add maturity label feature

ga4gh · Oct 23, 2024 · 8711806 · 8711806
1 parent fe29951
commit 8711806
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diff --git a/src/ga4gh/gks/metaschema/scripts/y2t.py b/src/ga4gh/gks/metaschema/scripts/y2t.py
@@ -65,6 +65,20 @@ def get_ancestor_with_attributes(class_name, proc):
 def main(proc_schema):
     for class_name, class_definition in proc_schema.defs.items():
         with open(proc_schema.def_fp / (class_name + '.rst'), "w") as f:
+            maturity = class_definition.get('maturity', '')
+            if maturity == 'draft':
+                print("""
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+                      
+                    """, file=f)
+            elif maturity == 'trial use':
+                print("""
+.. note:: This data class is at a **trial use** maturity level and may change
+    in future releases. Maturity levels are described in the :ref:`maturity-model`.
+                      
+                    """, file=f)
             print("**Computational Definition**\n", file=f)
             print(class_definition['description'], file=f)
             if proc_schema.class_is_passthrough(class_name):

diff --git a/tests/data/vrs/def/Adjacency.rst b/tests/data/vrs/def/Adjacency.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 The `Adjacency` class can represent either the termination of a sequence or the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence.

diff --git a/tests/data/vrs/def/Allele.rst b/tests/data/vrs/def/Allele.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 The state of a molecule at a :ref:`Location`.

diff --git a/tests/data/vrs/def/CopyNumberChange.rst b/tests/data/vrs/def/CopyNumberChange.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a system (e.g. genome, cell, etc.) relative to a baseline ploidy.

diff --git a/tests/data/vrs/def/CopyNumberCount.rst b/tests/data/vrs/def/CopyNumberCount.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`, within a system (e.g. genome, cell, etc.).

diff --git a/tests/data/vrs/def/Expression.rst b/tests/data/vrs/def/Expression.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 Representation of a variation by a specified nomenclature or syntax for a Variation object.  Common examples of expressions for the description of molecular variation include the HGVS  and ISCN nomenclatures.

diff --git a/tests/data/vrs/def/Haplotype.rst b/tests/data/vrs/def/Haplotype.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 An ordered set of co-occurring :ref:`variants <Variation>` on the same molecule.

diff --git a/tests/data/vrs/def/LengthExpression.rst b/tests/data/vrs/def/LengthExpression.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 A sequence expressed only by its length.

diff --git a/tests/data/vrs/def/LiteralSequenceExpression.rst b/tests/data/vrs/def/LiteralSequenceExpression.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 An explicit expression of a Sequence.

diff --git a/tests/data/vrs/def/Range.rst b/tests/data/vrs/def/Range.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 An inclusive range of values bounded by one or more integers.
diff --git a/tests/data/vrs/def/ReferenceLengthExpression.rst b/tests/data/vrs/def/ReferenceLengthExpression.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 An expression of a length of a sequence from a repeating reference.

diff --git a/tests/data/vrs/def/Residue.rst b/tests/data/vrs/def/Residue.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 A character representing a specific residue (i.e., molecular species) or groupings of these ("ambiguity codes"), using `one-letter IUPAC abbreviations <https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes>`_ for nucleic acids and amino acids.
diff --git a/tests/data/vrs/def/SequenceLocation.rst b/tests/data/vrs/def/SequenceLocation.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 A :ref:`Location` defined by an interval on a referenced :ref:`Sequence`.

diff --git a/tests/data/vrs/def/SequenceReference.rst b/tests/data/vrs/def/SequenceReference.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 A sequence of nucleic or amino acid character codes.

diff --git a/tests/data/vrs/def/SequenceString.rst b/tests/data/vrs/def/SequenceString.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 A character string of :ref:`Residues <Residue>` that represents a biological sequence using the conventional sequence order (5’-to-3’ for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.