diff --git a/CHANGELOG-publication-vignettes.md b/CHANGELOG-publication-vignettes.md new file mode 100644 index 0000000000..4fa1c1c6a8 --- /dev/null +++ b/CHANGELOG-publication-vignettes.md @@ -0,0 +1 @@ +- Add visualization vignettes section to publication page. \ No newline at end of file diff --git a/context/app/api/client.py b/context/app/api/client.py index 0d82edaa0b..d2e20f2e54 100644 --- a/context/app/api/client.py +++ b/context/app/api/client.py @@ -5,7 +5,7 @@ from flask import abort, current_app import requests - +import frontmatter from hubmap_commons.type_client import TypeClient from .client_utils import files_from_response @@ -209,6 +209,55 @@ def get_assay(name): vitessce_conf=vitessce_conf, vis_lifted_uuid=vis_lifted_uuid) + def _file_request(self, url, body_json=None): + headers = {'Authorization': 'Bearer ' + self.groups_token} if self.groups_token else {} + + if self.groups_token: + url += f"?token={self.groups_token}" + try: + response = ( + requests.get(url, headers=headers) + ) + except requests.exceptions.ConnectTimeout as error: + current_app.logger.error(error) + abort(504) + try: + response.raise_for_status() + except requests.exceptions.HTTPError as error: + current_app.logger.error(error.response.text) + status = error.response.status_code + if status in [400, 404]: + # The same 404 page will be returned, + # whether it's a missing route in portal-ui, + # or a missing entity in the API. + abort(status) + if status in [401]: + # I believe we have 401 errors when the globus credentials + # have expired, but are still in the flask session. + abort(status) + raise + return response.text + + def get_publication_vignettes(self, uuid): + vignettes_path = f"{current_app.config['ASSETS_ENDPOINT']}/{uuid}/vignettes/" + vignette_data = {} + + i = 1 + while True: + try: + vignette_dir_name = _get_vignette_dir_name(i) + description_text = self._file_request( + f"{vignettes_path}/{vignette_dir_name}/description.md") + metadata_content = frontmatter.loads(description_text) + vignette_data[vignette_dir_name] = { + **metadata_content.metadata, + 'vignette_description_md': metadata_content.content} + i += 1 + except Exception: + break + + return vignette_data + def _make_query(constraints, uuids): ''' @@ -463,3 +512,7 @@ def _get_latest_uuid(revisions): ] return max(clean_revisions, key=lambda revision: revision['revision_number'])['uuid'] + + +def _get_vignette_dir_name(vignette_number): + return f"vignette_{vignette_number:02}" diff --git a/context/app/routes_browse.py b/context/app/routes_browse.py index 318b72398b..ff26598b19 100644 --- a/context/app/routes_browse.py +++ b/context/app/routes_browse.py @@ -64,6 +64,9 @@ def details(type, uuid): 'vis_lifted_uuid': conf_cells_uuid.vis_lifted_uuid }) + if type == 'publication': + flask_data.update({'vignette_data': client.get_publication_vignettes(uuid)}) + template = 'base-pages/react-content.html' return render_template( template, diff --git a/context/app/static/js/components/Routes/Routes.jsx b/context/app/static/js/components/Routes/Routes.jsx index c87e3dbbb9..ce2f6decdd 100644 --- a/context/app/static/js/components/Routes/Routes.jsx +++ b/context/app/static/js/components/Routes/Routes.jsx @@ -48,6 +48,7 @@ function Routes({ flaskData }) { organs, organs_count, organ, + vignette_data, } = flaskData; const urlPath = window.location.pathname; const url = window.location.href; @@ -100,7 +101,7 @@ function Routes({ flaskData }) { if (urlPath.startsWith('/browse/publication/')) { return ( - + ); } @@ -296,6 +297,7 @@ Routes.propTypes = { organs: PropTypes.object, metadata: PropTypes.object, organs_count: PropTypes.number, + vignette_data: PropTypes.object, }), }; diff --git a/context/app/static/js/components/detailPage/visualization/Visualization/style.js b/context/app/static/js/components/detailPage/visualization/Visualization/style.js index 6b2e9d21f9..dad7aacde5 100644 --- a/context/app/static/js/components/detailPage/visualization/Visualization/style.js +++ b/context/app/static/js/components/detailPage/visualization/Visualization/style.js @@ -75,12 +75,13 @@ const StyledFooterText = styled(Typography)` `; const StyledDetailPageSection = styled(DetailPageSection)` + width: 100%; ${(props) => props.$vizIsFullscreen && css` z-index: ${props.theme.zIndex.visualization}; position: relative; - `} + `}; `; const bodyExpandedCSS = css` diff --git a/context/app/static/js/components/publications/PublicationVignette/PublicationVignette.jsx b/context/app/static/js/components/publications/PublicationVignette/PublicationVignette.jsx new file mode 100644 index 0000000000..757637165b --- /dev/null +++ b/context/app/static/js/components/publications/PublicationVignette/PublicationVignette.jsx @@ -0,0 +1,70 @@ +import React, { useContext, useEffect, useState } from 'react'; +import ReactMarkdown from 'react-markdown'; + +import { AppContext } from 'js/components/Providers'; +import VisualizationWrapper from 'js/components/detailPage/visualization/VisualizationWrapper'; + +import { fillUrls } from './utils'; + +async function fetchVitessceConf({ assetsEndpoint, uuid, filePath, groupsToken, vignetteDirName }) { + const urlHandler = (url, isZarr) => { + return `${url.replace('{{ base_url }}', `${assetsEndpoint}/${uuid}/data`)}${isZarr ? '' : `?token=${groupsToken}`}`; + }; + + const requestInitHandler = () => { + return { + headers: { Authorization: `Bearer ${groupsToken}` }, + }; + }; + const response = await fetch( + `${assetsEndpoint}/${uuid}/vignettes/${vignetteDirName}/${filePath}?token=${groupsToken}`, + { + headers: { + 'Content-Type': 'application/json', + }, + }, + ); + + if (!response.ok) { + console.error('Assets API failed', response); + return undefined; + } + const conf = await response.json(); + return fillUrls(conf, urlHandler, requestInitHandler); +} + +function PublicationVignette({ vignette, vignetteDirName, uuid }) { + const { assetsEndpoint, groupsToken } = useContext(AppContext); + + const [vitessceConfs, setVitessceConfs] = useState(undefined); + + useEffect(() => { + async function getAndSetVitessceConf() { + const figuresConfs = await Promise.all( + vignette.figures.map((figure) => { + return fetchVitessceConf({ assetsEndpoint, uuid, filePath: figure.file, groupsToken, vignetteDirName }); + }), + ); + setVitessceConfs(figuresConfs); + } + getAndSetVitessceConf(); + }, [assetsEndpoint, groupsToken, uuid, vignette.figures, vignetteDirName]); + + if (vitessceConfs) { + return ( + <> + {vignette.vignette_description_md} + + + ); + } + + return null; +} + +export default PublicationVignette; diff --git a/context/app/static/js/components/publications/PublicationVignette/index.js b/context/app/static/js/components/publications/PublicationVignette/index.js new file mode 100644 index 0000000000..ed320e09fb --- /dev/null +++ b/context/app/static/js/components/publications/PublicationVignette/index.js @@ -0,0 +1,3 @@ +import PublicationVignette from './PublicationVignette'; + +export default PublicationVignette; diff --git a/context/app/static/js/components/publications/PublicationVignette/utils.js b/context/app/static/js/components/publications/PublicationVignette/utils.js new file mode 100644 index 0000000000..ae32b4b1ae --- /dev/null +++ b/context/app/static/js/components/publications/PublicationVignette/utils.js @@ -0,0 +1,53 @@ +/** + * @param {object} config The "template" config containing URLs with "{{ base_url }}". + * @param {function} handleUrl Function that takes in a (potentially template) URL string and returns a filled-in URL string. + * @returns {object} The config with handleUrl having been called to process every URL. + */ +const fillUrls = (config, handleUrl, handleRequestInit) => { + return { + ...config, + datasets: config.datasets.map((datasetDef) => { + return { + ...datasetDef, + files: datasetDef.files.map((fileDef) => { + return { + ...fileDef, + ...(fileDef.url + ? { + url: handleUrl(fileDef.url, fileDef.fileType.includes('zarr')), + } + : {}), + ...(fileDef.fileType.includes('zarr') + ? { + requestInit: handleRequestInit(), + } + : {}), + ...(fileDef.options?.images + ? { + options: { + ...fileDef.options, + images: fileDef.options.images.map((imageDef) => { + return { + ...imageDef, + url: handleUrl(imageDef.url, false), + ...(imageDef.metadata?.omeTiffOffsetsUrl + ? { + metadata: { + ...imageDef.metadata, + omeTiffOffsetsUrl: handleUrl(imageDef.metadata.omeTiffOffsetsUrl, false), + }, + } + : {}), + }; + }), + }, + } + : {}), + }; + }), + }; + }), + }; +}; + +export { fillUrls }; diff --git a/context/app/static/js/components/publications/PublicationVisualizationsSection/PublicationsVisualizationSection.jsx b/context/app/static/js/components/publications/PublicationVisualizationsSection/PublicationsVisualizationSection.jsx new file mode 100644 index 0000000000..9ef47a7750 --- /dev/null +++ b/context/app/static/js/components/publications/PublicationVisualizationsSection/PublicationsVisualizationSection.jsx @@ -0,0 +1,43 @@ +import React, { useState } from 'react'; +import Accordion from '@material-ui/core/ExpansionPanel'; +import Typography from '@material-ui/core/Typography'; +import ArrowDropUpRoundedIcon from '@material-ui/icons/ArrowDropUpRounded'; + +import SectionHeader from 'js/shared-styles/sections/SectionHeader'; +import { DetailPageSection } from 'js/components/detailPage/style'; +import PublicationVignette from 'js/components/publications/PublicationVignette'; +import PrimaryColorAccordionSummary from 'js/shared-styles/accordions/PrimaryColorAccordionSummary'; +import { StyledAccordionDetails } from './style'; + +function PublicationsVisualizationSection({ vignette_data, uuid }) { + const [expandedIndex, setExpandedIndex] = useState(0); + + const handleChange = (i) => (event, isExpanded) => { + setExpandedIndex(isExpanded ? i : false); + }; + + return ( + + Visualizations + {Object.entries(vignette_data).map(([k, v], i) => { + return ( + + }> + {`Vignette ${i + 1}: ${v.name}`} + + + ; + + + ); + })} + + ); +} + +export default PublicationsVisualizationSection; diff --git a/context/app/static/js/components/publications/PublicationVisualizationsSection/index.js b/context/app/static/js/components/publications/PublicationVisualizationsSection/index.js new file mode 100644 index 0000000000..7d1b15d3db --- /dev/null +++ b/context/app/static/js/components/publications/PublicationVisualizationsSection/index.js @@ -0,0 +1,3 @@ +import PublicationsVisualizationSection from './PublicationsVisualizationSection'; + +export default PublicationsVisualizationSection; diff --git a/context/app/static/js/components/publications/PublicationVisualizationsSection/style.js b/context/app/static/js/components/publications/PublicationVisualizationsSection/style.js new file mode 100644 index 0000000000..3d63d34806 --- /dev/null +++ b/context/app/static/js/components/publications/PublicationVisualizationsSection/style.js @@ -0,0 +1,9 @@ +import styled from 'styled-components'; + +import AccordionDetails from '@material-ui/core/AccordionDetails'; + +const StyledAccordionDetails = styled(AccordionDetails)` + flex-direction: column; +`; + +export { StyledAccordionDetails }; diff --git a/context/app/static/js/pages/Publication/Publication.jsx b/context/app/static/js/pages/Publication/Publication.jsx index 5aa043182a..4a352d0ed5 100644 --- a/context/app/static/js/pages/Publication/Publication.jsx +++ b/context/app/static/js/pages/Publication/Publication.jsx @@ -6,13 +6,14 @@ import OutboundIconLink from 'js/shared-styles/Links/iconLinks/OutboundIconLink' import { getCombinedDatasetStatus, getSectionOrder } from 'js/components/detailPage/utils'; import ContributorsTable from 'js/components/detailPage/ContributorsTable/ContributorsTable'; import PublicationsDataSection from 'js/components/publications/PublicationsDataSection'; +import PublicationsVisualizationSection from 'js/components/publications/PublicationVisualizationsSection/'; import ProvSection from 'js/components/detailPage/provenance/ProvSection'; import DetailLayout from 'js/components/detailPage/DetailLayout'; import useEntityStore from 'js/stores/useEntityStore'; const entityStoreSelector = (state) => state.setAssayMetadata; -function Publication({ publication }) { +function Publication({ publication, vignette_data }) { const { title, uuid, @@ -35,7 +36,7 @@ function Publication({ publication }) { const setAssayMetadata = useEntityStore(entityStoreSelector); setAssayMetadata({ hubmap_id, entity_type, title, publication_venue }); - const sectionOrder = getSectionOrder(['summary', 'data', 'authors', 'provenance'], {}); + const sectionOrder = getSectionOrder(['summary', 'data', 'visualizations', 'authors', 'provenance'], {}); const combinedStatus = getCombinedDatasetStatus({ sub_status, status }); @@ -60,6 +61,7 @@ function Publication({ publication }) { {hasDOI && {doi_url}} + diff --git a/context/app/static/js/shared-styles/accordions/PrimaryColorAccordionSummary/index.js b/context/app/static/js/shared-styles/accordions/PrimaryColorAccordionSummary/index.js new file mode 100644 index 0000000000..0c2b52ad6a --- /dev/null +++ b/context/app/static/js/shared-styles/accordions/PrimaryColorAccordionSummary/index.js @@ -0,0 +1,3 @@ +import { PrimaryColorAccordionSummary } from './style'; + +export default PrimaryColorAccordionSummary; diff --git a/context/app/static/js/shared-styles/accordions/PrimaryColorAccordionSummary/style.js b/context/app/static/js/shared-styles/accordions/PrimaryColorAccordionSummary/style.js new file mode 100644 index 0000000000..5acf726310 --- /dev/null +++ b/context/app/static/js/shared-styles/accordions/PrimaryColorAccordionSummary/style.js @@ -0,0 +1,17 @@ +import styled, { css } from 'styled-components'; + +import AccordionSummary from '@material-ui/core/ExpansionPanelSummary'; + +const PrimaryColorAccordionSummary = styled(AccordionSummary)` + ${(props) => + props.$isExpanded && + css` + background-color: ${props.$isExpanded ? props.theme.palette.primary.main : '#E0E0E0'}; + + div > * { + color: ${props.$isExpanded ? '#fff' : props.theme.palette.text.primary}; + } + `} +`; + +export { PrimaryColorAccordionSummary }; diff --git a/context/package-lock.json b/context/package-lock.json index d722bb0eae..0294efda63 100644 --- a/context/package-lock.json +++ b/context/package-lock.json @@ -58,6 +58,7 @@ "react-hook-form": "^7.38.0", "react-intersection-observer": "^8.28.6", "react-joyride": "^2.2.1", + "react-markdown": "^8.0.6", "react-pdf": "^5.3.2", "react-spring": "^8.0.27", "react-vega": "^7.3.0", @@ -19107,6 +19108,14 @@ "resolved": "https://registry.npmjs.org/@types/d3-time-format/-/d3-time-format-2.3.1.tgz", "integrity": "sha512-fck0Z9RGfIQn3GJIEKVrp15h9m6Vlg0d5XXeiE/6+CQiBmMDZxfR21XtjEPuDeg7gC3bBM0SdieA5XF3GW1wKA==" }, + "node_modules/@types/debug": { + "version": "4.1.7", + "resolved": "https://registry.npmjs.org/@types/debug/-/debug-4.1.7.tgz", + "integrity": "sha512-9AonUzyTjXXhEOa0DnqpzZi6VHlqKMswga9EXjpXnnqxwLtdvPPtlO8evrI5D9S6asFRCQ6v+wpiUKbw+vKqyg==", + "dependencies": { + "@types/ms": "*" + } + }, "node_modules/@types/detect-browser": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/@types/detect-browser/-/detect-browser-4.0.0.tgz", @@ -19313,6 +19322,11 @@ "integrity": "sha512-fZQQafSREFyuZcdWFAExYjBiCL7AUCdgsk80iO0q4yihYYdcIiH28CcuPTGFgLOCC8RlW49GSQxdHwZP+I7CNg==", "dev": true }, + "node_modules/@types/ms": { + "version": "0.7.31", + "resolved": "https://registry.npmjs.org/@types/ms/-/ms-0.7.31.tgz", + "integrity": "sha512-iiUgKzV9AuaEkZqkOLDIvlQiL6ltuZd9tGcW3gwpnX8JbuiuhFlEGmmFXEXkN50Cvq7Os88IY2v0dkDqXYWVgA==" + }, "node_modules/@types/node": { "version": "14.18.36", "resolved": "https://registry.npmjs.org/@types/node/-/node-14.18.36.tgz", @@ -26446,6 +26460,27 @@ "@deck.gl/react": "8.8.27" } }, + "node_modules/decode-named-character-reference": { + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/decode-named-character-reference/-/decode-named-character-reference-1.0.2.tgz", + "integrity": "sha512-O8x12RzrUF8xyVcY0KJowWsmaJxQbmy0/EtnNtHRpsOcT7dFk5W598coHqBVpmWo1oQQfsCqfCmkZN5DJrZVdg==", + "dependencies": { + "character-entities": "^2.0.0" + }, + "funding": { + "type": "github", + "url": "https://github.com/sponsors/wooorm" + } + }, + "node_modules/decode-named-character-reference/node_modules/character-entities": { + "version": "2.0.2", + "resolved": "https://registry.npmjs.org/character-entities/-/character-entities-2.0.2.tgz", + "integrity": "sha512-shx7oQ0Awen/BRIdkjkvz54PnEEI/EjwXDSIZp86/KKdbafHh1Df/RYGBhn4hbe2+uKC9FnT5UCEdyPz3ai9hQ==", + "funding": { + "type": "github", + "url": "https://github.com/sponsors/wooorm" + } + }, "node_modules/decode-uri-component": { "version": "0.2.0", "resolved": "https://registry.npmjs.org/decode-uri-component/-/decode-uri-component-0.2.0.tgz", @@ -26807,6 +26842,14 @@ "node": ">=0.4.0" } }, + "node_modules/diff": { + "version": "5.1.0", + "resolved": "https://registry.npmjs.org/diff/-/diff-5.1.0.tgz", + "integrity": 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