. package/dist/composables/index.d.ts +2 -0
  41. package/dist/composables/index.js +4 -4
  42. package/dist/composables/useControlSchema.d.ts +11 -0
  43. package/dist/composables/useExperimentData.d.ts +11 -3
  44. package/dist/composables/useExperimentSamples.d.ts +42 -0
  45. package/dist/composables/usePlatformContext.d.ts +54 -0
  46. package/dist/{composables-D4Myb30a.js → composables-Bg7CFuNz.js} +5 -3
  47. package/dist/composables-Bg7CFuNz.js.map +1 -0
  48. package/dist/index.d.ts +4 -0
  49. package/dist/index.js +168 -6
  50. package/dist/index.js.map +1 -0
  51. package/dist/install.js +2 -2
  52. package/dist/instrument.d.ts +7 -0
  53. package/dist/lcms.d.ts +27 -0
  54. package/dist/permissions.d.ts +46 -0
  55. package/dist/stores/auth.d.ts +74 -2
  56. package/dist/stores/index.js +1 -1
  57. package/dist/styles.css +3316 -1216
  58. package/dist/templates/builders.d.ts +7 -3
  59. package/dist/templates/index.d.ts +2 -2
  60. package/dist/templates/index.js +2 -2
  61. package/dist/templates/presets.d.ts +12 -0
  62. package/dist/templates/types.d.ts +16 -1
  63. package/dist/{templates-BSlxwV2c.js → templates-BorLR_7p.js} +313 -3
  64. package/dist/templates-BorLR_7p.js.map +1 -0
  65. package/dist/types/auth.d.ts +2 -0
  66. package/dist/types/components.d.ts +32 -3
  67. package/dist/types/form-builder.d.ts +2 -1
  68. package/dist/types/index.d.ts +4 -1
  69. package/dist/types/instrument.d.ts +56 -0
  70. package/dist/types/platform.d.ts +3 -0
  71. package/dist/{useExperimentData-BbbdI5xT.js → useProtocolTemplates-n6AJqSqv.js} +534 -359
  72. package/dist/useProtocolTemplates-n6AJqSqv.js.map +1 -0
  73. package/dist/utils/rack.d.ts +47 -0
  74. package/package.json +1 -1
  75. package/src/__tests__/components/AppTopBar.test.ts +15 -0
  76. package/src/__tests__/components/BaseTabs.test.ts +15 -0
  77. package/src/__tests__/components/LcmsSequenceTable.test.ts +57 -0
  78. package/src/__tests__/components/ProgressBar.test.ts +18 -0
  79. package/src/__tests__/components/RackEditor.test.ts +125 -0
  80. package/src/__tests__/components/SampleSelector.test.ts +25 -0
  81. package/src/__tests__/components/SegmentedControl.test.ts +45 -0
  82. package/src/__tests__/components/SequenceProgressBar.test.ts +39 -0
  83. package/src/__tests__/components/SettingsModal.test.ts +83 -2
  84. package/src/__tests__/composables/useControlSchema.test.ts +4 -0
  85. package/src/__tests__/composables/useExperimentData.test.ts +23 -0
  86. package/src/__tests__/composables/useExperimentSamples.test.ts +91 -0
  87. package/src/__tests__/templates/templates.test.ts +86 -0
  88. package/src/__tests__/utils/instrument.test.ts +47 -0
  89. package/src/__tests__/utils/lcms.test.ts +73 -0
  90. package/src/__tests__/utils/permissions.test.ts +50 -0
  91. package/src/__tests__/utils/rack.test.ts +120 -0
  92. package/src/components/AppTopBar.vue +1 -0
  93. package/src/components/BaseTabs.vue +22 -1
  94. package/src/components/InstrumentAlertLog.vue +191 -0
  95. package/src/components/InstrumentStateBadge.vue +50 -0
  96. package/src/components/InstrumentStatusCard.vue +188 -0
  97. package/src/components/LcmsSequenceTable.vue +191 -0
  98. package/src/components/ProgressBar.vue +3 -0
  99. package/src/components/RackEditor.vue +73 -2
  100. package/src/components/SampleSelector.vue +28 -9
  101. package/src/components/SegmentedControl.story.vue +17 -0
  102. package/src/components/SegmentedControl.vue +14 -3
  103. package/src/components/SequenceProgressBar.vue +71 -0
  104. package/src/components/SettingsModal.vue +42 -2
  105. package/src/components/WellPlate.vue +142 -21
  106. package/src/components/index.ts +5 -0
  107. package/src/components/internal/WellEditPopupInternal.vue +1 -0
  108. package/src/composables/experimentDesignData.ts +182 -0
  109. package/src/composables/index.ts +14 -0
  110. package/src/composables/useAuth.ts +4 -0
  111. package/src/composables/useAutoGroup.ts +5 -1
  112. package/src/composables/useControlSchema.ts +21 -0
  113. package/src/composables/useExperimentData.ts +57 -16
  114. package/src/composables/useExperimentSamples.ts +142 -0
  115. package/src/index.ts +27 -0
  116. package/src/instrument.ts +90 -0
  117. package/src/lcms.ts +108 -0
  118. package/src/permissions.ts +143 -0
  119. package/src/stores/auth.ts +31 -3
  120. package/src/styles/components/instrument-monitor.css +478 -0
  121. package/src/styles/components/lcms-sequence-table.css +189 -0
  122. package/src/styles/components/sequence-progress-bar.css +63 -0
  123. package/src/styles/components/tabs.css +9 -0
  124. package/src/styles/components/well-edit-popup.css +7 -1
  125. package/src/styles/components/well-plate.css +5 -0
  126. package/src/styles/index.css +3 -0
  127. package/src/templates/builders.ts +201 -0
  128. package/src/templates/controlSchemas.ts +68 -0
  129. package/src/templates/index.ts +2 -0
  130. package/src/templates/presets.ts +23 -0
  131. package/src/templates/types.ts +17 -0
  132. package/src/types/auth.ts +3 -0
  133. package/src/types/components.ts +45 -3
  134. package/src/types/form-builder.ts +2 -1
  135. package/src/types/index.ts +35 -0
  136. package/src/types/instrument.ts +61 -0
  137. package/src/types/platform.ts +4 -0
  138. package/src/utils/rack.ts +209 -0
  139. package/dist/auth-CBG3bWEc.js.map +0 -1
  140. package/dist/components-5KSfsVqf.js.map +0 -1
  141. package/dist/composables-D4Myb30a.js.map +0 -1
  142. package/dist/templates-BSlxwV2c.js.map +0 -1
  143. package/dist/useExperimentData-BbbdI5xT.js.map +0 -1
@@ -1,7 +1,12 @@
1
- import { ref, computed, type Ref, type ComputedRef } from 'vue'
2
- import { useApi } from './useApi'
1
+ import { shallowRef, computed, type Ref, type ComputedRef } from 'vue'
2
+ import { useApi, type UseApiReturn } from './useApi'
3
3
  import { useRequestSyncState } from './useRequestSyncState'
4
- import type { TreeNode, SummaryData } from '../types'
4
+ import {
5
+ extractSampleNamesFromDesignData,
6
+ extractSampleOptionsFromDesignData,
7
+ unwrapExperimentDesignData,
8
+ } from './experimentDesignData'
9
+ import type { TreeNode, SummaryData, SelectOption } from '../types'
5
10
 
6
11
  export interface UseExperimentDataOptions {
7
12
  apiBaseUrl?: string
@@ -9,8 +14,14 @@ export interface UseExperimentDataOptions {
9
14
  }
10
15
 
11
16
  export interface UseExperimentDataReturn {
12
- /** Raw experiment data payload from `/experiments/{id}/data`, or null. */
17
+ /** Raw experiment data response from `/experiments/{id}/data`, or null. */
13
18
  data: Ref<Record<string, unknown> | null>
19
+ /** Plugin-defined design_data payload unwrapped from platform response shapes, or null. */
20
+ designData: ComputedRef<Record<string, unknown> | null>
21
+ /** Sample values extracted from design_data for SampleSelector-style components. */
22
+ sampleNames: ComputedRef<string[]>
23
+ /** Sample options extracted from design_data for select/dropdown components. */
24
+ sampleOptions: ComputedRef<SelectOption<string>[]>
14
25
  /** Hierarchy tree rows normalised from `tree_data` or `treeData`. */
15
26
  treeData: ComputedRef<TreeNode[]>
16
27
  /** Table rows normalised from `table_data` or `tableData`. */
@@ -24,54 +35,74 @@ export interface UseExperimentDataReturn {
24
35
  /** Timestamp of the last successful experiment data fetch, or null. */
25
36
  lastLoadedAt: Ref<Date | null>
26
37
  /** Fetch experiment data for an experiment id. */
27
- fetch: (experimentId: number) => Promise<void>
38
+ fetch: (experimentId: number) => Promise<Record<string, unknown> | null>
28
39
  /** Refetch the most recently fetched experiment id. */
29
40
  refresh: () => Promise<void>
41
+ /** Clear local experiment data and current fetch target. */
42
+ clear: () => void
30
43
  }
31
44
 
32
45
  /** Fetches and normalises experiment output data (tree, table, summary) from the platform API. */
33
46
  export function useExperimentData(
34
47
  options: UseExperimentDataOptions = {},
35
48
  ): UseExperimentDataReturn {
36
- const api = useApi({ baseUrl: options.apiBaseUrl })
37
-
38
- const data = ref<Record<string, unknown> | null>(null)
49
+ const data = shallowRef<Record<string, unknown> | null>(null)
39
50
  const request = useRequestSyncState('Failed to fetch experiment data')
40
51
  const isLoading = request.loading
41
52
  const error = request.error
42
53
  const lastLoadedAt = request.lastLoadedAt
43
54
  let lastExperimentId: number | null = null
55
+ let api: UseApiReturn | null = null
56
+
57
+ function getApi(): UseApiReturn {
58
+ api ??= useApi({ baseUrl: options.apiBaseUrl })
59
+ return api
60
+ }
61
+
62
+ const designData = computed<Record<string, unknown> | null>(() =>
63
+ unwrapExperimentDesignData(data.value),
64
+ )
65
+
66
+ const sampleNames = computed<string[]>(() =>
67
+ extractSampleNamesFromDesignData(designData.value),
68
+ )
69
+
70
+ const sampleOptions = computed<SelectOption<string>[]>(() =>
71
+ extractSampleOptionsFromDesignData(designData.value),
72
+ )
44
73
 
45
74
  const treeData = computed<TreeNode[]>(() => {
46
- if (!data.value) return []
47
- const tree = data.value.tree_data ?? data.value.treeData
75
+ if (!designData.value) return []
76
+ const tree = designData.value.tree_data ?? designData.value.treeData
48
77
  return Array.isArray(tree) ? tree as TreeNode[] : []
49
78
  })
50
79
 
51
80
  const tableData = computed<Record<string, unknown>[]>(() => {
52
- if (!data.value) return []
53
- const table = data.value.table_data ?? data.value.tableData
81
+ if (!designData.value) return []
82
+ const table = designData.value.table_data ?? designData.value.tableData
54
83
  return Array.isArray(table) ? table as Record<string, unknown>[] : []
55
84
  })
56
85
 
57
86
  const summaryData = computed<SummaryData | null>(() => {
58
- if (!data.value) return null
59
- const summary = data.value.summary_data ?? data.value.summaryData
87
+ if (!designData.value) return null
88
+ const summary = designData.value.summary_data ?? designData.value.summaryData
60
89
  if (summary && typeof summary === 'object' && 'metadata' in (summary as Record<string, unknown>)) {
61
90
  return summary as SummaryData
62
91
  }
63
92
  return null
64
93
  })
65
94
 
66
- async function fetchData(experimentId: number): Promise<void> {
95
+ async function fetchData(experimentId: number): Promise<Record<string, unknown> | null> {
67
96
  lastExperimentId = experimentId
68
97
  try {
69
98
  data.value = await request.run(
70
- () => api.get<Record<string, unknown>>(`/experiments/${experimentId}/data`),
99
+ () => getApi().get<Record<string, unknown>>(`/experiments/${experimentId}/data`),
71
100
  { success: 'load', errorMessage: 'Failed to fetch experiment data' },
72
101
  )
102
+ return data.value
73
103
  } catch {
74
104
  data.value = null
105
+ return null
75
106
  }
76
107
  }
77
108
 
@@ -81,8 +112,17 @@ export function useExperimentData(
81
112
  }
82
113
  }
83
114
 
115
+ function clear(): void {
116
+ data.value = null
117
+ lastExperimentId = null
118
+ request.clearError()
119
+ }
120
+
84
121
  return {
85
122
  data,
123
+ designData,
124
+ sampleNames,
125
+ sampleOptions,
86
126
  treeData,
87
127
  tableData,
88
128
  summaryData,
@@ -91,5 +131,6 @@ export function useExperimentData(
91
131
  lastLoadedAt,
92
132
  fetch: fetchData,
93
133
  refresh,
134
+ clear,
94
135
  }
95
136
  }
@@ -0,0 +1,142 @@
1
+ import {
2
+ computed,
3
+ inject,
4
+ toValue,
5
+ watch,
6
+ type ComputedRef,
7
+ type MaybeRefOrGetter,
8
+ type Ref,
9
+ } from 'vue'
10
+ import type { SelectOption } from '../types'
11
+ import { APP_EXPERIMENT_KEY } from './useAppExperiment'
12
+ import {
13
+ extractSampleNamesFromDesignData,
14
+ extractSampleOptionsFromDesignData,
15
+ unwrapExperimentDesignData,
16
+ type ExtractExperimentSamplesOptions,
17
+ } from './experimentDesignData'
18
+ import { parseExperimentId } from './platformContextHelpers'
19
+ import { useExperimentData } from './useExperimentData'
20
+
21
+ export type ExperimentIdSource = MaybeRefOrGetter<number | string | null | undefined>
22
+ export type ExperimentDesignDataSource = MaybeRefOrGetter<Record<string, unknown> | null | undefined>
23
+
24
+ export interface UseExperimentSamplesOptions extends ExtractExperimentSamplesOptions {
25
+ /** Experiment id to load from `/experiments/{id}/data`; defaults to provided AppExperiment context. */
26
+ experimentId?: ExperimentIdSource
27
+ /** Pre-fetched design_data or full platform design-data response. */
28
+ designData?: ExperimentDesignDataSource
29
+ /** API base URL override for platform calls. */
30
+ apiBaseUrl?: string
31
+ /** Auto-load when an experiment id becomes available. Defaults to true. */
32
+ immediate?: boolean
33
+ /** Enable or disable automatic loading while keeping derived samples reactive. Defaults to true. */
34
+ enabled?: MaybeRefOrGetter<boolean>
35
+ /** Use `useAppExperiment` provided state when `experimentId` is not set. Defaults to true. */
36
+ syncAppExperiment?: boolean
37
+ }
38
+
39
+ export interface UseExperimentSamplesReturn {
40
+ /** Experiment id currently used for automatic sample loading. */
41
+ experimentId: ComputedRef<number | undefined>
42
+ /** Raw `/experiments/{id}/data` response when loaded through the platform API. */
43
+ data: Ref<Record<string, unknown> | null>
44
+ /** Plugin-defined design_data payload from props or platform response. */
45
+ designData: ComputedRef<Record<string, unknown> | null>
46
+ /** SampleSelector-compatible string values extracted from design_data. */
47
+ samples: ComputedRef<string[]>
48
+ /** Select/dropdown-friendly sample options extracted from design_data. */
49
+ sampleOptions: ComputedRef<SelectOption<string>[]>
50
+ isLoading: Ref<boolean>
51
+ error: Ref<string | null>
52
+ lastLoadedAt: Ref<Date | null>
53
+ /** Fetch samples for a specific experiment id, defaulting to the resolved id. */
54
+ fetch: (experimentId?: number | string | null) => Promise<Record<string, unknown> | null>
55
+ /** Refetch the current experiment id. */
56
+ refresh: () => Promise<void>
57
+ /** Clear fetched platform data. */
58
+ clear: () => void
59
+ }
60
+
61
+ /** Loads experiment design_data and derives samples for SampleSelector-style UIs. */
62
+ export function useExperimentSamples(
63
+ options: UseExperimentSamplesOptions = {},
64
+ ): UseExperimentSamplesReturn {
65
+ const appExperiment = options.syncAppExperiment === false
66
+ ? undefined
67
+ : inject(APP_EXPERIMENT_KEY, undefined)
68
+ const experimentData = useExperimentData({ apiBaseUrl: options.apiBaseUrl })
69
+
70
+ const experimentId = computed<number | undefined>(() => {
71
+ const explicitId = parseExperimentId(toValue(options.experimentId))
72
+ return explicitId ?? parseExperimentId(appExperiment?.experimentId.value)
73
+ })
74
+
75
+ const explicitDesignData = computed<Record<string, unknown> | null>(() =>
76
+ unwrapExperimentDesignData(toValue(options.designData) ?? null),
77
+ )
78
+
79
+ const designData = computed<Record<string, unknown> | null>(() =>
80
+ explicitDesignData.value ?? experimentData.designData.value,
81
+ )
82
+
83
+ const extractOptions = computed<ExtractExperimentSamplesOptions>(() => ({
84
+ includeControls: options.includeControls,
85
+ }))
86
+
87
+ const samples = computed<string[]>(() =>
88
+ extractSampleNamesFromDesignData(designData.value, extractOptions.value),
89
+ )
90
+
91
+ const sampleOptions = computed<SelectOption<string>[]>(() =>
92
+ extractSampleOptionsFromDesignData(designData.value, extractOptions.value),
93
+ )
94
+
95
+ const enabled = computed(() => toValue(options.enabled) ?? true)
96
+
97
+ async function fetchSamples(
98
+ id: number | string | null | undefined = experimentId.value,
99
+ ): Promise<Record<string, unknown> | null> {
100
+ const parsedId = parseExperimentId(id)
101
+ if (parsedId === undefined) {
102
+ experimentData.clear()
103
+ return null
104
+ }
105
+ return experimentData.fetch(parsedId)
106
+ }
107
+
108
+ watch(
109
+ () => ({
110
+ designData: explicitDesignData.value,
111
+ enabled: enabled.value,
112
+ experimentId: experimentId.value,
113
+ }),
114
+ ({ designData: currentDesignData, enabled: isEnabled, experimentId: currentExperimentId }) => {
115
+ if (options.immediate === false || !isEnabled) return
116
+ if (currentDesignData) {
117
+ experimentData.clear()
118
+ return
119
+ }
120
+ if (currentExperimentId === undefined) {
121
+ experimentData.clear()
122
+ return
123
+ }
124
+ void experimentData.fetch(currentExperimentId)
125
+ },
126
+ { immediate: options.immediate !== false },
127
+ )
128
+
129
+ return {
130
+ experimentId,
131
+ data: experimentData.data,
132
+ designData,
133
+ samples,
134
+ sampleOptions,
135
+ isLoading: experimentData.isLoading,
136
+ error: experimentData.error,
137
+ lastLoadedAt: experimentData.lastLoadedAt,
138
+ fetch: fetchSamples,
139
+ refresh: experimentData.refresh,
140
+ clear: experimentData.clear,
141
+ }
142
+ }
package/src/index.ts CHANGED
@@ -19,6 +19,15 @@ export {
19
19
  // Stores
20
20
  export * from './stores'
21
21
 
22
+ // Permissions
23
+ export * from './permissions'
24
+
25
+ // Instrument monitoring
26
+ export * from './instrument'
27
+
28
+ // LCMS sequence helpers
29
+ export * from './lcms'
30
+
22
31
  // Utils
23
32
  export {
24
33
  hexToHsl,
@@ -26,6 +35,24 @@ export {
26
35
  deriveShade,
27
36
  type Hsl,
28
37
  } from './utils/color'
38
+ export {
39
+ LCMS_DEFAULT_CONTROL_POSITIONS,
40
+ createLcmsControlWellEditData,
41
+ getLcmsDefaultControlWellId,
42
+ lcmsPlateCellsToRack,
43
+ lcmsPlateCellsToRacks,
44
+ lcmsPlateTypeToRackFormat,
45
+ lcmsWellId,
46
+ parseLcmsWellId,
47
+ rackFormatToLcmsPlateType,
48
+ rackToLcmsPlateCells,
49
+ racksToLcmsPlateCells,
50
+ type LcmsControlSampleType,
51
+ type LcmsPlateCell,
52
+ type LcmsPlateCellsToRackOptions,
53
+ type LcmsPlateCellsToRacksOptions,
54
+ type LcmsPlateType,
55
+ } from './utils/rack'
29
56
 
30
57
  // Biology data templates
31
58
  export * from './templates'
@@ -0,0 +1,90 @@
1
+ import type { SequenceProgress } from './types'
2
+
3
+ export function sequenceProgressPercent(progress: SequenceProgress | null | undefined): number {
4
+ if (!progress || progress.total_samples <= 0) return 0
5
+ return Math.round(clamp((progress.current_sample / progress.total_samples) * 100, 0, 100))
6
+ }
7
+
8
+ export function sequenceSamplesRemaining(progress: SequenceProgress | null | undefined): number {
9
+ if (!progress) return 0
10
+ return Math.max(0, progress.total_samples - progress.current_sample)
11
+ }
12
+
13
+ export function estimateSequenceRemainingSeconds(
14
+ progress: SequenceProgress | null | undefined,
15
+ ): number | null {
16
+ if (!progress) return null
17
+ const samplesLeft = sequenceSamplesRemaining(progress)
18
+ if (samplesLeft <= 0) return 0
19
+
20
+ const explicit = progress.estimated_remaining_seconds
21
+ if (typeof explicit === 'number' && explicit > 0) return explicit
22
+
23
+ const avg = progress.avg_sample_seconds ?? average(progress.sample_durations)
24
+ if (typeof avg === 'number' && avg > 0) return samplesLeft * avg
25
+
26
+ const elapsed = progress.elapsed_seconds ?? 0
27
+ if (elapsed > 0 && progress.current_sample > 0) {
28
+ return (elapsed / progress.current_sample) * samplesLeft
29
+ }
30
+
31
+ return null
32
+ }
33
+
34
+ export function estimateSequenceFinishDate(
35
+ progress: SequenceProgress | null | undefined,
36
+ now = new Date(),
37
+ ): Date | null {
38
+ if (!progress) return null
39
+
40
+ const explicit = coerceDate(progress.estimated_finish_time)
41
+ if (explicit) return explicit
42
+
43
+ const remaining = estimateSequenceRemainingSeconds(progress)
44
+ if (remaining == null || remaining <= 0) return null
45
+ return new Date(now.getTime() + remaining * 1000)
46
+ }
47
+
48
+ export function formatSequenceRemaining(progress: SequenceProgress | null | undefined): string | null {
49
+ const remaining = estimateSequenceRemainingSeconds(progress)
50
+ if (remaining == null || remaining <= 0) return null
51
+
52
+ const minutes = remaining / 60
53
+ if (minutes < 1) return `${Math.round(remaining)}s left`
54
+ if (minutes < 60) return `~${Math.round(minutes)}m left`
55
+
56
+ const hours = Math.floor(minutes / 60)
57
+ const mins = Math.round(minutes % 60)
58
+ return mins > 0 ? `~${hours}h ${mins}m left` : `~${hours}h left`
59
+ }
60
+
61
+ export function formatSequenceEta(
62
+ progress: SequenceProgress | null | undefined,
63
+ locale?: Intl.LocalesArgument,
64
+ options: Intl.DateTimeFormatOptions = {},
65
+ ): string | null {
66
+ const finish = estimateSequenceFinishDate(progress)
67
+ if (!finish) return null
68
+ return finish.toLocaleTimeString(locale, {
69
+ hour: '2-digit',
70
+ minute: '2-digit',
71
+ ...options,
72
+ })
73
+ }
74
+
75
+ function average(values: readonly number[] | undefined): number | null {
76
+ if (!values?.length) return null
77
+ const usable = values.filter(value => Number.isFinite(value) && value >= 0)
78
+ if (usable.length === 0) return null
79
+ return usable.reduce((sum, value) => sum + value, 0) / usable.length
80
+ }
81
+
82
+ function coerceDate(value: string | Date | null | undefined): Date | null {
83
+ if (!value) return null
84
+ const date = value instanceof Date ? value : new Date(value)
85
+ return Number.isNaN(date.getTime()) ? null : date
86
+ }
87
+
88
+ function clamp(value: number, min: number, max: number): number {
89
+ return Math.min(max, Math.max(min, value))
90
+ }
package/src/lcms.ts ADDED
@@ -0,0 +1,108 @@
1
+ import type { LcmsPlateCell, LcmsPlateType } from './utils/rack'
2
+
3
+ export type LcmsPolarity = 'POS' | 'NEG' | 'BOTH'
4
+ export type LcmsContainerType = 'VIAL' | 'PLATE'
5
+
6
+ export interface LcmsSequenceItem {
7
+ sample_type: string
8
+ file_name: string
9
+ sample_id: string
10
+ path: string
11
+ instrument_method: string
12
+ position: string
13
+ injection_volume: number
14
+ }
15
+
16
+ export interface LcmsSequenceTableColumn {
17
+ key: keyof LcmsSequenceItem | 'index' | 'actions'
18
+ label: string
19
+ align?: 'left' | 'right'
20
+ }
21
+
22
+ export const DEFAULT_LCMS_SEQUENCE_COLUMNS: LcmsSequenceTableColumn[] = [
23
+ { key: 'index', label: '#' },
24
+ { key: 'sample_type', label: 'Type' },
25
+ { key: 'file_name', label: 'File Name' },
26
+ { key: 'position', label: 'Position' },
27
+ { key: 'instrument_method', label: 'Method' },
28
+ { key: 'injection_volume', label: 'Inj Vol', align: 'right' },
29
+ ]
30
+
31
+ export function extractLcmsCommonPrefix(fileNames: readonly string[]): string {
32
+ if (fileNames.length === 0) return ''
33
+ const stripped = fileNames.map(fileName => fileName.replace(/_\d{3}$/, ''))
34
+ const prefixes = stripped.map((fileName) => {
35
+ const match = fileName.match(/^(.+?)_(POS|NEG)_/i)
36
+ return match ? match[1] : fileName.replace(/_[^_]+$/, '')
37
+ })
38
+
39
+ let common = prefixes[0] ?? ''
40
+ for (const prefix of prefixes.slice(1)) {
41
+ while (common && !prefix.startsWith(common)) {
42
+ const index = common.lastIndexOf('_')
43
+ common = index > 0 ? common.substring(0, index) : common.substring(0, common.length - 1)
44
+ }
45
+ }
46
+ return common
47
+ }
48
+
49
+ export function extractLcmsSampleName(fileName: string, prefix = ''): string {
50
+ let name = fileName.replace(/_\d{3}$/, '')
51
+ if (prefix && name.startsWith(prefix)) {
52
+ name = name.substring(prefix.length).replace(/^_+/, '')
53
+ }
54
+ name = name.replace(/^(POS|NEG)_/i, '')
55
+ return name || fileName
56
+ }
57
+
58
+ export function lcmsWellIdFromPosition(position: string): string {
59
+ return position.includes(':') ? position.split(':').pop() ?? position : position
60
+ }
61
+
62
+ export function inferLcmsPlateTypeFromWellIds(wellIds: readonly string[]): LcmsPlateType | null {
63
+ let maxCol = 0
64
+ let maxRow = 0
65
+ for (const wellId of wellIds) {
66
+ const match = wellId.match(/^([A-Z])(\d+)$/i)
67
+ if (!match) continue
68
+ maxRow = Math.max(maxRow, match[1].toUpperCase().charCodeAt(0) - 64)
69
+ maxCol = Math.max(maxCol, Number(match[2]))
70
+ }
71
+ if (maxCol === 0 && maxRow === 0) return null
72
+ return maxCol <= 9 && maxRow <= 6 ? '54vial' : '96well'
73
+ }
74
+
75
+ export function reconstructLcmsPlateCellsFromSequenceItems(
76
+ items: readonly LcmsSequenceItem[],
77
+ ): { cells: LcmsPlateCell[]; plateType: LcmsPlateType } | null {
78
+ const unknownItems = items.filter(item => item.sample_type === 'Unknown')
79
+ if (unknownItems.length === 0) return null
80
+
81
+ const prefix = extractLcmsCommonPrefix(unknownItems.map(item => item.file_name))
82
+ const seen = new Set<string>()
83
+ const cells: LcmsPlateCell[] = []
84
+
85
+ for (const item of unknownItems) {
86
+ const wellId = lcmsWellIdFromPosition(item.position)
87
+ if (seen.has(wellId)) continue
88
+ seen.add(wellId)
89
+
90
+ const match = wellId.match(/^([A-Z])(\d+)$/i)
91
+ if (!match) continue
92
+ cells.push({
93
+ row: match[1].toUpperCase(),
94
+ column: Number(match[2]),
95
+ sample_name: extractLcmsSampleName(item.file_name, prefix),
96
+ })
97
+ }
98
+
99
+ if (cells.length === 0) return null
100
+ const plateType = inferLcmsPlateTypeFromWellIds(cells.map(cell => `${cell.row}${cell.column}`))
101
+ if (!plateType) return null
102
+ return { cells, plateType }
103
+ }
104
+
105
+ export function basenameFromWindowsPath(path: string | null | undefined): string {
106
+ if (!path) return ''
107
+ return path.split(/[\\/]/).pop() ?? path
108
+ }
@@ -0,0 +1,143 @@
1
+ export const ADMIN_ROLE = 'admin'
2
+
3
+ export const ADMIN_PANEL_PERMISSIONS = [
4
+ 'users.view',
5
+ 'users.invite',
6
+ 'users.manage',
7
+ 'platform.configure',
8
+ 'platform.view_logs',
9
+ 'plugins.configure',
10
+ 'plugins.install',
11
+ ] as const
12
+
13
+ export type AccessAudience = 'all' | 'admin' | 'user'
14
+ export type AccessAudienceInput = AccessAudience | readonly AccessAudience[]
15
+
16
+ export interface RoleInfo {
17
+ id?: number
18
+ slug: string
19
+ name?: string
20
+ color?: string
21
+ permissions?: readonly string[] | null
22
+ project_scope?: 'all' | 'assigned' | string
23
+ plugin_access?: readonly string[] | 'all' | null
24
+ }
25
+
26
+ export interface PermissionUser {
27
+ role?: string | null
28
+ role_obj?: RoleInfo | null
29
+ roleObj?: RoleInfo | null
30
+ permissions?: readonly string[] | null
31
+ }
32
+
33
+ export interface AccessPolicy {
34
+ audience?: AccessAudienceInput
35
+ visibleFor?: AccessAudienceInput
36
+ requiresAuth?: boolean
37
+ requiresAdmin?: boolean
38
+ permissions?: readonly string[]
39
+ anyPermissions?: readonly string[]
40
+ plugin?: string
41
+ }
42
+
43
+ export interface AccessControlled {
44
+ access?: AccessPolicy
45
+ visibleFor?: AccessAudienceInput
46
+ requiresAdmin?: boolean
47
+ permissions?: readonly string[]
48
+ anyPermissions?: readonly string[]
49
+ }
50
+
51
+ export function getRoleInfo(user: PermissionUser | null | undefined): RoleInfo | null {
52
+ return user?.roleObj ?? user?.role_obj ?? null
53
+ }
54
+
55
+ export function isAdminRole(role: string | null | undefined): boolean {
56
+ return role === ADMIN_ROLE
57
+ }
58
+
59
+ export function isAdminUser(user: PermissionUser | null | undefined): boolean {
60
+ return isAdminRole(user?.role) || getRoleInfo(user)?.slug === ADMIN_ROLE
61
+ }
62
+
63
+ export function getAccessAudience(user: PermissionUser | null | undefined): Exclude<AccessAudience, 'all'> {
64
+ return isAdminUser(user) ? 'admin' : 'user'
65
+ }
66
+
67
+ export function getUserPermissions(user: PermissionUser | null | undefined): string[] {
68
+ const rolePermissions = getRoleInfo(user)?.permissions
69
+ if (rolePermissions?.length) return [...rolePermissions]
70
+ return [...(user?.permissions ?? [])]
71
+ }
72
+
73
+ export function hasAllPermissions(
74
+ user: PermissionUser | null | undefined,
75
+ permissions: readonly string[] = [],
76
+ ): boolean {
77
+ if (permissions.length === 0) return true
78
+ if (isAdminUser(user)) return true
79
+ const granted = new Set(getUserPermissions(user))
80
+ return permissions.every(permission => granted.has(permission))
81
+ }
82
+
83
+ export function hasAnyPermission(
84
+ user: PermissionUser | null | undefined,
85
+ permissions: readonly string[] = [],
86
+ ): boolean {
87
+ if (permissions.length === 0) return true
88
+ if (isAdminUser(user)) return true
89
+ const granted = new Set(getUserPermissions(user))
90
+ return permissions.some(permission => granted.has(permission))
91
+ }
92
+
93
+ export function canAccessAdmin(user: PermissionUser | null | undefined): boolean {
94
+ return isAdminUser(user) || hasAnyPermission(user, ADMIN_PANEL_PERMISSIONS)
95
+ }
96
+
97
+ export function canAccessPlugin(
98
+ user: PermissionUser | null | undefined,
99
+ pluginName: string | null | undefined,
100
+ ): boolean {
101
+ if (!pluginName) return true
102
+ const access = getRoleInfo(user)?.plugin_access
103
+ if (!access || access === 'all') return true
104
+ return Array.isArray(access) && access.includes(pluginName)
105
+ }
106
+
107
+ export function normalizeAccessPolicy(rule: AccessControlled | AccessPolicy | undefined): AccessPolicy {
108
+ if (!rule) return {}
109
+ const { access: nested, ...direct } = rule as AccessPolicy & { access?: AccessPolicy }
110
+ return {
111
+ ...(nested ?? {}),
112
+ ...direct,
113
+ ...('visibleFor' in rule && rule.visibleFor !== undefined ? { visibleFor: rule.visibleFor } : {}),
114
+ ...('requiresAdmin' in rule && rule.requiresAdmin !== undefined ? { requiresAdmin: rule.requiresAdmin } : {}),
115
+ ...('permissions' in rule && rule.permissions !== undefined ? { permissions: rule.permissions } : {}),
116
+ ...('anyPermissions' in rule && rule.anyPermissions !== undefined ? { anyPermissions: rule.anyPermissions } : {}),
117
+ }
118
+ }
119
+
120
+ export function canAccessByPolicy(
121
+ user: PermissionUser | null | undefined,
122
+ rule: AccessControlled | AccessPolicy | undefined,
123
+ isAuthenticated = user !== null && user !== undefined,
124
+ ): boolean {
125
+ const policy = normalizeAccessPolicy(rule)
126
+ if (policy.requiresAuth && !isAuthenticated) return false
127
+ if (policy.requiresAdmin && !isAdminUser(user)) return false
128
+ if (!audienceAllowsUser(policy.visibleFor ?? policy.audience, user)) return false
129
+ if (!hasAllPermissions(user, policy.permissions)) return false
130
+ if (!hasAnyPermission(user, policy.anyPermissions)) return false
131
+ if (policy.plugin && !canAccessPlugin(user, policy.plugin)) return false
132
+ return true
133
+ }
134
+
135
+ function audienceAllowsUser(
136
+ audience: AccessAudienceInput | undefined,
137
+ user: PermissionUser | null | undefined,
138
+ ): boolean {
139
+ if (audience === undefined) return true
140
+ const allowed = Array.isArray(audience) ? audience : [audience]
141
+ if (allowed.includes('all')) return true
142
+ return allowed.includes(getAccessAudience(user))
143
+ }