chore(openchallenges): 2023-12-13 OC DB update (Sage-Bionetworks#2410)

* add new schemas for Doi, Url, Dates * indicate uniqueness for slugs/logins * add default value for counts * remove unneeded schemas * update API models and specs * add nullable properties * update table specifications * update list of required properties * remove depcrated org properties * update organizations dump file * challenge.description should not be null * remove deprecated challenge properties * update dump file; update mock objects; update TS scripts * update dump files using latest data * add regexp constraint * update java files * add new challenges * add organizations * update contribution roles * fix platforms * one last dump update * remove extra files * Update DateTime API schemas --------- Co-authored-by: Rongrong Chai <[email protected]> Co-authored-by: Thomas Schaffter <[email protected]>
mdsage1 · Dec 15, 2023 · 8df5976 · 8df5976
1 parent 39740de
commit 8df5976
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Showing 22 changed files with 191 additions and 149 deletions.
diff --git a/...ain/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeDto.java b/...ain/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeDto.java
@@ -480,7 +480,7 @@ public ChallengeDto createdAt(OffsetDateTime createdAt) {
   }
 
   /**
-   * Datetime when metadata was added to the OC database.
+   * Datetime when the object was added to the database.
    *
    * @return createdAt
    */
@@ -489,7 +489,7 @@ public ChallengeDto createdAt(OffsetDateTime createdAt) {
   @Schema(
       name = "createdAt",
       example = "2022-07-04T22:19:11Z",
-      description = "Datetime when metadata was added to the OC database.",
+      description = "Datetime when the object was added to the database.",
       required = true)
   public OffsetDateTime getCreatedAt() {
     return createdAt;
@@ -505,7 +505,7 @@ public ChallengeDto updatedAt(OffsetDateTime updatedAt) {
   }
 
   /**
-   * Datetime when metadata was last modified in the OC database.
+   * Datetime when the object was last modified in the database.
    *
    * @return updatedAt
    */
@@ -514,7 +514,7 @@ public ChallengeDto updatedAt(OffsetDateTime updatedAt) {
   @Schema(
       name = "updatedAt",
       example = "2022-07-04T22:19:11Z",
-      description = "Datetime when metadata was last modified in the OC database.",
+      description = "Datetime when the object was last modified in the database.",
       required = true)
   public OffsetDateTime getUpdatedAt() {
     return updatedAt;

diff --git a/apps/openchallenges/challenge-service/src/main/resources/db/challenges.csv b/apps/openchallenges/challenge-service/src/main/resources/db/challenges.csv
diff --git a/apps/openchallenges/challenge-service/src/main/resources/db/contribution_roles.csv b/apps/openchallenges/challenge-service/src/main/resources/db/contribution_roles.csv
@@ -1117,3 +1117,13 @@
 "1116","476","429","sponsor"
 "1117","476","339","sponsor"
 "1118","476","430","sponsor"
+"1119","477","431","challenge_organizer"
+"1120","478","432","challenge_organizer"
+"1121","480","434","challenge_organizer"
+"1122","480","435","challenge_organizer"
+"1123","480","436","challenge_organizer"
+"1124","480","437","challenge_organizer"
+"1125","480","411","challenge_organizer"
+"1126","480","438","challenge_organizer"
+"1127","481","439","challenge_organizer"
+"1128","481","439","sponsor"
diff --git a/apps/openchallenges/challenge-service/src/main/resources/db/incentives.csv b/apps/openchallenges/challenge-service/src/main/resources/db/incentives.csv
@@ -607,3 +607,6 @@
 "606","publication","473","2023-12-06 08:35:31"
 "607","monetary","474","2023-12-06 08:45:12"
 "608","monetary","476","2023-12-06 08:54:24"
+"609","monetary","477","2023-12-12 18:31:00"
+"610","other","480","2023-12-12 22:42:59"
+"611","other","481","2023-12-12 23:22:24"
diff --git a/apps/openchallenges/challenge-service/src/main/resources/db/platforms.csv b/apps/openchallenges/challenge-service/src/main/resources/db/platforms.csv
@@ -7,8 +7,8 @@
 "9","codalab","CodaLab","logo/codalab.jpg","https://codalab.lisn.upsaclay.fr/","2023-08-09 23:01:32","2023-10-19 21:50:30"
 "10","codabench","CodaBench","logo/codalab.jpg","https://www.codabench.org/","2023-08-09 23:01:32","2023-10-19 21:50:30"
 "13","eterna","Eterna","logo/eterna.svg","https://eternagame.org/","2023-08-09 23:01:32","2023-10-19 21:50:33"
-"14","nightingale-os","Nightingale OS","logo/nightingale-os.jpeg","https://app.nightingalescience.org/","2023-08-22 15:58:49","2023-12-06 01:10:23"
-"15","evalai","EvalAI","logo/evalai.png","https://eval.ai/","2023-09-15 16:00:34","2023-12-06 01:09:55"
-"16","cache","CACHE","logo/cache.png","https://cache-challenge.org/","2023-10-16 18:43:36","2023-12-06 01:09:56"
-"17","cameo","CAMEO","logo/cameo.png","https://www.cameo3d.org","2023-11-13 22:47:03","2023-12-06 01:09:56"
-"18","drivendata","DrivenData","logo/drivendata.jpg","https://www.drivendata.org/","2023-11-16 21:57:43","2023-12-06 01:09:57"
+"15","nightingale-os","Nightingale OS","logo/nightingale-os.jpeg","https://app.nightingalescience.org/contests","2023-08-22 15:58:49","2023-12-12 19:05:13"
+"16","evalai","EvalAI","logo/evalai.png","https://eval.ai/","2023-09-15 16:00:34","2023-12-12 18:18:37"
+"17","cache","CACHE","logo/cache.png","https://cache-challenge.org/","2023-10-16 18:43:36","2023-12-06 01:09:56"
+"18","cameo","CAMEO","logo/cameo.png","https://www.cameo3d.org","2023-11-13 22:47:03","2023-12-12 18:18:38"
+"19","drivendata","DrivenData","logo/drivendata.jpg","https://www.drivendata.org/","2023-11-16 21:57:43","2023-12-12 18:18:39"
diff --git a/apps/openchallenges/challenge-service/src/main/resources/db/submission_types.csv b/apps/openchallenges/challenge-service/src/main/resources/db/submission_types.csv
@@ -467,3 +467,8 @@
 "466","prediction_file","474","2023-12-06 08:45:12"
 "467","prediction_file","475","2023-12-06 08:52:21"
 "468","prediction_file","476","2023-12-06 08:54:24"
+"469","prediction_file","477","2023-12-12 18:31:00"
+"470","prediction_file","478","2023-12-12 21:54:25"
+"471","prediction_file","479","2023-12-12 22:41:48"
+"472","prediction_file","480","2023-12-12 22:42:59"
+"473","container_image","481","2023-12-12 23:22:24"
diff --git a/apps/openchallenges/challenge-service/src/main/resources/openapi.yaml b/apps/openchallenges/challenge-service/src/main/resources/openapi.yaml
@@ -679,13 +679,13 @@ components:
       format: date
       nullable: true
       type: string
-    CreatedDatetime:
-      description: Datetime when metadata was added to the OC database.
+    CreatedDateTime:
+      description: Datetime when the object was added to the database.
       example: 2022-07-04T22:19:11Z
       format: date-time
       type: string
-    ModifiedDatetime:
-      description: Datetime when metadata was last modified in the OC database.
+    UpdatedDateTime:
+      description: Datetime when the object was last modified in the database.
       example: 2022-07-04T22:19:11Z
       format: date-time
       type: string
@@ -810,12 +810,12 @@ components:
           minimum: 0
           type: integer
         createdAt:
-          description: Datetime when metadata was added to the OC database.
+          description: Datetime when the object was added to the database.
           example: 2022-07-04T22:19:11Z
           format: date-time
           type: string
         updatedAt:
-          description: Datetime when metadata was last modified in the OC database.
+          description: Datetime when the object was last modified in the database.
           example: 2022-07-04T22:19:11Z
           format: date-time
           type: string

diff --git a/...va/org/sagebionetworks/openchallenges/organization/service/model/dto/OrganizationDto.java b/...va/org/sagebionetworks/openchallenges/organization/service/model/dto/OrganizationDto.java
@@ -220,7 +220,7 @@ public OrganizationDto createdAt(OffsetDateTime createdAt) {
   }
 
   /**
-   * Datetime when metadata was added to the OC database.
+   * Datetime when the object was added to the database.
    *
    * @return createdAt
    */
@@ -229,7 +229,7 @@ public OrganizationDto createdAt(OffsetDateTime createdAt) {
   @Schema(
       name = "createdAt",
       example = "2022-07-04T22:19:11Z",
-      description = "Datetime when metadata was added to the OC database.",
+      description = "Datetime when the object was added to the database.",
       required = true)
   public OffsetDateTime getCreatedAt() {
     return createdAt;
@@ -245,7 +245,7 @@ public OrganizationDto updatedAt(OffsetDateTime updatedAt) {
   }
 
   /**
-   * Datetime when metadata was last modified in the OC database.
+   * Datetime when the object was last modified in the database.
    *
    * @return updatedAt
    */
@@ -254,7 +254,7 @@ public OrganizationDto updatedAt(OffsetDateTime updatedAt) {
   @Schema(
       name = "updatedAt",
       example = "2022-07-04T22:19:11Z",
-      description = "Datetime when metadata was last modified in the OC database.",
+      description = "Datetime when the object was last modified in the database.",
       required = true)
   public OffsetDateTime getUpdatedAt() {
     return updatedAt;

diff --git a/apps/openchallenges/organization-service/src/main/resources/db/contribution_roles.csv b/apps/openchallenges/organization-service/src/main/resources/db/contribution_roles.csv
@@ -1117,3 +1117,13 @@
 "1116","476","429","sponsor"
 "1117","476","339","sponsor"
 "1118","476","430","sponsor"
+"1119","477","431","challenge_organizer"
+"1120","478","432","challenge_organizer"
+"1121","480","434","challenge_organizer"
+"1122","480","435","challenge_organizer"
+"1123","480","436","challenge_organizer"
+"1124","480","437","challenge_organizer"
+"1125","480","411","challenge_organizer"
+"1126","480","438","challenge_organizer"
+"1127","481","439","challenge_organizer"
+"1128","481","439","sponsor"
diff --git a/apps/openchallenges/organization-service/src/main/resources/db/organizations.csv b/apps/openchallenges/organization-service/src/main/resources/db/organizations.csv
@@ -387,6 +387,7 @@
 "406","Biozentrum of the University of Basel","biozentrum","logo/biozentrum.jpg","http://www.biozentrum.unibas.ch/","The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. The primary focus is basic molecular and biomedical research and teaching.  It’s international and interdisciplinary research groups explore how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birth place of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.","3","2023-11-13 22:24:00","2023-11-21 00:17:11",""
 "407","National Institute of Aging","nia","logo/nih.png","https://www.nia.nih.gov/","NIA leads a broad scientific effort to understand the nature of aging and to extend the healthy, active years of life. NIA is the primary federal agency supporting and conducting Alzheimer's disease research.","3","2023-11-16 22:06:31","2023-11-21 00:13:03","NIA"
 "408","National Aeronautics and Space Administration","nasa","logo/nasa.jpg","https://www.nasa.gov/","NASA explores the unknown in air and space, innovates for the benefit of humanity, and inspires the world through discovery.","1","2023-11-16 22:08:34","2023-11-21 00:17:31","NASA"
+"411","DeepMind Technologies Limited","deepmind","logo/deepmind.png","","This organization may no longer exist, has rebranded, or has been merged under another organization.","1","2023-11-20 18:58:02","2023-11-21 00:19:11",""
 "414","CDC National Center for Injury Prevention and Control","ncipc","logo/cdc-ncipc.jpg","https://www.cdc.gov/injury/","For 30 years, CDC’s National Center for Injury Prevention and Control (Injury Center) has been a leader in protecting Americans from injury and violence so that individuals, families, and communities can be safe, healthy, and thriving. We work proactively with our partners to track trends, conduct research, raise awareness, and implement prevention programs.","1","2023-12-06 07:22:56","2023-12-06 08:50:23","NCIPC"
 "415","Centers for Disease Control and Prevention","cdc","logo/cdc.jpg","https://www.cdc.gov/injury/","CDC is the nation’s leading science-based, data-driven, service organization that protects the public’s health. For more than 70 years, we’ve put science into action to help children stay healthy so they can grow and learn; to help families, businesses, and communities fight disease and stay strong; and to protect the public’s health.","2","2023-12-06 07:26:44","2023-12-06 08:15:44","CDC"
 "416","United States Consumer Product Safety Commission","cpsc","logo/cpsc.jpg","https://www.cpsc.gov/","CPSC works to save lives and keep families safe by reducing the unreasonable risk of injuries and deaths associated with consumer products and fulfilling its vision to be the recognized global leader in consumer product safety. CPSC does this by: 1) Issuing and enforcing mandatory standards or banning consumer products if no feasible standard would adequately protect the public; 2) Obtaining the recall of products and arranging for a repair, replacement or refund for recalled products; 3) Researching potential product hazards; 4) Developing voluntary standards with standards organizations, manufacturers and businesses; 5) Informing and educating consumers directly and through traditional, online, and social media and by working with foreign, state and local governments and private organizations; and 6) Educating manufacturers worldwide about our regulations, supply chain integrity and development of safe products.","1","2023-12-06 07:29:21","2023-12-06 07:33:21","CPSC"
@@ -404,3 +405,11 @@
 "428","CDC National Survey of Family Growth","nsfg","logo/cdc-nchs.jpg","https://www.cdc.gov/nchs/nsfg/index.htm?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fnchs%2Fnsfg.htm","The National Survey of Family Growth (NSFG) gathers information on pregnancy and births, marriage and cohabitation, infertility, use of contraception, family life, and general and reproductive health. The survey results are used by the U.S. Department of Health and Human Services and others to plan health services and health education programs, and to do statistical studies of families, fertility, and health.","1","2023-12-06 08:49:39","2023-12-06 08:51:01","NSFG"
 "429","altLabs","altlabs","logo/altlabs.jpg","https://altlabs.tech/","altLabs is a research non-profit institution focused on the development and advancement of safety-promoting technologies. We collaborate with world-class researchers across diverse scientific fields to prioritize thoughtful solutions with long-term positive impact on a global scale. In a nutshell, we’re working to make the world a safer place.","1","2023-12-06 08:56:57","2023-12-06 08:59:34",""
 "430","iGEM","igem","logo/igem.jpg","https://igem.org/","iGEM educates the workforce and the leaders of the Synthetic Biology industry. The iGEM Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open, collaborative, and cooperative community.","1","2023-12-06 08:58:34","2023-12-06 08:59:36",""
+"431","Systems Neural Engineering Lab","snel","logo/snel.png","https://snel.ai/","Our lab at Emory University and the Georgia Institute of Technology sits at the intersection of systems neuroscience, neural engineering, and artificial intelligence, with dual goals of better understanding the nervous system and developing high-performing and robust brain-computer interfaces for people with paralysis.","1","2023-12-12 18:54:15","2023-12-12 18:56:43","SNEL"
+"432","Neural Prosthetics Translational Lab","nptl","logo/stanford.jpg","https://nptl.stanford.edu/","We conduct neuroscience, neuroengineering and translational research to better understand how the brain controls movement and to then design medical systems to assist people with paralysis. These medical systems are referred to as brain-computer interfaces (BCIs), brain-machine interfaces (BMIs) and intra-cortical neural prostheses. We conduct this research in our Neural Prosthetics Translational Lab (NPTL) which focuses on fundamental human neuroscience and translational research with people with paralysis. Prof. Jaimie Henderson and Prof. Krishna Shenoy are the PIs of the NPTL.","1","2023-12-12 21:54:51","2023-12-12 21:56:13","NPTL"
+"434","Georgia Institute of Technology","ga-tech","logo/gatech.jpg","https://www.gatech.edu/","The Georgia Institute of Technology is a leading research university committed to improving the human condition through advanced science and technology.","1","2023-12-12 23:01:56","2023-12-12 23:08:44",""
+"435","Samsung Advanced Institute of Technology AI Lab Montreal","sail-montreal","logo/samsung.jpg","https://www.sait.samsung.co.kr/saithome/main/main.do","SAIL Montreal (SAIT AI Lab Montreal) is a recently established academic-style research lab (in close collaboration with Mila) whose mission is to advance our fundamental understanding of deep learning technology and its applications. Headed by Simon Lacoste-Julien, professor in computer science at Université de Montréal and co-founding member of Mila, SAIL is located in Mila's corporate space at the heart of the Montreal AI ecosystem nearby Element AI, Borealis AI, FAIR, Microsoft Research and others where an open collaborative environment is encouraged.","1","2023-12-12 23:06:45","2023-12-12 23:11:43",""
+"436","Facebook AI Research","meta-ai","logo/meta.png","https://ai.meta.com/research/","(Renamed from Facebook AI Research). The Fundamental AI Research (FAIR) team at Meta seeks to further our fundamental understanding in both new and existing domains, covering the full spectrum of topics related to AI, with the mission of advancing the state-of-the-art of AI through open research for the benefit of all.  AI at Meta engages in cutting-edge applied research that can improve and power new product experiences at huge scale for our community. Building on AI at Meta's key principles of openness, collaboration, excellence, and scale, we make big, bold research investments focused on pushing the boundaries of AI to create a more connected world.","1","2023-12-12 23:11:50","2023-12-12 23:16:14",""
+"437","Université de Montréal","udem","logo/udem.png","https://www.umontreal.ca/en/","With its roots in Montreal and its eyes on the international horizon, the Université de Montréal is one of the world’s leading research universities.","1","2023-12-12 23:16:51","2023-12-12 23:18:13","UdeM"
+"438","Mila","mila","logo/mila.jpg","https://mila.quebec/en/","Located in the heart of Quebec’s AI ecosystem, Mila is a community of more than 1,200 researchers specializing in machine learning and dedicated to scientific excellence and innovation.","1","2023-12-12 23:19:27","2023-12-12 23:20:00",""
+"439","NeuroTechX","ntx","logo/ntx.jpg","https://neurotechx.com/","NeuroTechX is a non-profit organization whose mission is to facilitate the advancement of neurotechnology by providing key resources and learning opportunities, and by being leaders in local and worldwide technological initiatives. Our 3 pillars are “Community”, “Education”, and “Professional Development”.","1","2023-12-12 23:27:39","2023-12-12 23:28:16","NTX"
diff --git a/apps/openchallenges/organization-service/src/main/resources/openapi.yaml b/apps/openchallenges/organization-service/src/main/resources/openapi.yaml
@@ -271,13 +271,13 @@ components:
       maxLength: 500
       nullable: true
       type: string
-    CreatedDatetime:
-      description: Datetime when metadata was added to the OC database.
+    CreatedDateTime:
+      description: Datetime when the object was added to the database.
       example: 2022-07-04T22:19:11Z
       format: date-time
       type: string
-    ModifiedDatetime:
-      description: Datetime when metadata was last modified in the OC database.
+    UpdatedDateTime:
+      description: Datetime when the object was last modified in the database.
       example: 2022-07-04T22:19:11Z
       format: date-time
       type: string
@@ -333,12 +333,12 @@ components:
           minimum: 0
           type: integer
         createdAt:
-          description: Datetime when metadata was added to the OC database.
+          description: Datetime when the object was added to the database.
           example: 2022-07-04T22:19:11Z
           format: date-time
           type: string
         updatedAt:
-          description: Datetime when metadata was last modified in the OC database.
+          description: Datetime when the object was last modified in the database.
           example: 2022-07-04T22:19:11Z
           format: date-time
           type: string

diff --git a/libs/openchallenges/api-client-angular/src/lib/model/challenge.ts b/libs/openchallenges/api-client-angular/src/lib/model/challenge.ts
@@ -70,11 +70,11 @@ export interface Challenge {
      */
     starredCount: number;
     /**
-     * Datetime when metadata was added to the OC database.
+     * Datetime when the object was added to the database.
      */
     createdAt: string;
     /**
-     * Datetime when metadata was last modified in the OC database.
+     * Datetime when the object was last modified in the database.
      */
     updatedAt: string;
 }

diff --git a/libs/openchallenges/api-client-angular/src/lib/model/organization.ts b/libs/openchallenges/api-client-angular/src/lib/model/organization.ts
@@ -41,11 +41,11 @@ export interface Organization {
      */
     challengeCount?: number;
     /**
-     * Datetime when metadata was added to the OC database.
+     * Datetime when the object was added to the database.
      */
     createdAt: string;
     /**
-     * Datetime when metadata was last modified in the OC database.
+     * Datetime when the object was last modified in the database.
      */
     updatedAt: string;
     /**

diff --git a/libs/openchallenges/api-description/build/challenge.openapi.yaml b/libs/openchallenges/api-description/build/challenge.openapi.yaml
@@ -460,13 +460,13 @@ components:
       format: date
       nullable: true
       example: '2017-07-21'
-    CreatedDatetime:
-      description: Datetime when metadata was added to the OC database.
+    CreatedDateTime:
+      description: Datetime when the object was added to the database.
       type: string
       format: date-time
       example: '2022-07-04T22:19:11Z'
-    ModifiedDatetime:
-      description: Datetime when metadata was last modified in the OC database.
+    UpdatedDateTime:
+      description: Datetime when the object was last modified in the database.
       type: string
       format: date-time
       example: '2022-07-04T22:19:11Z'
@@ -517,9 +517,9 @@ components:
           minimum: 0
           example: 100
         createdAt:
-          $ref: '#/components/schemas/CreatedDatetime'
+          $ref: '#/components/schemas/CreatedDateTime'
         updatedAt:
-          $ref: '#/components/schemas/ModifiedDatetime'
+          $ref: '#/components/schemas/UpdatedDateTime'
       required:
         - id
         - slug