From 3beed199f6bbf2b2b304822ee8770902235f66ba Mon Sep 17 00:00:00 2001 From: khalifa-aly Date: Wed, 30 Aug 2023 14:50:25 -0500 Subject: [PATCH 001/114] Updating the structure definition to reflect the new design of the MolSeq --- .../structuredefinition-MolecularSequence.xml | 618 ++++++++++++------ 1 file changed, 414 insertions(+), 204 deletions(-) diff --git a/source/molecularsequence/structuredefinition-MolecularSequence.xml b/source/molecularsequence/structuredefinition-MolecularSequence.xml index ce23568c380..6bf114dd717 100644 --- a/source/molecularsequence/structuredefinition-MolecularSequence.xml +++ b/source/molecularsequence/structuredefinition-MolecularSequence.xml @@ -5,8 +5,11 @@ + - + @@ -14,9 +17,9 @@ - - - + @@ -94,7 +97,7 @@ - + @@ -110,85 +113,123 @@ - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - + + + + + + - - + - - - - + + + + + - + + + - - + + + @@ -198,8 +239,8 @@ - - + + @@ -209,8 +250,8 @@ - - + + @@ -226,17 +267,17 @@ - - - - - - - - - - - + @@ -250,161 +291,302 @@ - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - + + + + - + + + + + + + + + + + + - - - - - - - - - - - - - - - + + + + + - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - + + + + + + + + + + + - + + + + + + + + + - - - - - - - - - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - + - - - - - - - - - - - - + + + + + - + - - - - - - - - - - - - + + + + + + @@ -412,47 +594,75 @@ - - - - - + + + + + - + + - - - - - + + + + + - - - - + + + + - + - - - - - + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + From 2c3ddf5ac2d24b8e6107fa8134a0b5f4de88faf5 Mon Sep 17 00:00:00 2001 From: khalifa-aly Date: Wed, 30 Aug 2023 14:52:48 -0500 Subject: [PATCH 002/114] removing MolSeq from the patient compartment --- source/compartments.xml | 1817 ++++++++++++++++++++------------------- 1 file changed, 911 insertions(+), 906 deletions(-) diff --git a/source/compartments.xml b/source/compartments.xml index b4ecb32f1a8..c99e2d4c8d5 100644 --- a/source/compartments.xml +++ b/source/compartments.xml @@ -1,907 +1,912 @@ - - Grahame - Grahame Grieve - 2013-07-04T21:40:46Z - 2023-02-10T20:42:24Z - 16.00 - - - 747a3dc3-14ba-4528-94a7-b06f9d606003 - - - - - - - - - - 1 - False - False - - - - - - - - - - - - - - - - - - Name - Title - Description - Identification - Inclusion - - - patient - Patient - The set of resources associated with a particular patient - There is an instance of the patient compartment for each patient resource, and the identity of the compartment is the same as the patient. When a patient is linked to another patient resource, the records associated with the linked patient resource will not be returned as part of the compartment search. Those records will be returned only with another compartment search using the "id" for the linked patient resource. In cases where two patients have been merged rather than linked, associated resources should be moved to the target patient as part of the merge process, so the patient compartment for the target patient would include all relevant data, and the patient compartment for the source patient would include only the linked Patient and possibly remnant resources like AuditEvent. - The patient compartment includes any resources where the subject of the resource is the patient, and some other resources that are directly linked to resources in the patient compartment - - - encounter - Encounter - The set of resources associated with a particular encounter - There is an instance of the encounter compartment for each encounter resource, and the identity of the compartment is the same as the encounter - The encounter compartment includes any resources where the resource has an explicitly nominated encounter, and some other resources that themselves link to resources in the encounter compartment. Note that for many resources, the exact nature of the link to encounter can be ambiguous (e.g. for a DiagnosticReport, is it the encounter when it was initiated, or when it was reported?) - - - relatedPerson - RelatedPerson - The set of resources associated with a particular 'related person' - There is an instance of the relatedPerson compartment for each relatedPerson resource, and the identity of the compartment is the same as the relatedPerson - The relatedPerson compartment includes any resources where the resource is explicitly linked to relatedPerson (usually as author) - - - practitioner - Practitioner - The set of resources associated with a particular practitioner - There is an instance of the practitioner compartment for each Practitioner resource, and the identity of the compartment is the same as the Practitioner - The practitioner compartment includes any resources where the resource is explicitly linked to a Practitioner (usually as author, but other kinds of linkage exist) - - - device - Device - The set of resources associated with a particular device - There is an instance of the device compartment for each Device resource, and the identity of the compartment is the same as the Device - The device compartment includes any resources where the resource is explicitly linked to a Device (mostly subject or performer) - -
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