@abi-software/scaffoldvuer 1.3.3-beta.1 → 1.4.0-beta.0

package/src/services/scicrunchQueries.js

@@ -0,0 +1,280 @@
+const getOrganCuries = async (sparcApi, filetypes = [], species = []) => {
+  let params = new URLSearchParams();
+  filetypes.forEach((type) => {
+    params.append("filetypes", type);
+  });
+  species.forEach((name) => {
+    params.append("species", name);
+  });
+
+  const response = await fetch(`${sparcApi}/get-organ-curies/?${params}`);
+  const data = await response.json();
+
+  let organCuries = [];
+  data.uberon.array.forEach((pair) => {
+    const organCurie = {
+      id: pair.id.toUpperCase(),
+      name: pair.name,
+    };
+    organCuries.push(organCurie);
+  });
+
+  return organCuries;
+};
+
+const getFilesInfoForCuries = async (sparcApi, organCuries, filetypes) => {
+  const response = await fetch(`${sparcApi}/get-files-info-for-curies`, {
+    method: "POST",
+    body: JSON.stringify({
+      curies: organCuries.map((item) => item.id),
+      filetypes: filetypes,
+    }),
+    headers: {
+      "Content-Type": "application/json",
+    },
+  });
+  const data = await response.json();
+
+  return data;
+};
+
+const getFileNameFromPath = (filePath) => {
+  return filePath.substring(filePath.lastIndexOf("/") + 1);
+};
+
+const getBiolucidaThumbnailURL = (sparcApi, biolucidaId) => {
+  return `${sparcApi}/thumbnail/${biolucidaId}`;
+};
+
+const getBiolucidaThumbnails = async (sparcApi, organCuries, type) => {
+  try {
+    const data = await getFilesInfoForCuries(sparcApi, organCuries, [
+      "biolucida-2d",
+      "biolucida-3d",
+    ]);
+
+    if (data["files_info"]) {
+      let images = {};
+      for (const [key, value] of Object.entries(data["files_info"])) {
+        if (value.length > 0) {
+          let list = [];
+          value.forEach((entry) => {
+            const thumbnailURL = getBiolucidaThumbnailURL(
+              sparcApi,
+              entry.biolucida_id
+            );
+            if (entry.biolucida_id) {
+              let image = {
+                thumbnail: thumbnailURL,
+                resource: entry.file_path,
+                id: entry.id,
+                title: getFileNameFromPath(entry.file_path),
+                type: type,
+                link: thumbnailURL,
+                mimetype: entry.mimetype,
+                species: entry.species,
+                version: entry.version,
+              };
+              list.push(image);
+            }
+          });
+          images[key] = list;
+        }
+      }
+      return images;
+    }
+  } catch (error) {
+    console.error("Error:", error);
+  }
+  return {};
+};
+
+const getSegmentationThumbnailURL = (
+  sparcApi,
+  datasetId,
+  datasetVersion,
+  filePath
+) => {
+  return `${sparcApi}/thumbnail/neurolucida?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}`;
+};
+
+const getSegmentationThumbnails = async (sparcApi, organCuries, type) => {
+  try {
+    const data = await getFilesInfoForCuries(sparcApi, organCuries, [
+      "mbf-segmentation",
+    ]);
+
+    if (data["files_info"]) {
+      let images = {};
+      for (const [key, value] of Object.entries(data["files_info"])) {
+        if (value.length > 0) {
+          let list = [];
+          value.forEach((entry) => {
+            const thumbnailURL = getSegmentationThumbnailURL(
+              sparcApi,
+              entry.id,
+              entry.version,
+              entry.file_path
+            );
+            let image = {
+              thumbnail: thumbnailURL,
+              resource: entry.file_path,
+              id: entry.id,
+              title: getFileNameFromPath(entry.file_path),
+              type: type,
+              link: thumbnailURL,
+              mimetype: entry.mimetype,
+              species: entry.species,
+              version: entry.version,
+            };
+            list.push(image);
+          });
+          images[key] = list;
+        }
+      }
+      return images;
+    }
+  } catch (error) {
+    console.error("Error:", error);
+  }
+  return {};
+};
+
+const findEntryWithPathInArray = (entry, list, type) => {
+  if (entry && list) {
+    for (let i = 0; i < entry.isSourceOf.length; i++) {
+      for (let l = 0; l < list.length; l++) {
+        const item = list[l];
+        if (
+          entry.id === item.id &&
+          (!type || item.type === type) &&
+          entry.isSourceOf[i] === item.file_path
+        ) {
+          return item;
+        }
+      }
+    }
+  }
+  return undefined;
+};
+
+const getScaffoldThumbnailURL = (sparcApi, entry, list) => {
+  const viewEntry = findEntryWithPathInArray(
+    entry,
+    list,
+    "abi-scaffold-view-file"
+  );
+  const thumbnailEntry = findEntryWithPathInArray(
+    viewEntry,
+    list,
+    "abi-thumbnail"
+  );
+  if (thumbnailEntry) {
+    return `${sparcApi}/s3-resource/${thumbnailEntry.id}/files/${thumbnailEntry.file_path}`;
+  }
+  return undefined;
+};
+
+const getScaffoldThumbnails = async (sparcApi, organCuries, type) => {
+  try {
+    const data = await getFilesInfoForCuries(sparcApi, organCuries, [
+      "abi-thumbnail",
+      "abi-scaffold-metadata-file",
+      "abi-scaffold-view-file",
+    ]);
+
+    if (data["files_info"]) {
+      let images = {};
+      for (const [key, value] of Object.entries(data["files_info"])) {
+        if (value.length > 0) {
+          let list = [];
+          value.forEach((entry) => {
+            if (entry.type === "abi-scaffold-metadata-file") {
+              const thumbnailURL = getScaffoldThumbnailURL(
+                sparcApi,
+                entry,
+                value
+              );
+              if (thumbnailURL) {
+                let image = {
+                  thumbnail: thumbnailURL,
+                  resource: entry.file_path,
+                  id: entry.id,
+                  title: getFileNameFromPath(entry.file_path),
+                  type: type,
+                  link: thumbnailURL,
+                  species: entry.species,
+                  version: entry.version,
+                };
+                list.push(image);
+              }
+            }
+          });
+          images[key] = list;
+        }
+      }
+      return images;
+    }
+  } catch (error) {
+    console.error("Error:", error);
+  }
+  return {};
+};
+
+const getPlotThumbnailURL = (sparcApi, entry) => {
+  //None of the thumbnail for plot is properly annotated.
+  //We will use the first in is source of for testing.
+  if (entry.isSourceOf.length > 0) {
+    return `${sparcApi}/s3-resource/${entry.id}/files/${entry.isSourceOf[0]}`;
+  }
+  return undefined;
+};
+
+const getPlotThumbnails = async (sparcApi, organCuries, type) => {
+  try {
+    const data = await getFilesInfoForCuries(sparcApi, organCuries, [
+      "abi-plot",
+      "abi-thumbnail",
+    ]);
+
+    if (data["files_info"]) {
+      let images = {};
+      for (const [key, value] of Object.entries(data["files_info"])) {
+        if (value.length > 0) {
+          let list = [];
+          value.forEach((entry) => {
+            if (entry.type === "abi-plot") {
+              const thumbnailURL = getPlotThumbnailURL(sparcApi, entry);
+              if (thumbnailURL) {
+                let image = {
+                  thumbnail: thumbnailURL,
+                  resource: entry.file_path,
+                  id: entry.id,
+                  title: getFileNameFromPath(entry.file_path),
+                  type: type,
+                  link: thumbnailURL,
+                  species: entry.species,
+                  version: entry.version,
+                };
+                list.push(image);
+              }
+            }
+          });
+          images[key] = list;
+        }
+      }
+      return images;
+    }
+  } catch (error) {
+    console.error("Error:", error);
+  }
+  return {};
+};
+
+export {
+  getOrganCuries,
+  getBiolucidaThumbnails,
+  getSegmentationThumbnails,
+  getScaffoldThumbnails,
+  getPlotThumbnails,
+};

package/src/stores/settings.js

@@ -0,0 +1,46 @@
+import { defineStore } from "pinia";
+
+/* eslint-disable no-alert, no-console */
+
+export const useSettingsStore = defineStore("settings", {
+  state: () => {
+    return {
+      organCuries: [],
+      imageTypes: [],
+      imageThumbnails: {},
+    };
+  },
+  getters: {
+    imageTypeCached: (state) => (imageType) => {
+      return state.imageTypes.includes(imageType);
+    },
+    getImageThumbnails:
+      (state) =>
+        (imageType, uberonIds = undefined) => {
+          if (uberonIds) {
+            let thumbnails = {};
+            Object.entries(state.imageThumbnails).forEach(([key, value]) => {
+              if (uberonIds.includes(key)) {
+                thumbnails[key] = value.filter((item) => item.type === imageType);
+              }
+            });
+            return thumbnails;
+          }
+          return state.imageThumbnails;
+        },
+  },
+  actions: {
+    updateOrganCuries(organCuries) {
+      this.organCuries = organCuries;
+    },
+    updateImageThumbnails(imageType, imageThumbnails) {
+      this.imageTypes.push(imageType);
+      Object.keys(imageThumbnails).forEach((key) => {
+        if (!(key in this.imageThumbnails)) {
+          this.imageThumbnails[key] = [];
+        }
+        this.imageThumbnails[key].push(...imageThumbnails[key]);
+      });
+    },
+  },
+});