feat(portal): updated portal loader and added demo dataset (#4771)

* feat: added demo dataset for the portal model

backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/RD3v2Loader.java

@@ -34,6 +34,12 @@ public void run() {
       List<Row> rows = getProfilesFromAllModels("/portal", List.of());
       getSchema().migrate(Emx2.fromRowList(rows));
       MolgenisIO.fromClasspathDirectory("/_ontologies", getSchema(), false);
+      MolgenisIO.fromClasspathDirectory("/_settings/portal", getSchema(), false);
+
+      if (isIncludeDemoData()) {
+        MolgenisIO.fromClasspathDirectory("/_demodata/applications/portal", getSchema(), false);
+      }
+
       this.complete();
     } catch (Exception e) {
       this.completeWithError(e.getMessage());

data/_demodata/applications/portal/Biosamples.csv

@@ -0,0 +1,19 @@
+id,collected from individual,included in datasets.resource,included in datasets.name
+SAMEA10450711,Case1F,EGAS00001005702,EGAD00001008392
+SAMEA10450712,Case1C,EGAS00001005702,EGAD00001008392
+SAMEA10450713,Case1M,EGAS00001005702,EGAD00001008392
+SAMEA10450714,Case2C,EGAS00001005702,EGAD00001008392
+SAMEA10450715,Case2F,EGAS00001005702,EGAD00001008392
+SAMEA10450716,Case2M,EGAS00001005702,EGAD00001008392
+SAMEA10450723,Case3C,EGAS00001005702,EGAD00001008392
+SAMEA10450724,Case3F,EGAS00001005702,EGAD00001008392
+SAMEA10450725,Case3M,EGAS00001005702,EGAD00001008392
+SAMEA10450726,Case4C,EGAS00001005702,EGAD00001008392
+SAMEA10450728,Case4F,EGAS00001005702,EGAD00001008392
+SAMEA10450729,Case4M,EGAS00001005702,EGAD00001008392
+SAMEA10450730,Case5C,EGAS00001005702,EGAD00001008392
+SAMEA10450731,Case5M,EGAS00001005702,EGAD00001008392
+SAMEA10450732,Case5F,EGAS00001005702,EGAD00001008392
+SAMEA10450733,Case6C,EGAS00001005702,EGAD00001008392
+SAMEA10450734,Case6F,EGAS00001005702,EGAD00001008392
+SAMEA10450735,Case6M,EGAS00001005702,EGAD00001008392

data/_demodata/applications/portal/Clinical observations.csv

@@ -0,0 +1,9 @@
+id,individual,date saved in database
+7qOBAUD680,Case1C,2025-02-25
+7qOBAUD681,Case2C,2025-02-25
+7qOBAUD682,Case2M,2025-02-25
+7qOBAUD683,Case3C,2025-02-25
+7qOBAUD684,Case4C,2025-02-25
+7qOBAUD685,Case5C,2025-02-25
+7qOBAUD686,Case5M,2025-02-25
+7qOBAUD687,Case6C,2025-02-25

data/_demodata/applications/portal/Datasets.csv

@@ -0,0 +1,2 @@
+resource,name,label,since version,date created,dataset type,description,unit of observation,keywords
+EGAS00001005702,EGAD00001008392 ,Rare Disease Synthetic Dataset,2001-01-01,2025-02-27,Collected dataset,"The purpose of this project is to provide public human datasets for the study of rare diseases. The use of public human genomic background combined with the in-silico insertion of real disease-causing variants enable to have a representative dataset for testing purposes without facing ethical and legal issues associated with the use of human sensitive data. This project aims to help development of technical implementations for rare disease data integration, analysis, discovery,  and federated access.",sample,"Sex/gender,Family and household structure,Health-related characteristics,Diseases"

data/_demodata/applications/portal/Disease history.csv

@@ -0,0 +1,6 @@
+part of clinical observation,disease
+7qOBAUD680,Central core disease
+7qOBAUD684,Mitochondrial DNA depletion syndrome
+7qOBAUD687,Central core disease
+7qOBAUD685,Hereditary breast cancer
+7qOBAUD686,Hereditary breast cancer

data/_demodata/applications/portal/Gender at birth.csv

@@ -0,0 +1,14 @@
+name,definition,codesystem,code,ontologyTermURI
+assigned U at birth,An assignment of an 'U' gender shortly after birth. Note that 'U' is only available in certain jurisdictions on birth certificates.,GSSO,9511,http://purl.obolibrary.org/obo/GSSO_009511
+assigned X at birth,An assignment of an 'X' gender shortly after birth. Note that 'X' is only available in certain jurisdictions on birth certificates.,GSSO,9486,http://purl.obolibrary.org/obo/GSSO_009486
+assigned diverse at birth,"An assignment of a diverse gender marker shortly after birth. Note that 'diverse' is only available in certain jurisdictions on birth certificates. Further, note that 'diverse' itself is not a gender, but is a legal gender in this context.",GSSO,9512,http://purl.obolibrary.org/obo/GSSO_009512
+assigned eunuch at birth,"An assignment of a 'eunuch' gender marker shortly after birth. Note that 'eunuch' is only available in certain jurisdictions on birth certificates. Further, note that 'eunuch' itself is not a gender, but is a legal gender in this context. This term may also be offensive depending on the context.",GSSO,9513,http://purl.obolibrary.org/obo/GSSO_009513
+assigned female at birth,An assignment of a female gender shortly after birth.,GSSO,123,http://purl.obolibrary.org/obo/GSSO_000123
+assigned indeterminate at birth,"An assignment of an indeterminate gender marker shortly after birth. Note that 'indeterminate' is only available in certain jurisdictions on birth certificates. Further, note that 'indeterminate' itself is not a gender, but is a legal gender in this context.",GSSO,9509,http://purl.obolibrary.org/obo/GSSO_009509
+assigned intersex at birth,"An assignment of an intersex gender marker shortly after birth. Note that 'intersex' is only available in certain jurisdictions on birth certificates. Further, note that 'intersex' itself is not a gender, but is a legal gender in this context.",GSSO,9488,http://purl.obolibrary.org/obo/GSSO_009488
+assigned male at birth,An assignment of a male gender shortly after birth.,GSSO,124,http://purl.obolibrary.org/obo/GSSO_000124
+assigned no gender at birth,"Use in situations where no gender was assigned at birth, i.e. no birth certificate was issued shortly after birth or no birth certificate gender was recorded.",GSSO,9487,http://purl.obolibrary.org/obo/GSSO_009487
+assigned nonbinary at birth,An assignment of a nonbinary gender shortly after birth. Note that 'nonbinary' is only available in certain jurisdictions on birth certificates.,GSSO,9510,http://purl.obolibrary.org/obo/GSSO_009510
+assigned other at birth,An assignment of an 'other' gender marker shortly after birth. Note that 'other' is only available in certain jurisdictions on birth certificates.,GSSO,9507,http://purl.obolibrary.org/obo/GSSO_009507
+assigned third gender at birth,"An assignment of a 'third gender' gender marker shortly after birth. Note that 'third gender' is only available in certain jurisdictions on birth certificates. Further, note that 'third gender' itself is not a gender, but is a legal gender in this context. This term may also be offensive depending on the context.",GSSO,9514,http://purl.obolibrary.org/obo/GSSO_009514
+assigned unspecified at birth,An assignment of an 'unspecified' gender shortly after birth. Note that 'unspecified' is only available in certain jurisdictions on birth certificates.,GSSO,9515,http://purl.obolibrary.org/obo/GSSO_009515

data/_demodata/applications/portal/Individuals.csv

@@ -0,0 +1,19 @@
+id,gender at birth,pedigree,included in datasets.resource,included in datasets.name
+Case1F,assigned male at birth,Case1,EGAS00001005702,EGAD00001008392
+Case1C,assigned male at birth,Case1,EGAS00001005702,EGAD00001008392
+Case1M,assigned female at birth,Case1,EGAS00001005702,EGAD00001008392
+Case2C,assigned male at birth,Case2,EGAS00001005702,EGAD00001008392
+Case2F,assigned male at birth,Case2,EGAS00001005702,EGAD00001008392
+Case2M,assigned female at birth,Case2,EGAS00001005702,EGAD00001008392
+Case3C,assigned male at birth,Case3,EGAS00001005702,EGAD00001008392
+Case3F,assigned male at birth,Case3,EGAS00001005702,EGAD00001008392
+Case3M,assigned female at birth,Case3,EGAS00001005702,EGAD00001008392
+Case4C,assigned male at birth,Case4,EGAS00001005702,EGAD00001008392
+Case4F,assigned male at birth,Case4,EGAS00001005702,EGAD00001008392
+Case4M,assigned female at birth,Case4,EGAS00001005702,EGAD00001008392
+Case5C,assigned female at birth,Case5,EGAS00001005702,EGAD00001008392
+Case5M,assigned female at birth,Case5,EGAS00001005702,EGAD00001008392
+Case5F,assigned male at birth,Case5,EGAS00001005702,EGAD00001008392
+Case6C,assigned male at birth,Case6,EGAS00001005702,EGAD00001008392
+Case6F,assigned male at birth,Case6,EGAS00001005702,EGAD00001008392
+Case6M,assigned female at birth,Case6,EGAS00001005702,EGAD00001008392

data/_demodata/applications/portal/Pedigree members.csv

@@ -0,0 +1,19 @@
+pedigree,individual,relative,relation
+Case1,Case1C,Case1C,Patient
+Case1,Case1F,Case1C,Biological Father
+Case1,Case1M,Case1C,Biological Mother
+Case2,Case2C,Case2C,Patient
+Case2,Case2F,Case2C,Biological Father
+Case2,Case2M,Case2C,Biological Mother
+Case3,Case3C,Case3C,Patient
+Case3,Case3F,Case3C,Biological Father
+Case3,Case3M,Case3C,Biological Mother
+Case4,Case4C,Case4C,Patient
+Case4,Case4F,Case4C,Biological Father
+Case4,Case4M,Case4C,Biological Mother
+Case5,Case5C,Case5C,Patient
+Case5,Case5F,Case5C,Biological Father
+Case5,Case5M,Case5C,Biological Mother
+Case6,Case6C,Case6C,Patient
+Case6,Case6F,Case6C,Biological Father
+Case6,Case6M,Case6C,Biological Mother

data/_demodata/applications/portal/Pedigree.csv

@@ -0,0 +1,7 @@
+identifier
+Case1
+Case2
+Case3
+Case4
+Case5
+Case6

data/_demodata/applications/portal/Phenotype observations.csv

@@ -0,0 +1,4 @@
+part of clinical observation,type
+7qOBAUD681,Macular dystrophy
+7qOBAUD682,Macular dystrophy
+7qOBAUD683,Limb-girdle muscular dystrophy

data/_demodata/applications/portal/Resources.csv

@@ -0,0 +1,2 @@
+id,name,website,type,description,cohort type,clinical study type,start year,status,number of participants,number of participants with samples,release type
+EGAS00001005702,Human genomic and phenotypic synthetic data for the study of rare diseases,https://ega-archive.org/studies/EGAS00001005702,Rare disease,"The purpose of this dataset is to facilitate development of technical implementations for rare disease data integration, analysis, discovery, and federated access. This synthetic dataset includes clinical and genomic data from 6 rare disease cases. It consists of 18 whole genomes (6 index cases with their parents) which have genetic background based on public human data sequenced in the context of the Illumina Platinum initiative (Eberle, MA et al. (2017)) and made available by the HapMap project (https://www.genome.gov/10001688/international-hapmap-project). In each of the cases, real causative variants correlating with the phenotypic data provided were spiked-in. The cases included in this synthetic dataset correspond to the following type of disorders: CASE 1- Congenital myasthenic syndrome (Autosomal Dominant -de novo variant), CASE 2- Macular dystrophy (Autosomal Dominant), CASE 3- Muscular dystrophy (Autosomal Recessive-compound heterozygous variants), CASE 4- Mitochondrial disorder (Autosomal Recessive-consanguineous case - homozygous variant), CASE 5- Breast cancer (Autosomal Dominant), CASE 6- Similar as case 1 for patient matchmaking tests: Congenital myasthenic syndrome (Autosomal Dominant-de novo variant) For each case you will be able to download the following data: clinical information (phenopackets per individual and pedigree per family), raw genomic data (FASTQ and BAMs) and processed genomic data (vcfs). When using the data, the following should be acknowledged: the RD-Connect GPAP (https://platform.rd-connect.eu/), EC H2020 project EJP-RD (grant # 825575), EC H2020 project B1MG (grant # 951724) and Generalitat de Catalunya VEIS project (grant # 001-P-001647).",Other type,Primary data collection,2021,Finalised,6,6,Closed dataset