diff --git a/.github/workflows/update_dev_docs.yml b/.github/workflows/update_dev_docs.yml index 65571aa8..92d79009 100644 --- a/.github/workflows/update_dev_docs.yml +++ b/.github/workflows/update_dev_docs.yml @@ -21,6 +21,16 @@ jobs: python-version: '3.10' - name: Install dependencies run: uv sync --locked --group dev --group docs + - name: Set up Node.js + uses: actions/setup-node@v4 + with: + node-version: "20" + - name: Build documentation widgets + run: | + npm --prefix diagram-app ci + npm --prefix diagram-app run build + npm --prefix qc-tree-app ci + npm --prefix qc-tree-app run build - name: Generate docs run: | uv run python src/biodata_schema/utils/docs/model_generator.py diff --git a/.gitignore b/.gitignore index ba73fec7..694c7703 100644 --- a/.gitignore +++ b/.gitignore @@ -147,10 +147,14 @@ examples/*.json !diagram-app/package.json !diagram-app/package-lock.json !diagram-app/tsconfig.json +!qc-tree-app/package.json +!qc-tree-app/package-lock.json +!qc-tree-app/tsconfig.json # diagram-app (React Flow schema diagram embedded in the docs front page) diagram-app/node_modules/ docs/source/_static/schema-diagram/ +docs/source/_static/qc-tree-app/ docs/base/models/* .github/copilot-instructions.md schema_tree.md diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ec58f06b..d49f4e9c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,6 +10,8 @@ build: pre_build: - npm --prefix diagram-app ci - npm --prefix diagram-app run build + - npm --prefix qc-tree-app ci + - npm --prefix qc-tree-app run build python: install: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index fff4608b..651c1d86 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -51,6 +51,13 @@ npm --prefix diagram-app ci npm --prefix diagram-app run build ``` +The quality-control page embeds the interactive hierarchy builder (`qc-tree-app/`). Build its JS/CSS bundle before building the docs as well: + +```bash +npm --prefix qc-tree-app ci +npm --prefix qc-tree-app run build +``` + Then to create the documentation html files, run: ```bash diff --git a/docs/base/core/quality_control.md b/docs/base/core/quality_control.md index a9e99065..f102f4da 100644 --- a/docs/base/core/quality_control.md +++ b/docs/base/core/quality_control.md @@ -10,21 +10,26 @@ Every [QCMetric](#qcmetric) has a `Status` which takes the value of the metric a ## Details -### Metrics +The metrics defined during quality control should define whether or not an asset can be used for analysis and the properties of an asset that could influence how an analysis is performed. There are two levels of QC: -Each [QCMetric](#qcmetric) is a single value or array of values that can be computed, or observed, about one modality in a data asset. These can have any type. Metrics should be significant: i.e. whether they pass or fail should matter for the modality. Metrics need to be human understandable. If you find yourself generating more than fifty metrics for a modality you should group them together (i.e. make the value a dictionary combining similar metrics and the rule an evaluation of multiple fields in the dictionary). +- Quality control metrics that are **not allowed to fail** are metrics that at `stage:raw` would prevent an asset from being processed or that at `stage:processing` would prevent an asset from being analyzed. This is a very high bar. If the goals of the data acquisition were met (regardless of whether *experimental* goals were met), then all metrics that are 'not allowed to fail' should be passing. +- All other metrics should be **allowed to fail**. -Each [QCMetric](#qcmetric) has a [Status](#status). The [Status](#status) should depend directly on the `QCMetric.value`, either by a simple function: "value>5", or by a qualitative rule: "Field of view includes visual areas". The `QCMetric.description` field should describe the rule used to set the status. Metrics can be evaluated multiple times, in which case the new status should be appended the `QCMetric.status_history`. +For example, if the goal of an acquisition was to collect behavior and fiber photometry, the 'not allowed to fail' metrics should define whether the behavior and fiber photometry data can be analyzed. Metrics that are allowed to fail could include whether the data meets various thresholds of behavior engagement, the signal to noise ratio of the data, and other potentially valuable (but not critical) metrics. -Each [QCMetric](#qcmetric) is annotated with three pieces of additional metadata: the [Stage](#stage) during which it was evaluated, the [Modality](biodata_models/modalities.md#modality) of the evaluated data, and [tags](#tags). +Metrics that *can fail* are identified by the `QualityControl.allow_tag_failures` field, details below. -### Curations +### Metrics + +Each [QCMetric](#qcmetric) is a single value or array of values that can be computed, or observed, about one modality in a data asset. These can have any type. Metrics should be significant: i.e. whether they pass or fail should matter for the modality. Metrics need to be human understandable. If you find yourself generating more metrics than a human can reasonably parse for a modality you should group them together (i.e. make the value a dictionary combining similar metrics). -If you find yourself computing a value for something smaller than an entire modality of data in an asset you are performing *curation*, i.e. you are determining the status of a subset of a modality in the data asset. We provide the [CurationMetric](#curationmetric) for this purpose. You should put a dictionary in the `CurationMetric.value` field that contains a mapping between the subsets (usually neurons, ROIs, channels, etc) and their values. +Each [QCMetric](#qcmetric) has a [Status](#status). The [Status](#status) should depend directly on the `QCMetric.value`, either by a simple function: "value>5", or by a qualitative rule: "Field of view includes visual areas". The `QCMetric.description` field should describe the rule used to set the status. The status of a metric should be appended the `QCMetric.status_history`. + +Each [QCMetric](#qcmetric) is annotated with three pieces of additional metadata: the [Stage](#stage) during which it was evaluated, the [Modality](biodata_models/modalities.md#modality) of the evaluated data, and [tags](#tags). ### Tags -`tags` are groups of descriptors that define how metrics are organized hierarchically, making it easier to visualize metrics. Good tag keys (groups) are things like "probe" and good tag values are things like "Probe A" or just "A". +`tags` are groups of descriptors that define how metrics are grouped hierarchically, making it easier to visualize metrics. Good tag keys (groups) are things like "probe" and good tag values (group members) are things like "Probe A" or just "A". ```python # For an electrophysiology metric @@ -39,7 +44,19 @@ tags = { } ``` -Use the `QualityControl.default_grouping` list to define how users should organize a visualization by default. In almost all cases *modality should be the top-level grouping*. For example, building on the example above you might group by: `["modality", ("probe", "video"), "shank"]` to get a tree split by modality first (which naturally splits ephys and behavior-videos tags into two groups), then by which probe or video a metric belongs to, and finally only for probes the individual shanks are split into groups. +When multiple QC stages are selected, they split at the top of the hierarchy. Multiple modalities split at the next level, or at the top when only one stage is selected. These fixed levels are followed by the tag levels in `QualityControl.default_grouping`. For example, `["stage", "modality", ("probe", "video"), "shank"]` groups first by stage, then by modality, then by probe or video at the same level, and finally by shank. + +Use the builder to define tag keys and values, drag tag keys into level buckets, and preview the resulting hierarchy: + +```{raw} html + +
+ +``` + +### Curations + +If you find yourself computing a value for something that is smaller than an entire modality of data and is repeated (e.g. neurons) in an asset you are performing *curation*, i.e. you are determining the status of a subset of a modality in the data asset. We provide the [CurationMetric](#curationmetric) for this purpose. You should put a dictionary in the `CurationMetric.value` field that contains a mapping between the subsets (usually neurons, ROIs, channels, etc) and their values. ### QualityControl.evaluate_status() @@ -53,6 +70,16 @@ Then, given the status of all the remaining metrics in the group: 2. If any metric is pending and the rest pass the evaluation is pending 3. If all metrics pass the evaluation passes +### QualityControl.status + +The `QualityControl.status` field is a dictionary that maps individual tag `key:value` pairs to their status. For example a typical status dictionary might look like this: + +``` +{ + "modality:behavior": "PASS", +} +``` + **Q: What is a metric reference?** Each [QCMetric](#qcmetric) should include a `QCMetric.reference`. References should be publicly accessible images, figures, multi-panel figures, and videos that support the metric value/status or provide the information necessary for manual annotation. diff --git a/docs/source/quality_control.md b/docs/source/quality_control.md index 22b77551..876ddd8f 100644 --- a/docs/source/quality_control.md +++ b/docs/source/quality_control.md @@ -10,21 +10,26 @@ Every [QCMetric](#qcmetric) has a `Status` which takes the value of the metric a ## Details -### Metrics +The metrics defined during quality control should define whether or not an asset can be used for analysis and the properties of an asset that could influence how an analysis is performed. There are two levels of QC: -Each [QCMetric](#qcmetric) is a single value or array of values that can be computed, or observed, about one modality in a data asset. These can have any type. Metrics should be significant: i.e. whether they pass or fail should matter for the modality. Metrics need to be human understandable. If you find yourself generating more than fifty metrics for a modality you should group them together (i.e. make the value a dictionary combining similar metrics and the rule an evaluation of multiple fields in the dictionary). +- Quality control metrics that are **not allowed to fail** are metrics that at `stage:raw` would prevent an asset from being processed or that at `stage:processing` would prevent an asset from being analyzed. This is a very high bar. If the goals of the data acquisition were met (regardless of whether *experimental* goals were met), then all metrics that are 'not allowed to fail' should be passing. +- All other metrics should be **allowed to fail**. -Each [QCMetric](#qcmetric) has a [Status](#status). The [Status](#status) should depend directly on the `QCMetric.value`, either by a simple function: "value>5", or by a qualitative rule: "Field of view includes visual areas". The `QCMetric.description` field should describe the rule used to set the status. Metrics can be evaluated multiple times, in which case the new status should be appended the `QCMetric.status_history`. +For example, if the goal of an acquisition was to collect behavior and fiber photometry, the 'not allowed to fail' metrics should define whether the behavior and fiber photometry data can be analyzed. Metrics that are allowed to fail could include whether the data meets various thresholds of behavior engagement, the signal to noise ratio of the data, and other potentially valuable (but not critical) metrics. -Each [QCMetric](#qcmetric) is annotated with three pieces of additional metadata: the [Stage](#stage) during which it was evaluated, the [Modality](biodata_models/modalities.md#modality) of the evaluated data, and [tags](#tags). +Metrics that *can fail* are identified by the `QualityControl.allow_tag_failures` field, details below. -### Curations +### Metrics + +Each [QCMetric](#qcmetric) is a single value or array of values that can be computed, or observed, about one modality in a data asset. These can have any type. Metrics should be significant: i.e. whether they pass or fail should matter for the modality. Metrics need to be human understandable. If you find yourself generating more metrics than a human can reasonably parse for a modality you should group them together (i.e. make the value a dictionary combining similar metrics). -If you find yourself computing a value for something smaller than an entire modality of data in an asset you are performing *curation*, i.e. you are determining the status of a subset of a modality in the data asset. We provide the [CurationMetric](#curationmetric) for this purpose. You should put a dictionary in the `CurationMetric.value` field that contains a mapping between the subsets (usually neurons, ROIs, channels, etc) and their values. +Each [QCMetric](#qcmetric) has a [Status](#status). The [Status](#status) should depend directly on the `QCMetric.value`, either by a simple function: "value>5", or by a qualitative rule: "Field of view includes visual areas". The `QCMetric.description` field should describe the rule used to set the status. The status of a metric should be appended the `QCMetric.status_history`. + +Each [QCMetric](#qcmetric) is annotated with three pieces of additional metadata: the [Stage](#stage) during which it was evaluated, the [Modality](biodata_models/modalities.md#modality) of the evaluated data, and [tags](#tags). ### Tags -`tags` are groups of descriptors that define how metrics are organized hierarchically, making it easier to visualize metrics. Good tag keys (groups) are things like "probe" and good tag values are things like "Probe A" or just "A". +`tags` are groups of descriptors that define how metrics are grouped hierarchically, making it easier to visualize metrics. Good tag keys (groups) are things like "probe" and good tag values (group members) are things like "Probe A" or just "A". ```python # For an electrophysiology metric @@ -39,7 +44,19 @@ tags = { } ``` -Use the `QualityControl.default_grouping` list to define how users should organize a visualization by default. In almost all cases *modality should be the top-level grouping*. For example, building on the example above you might group by: `["modality", ("probe", "video"), "shank"]` to get a tree split by modality first (which naturally splits ephys and behavior-videos tags into two groups), then by which probe or video a metric belongs to, and finally only for probes the individual shanks are split into groups. +When multiple QC stages are selected, they split at the top of the hierarchy. Multiple modalities split at the next level, or at the top when only one stage is selected. These fixed levels are followed by the tag levels in `QualityControl.default_grouping`. For example, `["stage", "modality", ("probe", "video"), "shank"]` groups first by stage, then by modality, then by probe or video at the same level, and finally by shank. + +Use the builder to define tag keys and values, drag tag keys into level buckets, and preview the resulting hierarchy: + +```{raw} html + +
+ +``` + +### Curations + +If you find yourself computing a value for something that is smaller than an entire modality of data and is repeated (e.g. neurons) in an asset you are performing *curation*, i.e. you are determining the status of a subset of a modality in the data asset. We provide the [CurationMetric](#curationmetric) for this purpose. You should put a dictionary in the `CurationMetric.value` field that contains a mapping between the subsets (usually neurons, ROIs, channels, etc) and their values. ### QualityControl.evaluate_status() @@ -53,6 +70,16 @@ Then, given the status of all the remaining metrics in the group: 2. If any metric is pending and the rest pass the evaluation is pending 3. If all metrics pass the evaluation passes +### QualityControl.status + +The `QualityControl.status` field is a dictionary that maps individual tag `key:value` pairs to their status. For example a typical status dictionary might look like this: + +``` +{ + "modality:behavior": "PASS", +} +``` + **Q: What is a metric reference?** Each [QCMetric](#qcmetric) should include a `QCMetric.reference`. References should be publicly accessible images, figures, multi-panel figures, and videos that support the metric value/status or provide the information necessary for manual annotation. diff --git a/qc-tree-app/.gitignore b/qc-tree-app/.gitignore new file mode 100644 index 00000000..b9470778 --- /dev/null +++ b/qc-tree-app/.gitignore @@ -0,0 +1,2 @@ +node_modules/ +dist/ diff --git a/qc-tree-app/index.html b/qc-tree-app/index.html new file mode 100644 index 00000000..0321f75e --- /dev/null +++ b/qc-tree-app/index.html @@ -0,0 +1,17 @@ + + + + + + QC Tree Builder + + + +
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} + } + }, + "node_modules/yallist": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", + "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", + "dev": true, + "license": "ISC" + } + } +} diff --git a/qc-tree-app/package.json b/qc-tree-app/package.json new file mode 100644 index 00000000..03f6c44f --- /dev/null +++ b/qc-tree-app/package.json @@ -0,0 +1,22 @@ +{ + "name": "biodata-schema-qc-tree-app", + "private": true, + "version": "0.1.0", + "type": "module", + "scripts": { + "dev": "vite --host 127.0.0.1", + "build": "tsc --noEmit && vite build", + "preview": "vite preview --host 127.0.0.1" + }, + "dependencies": { + "react": "^18.3.1", + "react-dom": "^18.3.1" + }, + "devDependencies": { + "@types/react": "^18.3.12", + "@types/react-dom": "^18.3.1", + "@vitejs/plugin-react": "^4.3.4", + "typescript": "^5.6.3", + "vite": "^5.4.11" + } +} diff --git a/qc-tree-app/src/QCWidget.tsx b/qc-tree-app/src/QCWidget.tsx new file mode 100644 index 00000000..b1d457d1 --- /dev/null +++ b/qc-tree-app/src/QCWidget.tsx @@ -0,0 +1,407 @@ +import { useState, type DragEvent } from "react"; +import type { + FixedSelections, + GroupField, + GroupStep, + HierarchyStep, + TagDefinition, + TreeBranch, +} from "./widgetTypes"; +import { buildTree, fieldKey, formatDefaultGrouping } from "./widgetTree"; +import { MODALITIES, QC_STAGES, type Modality, type Stage } from "./vocabularies"; + +const FIELD_DRAG_TYPE = "application/x-qc-tree-field"; +const STEP_DRAG_TYPE = "application/x-qc-tree-step"; + +const initialTags: TagDefinition[] = [ + { id: "probe", key: "probe", values: "A, B", modalityScope: "ecephys" }, + { id: "video", key: "video", values: "left body, right body", modalityScope: "behavior-videos" }, + { id: "shank", key: "shank", values: "0, 1", modalityScope: "ecephys" }, +]; + +const initialGrouping: GroupStep[] = [ + { id: "group-probe-video", fields: ["tag:probe", "tag:video"] }, + { id: "group-shank", fields: ["tag:shank"] }, +]; + +const initialModalities: Modality[] = ["ecephys", "behavior", "behavior-videos"]; +const initialStages: Stage[] = ["Raw data", "Processing"]; + +function makeId(): string { + return crypto.randomUUID(); +} + +function toggleValue(values: Value[], value: Value): Value[] { + return values.includes(value) ? values.filter((item) => item !== value) : [...values, value]; +} + +function getFieldOptions(tags: TagDefinition[]): GroupField[] { + const options: GroupField[] = []; + const seenKeys = new Set(); + + for (const tag of tags) { + const key = tag.key.trim(); + if (!key || seenKeys.has(key)) continue; + seenKeys.add(key); + options.push(`tag:${tag.id}`); + } + + return options; +} + +function TreeList({ branches, root = false }: { branches: TreeBranch[]; root?: boolean }) { + if (!branches.length) return null; + + return ( + + ); +} + +export default function QCWidget() { + const [tags, setTags] = useState(initialTags); + const [grouping, setGrouping] = useState(initialGrouping); + const [modalities, setModalities] = useState(initialModalities); + const [stages, setStages] = useState(initialStages); + const selections: FixedSelections = { modalities, stages }; + const effectiveGrouping: HierarchyStep[] = []; + if (stages.length > 1) { + effectiveGrouping.push({ id: "fixed-stage", fields: ["stage"], fixed: true }); + } + if (modalities.length > 1) { + effectiveGrouping.push({ id: "fixed-modality", fields: ["modality"], fixed: true }); + } + const fixedGrouping = [...effectiveGrouping]; + effectiveGrouping.push( + ...grouping + .filter((step) => step.fields.length > 0) + .map((step) => ({ ...step, fixed: false })), + ); + const tree = buildTree(effectiveGrouping, tags, selections); + const fieldOptions = getFieldOptions(tags); + const activeFields = new Set(grouping.flatMap((step) => step.fields)); + const availableFields = fieldOptions.filter((field) => !activeFields.has(field)); + const groupingCode = formatDefaultGrouping(effectiveGrouping, tags); + + function removeField(field: GroupField) { + setGrouping((current) => + current.map((step) => ({ ...step, fields: step.fields.filter((item) => item !== field) })), + ); + } + + function placeField(field: GroupField, targetId?: string) { + setGrouping((current) => { + const source = current.find((step) => step.fields.includes(field)); + if (source?.id === targetId) return current; + + const next = current.map((step) => ({ + ...step, + fields: step.fields.filter((item) => item !== field), + })); + const target = next.find((step) => step.id === targetId); + + if (target) { + return next.map((step) => + step.id === targetId ? { ...step, fields: [...step.fields, field] } : step, + ); + } + return [...next, { id: makeId(), fields: [field] }]; + }); + } + + function addLevel() { + setGrouping((current) => [...current, { id: makeId(), fields: [] }]); + } + + function moveStep(stepId: string, targetId?: string) { + setGrouping((current) => { + if (stepId === targetId) return current; + const sourceIndex = current.findIndex((step) => step.id === stepId); + if (sourceIndex < 0) return current; + + const next = [...current]; + const [step] = next.splice(sourceIndex, 1); + const targetIndex = targetId ? next.findIndex((item) => item.id === targetId) : next.length; + next.splice(targetIndex < 0 ? next.length : targetIndex, 0, step); + return next; + }); + } + + function handleDrop(event: DragEvent, targetId?: string) { + event.preventDefault(); + event.stopPropagation(); + const field = event.dataTransfer.getData(FIELD_DRAG_TYPE) as GroupField; + const stepId = event.dataTransfer.getData(STEP_DRAG_TYPE); + + if (field) placeField(field, targetId); + else if (stepId) moveStep(stepId, targetId); + } + + function startFieldDrag(event: DragEvent, field: GroupField) { + event.dataTransfer.effectAllowed = "copyMove"; + event.dataTransfer.setData(FIELD_DRAG_TYPE, field); + } + + function startStepDrag(event: DragEvent, stepId: string) { + event.dataTransfer.effectAllowed = "move"; + event.dataTransfer.setData(STEP_DRAG_TYPE, stepId); + } + + function updateTag(tagId: string, change: Partial) { + setTags((current) => current.map((tag) => (tag.id === tagId ? { ...tag, ...change } : tag))); + } + + function addTag() { + setTags((current) => [ + ...current, + { id: makeId(), key: "", values: "", modalityScope: "all" }, + ]); + } + + function removeTag(tagId: string) { + setTags((current) => current.filter((tag) => tag.id !== tagId)); + removeField(`tag:${tagId}`); + } + + function updateVocabulary( + values: Value[], + value: Value, + update: (next: Value[]) => void, + ) { + update(toggleValue(values, value)); + } + + return ( +
+
+
+
+
+ Stage values {stages.length} selected +
+ {QC_STAGES.map((stage) => ( + + ))} +
+
+ +
+ Modality values {modalities.length} selected +
+ {MODALITIES.map((modality) => ( + + ))} +
+
+
+ +
+
Tag definitions
+
+ + {tags.map((tag) => ( +
+ updateTag(tag.id, { key: event.currentTarget.value })} + placeholder="tag key" + value={tag.key} + /> + updateTag(tag.id, { values: event.currentTarget.value })} + placeholder="A, B" + value={tag.values} + /> + + +
+ ))} +
+ +
+ +
+
default_grouping
+
+
+ Available tags + Drag keys into a level +
+
+ {availableFields.map((field) => ( + + ))} + {availableFields.length === 0 && ( + All tag keys are in a level + )} +
+
+ +
    event.preventDefault()} + onDrop={(event) => handleDrop(event)} + > + {fixedGrouping.map((step, index) => ( +
  1. + + {index + 1} +
    + {step.fields.map((field) => ( + + + + ))} +
    +
    2. + ))} + {grouping.map((step, index) => { + const levelNumber = fixedGrouping.length + index + 1; + return ( +
  2. event.preventDefault()} + onDrop={(event) => handleDrop(event, step.id)} + > +
    + + Level {levelNumber} + Multiple keys form a tuple + +
    +
    + {step.fields.map((field) => ( + startFieldDrag(event, field)} + title={`Drag ${fieldKey(field, tags)} to another level`} + > + {fieldKey(field, tags)} + + + ))} + {step.fields.length === 0 && ( + Drop tag keys here + )} +
    +
    3. + ); + })} + {fixedGrouping.length + grouping.length === 0 && ( +
  3. Add a level, then drag tag keys into it.
    4. + )} +
+ + + + + {groupingCode} + +
+
+ +
+ {tree.length ? ( + + ) : ( +

Choose a grouping field and values to preview the hierarchy.

+ )} +
+
+
+ ); +} \ No newline at end of file diff --git a/qc-tree-app/src/main.tsx b/qc-tree-app/src/main.tsx new file mode 100644 index 00000000..e63ae974 --- /dev/null +++ b/qc-tree-app/src/main.tsx @@ -0,0 +1,31 @@ +import React from "react"; +import ReactDOM from "react-dom/client"; +import App from "./QCWidget"; +import "./qcWidget.css"; + +function mount(element: HTMLElement) { + if (element.dataset.mounted) return; + element.dataset.mounted = "true"; + ReactDOM.createRoot(element).render( + + + , + ); +} + +function mountAll() { + const targets = document.querySelectorAll(".qc-tree-app"); + if (targets.length) { + targets.forEach(mount); + return; + } + + const standaloneRoot = document.getElementById("root"); + if (standaloneRoot) mount(standaloneRoot); +} + +if (document.readyState === "loading") { + document.addEventListener("DOMContentLoaded", mountAll); +} else { + mountAll(); +} diff --git a/qc-tree-app/src/qcWidget.css b/qc-tree-app/src/qcWidget.css new file mode 100644 index 00000000..5c56ebf5 --- /dev/null +++ b/qc-tree-app/src/qcWidget.css @@ -0,0 +1,560 @@ +.qc-tree-widget { + --qc-border: var(--color-foreground-border, #d8d8d8); + --qc-muted: var(--color-foreground-muted, #666); + --qc-link: var(--color-brand-content, #0645ad); + --qc-background: var(--color-background-primary, #fff); + --qc-background-muted: var(--color-background-secondary, #f7f7f7); + box-sizing: border-box; + width: 100%; + color: var(--color-foreground-primary, inherit); + font: inherit; + font-size: 0.9em; + line-height: 1.45; + container-name: qc-widget; + container-type: inline-size; + border: 1px solid var(--qc-border); + background: var(--qc-background); +} + +.qc-tree-widget *, +.qc-tree-widget *::before, +.qc-tree-widget *::after { + box-sizing: border-box; +} + +.qc-tree-widget button, +.qc-tree-widget input, +.qc-tree-widget select { + max-width: 100%; + color: inherit; + font: inherit; +} + +.qc-tree-widget button { + cursor: pointer; +} + +.qc-tree-widget :focus-visible { + outline: 2px solid var(--qc-link); + outline-offset: 2px; +} + +.qc-widget-layout { + display: grid; + grid-template-columns: minmax(0, 1fr); + min-width: 0; +} + +.qc-controls { + min-width: 0; + padding: 12px; +} + +.qc-vocabulary { + min-width: 0; + border-bottom: 1px solid var(--qc-border); + padding-bottom: 8px; +} + +.qc-label { + margin-bottom: 6px; + color: var(--qc-muted); + font-family: ui-monospace, SFMono-Regular, Consolas, monospace; + font-size: 0.83em; + font-weight: 600; +} + +.qc-step-fields, +.qc-vocabulary-options, +.qc-stage-options { + display: flex; + flex-wrap: wrap; + align-items: center; + gap: 5px; +} + +.qc-field-options { + display: flex; + flex-direction: column; + align-items: stretch; + gap: 4px; + margin-bottom: 8px; +} + +.qc-field-options-heading { + display: flex; + justify-content: space-between; + gap: 8px; + color: var(--qc-muted); + font-size: 0.76em; +} + +.qc-field-options-heading span:last-child { + text-align: right; +} + +.qc-field-option-list { + display: flex; + flex-wrap: wrap; + align-items: center; + gap: 5px; +} + +.qc-no-available-tags { + color: var(--qc-muted); + font-size: 0.8em; +} + +.qc-field-option { + min-height: 27px; + border: 1px solid var(--qc-border); + border-radius: 2px; + background: var(--qc-background); + padding: 2px 7px; + color: var(--qc-link) !important; + font-family: ui-monospace, SFMono-Regular, Consolas, monospace !important; + font-size: 0.82em !important; +} + +.qc-field-option:hover { + border-color: var(--qc-link); + background: var(--qc-background-muted); +} + +.qc-grouping-list { + display: flex; + flex-direction: column; + align-items: stretch; + min-height: 39px; + margin: 8px 0 0; + padding: 0; + list-style: none; + gap: 5px; +} + +.qc-grouping-list.is-empty { + border: 1px dashed var(--qc-border); + padding: 6px; +} + +.qc-grouping-empty { + color: var(--qc-muted); + font-size: 0.85em; + list-style: none; +} + +.qc-grouping-step { + display: flex; + width: 100%; + flex: 0 0 auto; + min-width: 0; + min-height: 32px; + align-items: center; + gap: 6px; + border: 1px solid var(--qc-border); + background: var(--qc-background); + padding: 2px 5px 2px 2px; +} + +.qc-grouping-step.is-fixed { + background: var(--qc-background-muted); +} + +.qc-level-bucket { + flex-direction: column; + align-items: stretch; + gap: 0; + overflow: hidden; + padding: 0; +} + +.qc-level-header { + display: flex; + min-width: 0; + min-height: 34px; + align-items: center; + gap: 6px; + padding: 2px 6px 2px 2px; +} + +.qc-level-title { + flex: 0 0 auto; + font-size: 0.84em; +} + +.qc-level-hint { + min-width: 0; + overflow: hidden; + color: var(--qc-muted); + font-size: 0.72em; + text-overflow: ellipsis; + white-space: nowrap; +} + +.qc-remove-level { + flex: 0 0 auto; + margin-left: auto; + border: 0; + background: transparent; + color: var(--qc-muted); + font-size: 0.72em; +} + +.qc-remove-level:hover { + color: var(--qc-link); +} + +.qc-level-dropzone { + display: flex; + min-height: 45px; + flex-wrap: wrap; + align-content: flex-start; + align-items: center; + gap: 5px; + margin: 0 6px 6px; + border: 1px dashed var(--qc-border); + padding: 6px; +} + +.qc-drop-hint { + color: var(--qc-muted); + font-size: 0.78em; +} + +.qc-level-tag { + display: inline-flex; + min-height: 27px; + align-items: center; + gap: 5px; + border: 1px solid var(--qc-border); + background: var(--qc-background-muted); + padding: 2px 4px 2px 7px; + cursor: grab; +} + +.qc-level-tag:active { + cursor: grabbing; +} + +.qc-level-tag code { + color: var(--qc-link); + font-size: 0.82em; +} + +.qc-level-tag button { + width: 18px; + height: 19px; + border: 0; + background: transparent; + color: var(--qc-muted); + font-size: 1.1em; + line-height: 1; +} + +.qc-add-level { + margin-top: 7px; + border: 0; + background: transparent; + padding: 2px 0; + color: var(--qc-link) !important; + font-size: 0.82em !important; +} + +.qc-fixed-lock { + width: 32px; + flex: 0 0 32px; + color: var(--qc-muted); + font-size: 0.62em; + text-align: center; + text-transform: uppercase; +} + +.qc-drag-handle { + display: grid; + width: 19px; + height: 24px; + flex: 0 0 19px; + place-items: center; + border: 0; + background: transparent; + color: var(--qc-muted) !important; + cursor: grab !important; + font-size: 0.75em !important; +} + +.qc-step-number { + width: 13px; + color: var(--qc-muted); + font-size: 0.75em; + text-align: center; +} + +.qc-step-fields { + display: flex; + flex: 1 1 auto; + flex-wrap: wrap; + min-width: 0; +} + +.qc-step-field { + display: inline-flex; + min-height: 23px; + align-items: center; + gap: 4px; + color: var(--qc-link); + font-size: 0.82em; +} + +.qc-step-field code { + color: inherit; + font-size: 0.95em; +} + +.qc-step-field > .qc-fixed-field:disabled { + width: auto; + height: auto; + flex: 0 0 auto; + border: 0; + background: transparent; + color: var(--qc-muted); + cursor: not-allowed; + font-family: ui-monospace, SFMono-Regular, Consolas, monospace; + font-size: 0.95em; + opacity: 1; + padding: 0; + white-space: nowrap; +} + +.qc-step-field > button { + width: 17px; + height: 19px; + border: 0; + background: transparent; + color: var(--qc-muted); + font-size: 1.15em; + line-height: 1; +} + +.qc-step-field > button:hover, +.qc-remove-tag:hover { + color: var(--qc-link); +} + +.qc-or { + margin: 0 2px 0 4px; + color: var(--qc-muted); + font-size: 0.85em; +} + +.qc-grouping-code { + display: block; + overflow-wrap: anywhere; + margin-top: 8px; + border-left: 2px solid var(--qc-border); + background: var(--qc-background-muted); + padding: 5px 8px; + color: var(--color-foreground-primary, #222); + font-size: 0.8em; +} + +.qc-tag-definitions { + margin-top: 10px; + border-top: 1px solid var(--qc-border); + padding-top: 7px; +} + +.qc-tag-definitions-title, +.qc-modality-picker legend { + margin-bottom: 5px; + color: var(--qc-link); + font-size: 0.86em; +} + +.qc-modality-picker { + min-width: 0; + margin: 0; + border: 0; + padding: 0; +} + +.qc-tag-table { + min-width: 0; + margin-top: 7px; +} + +.qc-tag-headings, +.qc-tag-row { + display: grid; + grid-template-columns: minmax(64px, 0.8fr) minmax(74px, 1.2fr) minmax(74px, 0.7fr) 20px; + align-items: center; + gap: 5px; +} + +.qc-tag-headings { + margin: 0 0 3px; + color: var(--qc-muted); + font-size: 0.72em; +} + +.qc-tag-row + .qc-tag-row { + margin-top: 4px; +} + +.qc-tag-row input, +.qc-tag-row select { + width: 100%; + min-width: 0; + height: 27px; + border: 1px solid var(--qc-border); + border-radius: 2px; + background: var(--qc-background); + padding: 2px 5px; + font-size: 0.78em; +} + +.qc-tag-row input { + font-family: ui-monospace, SFMono-Regular, Consolas, monospace; +} + +.qc-tag-row select { + padding-right: 2px; +} + +.qc-remove-tag { + width: 20px; + height: 24px; + border: 0; + background: transparent; + color: var(--qc-muted); + font-size: 1.15em; +} + +.qc-add-tag { + margin-top: 6px; + border: 0; + background: transparent; + padding: 2px 0; + color: var(--qc-link) !important; + font-size: 0.82em !important; +} + +.qc-modality-picker legend span, +.qc-stage-picker legend span { + color: var(--qc-muted); + font-size: 0.9em; +} + +.qc-vocabulary-options { + padding: 6px 2px 2px; +} + +.qc-vocabulary-options label, +.qc-stage-options label { + display: inline-flex; + align-items: center; + gap: 3px; + color: var(--color-foreground-primary, inherit); + font-size: 0.76em; + white-space: nowrap; +} + +.qc-tree-widget input[type="checkbox"] { + width: 13px; + height: 13px; + margin: 0; + accent-color: var(--qc-link); +} + +.qc-stage-picker { + min-width: 0; + margin: 0 0 7px; + border: 0; + padding: 0; +} + +.qc-stage-picker legend, +.qc-modality-picker legend { + padding: 0; +} + +.qc-stage-picker legend { + margin-bottom: 4px; + color: var(--qc-link); + font-size: 0.86em; +} + +.qc-stage-options { + gap: 5px 10px; +} + +.qc-tree-preview { + min-width: 0; + min-height: 120px; + border-top: 1px solid var(--qc-border); + background: var(--qc-background); + padding: 12px; +} + +.qc-tree-list { + min-width: 0; + margin: 0; + padding: 0; + list-style: none; +} + +.qc-tree-list[role="group"] { + margin-left: 8px; + border-left: 1px solid var(--qc-border); + padding-left: 12px; +} + +.qc-tree-branch { + position: relative; + min-width: 0; + padding: 3px 0; + list-style: none; +} + +.qc-tree-list[role="group"] > .qc-tree-branch::before { + position: absolute; + top: 14px; + left: -12px; + width: 11px; + border-top: 1px solid var(--qc-border); + content: ""; +} + +.qc-tree-entry { + display: flex; + min-width: 0; + align-items: baseline; + gap: 8px; + overflow-wrap: anywhere; +} + +.qc-tree-entry code { + flex: 0 0 auto; + color: var(--qc-link); + font-size: 0.78em; +} + +.qc-tree-entry span { + font-size: 0.86em; +} + +.qc-tree-empty { + margin: 0; + color: var(--qc-muted); + font-size: 0.84em; +} + +@container qc-widget (min-width: 760px) { + .qc-widget-layout { + grid-template-columns: minmax(0, 1fr) minmax(0, 1fr); + } + + .qc-tree-preview { + border-top: 0; + border-left: 1px solid var(--qc-border); + } +} \ No newline at end of file diff --git a/qc-tree-app/src/vocabularies.ts b/qc-tree-app/src/vocabularies.ts new file mode 100644 index 00000000..0e60a4e1 --- /dev/null +++ b/qc-tree-app/src/vocabularies.ts @@ -0,0 +1,28 @@ +export const QC_STAGES = ["Raw data", "Processing", "Analysis", "Multi-asset"] as const; +export type Stage = (typeof QC_STAGES)[number]; + +export const MODALITIES = [ + { name: "Barcoded anatomy resolved by sequencing", abbreviation: "BARseq" }, + { name: "Behavior", abbreviation: "behavior" }, + { name: "Behavior videos", abbreviation: "behavior-videos" }, + { name: "Brightfield microscopy", abbreviation: "brightfield" }, + { name: "Confocal microscopy", abbreviation: "confocal" }, + { name: "Extracellular electrophysiology", abbreviation: "ecephys" }, + { name: "Electron microscopy", abbreviation: "EM" }, + { name: "Electromyography", abbreviation: "EMG" }, + { name: "Fiber photometry", abbreviation: "fib" }, + { name: "Fluorescence micro-optical sectioning tomography", abbreviation: "fMOST" }, + { name: "Intracellular electrophysiology", abbreviation: "icephys" }, + { name: "Intrinsic signal imaging", abbreviation: "ISI" }, + { name: "Multiplexed analysis of projections by sequencing", abbreviation: "MAPseq" }, + { name: "Multiplexed error-robust fluorescence in situ hybridization", abbreviation: "merfish" }, + { name: "Magnetic resonance imaging", abbreviation: "MRI" }, + { name: "One-photon imaging", abbreviation: "one-photon" }, + { name: "Planar optical physiology", abbreviation: "pophys" }, + { name: "Single cell RNA sequencing", abbreviation: "scRNAseq" }, + { name: "Random access projection microscopy", abbreviation: "slap2" }, + { name: "Selective plane illumination microscopy", abbreviation: "SPIM" }, + { name: "Serial two-photon tomogrophy", abbreviation: "STPT" }, +] as const; + +export type Modality = (typeof MODALITIES)[number]["abbreviation"]; diff --git a/qc-tree-app/src/widgetTree.ts b/qc-tree-app/src/widgetTree.ts new file mode 100644 index 00000000..02f21a55 --- /dev/null +++ b/qc-tree-app/src/widgetTree.ts @@ -0,0 +1,95 @@ +import type { FixedSelections, HierarchyField, HierarchyStep, TagDefinition, TreeBranch } from "./widgetTypes"; +import type { Modality, Stage } from "./vocabularies"; + +type TreeContext = { + modality?: Modality; + stage?: Stage; +}; + +type Candidate = { + key: string; + value: string; + context: TreeContext; +}; + +export function fieldKey(field: HierarchyField, tags: TagDefinition[]): string { + if (field === "modality" || field === "stage") return field; + return tags.find((tag) => `tag:${tag.id}` === field)?.key.trim() || "tag"; +} + +export function formatDefaultGrouping(grouping: HierarchyStep[], tags: TagDefinition[]): string { + const entries = grouping.map((step) => { + const keys = step.fields.map((field) => JSON.stringify(fieldKey(field, tags))); + return keys.length === 1 ? keys[0] : `(${keys.join(", ")})`; + }); + + return `default_grouping = [${entries.join(", ")}]`; +} + +function candidatesForField( + field: HierarchyField, + context: TreeContext, + tags: TagDefinition[], + selections: FixedSelections, +): Candidate[] { + if (field === "modality") { + if (context.modality) return []; + return selections.modalities.map((value) => ({ + key: "modality", + value, + context: { ...context, modality: value }, + })); + } + + if (field === "stage") { + if (context.stage) return []; + return selections.stages.map((value) => ({ + key: "stage", + value, + context: { ...context, stage: value }, + })); + } + + const tag = tags.find((item) => `tag:${item.id}` === field); + if (!tag || (context.modality && tag.modalityScope !== "all" && tag.modalityScope !== context.modality)) { + return []; + } + + return Array.from(new Set(tag.values.split(",").map((value) => value.trim()).filter(Boolean))).map((value) => ({ + key: fieldKey(field, tags), + value, + context, + })); +} + +function buildLevel( + grouping: HierarchyStep[], + tags: TagDefinition[], + selections: FixedSelections, + depth: number, + context: TreeContext, +): TreeBranch[] { + const step = grouping[depth]; + if (!step) return []; + + return step.fields.flatMap((field) => + candidatesForField(field, context, tags, selections).map((candidate) => ({ + id: `${step.id}:${field}:${candidate.value}`, + key: candidate.key, + value: candidate.value, + children: buildLevel(grouping, tags, selections, depth + 1, candidate.context), + })), + ); +} + +export function buildTree( + grouping: HierarchyStep[], + tags: TagDefinition[], + selections: FixedSelections, +): TreeBranch[] { + const context = { + ...(selections.modalities.length === 1 ? { modality: selections.modalities[0] } : {}), + ...(selections.stages.length === 1 ? { stage: selections.stages[0] } : {}), + }; + return buildLevel(grouping, tags, selections, 0, context); +} \ No newline at end of file diff --git a/qc-tree-app/src/widgetTypes.ts b/qc-tree-app/src/widgetTypes.ts new file mode 100644 index 00000000..0411cb3c --- /dev/null +++ b/qc-tree-app/src/widgetTypes.ts @@ -0,0 +1,35 @@ +import type { Modality, Stage } from "./vocabularies"; + +export type TagDefinition = { + id: string; + key: string; + values: string; + modalityScope: Modality | "all"; +}; + +export type GroupField = `tag:${string}`; + +export type HierarchyField = "modality" | "stage" | GroupField; + +export type GroupStep = { + id: string; + fields: GroupField[]; +}; + +export type HierarchyStep = { + id: string; + fields: HierarchyField[]; + fixed?: boolean; +}; + +export type FixedSelections = { + modalities: Modality[]; + stages: Stage[]; +}; + +export type TreeBranch = { + id: string; + key: string; + value: string; + children: TreeBranch[]; +}; \ No newline at end of file diff --git a/qc-tree-app/tsconfig.json b/qc-tree-app/tsconfig.json new file mode 100644 index 00000000..a627621e --- /dev/null +++ b/qc-tree-app/tsconfig.json @@ -0,0 +1,16 @@ +{ + "compilerOptions": { + "target": "ES2020", + "useDefineForClassFields": true, + "lib": ["ES2020", "DOM", "DOM.Iterable"], + "module": "ESNext", + "skipLibCheck": true, + "moduleResolution": "bundler", + "resolveJsonModule": true, + "isolatedModules": true, + "noEmit": true, + "jsx": "react-jsx", + "strict": true + }, + "include": ["src"] +} diff --git a/qc-tree-app/vite.config.ts b/qc-tree-app/vite.config.ts new file mode 100644 index 00000000..3d802f4f --- /dev/null +++ b/qc-tree-app/vite.config.ts @@ -0,0 +1,26 @@ +import { defineConfig } from "vite"; +import react from "@vitejs/plugin-react"; +import { dirname, resolve } from "node:path"; +import { fileURLToPath } from "node:url"; + +const root = dirname(fileURLToPath(import.meta.url)); + +export default defineConfig(({ command }) => ({ + root, + plugins: [react()], + server: { host: "127.0.0.1", port: 5174, strictPort: false }, + ...(command === "build" ? { define: { "process.env.NODE_ENV": JSON.stringify("production") } } : {}), + build: { + outDir: resolve(root, "../docs/source/_static/qc-tree-app"), + emptyOutDir: false, + cssCodeSplit: false, + lib: { + entry: resolve(root, "src/main.tsx"), + formats: ["es"], + fileName: () => "qc-tree-app.js", + }, + rollupOptions: { + output: { assetFileNames: "qc-tree-app.[ext]" }, + }, + }, +}));