Changes to the structure - we use lists now instead of strings where it makes sense. This allows us to have multiple values where in makes sense

4 files changed, 44 insertions, 61 deletions

diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
new file mode 100644
index 0000000..0a6d910
--- /dev/null
+++ b/example/maximum_metadata_example.yaml
@@ -0,0 +1,44 @@
+id: placeholder
+
+host:
+    host_id: XX1
+    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+    host_sex: http://purl.obolibrary.org/obo/PATO_0000384
+    host_age: 20
+    host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
+    host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
+    host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
+    host_vaccination: [vaccines1,vaccine2]
+    additional_host_information: Optional free text field for addtional information
+
+sample:
+    sample_id: Id of the sample as defined by the submitter 
+    collector_name: Name of the person that took the sample
+    collecting_institution: Institute that was responsible of sampling  
+    specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835]
+    collection_date: "2020-01-01"
+    collection_location: http://www.wikidata.org/entity/Q148
+    sample_storage_conditions: frozen specimen
+    source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence]
+    additional_collection_information: Optional free text field for addtional information
+
+virus:
+    virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
+    virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
+
+technology:
+    sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
+    sequence_assembly_method: Protocol used for assembly
+    sequencing_coverage: [70, 100]
+    additional_technology_information: Optional free text field for addtional information
+
+submitter:
+    submitter_name: [John Doe]
+    submitter_address: John Doe's adress
+    originating_lab: John Doe kitchen
+    lab_address: John Doe's address
+    provider_sample_id: XXX1
+    submitter_sample_id: XXX2
+    authors: [John Doe, Joe Boe, Jonny Oe]
+    submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
+    additional_submitter_information: Optional free text field for addtional information
\ No newline at end of file
diff --git a/example/metadata.yaml b/example/metadata.yaml
deleted file mode 100644
index a76616c..0000000
--- a/example/metadata.yaml
+++ /dev/null
@@ -1,43 +0,0 @@
-id: placeholder
-
-host:
-    host_id: XX1
-    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
-    host_sex: http://purl.obolibrary.org/obo/NCIT_C27993
-    host_age: 20
-    host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
-    host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
-    host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
-    host_vaccination: List of vaccines given to the host (RRIDs?)
-    additional_host_information: Field for additional host information
-
-sample:
-    sample_id: Id of the sample as defined by the submitter 
-    collector_name: Name of the person that took the sample
-    collecting_institution: Institute that was responsible of sampling  
-    specimen_source: http://purl.obolibrary.org/obo/NCIT_C155831
-    specimen_source2: http://purl.obolibrary.org/obo/NCIT_C155835
-    collection_date: "2020-01-01"
-    collection_location: http://www.wikidata.org/entity/Q148
-    sample_storage_conditions: XXX
-    additional_collection_information: XXX
-
-virus:
-    virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
-    virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
-
-technology:
-    sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0009173
-    sample_sequencing_technology2: http://www.ebi.ac.uk/efo/EFO_0009173
-    sequence_assembly_method: Protocol used for assembly
-    sequencing_coverage: 70
-
-submitter:
-    submitter_name: John Doe
-    submitter_address: John Doe's adress
-    originating_lab: John Doe kitchen
-    lab_address: John Doe's address
-    provider_sample_id: HmX
-    submitter_sample_id: xXx
-    authors: John Doe et all
-    submitter_orcid: https://orcid.org/0000-0000-0000-0000
\ No newline at end of file
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
deleted file mode 100644
index 0e36a25..0000000
--- a/example/minimal_example.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-id: placeholder
-
-host:
-    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
-
-sample:
-    sample_id: XX
-    collection_date: 2020-01
-    collection_location: http://www.wikidata.org/entity/Q148
-
-virus:
-    virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
-
-technology:
-    sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0008632
-
-submitter:
-    authors: John Doe
\ No newline at end of file
diff --git a/example/minimal_metadata_example.yaml b/example/minimal_metadata_example.yaml
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/example/minimal_metadata_example.yaml