Merge branch 'rebase-in-time'

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:21.3.0 as base
+FROM node:21.3.0 AS base
 ENV PUPPETEER_SKIP_CHROMIUM_DOWNLOAD true
 RUN echo "Installing system dependencies (git+puppeteer deps)..." \
   && apt-get update \
@@ -16,32 +16,32 @@ RUN npm i -g ts-node
 USER node
 WORKDIR /app
 
-FROM base as prepare_system
+FROM base AS prepare_system
 USER root
 RUN echo "Installing system deps..." && apt-get -y update && apt-get -y install r-base python3-dev python3-pip python3-venv pkg-config libhdf5-dev && rm -rf /var/lib/apt/lists/*
 ENV PYTHON_BIN="python3"
 USER node
 
-FROM prepare_system as prepare_r
+FROM prepare_system AS prepare_r
 USER root
 COPY --chown=node:node cli/setup.R /app/setup.R
 RUN echo "Running setup.R..." && R -e "source('/app/setup.R')" && rm /app/setup.R
 USER node
 
-FROM base as prepare_src
+FROM base AS prepare_src
 COPY --chown=node:node . /app
 
-FROM prepare_src as prepare_package_json
+FROM prepare_src AS prepare_package_json
 RUN find /app -type d -name "node_modules" -exec rm -rf {} + \
   && find /app -type f -a \! \( -name "package.json" -o -name "package-lock.json" -o -name ".puppeteerrc.cjs" \) -delete \
   && find /app -type d -empty -delete
 
-FROM prepare_src as prepare_requirements_txt
+FROM prepare_src AS prepare_requirements_txt
 RUN find /app -type d -name "node_modules" -exec rm -rf {} + \
   && find /app -type f -a \! \( -name "requirements.txt" -o -name "enumerate-requirements.ts" \) -delete \
   && find /app -type d -empty -delete
 
-FROM base as prepare_npm_i
+FROM base AS prepare_npm_i
 COPY --from=prepare_package_json /app /app
 RUN echo "Installing NodeJS dependencies..." && npm i
 
@@ -56,18 +56,18 @@ RUN mv /app/requirements.txt /tmp/requirements.txt \
   && chown node:node /app/requirements.txt
 USER node
 
-FROM prepare_src as prepare_build
+FROM prepare_src AS prepare_build
 COPY --from=prepare_npm_i /app /app
 RUN echo "Building app..." && LANDING_PAGE=/graph/extend PUBLIC_URL=https://playbook-workflow-builder.cloud npm run build
 
-FROM prepare_system as prepare_python
+FROM prepare_system AS prepare_python
 COPY --from=prepare_requirements_txt_complete /app /app
 USER root
 RUN echo "Installing python dependencies..." && python3 -m pip install --break-system-packages -r /app/requirements.txt && rm /app/requirements.txt
 USER node
 
 # TARGET: dev -- development environment with dependencies to run dev tools
-FROM prepare_system as dev
+FROM prepare_system AS dev
 USER root
 RUN echo "Installing dev deps..." \
   && apt-get -y update \
@@ -98,13 +98,13 @@ COPY --from=prepare_python /usr/local/lib/ /usr/local/lib/
 CMD ["/bin/bash"]
 
 # TARGET: app_minimal -- production server with dependencies to run just the webserver
-FROM base as app_minimal
+FROM base AS app_minimal
 COPY --from=prepare_build /app /app
 ENV PORT 3000
 CMD ["npm", "run", "start"]
 
 # TARGET: app -- production server with dependencies to run everything
-FROM prepare_system as app
+FROM prepare_system AS app
 COPY --from=prepare_r /usr/local/lib/ /usr/local/lib/
 COPY --from=prepare_python /usr/local/lib/ /usr/local/lib/
 COPY --from=prepare_build /app /app

app/api/v1/user/playbooks/index.ts

@@ -229,6 +229,9 @@ export const UpdateUserPlaybook = API.post('/api/v1/user/playbooks/[id]/update')
     )
     if (fpl === undefined) throw new NotFoundError()
     fpl = fpl.rebasePlaybookMetadata(fpl, await fpprg.resolvePlaybookMetadata(inputs.body.playbook_metadata)).head
+    fpl = await fpprg.upsertFPL(fpl)
+    if (fpl === undefined) throw new NotFoundError()
+    fpl = await fpl.rebaseInTime()
     if (fpl === undefined) throw new NotFoundError()
     fpl = await fpprg.upsertFPL(fpl)
     const session = await getServerSessionWithId(req, res)

app/fragments/graph/catalog.tsx

@@ -10,7 +10,7 @@ const InputGroup = dynamic(() => import('@blueprintjs/core').then(({ InputGroup
 
 type KVCounts = { [key: string]: { [val: string]: number } }
 
-export default function Catalog<T extends { spec: string, meta?: { pagerank?: number, tags?: Record<string, Record<string, number>> } }>({ items, weights, serialize, children }: {
+export default function Catalog<T extends { spec: string, meta?: { pagerank?: number, tags?: Record<string, Record<string, number>>, external?: boolean } }>({ items, weights, serialize, children }: {
   items: Array<T>,
   weights: Record<string, number>,
   serialize: (item: T) => string,
@@ -27,6 +27,7 @@ export default function Catalog<T extends { spec: string, meta?: { pagerank?: nu
     for (const k in items) {
       const item = items[k]
       const item_meta = item.meta||{}
+      item_meta.tags = item_meta.tags||{}
       item_search_ts[k] = tsvector(serialize(item))
       pagerank_max = Math.max(item_meta.pagerank||0, pagerank_max)
       weight_max = Math.max(weights[item.spec]||0, weight_max)

app/fragments/graph/cell.tsx

@@ -3,13 +3,16 @@ import type KRG from '@/core/KRG'
 import dynamic from 'next/dynamic'
 import { Metapath, useMetapathOutput } from '@/app/fragments/metapath'
 import Head from 'next/head'
+import { useRouter } from 'next/router'
 import { useStory } from '@/app/fragments/story'
 import SafeRender from '@/utils/saferender'
 import { Abstract, FigureCaption, Methods, References } from './story'
+import { z } from 'zod'
 
 const Prompt = dynamic(() => import('@/app/fragments/graph/prompt'))
 
 export default function Cell({ session_id, krg, id, head, metapath }: { session_id?: string, krg: KRG, id: string, head: Metapath, metapath: Metapath[] }) {
+  const router = useRouter()
   const processNode = krg.getProcessNode(head.process.type)
   const { data: { output, outputNode }, status, error: outputError, mutate } = useMetapathOutput({ krg, head })
   const story = useStory()
@@ -52,11 +55,13 @@ export default function Cell({ session_id, krg, id, head, metapath }: { session_
               : <SafeRender component={outputNode.view} props={output} />}
             <FigureCaption id={head.id} story={{ ...story, ast: astFiltered }} />
             <References story={{ ...story, ast: astFiltered }} />
+            {head.process.timestamp ? <div className="alert alert-info">Saved computation from {new Date(head.process.timestamp).toLocaleString()}</div> : null}
             <button
               className="btn btn-primary"
               onClick={async (evt) => {
-                const req = await fetch(`${session_id ? `/api/socket/${session_id}` : ''}/api/db/process/${head.process.id}/output/delete`, { method: 'POST' })
-                const res = await req.text()
+                const req = await fetch(`${session_id ? `/api/socket/${session_id}` : ''}/api/db/fpl/${id}/recompute/${head.id}`, { method: 'POST' })
+                const res = z.object({ head: z.string(), rebased: z.string() }).parse(await req.json())
+                router.push(`${session_id ? `/session/${session_id}` : ''}/graph/${res.head}${res.head !== res.rebased ? `/node/${res.rebased}` : ''}`, undefined, { shallow: true })
                 mutate()
               }}
             >Recompute</button>

app/fragments/graph/extend.tsx

@@ -48,7 +48,9 @@ export default function Extend({ session_id, krg, id, head, metapath }: { sessio
       </Head>
       <Catalog<ProcessMetaNode & ({}|{ onClick: (_: { router: NextRouter, id: string, head: Metapath }) => void })>
         items={[
-          ...krg.getNextProcess(processNode ? processNode.output.spec : '').filter(proc => proc.meta.hidden !== true),
+          ...krg.getNextProcess(processNode ? processNode.output.spec : '')
+            .filter(proc => proc.meta.hidden !== true)
+            .map(proc => ({ ...proc, meta: { ...proc.meta, tags: { ...(proc.meta.tags??{}), External: { [proc.meta.external ? 'True': 'False']: 1 } } } })),
           ...SuggestionEdges(processNode ? processNode.output : undefined),
         ]}
         serialize={item => [

app/pages/api/db/fpl/[fpl_id]/recompute/[rebase_id].ts

@@ -0,0 +1,35 @@
+import fpprg from '@/app/fpprg'
+import { z } from 'zod'
+import { Process } from '@/core/FPPRG'
+import handler from '@/utils/next-rest'
+import { NotFoundError, UnsupportedMethodError } from '@/spec/error'
+
+const QueryType = z.object({
+  fpl_id: z.string(),
+  rebase_id: z.string(),
+})
+
+export default handler(async (req, res) => {
+  if (req.method !== 'POST') throw new UnsupportedMethodError(req.method)
+  const { fpl_id, rebase_id } = QueryType.parse(req.query)
+  const rebase = await fpprg.getFPL(rebase_id)
+  if (rebase === undefined) throw new NotFoundError()
+  const old_process = rebase.process
+  const old_fpl = await fpprg.getFPL(fpl_id)
+  if (old_fpl === undefined) throw new NotFoundError()
+  if (old_process.timestamp !== undefined) {
+    const new_process = await fpprg.upsertProcess(new Process(
+      old_process.type,
+      old_process.data,
+      old_process.inputs,
+    ))
+    const { rebased, head } = old_fpl.rebase(old_process, new_process)
+    const fpl = await fpprg.upsertFPL(head)
+    res.status(200).json({ head: fpl.id, rebased: rebased.id })
+  } else {
+    const resolved = await fpprg.getResolved(old_process.id)
+    if (resolved === undefined) throw new NotFoundError()
+    await fpprg.deleteResolved(resolved)
+    res.status(200).json({ head: fpl_id, rebased: rebase_id })
+  }
+})

components/MW/metgene_summary/index.tsx

@@ -32,6 +32,7 @@ export const MetGeneSearch = MetaNode('MetGeneSearch')
     description: 'Identify gene-centric information from Metabolomics.',
     icon: [metgene_icon],
     pagerank: 2,
+    external: true,
   })
   .inputs({ gene: GeneTerm })
   .output(MetGeneSummary)

components/data/limma_voom/package.json

@@ -1,7 +1,7 @@
 {
   "name": "limma_voom",
   "version": "1.0.0",
-  "license": "CC-BY-4.0",
+  "license": "GPL-2.0-or-later",
   "author": "Alex Agris <[email protected]>",
   "private": true,
   "dependencies": {

components/data/pca_transformation/package.json

@@ -1,7 +1,7 @@
 {
   "name": "pca-transformation",
   "version": "1.0.0",
-  "license": "CC-BY-4.0",
+  "license": "GPL-3.0-or-later",
   "author": "Juncheng Pan <[email protected]>",
   "private": true,
   "dependencies": {

components/lincs/l1000-reverse-search/index.tsx

@@ -61,6 +61,7 @@ export const LINCSL1000ReverseSearch = MetaNode('LINCSL1000ReverseSearch')
     description: 'Identify RNA-seq-like LINCS L1000 Signatures which reverse the expression of the gene.',
     icon: [lincs_icon],
     pagerank: 2,
+    external: true,
   })
   .inputs({ gene: GeneTerm })
   .output(LINCSL1000ReverseSearchDashboard)

components/service/enrichr/index.tsx

@@ -568,6 +568,7 @@ export const EnrichrTermTSearch = [
       label: `Extract Gene Sets Containing the ${T.label} in the Set Label`,
       icon: [...array.ensureArray(T.icon), enrichr_icon],
       description: `Find ${T.label} Terms in Enrichr Libraries`,
+      external: true,
     })
     .inputs({ term: TermT })
     .output(EnrichrTermSearchResults)