Merge pull request #8 from BBMRI-cz/CI_pipeline

Ci pipeline
BBMRI-cz · Oct 14, 2024 · 5fdca16 · 5fdca16
2 parents 8bce00c + 018dd12
commit 5fdca16
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diff --git a/MiabisOnFHIR/input/fsh/codeSystems/CollectionDatasetTypeCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/CollectionDatasetTypeCS.fsh
@@ -2,7 +2,7 @@ CodeSystem: CollectionDatasetTypeCS
 Id: miabis-collection-dataset-typeCS
 Title: "MIABIS Collection Dataset Type"
 Description: "Codes describing the type of dataset that is part of a collection."
-// create these : Lifestyle dataset, Environmental dataset, Physiological dataset, Biochemical dataset, Clinical dataset, Psychological dataset, Genomic dataset, Proteomic dataset, Metabolomic dataset, Body (Radiological) image, Whole slide image, Photo image, Genealogical records, Other.
+
 * #Lifesyle "Lifestyle dataset"
 * #Environmental "Environmental dataset"
 * #Physiological "Physiological dataset"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/biobankBioprocessingAndAnalyticasCapCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/biobankBioprocessingAndAnalyticasCapCS.fsh
@@ -3,7 +3,6 @@ Id: miabis-bioprocessing-and-analytical-capabilities-cs
 Title: "Bioprocessing and Analytical Capabilities Code System"
 Description: "Code system representing the bioprocessing and analytical services that the biobank can offer to the clients. "
 
-// Biochemical analyses, Genomics, Nucleic acid extraction, Proteomics, Metabolomics, Histology, Cell-lines processing, Virology, Sample processing, Sample shipping, Sample quality control services, Other
 * #BioChemAnalyses "Biochemical analyses"
 * #Genomics "Genomics"
 * #NucleicAcidExtraction "Nucleic acid extraction"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/biobankOrganisationalCapabilitiesCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/biobankOrganisationalCapabilitiesCS.fsh
@@ -2,7 +2,7 @@ CodeSystem: OrganisationalCapabilitiesCS
 Id: miabis-organisational-capabilities-cs
 Title: "Organisational Capabilities"
 Description: "This code system represents the organisational capabilities and services that the biobank can provide to support clients."
-// Recontact with donors, Facilitating clinical trials, Setting up prospective collections, Access to omics data, Access to laboratory analysis data, Access to donors'clinical data, Access to pathology archive, Access to radiology archive, Access to national medical registries, Other
+
 *  #RecontactDonors "Recontact with donors"
 *  #ClinicalTrials "Facilitating clinical trials"
 *  #ProspectiveCollections "Setting up prospective collections"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/collectionDesignCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/collectionDesignCS.fsh
@@ -3,7 +3,6 @@ Id: miabis-collection-design-cs
 Title: "MIABIS Collection Design code System"
 Description: "Codes describing the overall design of the collection that explains how the collection was/is built up."
 
-// Case-control, Cross-sectional, Longitudinal cohort, Twin-study, Quality control study, Population-based cohort, Disease-specific cohort, Birth cohort, Microbial collection (if applicable with resistance data), Reference collection, Rare disease collection, Other.
 * #CaseControl "Case-control"
 * #CrossSectional "Cross-sectional"
 * #LongitudinalCohort "Longitudinal cohort"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/inclusionCriteriaCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/inclusionCriteriaCS.fsh
@@ -2,7 +2,7 @@ CodeSystem: InclusionCriteriaCS
 Id: miabis-inclusion-criteria-cs
 Title: "Inclusion Criteria"
 Description: "Code system describing information on type of parameters that determine which subjects will become collection participant"
-// Health status, Hospital patient, Use of medication, Gravidity, Age group, Familial status, Sex, Country of residence, Ethnic origin, Population representative sampling, Lifestyle/Exposure, Other
+
 * #HealthStatus "Health status"
 * #HospitalPatient "Hospital patient"
 * #UseOfMedication "Use of medication"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/materialTypeCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/materialTypeCS.fsh
@@ -3,7 +3,7 @@ Id: miabis-material-type-CS
 Title: "MIABIS Material Type Code System"
 Description: "Codes for the material type of a sample"
 
-// Codes are taken from https://github.com/BBMRI-ERIC/miabis/blob/master/Structured-data-and-lists.md#miabis-20-14
+
 
 * #Blood "Blood that has not been separated into its various components"
 * #DNA "DNA"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/networkCommonCollaborationTopicCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/networkCommonCollaborationTopicCS.fsh
@@ -3,7 +3,7 @@ Id: miabis-common-collaboration-topics-cs
 Title: "Common Collaboration Topics Code System"
 Description: "Codes describing topics that the network partners collaborate on"
 
-// Common charter, Common SOPs, Common data access policy, Common sample access, policy, Common MTA, Common image access policy, Common image MTA, Common representation, Common URL, Other.
+
 * #Charter "Common Charter"
 * #SOP "Common SOPs"
 * #DataAccessPolicy "Common data access policy"

diff --git a/MiabisOnFHIR/input/fsh/codeSystems/sampleCollectionSettingCS.fsh b/MiabisOnFHIR/input/fsh/codeSystems/sampleCollectionSettingCS.fsh
@@ -3,7 +3,7 @@ Id: miabis-sample-collection-setting-cs
 Title: "MIABIS Sample Collection Setting Code System"
 Description: "Code set for the context in which the sample collection was conducted."
 
-// Routine health care setting, Clinical trial, Research study, Public health/population based study, Museum and/or archeological collection, Environment, Unknown, Other.
+
 * #RoutineHealthCare "Routine health care setting"
 * #ClinicalTrial "Clinical trial"
 * #ResearchStudy "Research study"

diff --git a/MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh b/MiabisOnFHIR/input/fsh/instances/collectionInstance.fsh
@@ -38,7 +38,7 @@ Description: "example of a collection instance"
 
 * extension[numberOfSubjects].valueInteger = 100
 * extension[inclusionCriteria].valueCodeableConcept = InclusionCriteriaCS#HealthStatus
-
+* extension[MemberEntity].valueReference = Reference(Specimen/sampleId)
 
 
 
diff --git a/MiabisOnFHIR/input/fsh/profiles/collectionList.fsh b/MiabisOnFHIR/input/fsh/profiles/collectionList.fsh
diff --git a/MiabisOnFHIR/input/fsh/profiles/condition.fsh b/MiabisOnFHIR/input/fsh/profiles/condition.fsh
@@ -16,8 +16,8 @@ Description: "This profile represents a condition, which is linked to sample and
 * code 0..1 MS
 * code ^short = "ICD-10 Code representing diagnosis of the patient."
 * code ^definition = "The ICD-10 code of the condition. This code is used to represent only the diagnosis of the patient. It is not used to represent the condition of the sample. For the condition of the sample, use the stage.assessment element."
-* code from http://hl7.org/fhir/ValueSet/icd-10
+* code from DiagnosisVS
 * stage.assessment only Reference(DiagnosisReport)
 * stage.assessment 1.. MS
 * stage.assessment ^short = "Diagnostic Report"
-* stage.assessment ^definition = "This element is used to link the condition to the sample and to the diagnosis of the said sample. It is used to represent the condition of the sample. For the diagnosis of the patient, use the code element."
+* stage.assessment ^definition = "This element is used to link the condition to the sample and to the diagnosis of the said sample. It is used to represent the condition of the sample. For the diagnosis of the patient (which is not linked to a specific sample, ie condition that patient has been diagnoses elsewhere), use the code element."
diff --git a/MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh b/MiabisOnFHIR/input/fsh/profiles/diagnosticReport.fsh
@@ -2,11 +2,11 @@ Profile: DiagnosisReport
 Parent: DiagnosticReport
 Id: miabis-diagnosis-report
 Title: "Diagnosis Report"
-Description: "provides information about the diagnosis linked to sample"
+Description: "Diagnosis Report provides information about the diagnosis linked to sample"
 
 * identifier 0..1 MS
-* identifier ^short = "ID of Condition"
-* identifier ^definition = "A unique identifier for the condition."
+* identifier ^short = "ID of Diagnosis Report"
+* identifier ^definition = "A unique identifier for the Diagnosis Report."
 
 * status = #final
 

diff --git a/MiabisOnFHIR/input/fsh/profiles/donor.fsh b/MiabisOnFHIR/input/fsh/profiles/donor.fsh
@@ -18,5 +18,5 @@ Description: "Sample donor is a person who is a source of either a biological ma
 * birthDate ^definition = " Date of birth is required when Event date in Event resource is used, otherwise partial date, as in birth year, can be used"
 
 * extension contains DatasetTypeExtension named datasetType 0.. MS
-* extension ^short = "Data categories"
+* extension[datasetType] ^short = "Data categories"
 * extension[datasetType] ^definition = "The data categories from which data are available or can be linked to the sample donor. Can be several values"
diff --git a/MiabisOnFHIR/input/fsh/profiles/managingPerson.fsh b/MiabisOnFHIR/input/fsh/profiles/managingPerson.fsh
diff --git a/MiabisOnFHIR/input/fsh/profiles/networkList.fsh b/MiabisOnFHIR/input/fsh/profiles/networkList.fsh
diff --git a/MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh b/MiabisOnFHIR/input/fsh/profiles/networkOrg.fsh
@@ -14,7 +14,7 @@ Description: "Network Organization represent a formal part of a network member,
 * telecom ^short = "Complete http-address for the network."
 * telecom.system = #url
 * telecom.value 0..1 MS
-* telecom.value ^short = "URL of the collection."
+* telecom.value ^short = "URL of the network."
 * active 0..1 MS
 * active ^short = "The state of the network functions."
 * active ^definition = "The state of the network functions."

diff --git a/MiabisOnFHIR/input/fsh/profiles/sample.fsh b/MiabisOnFHIR/input/fsh/profiles/sample.fsh
@@ -8,16 +8,16 @@ Description: "Sample is a portion or quantity of biological material that is col
 
 * identifier 1..1 MS
 * identifier ^short = "Sample ID"
-* identifier ^definition = "Unique ID of the sample within a sample collection."
+* identifier ^definition = "Unique ID of the sample usually given by the data provider."
 
 * collection.collectedDateTime ^short = "Sample creation date and time"
-* collection.collectedDateTime ^definition =  "The date and time the sample was created in the form previously described in detailedSampleType. Date/time format must be ISO8601-compliant or partial, for example, YYYY"
+* collection.collectedDateTime ^definition =  "The date and time the sample was created."
 * collection.collectedDateTime 0..1 MS
 
 * type from DetailedSampleTypeVS
 * type 1..1 MS
 * type ^short = "Detailed Sample type"
-* type ^definition = "The type of biological specimen intended for testing diagnostics, disease propagation, treatment, or for research purposes."
+* type ^definition = "The type of biological specimen."
 
 * collection.bodySite.coding obeys SpecimenOntologyInvariant
 * collection.bodySite.coding 0..1 MS 

diff --git a/MiabisOnFHIR/input/fsh/valueSets/SampleSourceVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/SampleSourceVS.fsh
@@ -1,5 +1,5 @@
 ValueSet: SampleSourceVS
-Id: miabis-sample-source-VS
+Id: miabis-sample-source-vs
 Title: "Sample Source Value Set"
 Description: "Value set containing the possible sources of a sample."
 

diff --git a/MiabisOnFHIR/input/fsh/valueSets/collectionDatasetTypeVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/collectionDatasetTypeVS.fsh
@@ -1,5 +1,5 @@
 ValueSet: CollectionDatasetTypeVS
-Id: miabis-collection-dataset-type
+Id: miabis-collection-dataset-type-vs
 Title: "MIABIS Collection Dataset Type"
 Description: "Value set containing codes describing the type of dataset that is part of a collection."
 * include codes from system CollectionDatasetTypeCS
diff --git a/MiabisOnFHIR/input/fsh/valueSets/datasetTypeVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/datasetTypeVS.fsh
@@ -1,5 +1,5 @@
 ValueSet: DatasetTypeVS
-Id: miabis-dataset-type
+Id: miabis-dataset-type-vs
 Title: "dataset type Value Set"
 Description: "The data categories from which data are available or can be linked to the sample donor. Can be one or more of the provided values"
 

diff --git a/MiabisOnFHIR/input/fsh/valueSets/materialTypeVS.fsh b/MiabisOnFHIR/input/fsh/valueSets/materialTypeVS.fsh
@@ -1,5 +1,5 @@
 ValueSet: MaterialTypeVS
-Id: miabis-material-type-VS
+Id: miabis-material-type-vs
 Title: "Material Type Value Set"
 Description: "Value set containing codes for the material type of the sample."
Original file line number	Diff line number	Diff line change
Expand Up		@@ -38,7 +38,7 @@ Description: "example of a collection instance"

		* extension[numberOfSubjects].valueInteger = 100
		* extension[inclusionCriteria].valueCodeableConcept = InclusionCriteriaCS#HealthStatus

		* extension[MemberEntity].valueReference = Reference(Specimen/sampleId)