Merging staging branch into prod branch

chanzuckerberg · Oct 10, 2024 · f52fce9 · f52fce9
2 parents cb38f31 + 956986b
commit f52fce9
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Showing 23 changed files with 189 additions and 94 deletions.
diff --git a/backend/curation/api/curation-api.yml b/backend/curation/api/curation-api.yml
@@ -762,7 +762,7 @@ components:
     batch_condition:
       description: |
         These keys define the batches that a normalization or integration algorithm should be aware of.
-        [batch condition schema](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#batch_condition)
+        [batch condition schema](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#batch_condition)
 
       type: array
       items:
@@ -774,7 +774,7 @@ components:
         Citation that includes downloadable permalink to h5ad artifact for this dataset, a permalink to collection it 
         belongs to in CZ CELLxGENE Discover, and--if applicable--the Publication DOI associated with the dataset.
         See details about the exact format in the 
-        [schema definition](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#citation)
+        [schema definition](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#citation)
       type: string
       nullable: true
     collection_list:
@@ -1027,7 +1027,7 @@ components:
           type: integer
         cell_type:
           description: |
-            [cell type label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#cell_type)
+            [cell type label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#cell_type)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1042,7 +1042,7 @@ components:
           $ref: "#/components/schemas/default_embedding"
         development_stage:
           description: |
-            [development stage label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#development_stage)
+            [development stage label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#development_stage)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1069,7 +1069,7 @@ components:
           type: number
         title:
           description: |
-            [title](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#title)
+            [title](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#title)
           nullable: true
           type: string
         organism:
@@ -1096,14 +1096,14 @@ components:
           type: string
         self_reported_ethnicity:
           description: |
-            [self reported ethnicity label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#self_reported_ethnicity)
+            [self reported ethnicity label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#self_reported_ethnicity)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
           type: array
         sex:
           description: |
-            [sex label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#sex)
+            [sex label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#sex)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1135,7 +1135,7 @@ components:
           type: integer
         cell_type:
           description: |
-            [cell type label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#cell_type)
+            [cell type label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#cell_type)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1158,7 +1158,7 @@ components:
           $ref: "#/components/schemas/dataset_version_id"
         development_stage:
           description: |
-            [development stage label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#development_stage)
+            [development stage label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#development_stage)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1177,7 +1177,7 @@ components:
           type: number
         title:
           description: |
-            [title](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#title)
+            [title](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#title)
           nullable: true
           type: string
         organism:
@@ -1205,14 +1205,14 @@ components:
           type: string
         self_reported_ethnicity:
           description: |
-            [self reported ethnicity label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#self_reported_ethnicity)
+            [self reported ethnicity label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#self_reported_ethnicity)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
           type: array
         sex:
           description: |
-            [sex label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#sex)
+            [sex label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#sex)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1246,7 +1246,7 @@ components:
           type: integer
         cell_type:
           description: |
-            [cell type label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#cell_type)
+            [cell type label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#cell_type)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1268,7 +1268,7 @@ components:
           $ref: "#/components/schemas/default_embedding"
         development_stage:
           description: |
-            [development stage label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#development_stage)
+            [development stage label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#development_stage)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1293,7 +1293,7 @@ components:
           type: number
         title:
           description: |
-            [title](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#title)
+            [title](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#title)
           nullable: true
           type: string
         organism:
@@ -1310,14 +1310,14 @@ components:
           type: string
         self_reported_ethnicity:
           description: |
-            [self reported ethnicity label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#self_reported_ethnicity)
+            [self reported ethnicity label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#self_reported_ethnicity)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
           type: array
         sex:
           description: |
-            [sex label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#sex)
+            [sex label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#sex)
           default: []
           items:
             $ref: "#/components/schemas/ontology_element"
@@ -1333,21 +1333,21 @@ components:
       type: object
     dataset_assay:
       description: |
-        [assay label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#assay)
+        [assay label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#assay)
       default: []
       items:
         $ref: "#/components/schemas/ontology_element"
       type: array
     dataset_disease:
       description: |
-        [disease label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#disease)
+        [disease label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#disease)
       default: []
       items:
         $ref: "#/components/schemas/ontology_element"
       type: array
     dataset_organism:
       description: |
-        [organism label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#organism)
+        [organism label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#organism)
       default: []
       items:
         $ref: "#/components/schemas/ontology_element"
@@ -1360,7 +1360,7 @@ components:
       type: string
     dataset_tissue:
       description: |
-        [tissue label](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#tissue)
+        [tissue label](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#tissue)
       default: []
       items:
         allOf:
@@ -1421,7 +1421,7 @@ components:
         CELLxGENE Discover runs a heuristic to detect the approximate distribution
         of the data in X so that it can accurately calculate statistical properties
         of the data. This field enables the curator to override this heuristic and
-        specify the data distribution explicitly. [x_approximate_distribution](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#x_approximate_distribution)
+        specify the data distribution explicitly. [x_approximate_distribution](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#x_approximate_distribution)
       enum:
         - COUNT
         - NORMAL
@@ -1482,7 +1482,7 @@ components:
       nullable: true
     is_primary_data:
       description: |
-        [is_primary_data](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#is_primary_data)
+        [is_primary_data](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#is_primary_data)
 
         Describes whether cellular observations for this Dataset are all
         canonical (True), all non-canonical (False), or contain a mixture (True, False).
@@ -1603,21 +1603,21 @@ components:
       properties:
         is_single:
           description: |
-            [is_single](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#is_single)
+            [is_single](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#is_single)
 
             Flag indicating if a spatial dataset represents one Space Ranger output for a single tissue section or the
             output for a single array on a puck.
           type: boolean
         has_fullres:
           description: |
-            [has_fullres](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#spatiallibrary_idimagesfullres)
+            [has_fullres](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#spatiallibrary_idimagesfullres)
 
             Flag indicating if a spatial dataset's metadata includes a numpy.ndarray representing the full resolution 
             image.
           type: boolean
     suspension_type:
       description: |
-        [suspension_type](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#suspension_type)
+        [suspension_type](https://chanzuckerberg.github.io/single-cell-curation/latest-schema.html#suspension_type)
 
         List of unique suspension types represented in the dataset, corresponding to dataset's assay(s).
         Possible item values are 'nucleus', 'cell', and/or 'na'.

diff --git a/backend/layers/processing/publish_revisions.py b/backend/layers/processing/publish_revisions.py
@@ -14,6 +14,7 @@
 import os
 from typing import Dict, List
 
+from backend.common.providers.crossref_provider import CrossrefProvider
 from backend.layers.business.business import BusinessLogic
 from backend.layers.business.entities import CollectionQueryFilter
 from backend.layers.common.entities import (
@@ -100,7 +101,7 @@ def run(self):
     business_logic = BusinessLogic(
         DatabaseProvider(),
         None,
-        None,
+        CrossrefProvider(),
         None,
         S3Provider(),
         UriProvider(),

diff --git a/...sts/features/cellGuide/cellGuide.test.ts-snapshots/landing-seoMetaTags-chromium-linux.txt b/...sts/features/cellGuide/cellGuide.test.ts-snapshots/landing-seoMetaTags-chromium-linux.txt
@@ -1 +1 @@
-["<meta charset=\"utf-8\">","<meta name=\"description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta name=\"viewport\" content=\"width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">"]
+["<meta charset=\"utf-8\">","<meta id=\"newsletter-signup-meta\" name=\"viewport\" content=\"width=device-width, initial-scale=1\">","<meta name=\"description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">"]
diff --git a/..._/tests/features/cellGuide/cellGuide.test.ts-snapshots/landing-seoMetaTags-edge-linux.txt b/..._/tests/features/cellGuide/cellGuide.test.ts-snapshots/landing-seoMetaTags-edge-linux.txt
@@ -1 +1 @@
-["<meta charset=\"utf-8\">","<meta name=\"description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta name=\"viewport\" content=\"width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">"]
+["<meta charset=\"utf-8\">","<meta id=\"newsletter-signup-meta\" name=\"viewport\" content=\"width=device-width, initial-scale=1\">","<meta name=\"description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">"]
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		["<meta charset=\"utf-8\">","<meta name=\"description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta name=\"viewport\" content=\"width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">"]
		["<meta charset=\"utf-8\">","<meta id=\"newsletter-signup-meta\" name=\"viewport\" content=\"width=device-width, initial-scale=1\">","<meta name=\"description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Explore single-cell transcriptomics data in CellGuide, a comprehensive resource that empowers researchers with deep insights into the intricacies of cell types\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"CellGuide Cell Types and Cell Tissues - CZ CELLxGENE\">"]