Merge pull request #262 from EGA-archive/develop

Develop
EGA-archive · Jan 9, 2024 · 7b3630f · 7b3630f
2 parents 58998f8 + d5aff22
commit 7b3630f
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Showing 8 changed files with 149 additions and 21 deletions.
diff --git a/README.md b/README.md
@@ -20,6 +20,7 @@ To give the right permissions for AAI you will need to set the permissions of th
 docker exec beacon-permissions bash permissions/permissions-ui/start.sh
 ```
 Please, bear in mind that the name of the user has to be the same that you used when creating the user in LS or in IDP, whatever the AAI method you are working with.
+To give a user a certain type of response for their queries, please modify this file [response_type.yml](https://github.com/EGA-archive/beacon2-ri-api/blob/master/beacon/request/response_type.yml) adding the maximum type of response you want to allow every user.
 
 Also, you will need to edit the file [conf.py](beacon/conf.py) and introduce the domain where your keycloak is being hosted inside **ldp_user_info** and the issuers you trust for your token inside **trusted_issuers**. In case you want to run your local container, use this configuration:
 ```bash

diff --git a/beacon/db/g_variants.py b/beacon/db/g_variants.py
@@ -38,18 +38,18 @@ def generate_position_filter_start(key: str, value: List[int]) -> List[Alphanume
     if len(value) == 1:
         filters.append(AlphanumericFilter(
             id=VARIANTS_PROPERTY_MAP[key],
-            value=[value[0]],
+            value=value[0],
             operator=Operator.GREATER_EQUAL
         ))
     elif len(value) == 2:
         filters.append(AlphanumericFilter(
             id=VARIANTS_PROPERTY_MAP[key],
-            value=[value[0]],
+            value=value[0],
             operator=Operator.GREATER_EQUAL
         ))
         filters.append(AlphanumericFilter(
             id=VARIANTS_PROPERTY_MAP[key],
-            value=[value[1]],
+            value=value[1],
             operator=Operator.LESS_EQUAL
         ))
     return filters
@@ -61,18 +61,18 @@ def generate_position_filter_end(key: str, value: List[int]) -> List[Alphanumeri
     if len(value) == 1:
         filters.append(AlphanumericFilter(
             id=VARIANTS_PROPERTY_MAP[key],
-            value=[value[0]],
+            value=value[0],
             operator=Operator.LESS_EQUAL
         ))
     elif len(value) == 2:
         filters.append(AlphanumericFilter(
             id=VARIANTS_PROPERTY_MAP[key],
-            value=[value[0]],
+            value=value[0],
             operator=Operator.GREATER_EQUAL
         ))
         filters.append(AlphanumericFilter(
             id=VARIANTS_PROPERTY_MAP[key],
-            value=[value[1]],
+            value=value[1],
             operator=Operator.LESS_EQUAL
         ))
     return filters

diff --git a/beacon/response/build_response.py b/beacon/response/build_response.py
@@ -49,6 +49,7 @@ def build_response_summary(exists, qparams, num_total_results):
 
 
 def build_response_summary_by_dataset(exists, num_total_results, response_dict):
+    LOG.debug(response_dict)
     count=0
     try:
         for k,v in response_dict.items():
@@ -174,7 +175,7 @@ def build_beacon_resultset_response_by_dataset(data,
             dataset_id = dataset_dict['dataset']
             response_dict[dataset_id] = []
             dataset_ids_list.append(dataset_id)
-
+    LOG.debug(include)
     if include == 'MISS':
         for doc in data:
             for dataset_dict in list_of_dataset_dicts:
@@ -311,14 +312,16 @@ def build_beacon_resultset_response_by_dataset(data,
                                 dataset_id = dataset_dict['dataset']
                                 response_dict[dataset_id].append(doc)
                     else:
-                            if doc['id'] in dataset_dict['ids']:
-                                dataset_id = dataset_dict['dataset']
-                                response_dict[dataset_id].append(doc)
-                            elif doc['id'] in dataset_dict['ids']:
-                                dataset_id = dataset_dict['dataset']
-                                response_dict[dataset_id].append(doc)
+                        #LOG.debug(doc['id'])
+                        if doc['id'] in dataset_dict['ids']:
+                            dataset_id = dataset_dict['dataset']
+                            response_dict[dataset_id].append(doc)
+                        elif doc['id'] in dataset_dict['ids']:
+                            dataset_id = dataset_dict['dataset']
+                            response_dict[dataset_id].append(doc)
                 except Exception as e:
                     pass
+    #LOG.debug(response_dict)
 
     limit= qparams.query.pagination.limit
     length_to_rest=0
@@ -338,10 +341,11 @@ def build_beacon_resultset_response_by_dataset(data,
             length_to_rest = len(response_dict[dataset_id])
         else:
             start_record = start_record - len(response_dict[dataset_id])
+
 
 
 
-
+    LOG.debug(response_dict)
     beacon_response = {
         'meta': build_meta(qparams, entity_schema, Granularity.RECORD),
         'responseSummary': build_response_summary_by_dataset(num_total_results > 0, num_total_results, response_dict),

diff --git a/deploy/README.md b/deploy/README.md
@@ -61,6 +61,11 @@ docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:example@12
 
 This loads the JSON files inside of the `data` folder into the MongoDB database container.
 
+#### List the ids
+
+After deploying all the data, you will need to tell the beacon which are the individual and biosample ids belonging to each dataset and cohort. In order to do that, please, add the name of each dataset with the respective array of all the ids together in this file [datasets.yml](https://github.com/EGA-archive/beacon2-ri-api/blob/master/beacon/request/datasets.yml).
+Then, repeat the same for the cohorts modifying this file [cohorts.yml](https://github.com/EGA-archive/beacon2-ri-api/blob/master/beacon/request/cohorts.yml).
+
 #### Create the indexes
 
 You can create the necessary indexes running the following Python script:
@@ -188,7 +193,7 @@ But you can also use complex filters:
     "query": {
         "filters": [
             {
-                "id": "UBERON:0001256",
+                "id": "UBERON:0000178",
                 "scope": "biosamples",
                 "includeDescendantTerms": false
             }

diff --git a/deploy/data/cohorts.json b/deploy/data/cohorts.json
@@ -1 +1 @@
-[{"cohortType": "study-defined", "collectionEvents": [{"eventDiseases": {"availability": true, "availabilityCount": 1705, "distribution": {"diseases": {"acutebronchitis": 121, "agranulocytosis": 111, "asthma": 134, "bipolaraffectivedisorder": 134, "cardiomyopathy": 133, "dentalcaries": 139, "eatingdisorders": 134, "fibrosisandcirrhosisofliver": 132, "gastro-oesophagealrefluxdisease": 140, "haemorrhoids": 127, "influenzaduetocertainidentifiedinfluenzavirus": 135, "insulin-dependentdiabetesmellitus": 165, "irondeficiencyanaemia": 142, "multiplesclerosis": 125, "obesity": 136, "sarcoidosis": 136, "schizophrenia": 138, "thyroiditis": 141, "varicoseveinsoflowerextremities": 139}}}, "eventEthnicities": {"availability": true, "availabilityCount": 2287, "distribution": {"ethnicities": {"African": 119, "AnyotherAsianbackground": 120, "AnyotherBlackbackground": 104, "Anyothermixedbackground": 92, "Anyotherwhitebackground": 114, "AsianorAsianBritish": 125, "Bangladeshi": 96, "BlackorBlackBritish": 131, "British": 114, "Caribbean": 127, "Chinese": 100, "Indian": 110, "Irish": 111, "Mixed": 127, "Otherethnicgroup": 116, "Pakistani": 115, "White": 105, "WhiteandAsian": 114, "WhiteandBlackAfrican": 115, "WhiteandBlackCaribbean": 132}}}, "eventGenders": {"availability": true, "availabilityCount": 1597, "distribution": {"genders": {"female": 1271, "male": 1233}}}}], "id": "CINECA_synthetic_cohort_UK1", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P65Y"}, "start": {"iso8601duration": "P18Y"}}, "genders": [{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}], "locations": [{"id": "GAZ:00150372", "label": "UK"}]}, "name": "CINECA synthetic cohort UK1"}]
+[{"cohortType": "study-defined", "collectionEvents": [{"eventDiseases": {"availability": true, "availabilityCount": 1705, "distribution": {"diseases": {"acutebronchitis": 121, "agranulocytosis": 111, "asthma": 134, "bipolaraffectivedisorder": 134, "cardiomyopathy": 133, "dentalcaries": 139, "eatingdisorders": 134, "fibrosisandcirrhosisofliver": 132, "gastro-oesophagealrefluxdisease": 140, "haemorrhoids": 127, "influenzaduetocertainidentifiedinfluenzavirus": 135, "insulin-dependentdiabetesmellitus": 165, "irondeficiencyanaemia": 142, "multiplesclerosis": 125, "obesity": 136, "sarcoidosis": 136, "schizophrenia": 138, "thyroiditis": 141, "varicoseveinsoflowerextremities": 139}}}, "eventEthnicities": {"availability": true, "availabilityCount": 2287, "distribution": {"ethnicities": {"African": 119, "AnyotherAsianbackground": 120, "AnyotherBlackbackground": 104, "Anyothermixedbackground": 92, "Anyotherwhitebackground": 114, "AsianorAsianBritish": 125, "Bangladeshi": 96, "BlackorBlackBritish": 131, "British": 114, "Caribbean": 127, "Chinese": 100, "Indian": 110, "Irish": 111, "Mixed": 127, "Otherethnicgroup": 116, "Pakistani": 115, "White": 105, "WhiteandAsian": 114, "WhiteandBlackAfrican": 115, "WhiteandBlackCaribbean": 132}}}, "eventGenders": {"availability": true, "availabilityCount": 1597, "distribution": {"genders": {"female": 1271, "male": 1233}}}, "eventLocations": {"availability": true, "availabilityCount": 1597, "distribution": {"locations": {"England": 322, "NorthernIreland": 317, "RepublicofIreland": 311, "Scotland": 308, "Wales": 339}}}}], "id": "CINECA_synthetic_cohort_UK1", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P65Y"}, "start": {"iso8601duration": "P18Y"}}, "genders": [{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}], "locations": [{"id": "GAZ:00150372", "label": "UK"}]}, "name": "CINECA synthetic cohort UK1"}]
diff --git a/deploy/data/cohorts_av.json b/deploy/data/cohorts_av.json
@@ -0,0 +1,115 @@
+[
+    {
+        "cohortType": "study-defined",
+        "collectionEvents": [
+            {
+                "eventDiseases": {
+                    "availability": true,
+                    "availabilityCount": 1700,
+                    "distribution": {
+                        "diseases": {
+                            "acutebronchitis": 121,
+                            "agranulocytosis": 111,
+                            "asthma": 134,
+                            "bipolaraffectivedisorder": 134,
+                            "cardiomyopathy": 133,
+                            "dentalcaries": 135,
+                            "eatingdisorders": 134,
+                            "fibrosisandcirrhosisofliver": 132,
+                            "gastro-oesophagealrefluxdisease": 140,
+                            "haemorrhoids": 127,
+                            "influenzaduetocertainidentifiedinfluenzavirus": 135,
+                            "insulin-dependentdiabetesmellitus": 165,
+                            "irondeficiencyanaemia": 142,
+                            "multiplesclerosis": 125,
+                            "obesity": 136,
+                            "sarcoidosis": 136,
+                            "schizophrenia": 138,
+                            "thyroiditis": 141,
+                            "varicoseveinsoflowerextremities": 139
+                        }
+                    }
+                },
+                "eventEthnicities": {
+                    "availability": true,
+                    "availabilityCount": 54,
+                    "distribution": {
+                        "ethnicities": {
+                            "African": 3,
+                            "AnyotherAsianbackground": 4,
+                            "AnyotherBlackbackground": 4,
+                            "Anyothermixedbackground": 2,
+                            "Anyotherwhitebackground": 2,
+                            "AsianorAsianBritish": 4,
+                            "Bangladeshi": 3,
+                            "BlackorBlackBritish": 2,
+                            "British": 4,
+                            "Caribbean": 2,
+                            "Chinese": 4,
+                            "Indian": 2,
+                            "Irish": 3,
+                            "Mixed": 2,
+                            "Otherethnicgroup": 4,
+                            "Pakistani": 2,
+                            "White": 2,
+                            "WhiteandAsian": 3,
+                            "WhiteandBlackAfrican": 3,
+                            "WhiteandBlackCaribbean": 1
+                        }
+                    }
+                },
+                "eventGenders": {
+                    "availability": true,
+                    "availabilityCount": 3,
+                    "distribution": {
+                        "genders": {
+                            "female": 2,
+                            "male": 1
+                        }
+                    }
+                },
+                "eventLocations": {
+                    "availability": true,
+                    "availabilityCount": 1597,
+                    "distribution": {
+                        "locations": {
+                            "England": 2,
+                            "NorthernIreland": 2,
+                            "RepublicofIreland": 3,
+                            "Scotland": 4,
+                            "Wales": 5
+                        }
+                    }
+                }
+            }
+        ],
+        "id": "AV_synthetic_cohort",
+        "inclusionCriteria": {
+            "ageRange": {
+                "end": {
+                    "iso8601duration": "P65Y"
+                },
+                "start": {
+                    "iso8601duration": "P18Y"
+                }
+            },
+            "genders": [
+                {
+                    "id": "NCIT:C16576",
+                    "label": "female"
+                },
+                {
+                    "id": "NCIT:C20197",
+                    "label": "male"
+                }
+            ],
+            "locations": [
+                {
+                    "id": "GAZ:00150372",
+                    "label": "UK"
+                }
+            ]
+        },
+        "name": "AV synthetic cohort"
+    }
+]
diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
@@ -179,8 +179,8 @@ services:
       - 3000:3000
     stdin_open: true
     volumes:
-      - ./frontend/.env:/frontend/.env
-      - ./frontend/src/config.json:/frontend/src/config.json
+      - ../frontend/.env:/frontend/.env
+      - ../frontend/src/config.json:/frontend/src/config.json
 
 
 
diff --git a/frontend/Dockerfile b/frontend/Dockerfile
@@ -1,13 +1,16 @@
 FROM node:19.0-alpine
 
 # set working directory
-WORKDIR /usr/src/app
+WORKDIR ./frontend
 
 # add _/usr/src/app/node_modules/.bin_ to $PATH
-ENV PATH /usr/src/app/node_modules/.bin:$PATH
+ENV PATH /frontend/node_modules/.bin:$PATH
 
 # install app dependencies
 COPY package.json .
 COPY yarn.lock .
+COPY public ./public
+COPY src ./src
 
-RUN yarn install --production
+
+RUN yarn install --production
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		[{"cohortType": "study-defined", "collectionEvents": [{"eventDiseases": {"availability": true, "availabilityCount": 1705, "distribution": {"diseases": {"acutebronchitis": 121, "agranulocytosis": 111, "asthma": 134, "bipolaraffectivedisorder": 134, "cardiomyopathy": 133, "dentalcaries": 139, "eatingdisorders": 134, "fibrosisandcirrhosisofliver": 132, "gastro-oesophagealrefluxdisease": 140, "haemorrhoids": 127, "influenzaduetocertainidentifiedinfluenzavirus": 135, "insulin-dependentdiabetesmellitus": 165, "irondeficiencyanaemia": 142, "multiplesclerosis": 125, "obesity": 136, "sarcoidosis": 136, "schizophrenia": 138, "thyroiditis": 141, "varicoseveinsoflowerextremities": 139}}}, "eventEthnicities": {"availability": true, "availabilityCount": 2287, "distribution": {"ethnicities": {"African": 119, "AnyotherAsianbackground": 120, "AnyotherBlackbackground": 104, "Anyothermixedbackground": 92, "Anyotherwhitebackground": 114, "AsianorAsianBritish": 125, "Bangladeshi": 96, "BlackorBlackBritish": 131, "British": 114, "Caribbean": 127, "Chinese": 100, "Indian": 110, "Irish": 111, "Mixed": 127, "Otherethnicgroup": 116, "Pakistani": 115, "White": 105, "WhiteandAsian": 114, "WhiteandBlackAfrican": 115, "WhiteandBlackCaribbean": 132}}}, "eventGenders": {"availability": true, "availabilityCount": 1597, "distribution": {"genders": {"female": 1271, "male": 1233}}}}], "id": "CINECA_synthetic_cohort_UK1", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P65Y"}, "start": {"iso8601duration": "P18Y"}}, "genders": [{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}], "locations": [{"id": "GAZ:00150372", "label": "UK"}]}, "name": "CINECA synthetic cohort UK1"}]
		[{"cohortType": "study-defined", "collectionEvents": [{"eventDiseases": {"availability": true, "availabilityCount": 1705, "distribution": {"diseases": {"acutebronchitis": 121, "agranulocytosis": 111, "asthma": 134, "bipolaraffectivedisorder": 134, "cardiomyopathy": 133, "dentalcaries": 139, "eatingdisorders": 134, "fibrosisandcirrhosisofliver": 132, "gastro-oesophagealrefluxdisease": 140, "haemorrhoids": 127, "influenzaduetocertainidentifiedinfluenzavirus": 135, "insulin-dependentdiabetesmellitus": 165, "irondeficiencyanaemia": 142, "multiplesclerosis": 125, "obesity": 136, "sarcoidosis": 136, "schizophrenia": 138, "thyroiditis": 141, "varicoseveinsoflowerextremities": 139}}}, "eventEthnicities": {"availability": true, "availabilityCount": 2287, "distribution": {"ethnicities": {"African": 119, "AnyotherAsianbackground": 120, "AnyotherBlackbackground": 104, "Anyothermixedbackground": 92, "Anyotherwhitebackground": 114, "AsianorAsianBritish": 125, "Bangladeshi": 96, "BlackorBlackBritish": 131, "British": 114, "Caribbean": 127, "Chinese": 100, "Indian": 110, "Irish": 111, "Mixed": 127, "Otherethnicgroup": 116, "Pakistani": 115, "White": 105, "WhiteandAsian": 114, "WhiteandBlackAfrican": 115, "WhiteandBlackCaribbean": 132}}}, "eventGenders": {"availability": true, "availabilityCount": 1597, "distribution": {"genders": {"female": 1271, "male": 1233}}}, "eventLocations": {"availability": true, "availabilityCount": 1597, "distribution": {"locations": {"England": 322, "NorthernIreland": 317, "RepublicofIreland": 311, "Scotland": 308, "Wales": 339}}}}], "id": "CINECA_synthetic_cohort_UK1", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P65Y"}, "start": {"iso8601duration": "P18Y"}}, "genders": [{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}], "locations": [{"id": "GAZ:00150372", "label": "UK"}]}, "name": "CINECA synthetic cohort UK1"}]