Merge branch 'fix-importer-exporter-issues' into fix-duo-codes

elixir-luxembourg · Oct 24, 2023 · 9e67566 · 9e67566
2 parents 1292478 + 42a50d7
commit 9e67566
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diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -3,6 +3,8 @@ name: Docker Image CI
 on:
   push:
     branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
 
 env:
   REGISTRY: ghcr.io

diff --git a/Dockerfile b/Dockerfile
@@ -2,8 +2,25 @@ FROM python:3.9.6-slim
 ENV PYTHONUNBUFFERED 1
 RUN mkdir -p /code/log /static \
     && apt-get update \
-    && apt-get install -yq libsasl2-dev python-dev libldap2-dev git libssl-dev build-essential \
+    && apt-get install -yq libsasl2-dev python-dev libldap2-dev git libssl-dev build-essential wget \
     && rm -rf /var/lib/apt/lists/*
+
+# Install node 
+RUN apt-get update \
+    && apt-get install -y ca-certificates curl gnupg
+RUN mkdir -p /etc/apt/keyrings
+RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg
+RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_18.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list
+RUN apt-get update \
+    && apt-get install -y nodejs
+
+COPY web/static /static
+
+# Install npm dependencies
+RUN cd /static/vendor \
+    && npm ci \
+    && npm run-script build
+
 WORKDIR /code
 
 # Copy the list of Python dependencies

diff --git a/README.md b/README.md
@@ -58,7 +58,6 @@ You are encouraged to try Daisy for yourself using our [DEMO deployment](https:/
 1. Create initial data in the database
 
     ```bash
-    docker-compose exec web bash -c "apt update && apt install -y wget"
     docker-compose exec web bash -c "cd core/fixtures/ && wget https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/edda.json && wget https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hpo.json && wget https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hdo.json && wget https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hgnc.json"
     docker-compose exec web python manage.py load_initial_data
     ```

diff --git a/core/fixtures/json_schemas/elu-core.json b/core/fixtures/json_schemas/elu-core.json
@@ -1,13 +1,10 @@
 {
-  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-core.json",
+  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-core.json",
   "title": "ELIXIR Luxembourg Core json schema",
   "description": "Schema containing core attributes for any json serialisable ELIXIR Luxembourg record.",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "object",
-  "required": [
-    "source",
-    "name"
-  ],
+  "required": ["source", "name"],
   "properties": {
     "source": {
       "type": "string",
@@ -20,7 +17,7 @@
       "type": "string"
     },
     "description": {
-      "type":  ["string", "null"]
+      "type": ["string", "null"]
     },
     "external_id": {
       "type": ["string", "null"]
@@ -32,7 +29,7 @@
       "type": ["string", "null"]
     },
     "url": {
-      "type":  ["string", "null"]
+      "type": ["string", "null"]
     },
     "contacts": {
       "type": "array",
@@ -46,7 +43,6 @@
             "type": "string"
           },
           "role": {
-            "type": "string",
             "enum": [
               "Principal_Investigator",
               "Researcher",
@@ -70,15 +66,8 @@
             }
           }
         },
-        "required": [
-          "first_name",
-          "last_name",
-          "role",
-          "email",
-          "affiliations"
-        ]
+        "required": ["first_name", "last_name", "role", "email", "affiliations"]
       }
     }
   }
 }
-
diff --git a/core/fixtures/json_schemas/elu-dataset.json b/core/fixtures/json_schemas/elu-dataset.json
@@ -1,12 +1,12 @@
 {
-  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-dataset.json",
+  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-dataset.json",
   "title": "ELIXIR Luxembourg Datasets Schema",
   "description": "A JSON Schema for describing biomedical research Datasets.",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "object",
   "allOf": [
     {
-      "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-core.json"
+      "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-core.json"
     }
   ],
   "properties": {
@@ -43,8 +43,8 @@
     "elu:storage": {
       "type": "object",
       "properties": {
-        "platform": {"type": "string"},
-        "location": {"type": "string"},
+        "platform": { "type": "string" },
+        "location": { "type": "string" },
         "accesses": {
           "type": "array",
           "items": {
@@ -56,8 +56,8 @@
     "elu:transfer": {
       "type": "object",
       "properties": {
-        "partner": {"type": "string"},
-        "transfer_details": {"type": ["string", "null"]},
+        "partner": { "type": "string" },
+        "transfer_details": { "type": ["string", "null"] },
         "transfer_date": {
           "type": ["string", "null"],
           "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
@@ -76,20 +76,12 @@
         "legal_basis_codes": {
           "type": "array",
           "items": {
-            "type": "string",
-            "enum": [
-              "6.1(a)",
-              "6.1(b)",
-              "6.1(c)",
-              "6.1(d)",
-              "6.1(e)",
-              "6.1(f)"
-            ]
-          }},
+            "enum": ["6.1(a)", "6.1(b)", "6.1(c)", "6.1(d)", "6.1(e)", "6.1(f)"]
+          }
+        },
         "personal_data_codes": {
           "type": "array",
           "items": {
-            "type": "string",
             "enum": [
               "Standard",
               "Special",
@@ -107,10 +99,7 @@
           "type": "string"
         }
       },
-      "required": [
-        "legal_basis_codes",
-        "personal_data_codes"
-      ]
+      "required": ["legal_basis_codes", "personal_data_codes"]
     },
     "elu:data": {
       "type": "object",
@@ -124,25 +113,24 @@
             "type": "object",
             "properties": {
               "use_class": {
-                "type": "string",
                 "enum": [
                   "NRES",
-                  "GRU(CC)",
-                  "HMB(CC)",
-                  "DS-[XX](CC)",
+                  "GRU",
+                  "HMB",
+                  "DS",
                   "POA",
-                  "RS-[XX]",
+                  "RS",
                   "RUO",
                   "NMDS",
                   "GSO",
                   "NPU",
                   "PUB",
-                  "COL-[XX]",
+                  "COL",
                   "RTN",
                   "IRB",
-                  "GS-[XX]",
-                  "MOR-[XX]",
-                  "TS-[XX]",
+                  "GS",
+                  "MOR",
+                  "TS",
                   "US",
                   "PS",
                   "IS",
@@ -154,7 +142,6 @@
                 "type": "string"
               },
               "use_restriction_rule": {
-                "type": "string",
                 "enum": [
                   "OBLIGATION",
                   "PERMISSION",
@@ -172,16 +159,12 @@
                 }
               }
             },
-            "required": [
-              "use_class_note",
-              "use_restriction_rule"
-            ]
+            "required": ["use_class_note", "use_restriction_rule"]
           }
         },
         "data_types": {
           "type": "array",
           "items": {
-            "type": "string",
             "enum": [
               "ATAC-seq",
               "Biometric_data",
@@ -223,34 +206,21 @@
           "type": "string"
         },
         "access_category": {
-          "type": ["string", "null"],
           "enum": [
             "open_access",
             "controlled_access",
-            "registered_access"
+            "registered_access",
+            null
           ]
         },
         "subjects_category": {
-          "type": "string",
-          "enum": [
-            "cases",
-            "controls",
-            "cases_and_controls"
-          ]
+          "enum": ["cases", "controls", "cases_and_controls"]
         },
         "de_identification": {
-          "type": "string",
-          "enum": [
-            "anonymization",
-            "pseudonymization"
-          ]
+          "enum": ["anonymization", "pseudonymization"]
         },
         "consent_status": {
-          "enum": [
-            "heterogeneous",
-            "homogeneous",
-            null
-          ]
+          "enum": ["heterogeneous", "homogeneous", null]
         },
         "consent_status_description": {
           "type": "string"
@@ -259,10 +229,10 @@
           "type": ["boolean", "null"]
         },
         "special_subjects_description": {
-          "type": "string"
+          "type": ["string", "null"]
         },
         "embargo_date": {
-          "type": ["string","null"],
+          "type": ["string", "null"],
           "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
         },
         "storage_end_date": {
@@ -276,4 +246,3 @@
     }
   }
 }
-
diff --git a/core/fixtures/json_schemas/elu-institution.json b/core/fixtures/json_schemas/elu-institution.json
@@ -1,45 +1,36 @@
 {
-  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-institution.json",
+  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-institution.json",
   "title": "ELIXIR Luxembourg Partner Schema",
   "description": "A JSON Schema for describing partners institutes.",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "object",
-  "allOf": [{
-    "$ref": "#/definitions/elu:partner"
-  }],
+  "allOf": [
+    {
+      "$ref": "#/definitions/elu:partner"
+    }
+  ],
   "definitions": {
     "elu:partner": {
       "type": "object",
       "allOf": [
         {
-          "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-core.json"
+          "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-core.json"
         }
       ],
       "properties": {
         "is_clinical": {
           "type": "boolean"
         },
         "geo_category": {
-          "type": "string",
-          "enum": [
-            "National",
-            "EU",
-            "Non_EU",
-            "International"
-          ]
+          "enum": ["National", "EU", "Non_EU", "International"]
         },
         "sector_category": {
-          "type": "string",
-          "enum": [
-            "PUBLIC",
-            "PRIVATE_P",
-            "PRIVATE_NP"
-          ]
+          "enum": ["PUBLIC", "PRIVATE_P", "PRIVATE_NP"]
         },
         "address": {
           "type": ["string", "null"]
         },
-        "country_code":{
+        "country_code": {
           "title": "ISO 3166-1 Alpha-2 Country code",
           "type": ["string", "null"],
           "pattern": "^[A-Z]{2}$"
@@ -48,4 +39,3 @@
     }
   }
 }
-
diff --git a/core/fixtures/json_schemas/elu-project.json b/core/fixtures/json_schemas/elu-project.json
@@ -1,18 +1,20 @@
 {
-  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-project.json",
+  "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-project.json",
   "title": "ELIXIR Luxembourg Projects Schema",
   "description": "A JSON Schema for describing biomedical research Projects.",
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "object",
-  "allOf": [{
-    "$ref": "#/definitions/elu:project"
-  }],
+  "allOf": [
+    {
+      "$ref": "#/definitions/elu:project"
+    }
+  ],
   "definitions": {
     "elu:project": {
       "type": "object",
       "allOf": [
         {
-          "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.5/schemas/elu-study.json"
+          "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.6/schemas/elu-study.json"
         }
       ],
       "properties": {
@@ -32,4 +34,3 @@
     }
   }
 }
-