From 730d83af354207dd62cae774396015a58704a983 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 31 Oct 2023 07:59:08 -0500
Subject: [PATCH 01/11] Removed prototype calls to Cells API.

---
 src/hs_ontology_api/routes/neo4j_logic.py | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/src/hs_ontology_api/routes/neo4j_logic.py b/src/hs_ontology_api/routes/neo4j_logic.py
index 3eba1d4..f4ca2a8 100644
--- a/src/hs_ontology_api/routes/neo4j_logic.py
+++ b/src/hs_ontology_api/routes/neo4j_logic.py
@@ -628,16 +628,10 @@ def query_cypher_dataset_info(sab: str) -> str:
 def genedetail_get_logic(neo4j_instance, gene_id: str) -> List[GeneDetail]:
     """
     Returns detailed information on a gene, based on an input list of HGNC identifiers in the request body of a POST.
+    :param neo4j_instance: instance of neo4j connection
+    :param gene_id: HGNC identifier for a gene
     """
     # response list
-
-    # Read indexed cell-type data from Cells API.
-    # The cells_client was instantiated at startup.
-    oc = current_app.cells_client
-
-    # The current prototype call reads a CSV of static information obtained from
-    # prior calls to the Cells API.
-    cellsapi_celltypes = oc.celltypes_for_gene_csv(gene_id)
     genedetails: [GeneDetail] = []
 
     # Load annotated Cypher query from the cypher directory.

From d33daaabcbca4af8909f9ddf4380b698371afce8 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 31 Oct 2023 10:04:17 -0500
Subject: [PATCH 02/11] Proposed endpoints for proteins; protein; celltypes;
 and celltype

---
 hs-ontology-api-spec.yaml | 355 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 349 insertions(+), 6 deletions(-)

diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
index e103e36..e390636 100644
--- a/hs-ontology-api-spec.yaml
+++ b/hs-ontology-api-spec.yaml
@@ -392,7 +392,6 @@ paths:
           description: No genes that satisfied the criteria were found. This usually means that there are no genes with HGNC approved symbols that start with the string specified in the *starts_with* parameter.
         '5XX':
           description: Unexpected error
-
   /gene/{id}:
     get:
       operationId: gene_detail_get
@@ -418,6 +417,140 @@ paths:
           description: No information for gene with HGNC identifier *id*.
         '5XX':
           description: Unexpected error
+  /proteins:
+    get:
+      operationId: protein_list_get
+      summary: Return high-level information on a set of proteins specified by pagination parameters.
+      parameters:
+        - name: page
+          in: query
+          required: false
+          description: Offset set of proteins of count=proteinsperpage. Can be a non-negative number or the words "first" or "last".
+          schema:
+            type: string
+            default: 1
+          example: 1
+        - name: proteinsperpage
+          in: query
+          required: false
+          description: Number of proteins per "page" to return. Can be a nonzero number.
+          schema:
+            type: string
+            default: 10
+        - name: starts_with
+          in: query
+          required: false
+          description: Optional *case-insensitive* string by which to filter by UniProtKB protein name.
+          schema:
+            type: string
+            example: M
+      responses:
+        '200':
+          description: high-level information on proteins specified by UniProtKB identifiers.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/ProteinListResponse'
+        '400':
+          description: Invalid parameter--e.g., *proteinsperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
+        '404':
+          description: No proteins that satisfied the criteria were found. This usually means that there are no proteins with UniprotKB names that start with the string specified in the *starts_with* parameter.
+        '5XX':
+          description: Unexpected error
+  /protein/{id}:
+    get:
+      operationId: protein_detail_get
+      summary: Return detailed information on a protein specified by a UniProtKB identifier.
+      parameters:
+        - name: id
+          in: path
+          required: true
+          description: Case-insensitive UniProtKB identifier
+          schema:
+            type: string
+            example: Q13201
+      responses:
+        '200':
+          description: detailed information on the protein specified by a UniProtKB identifier.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/ProteinDetailResponse'
+        '404':
+          description: No information for protein with UniProtKB identifier *id*.
+        '5XX':
+          description: Unexpected error
+  /celltypes:
+    get:
+      operationId: celltype_list_get
+      summary: Return high-level information on a set of cell types specified by pagination parameters.
+      parameters:
+        - name: page
+          in: query
+          required: false
+          description: Offset set of genes of count=celltypesperpage. Can be a non-negative number or the words "first" or "last".
+          schema:
+            type: string
+            default: 1
+          example: 1
+        - name: celltypesperpage
+          in: query
+          required: false
+          description: Number of cell types per "page" to return. Can be a nonzero number.
+          schema:
+            type: string
+            default: 10
+        - name: starts_with
+          in: query
+          required: false
+          description: Optional *case-insensitive* string by which to filter by cell type name.
+          schema:
+            type: string
+            example: E
+      responses:
+        '200':
+          description: high-level information on cell types specified by Cell Ontology.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/CellTypeListResponse'
+        '400':
+          description: Invalid parameter--e.g., *celltypesperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
+        '404':
+          description: No cell types that satisfied the criteria were found. This usually means that there are no cell types with names that start with the string specified in the *starts_with* parameter.
+        '5XX':
+          description: Unexpected error
+  /celltype/{id}:
+    get:
+      operationId: celltype_detail_get
+      summary: Return detailed information on a cell type specified by a name.
+      parameters:
+        - name: id
+          in: path
+          required: true
+          description: case-insensitive Cell Ontology identifier in format CL{id}
+          schema:
+            type: string
+            example: CL0002138
+      responses:
+        '200':
+          description: detailed information on the cell type specified by a Cell Ontology identifier.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/CellTypeDetailResponse'
+        '404':
+          description: No information for cell type with identifier *id*.
+        '5XX':
+          description: Unexpected error
 components:
   schemas:
     AssayTypePropertyInfo:
@@ -591,7 +724,7 @@ components:
             - SenNet
     GeneListResponse:
       type: object
-      description: High-level information on a set of genes requested by the gene_list endpoint.
+      description: High-level information on a set of genes requested by the genes endpoint.
       properties:
         genes:
           type: array
@@ -613,11 +746,11 @@ components:
                 example: Multimerin is a massive, soluble protein found in....
         genes_per_page:
           type: number
-          description: value of genesperpage paramater from the gene_list endpoint
+          description: value of genesperpage parameter from the gene_list endpoint
           example: 3
         page:
           type: number
-          description: value of page paramater from the gene_list endpoint
+          description: value of page parameter from the gene_list endpoint
           example: 1
         total_pages:
           type: number
@@ -633,7 +766,7 @@ components:
           example: 500
     GeneDetailResponse: # JAS Sept 2023
       type: object
-      description: Detailed information on a gene.
+      description: Detailed information on a gene requested by the gene endpoint
       properties:
         alias_names:
           type: array
@@ -734,4 +867,214 @@ components:
         summary:
           type: string
           description: RefSeq summary of the gene
-          example: Multimerin is a massive, soluble protein found in....
\ No newline at end of file
+          example: Multimerin is a massive, soluble protein found in....
+    ProteinListResponse:
+      type: object
+      description: High-level list of proteins with pagination details, requested by the proteins endpoint.
+      properties:
+        proteins:
+          type: array
+          description: protein information
+          items:
+            type: object
+            properties:
+              id:
+                type: string
+                description: UniProtKB identifier
+                example: Q13201
+              entry_name:
+                type: string
+                description: UniProtKB Entry Name
+                example: MMRN1_HUMAN
+              recommended_name:
+                type: string
+                description: UniProtKB Recommended Name
+                example: multimerin-1
+        proteins_per_page:
+          type: number
+          description: value of proteinsperpage parameter from the proteins endpoint
+          example: 3
+        page:
+          type: number
+          description: value of page parameter from the proteins endpoint
+          example: 1
+        total_pages:
+          type: number
+          description: total number of "pages" based on the values of proteinsperpage and the total number of proteins
+          example: 14381
+        starts_with:
+          type: string
+          description: value of starts_with from the proteins endpoint
+          example: M
+        protein_count:
+          type: number
+          description: Count of proteins. If starts_with is non-null, the count is that of the proteins with names that start with the value of starts_with.
+          example: 500
+    ProteinDetailResponse:
+      type: object
+      description: Detailed information on a protein requested by the protein endpoint
+      properties:
+        id:
+          type: string
+          description: UniProtKB identifier
+          example: Q13201
+        entry_name:
+          type: string
+          description: UniProtKB Entry Name
+          example: MMRN1_HUMAN
+        recommended_name:
+          type: string
+          description: UniProtKB Recommended Name
+          example: multimerin-1
+        synonyms:
+          type: array
+          description: alternative names
+          items:
+            type: string
+          example: [EMILIN-4,Elastin microfibril interface located protein 4 (Elastin microfibril interfacer 4),Endothelial cell multimerin]
+        references:
+          type: array
+          description: Array of links to protein databases
+          items:
+            type: object
+            properties:
+              source:
+                type: string
+                description: protein database name
+                example: uniprotkb
+              entry:
+                type: string
+                description: description of protein in source--e.g., the "function" in UniProtKB
+                example: Carrier protein for platelet (but not plasma) factor V/Va. Plays a role…
+              url:
+                type: string
+                description: URL to reference site
+                example: https://www.ncbi.nlm.nih.gov/gene/22915
+              curation:
+                type: string
+                description: method of curation
+                enum:
+                  - swissprot
+                  - trembl
+        organisms:
+          type: array
+          description: array of relevant organism, named in binomial nomenclature
+          items:
+            type: string
+            example: [Homo sapiens]
+    CellTypeListResponse:
+      type: object
+      description: High-level list of cell types with pagination details, requested by the celltypes endpoint.
+      properties:
+        proteins:
+          type: array
+          description: cell type information
+          items:
+            type: object
+            properties:
+              id:
+                type: string
+                description: Cell Ontology code
+                example: CL:0002138
+              name:
+                type: string
+                description: Preferred term for the cell type from Cell Ontology
+                example: endothelial cell of lymphatic vessel
+              definition:
+                type: string
+                description: Definition of the cell type from Cell Ontology
+                example: A endothelial cell of a lymphatic vessel. The border of…
+        celltypes_per_page:
+          type: number
+          description: value of celltypesperpage parameter from the celltypes endpoint
+          example: 3
+        page:
+          type: number
+          description: value of page parameter from the celltypes endpoint
+          example: 1
+        total_pages:
+          type: number
+          description: total number of "pages" based on the values of celltypesperpage and the total number of celltypes
+          example: 14381
+        starts_with:
+          type: string
+          description: value of starts_with from the celltypes endpoint
+          example: E
+        cell_type_count:
+          type: number
+          description: Count of cell types. If starts_with is non-null, the count is that of the cell types with names that start with the value of starts_with.
+          example: 500
+    CellTypeDetailResponse:
+      type: object
+      description: Detailed information on a cell type requested by the celltype endpoint
+      properties:
+        id:
+          type: string
+          description: Cell Ontology code
+          example: CL:0002138
+        name:
+          type: string
+          description: Preferred term for the cell type from Cell Ontology
+          example: endothelial cell of lymphatic vessel
+        definition:
+          type: string
+          description: Definition of the cell type from Cell Ontology
+          example: A endothelial cell of a lymphatic vessel. The border of…
+        biomarkers:
+          type: array
+          description: Array of biomarkers associated with the cell type
+          items:
+            type: object
+            properties:
+              reference:
+                type: string
+                description: source for association between cell type and biomarker
+                enum:
+                  - Human Reference Atlas
+                  - Cells
+              biomarker_type:
+                type: string
+                description: type of biomarker
+                enum:
+                  - gene
+                  - protein
+                  - lipid
+                  - metabolite
+              entry:
+                type: object
+                description: Encoded entry in reference
+                properties:
+                  vocabulary:
+                    type: string
+                    description: vocabulary for entry
+                    example: hgnc
+                  id:
+                    type: string
+                    description: identifier for entry in vocabulary
+                    example: 7178
+                  symbol:
+                    type: string
+                    description: symbol for entry in vocabulary
+                    example: MMRN1
+                  name:
+                    type: string
+                    description: preferred term for entry in vocabulary
+                    example: multimerin-1
+        organs:
+          type: array
+          description: Organs associated with the cell type, based on relationships in the Human Resource Atlas and Azimuth
+          items:
+            type: object
+            properties:
+              id:
+                type: string
+                description: Identifier (code) for the organ in source
+                example: 0000948
+              source:
+                type: string
+                description: Source vocabulary for id for organ
+                example: UBERON
+              name:
+                type: string
+                description: Name (preferred term) for organ in source
+                example: heart
\ No newline at end of file

From b138cb072cd38c1bf1afa3854895af2ae0824351 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 31 Oct 2023 10:24:05 -0500
Subject: [PATCH 03/11] Proposed endpoints for proteins; protein; celltypes;
 and celltype

---
 src/hs_ontology_api/routes/neo4j_logic.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/hs_ontology_api/routes/neo4j_logic.py b/src/hs_ontology_api/routes/neo4j_logic.py
index f4ca2a8..c3a93ba 100644
--- a/src/hs_ontology_api/routes/neo4j_logic.py
+++ b/src/hs_ontology_api/routes/neo4j_logic.py
@@ -657,9 +657,6 @@ def genedetail_get_logic(neo4j_instance, gene_id: str) -> List[GeneDetail]:
                                record.get('cell_types_code_definition'),
                                record.get('cell_types_codes_organ'),record.get('cell_types_codes_source')).serialize()
 
-                # Append cell type information from Cells API.
-                for cell_type in cellsapi_celltypes:
-                    genedetail['cell_types'].append(cell_type)
                 genedetails.append(genedetail)
 
             except KeyError:

From 909521d4230e24c1c8e44ff3276ccf19b62e6594 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Wed, 1 Nov 2023 11:07:34 -0500
Subject: [PATCH 04/11] Proposed endpoints to replace use of
 field_descriptions.yaml, field_types.yaml, field_entities.yaml,
 field_assays.yaml, and field_schemas.yaml in ingest-validation-tools.

---
 hs-ontology-api-spec.yaml | 289 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 288 insertions(+), 1 deletion(-)

diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
index e390636..562c2e7 100644
--- a/hs-ontology-api-spec.yaml
+++ b/hs-ontology-api-spec.yaml
@@ -551,6 +551,132 @@ paths:
           description: No information for cell type with identifier *id*.
         '5XX':
           description: Unexpected error
+  /field_descriptions:
+    get:
+      operationId: field_descriptions_get
+      summary: Return descriptions for ingest metadata fields. Replacement for field_descriptions.yaml.
+      responses:
+        '200':
+          description: Ingest metadata fields and descriptions
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/FieldDescriptionsResponse'
+        '5XX':
+          description: Unexpected error
+  /field_types:
+    get:
+      operationId: field_types_get
+      summary: Return data types for ingest metadata fields. Replacement for field_types.yaml.
+      responses:
+        '200':
+          description: Ingest metadata fields mapped to XSD data types.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/FieldTypesResponse'
+        '5XX':
+          description: Unexpected error
+  /field_entities:
+    get:
+      operationId: field_entities_get
+      summary: Return associations between ingest metadata fields and the provenance entities of an application. Replacement for field_types.yaml.
+      parameters:
+        - name: application_context
+          in: query
+          required: true
+          description: Filter to indicate application context
+          schema:
+            type: string
+            default: HUBMAP
+            enum:
+              - HUBMAP
+              - SENNET
+              - hubmap
+              - sennet
+              - HuBMAP
+              - SenNet
+      responses:
+        '200':
+          description: Associations between ingest metadata fields and application-specific provenance entities.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/FieldEntitiesResponse'
+        '400':
+          description: missing application context
+        '5XX':
+          description: Unexpected error
+  /field_assays:
+    get:
+      operationId: field_assays_get
+      summary: Return associations between ingest metadata fields and the "assays" (dataset data types) for an application. Replacement for field_assays.yaml.
+      parameters:
+        - name: application_context
+          in: query
+          required: true
+          description: Filter to indicate application context
+          schema:
+            type: string
+            default: HUBMAP
+            enum:
+              - HUBMAP
+              - SENNET
+              - hubmap
+              - sennet
+              - HuBMAP
+              - SenNet
+      responses:
+        '200':
+          description: Associations between ingest metadata fields and application-specific assays/dataset types.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/FieldAssaysResponse'
+        '400':
+          description: missing application context
+        '5XX':
+          description: Unexpected error
+  /field_schemas:
+    get:
+      operationId: field_schemas_get
+      summary: Return associations between ingest metadata fields and metadata schemas for an application. Replacement for field_schemas.yaml.
+      parameters:
+        - name: application_context
+          in: query
+          required: true
+          description: Filter to indicate application context
+          schema:
+            type: string
+            default: HUBMAP
+            enum:
+              - HUBMAP
+              - SENNET
+              - hubmap
+              - sennet
+              - HuBMAP
+              - SenNet
+      responses:
+        '200':
+          description: Associations between ingest metadata fields and application-specific metadata schemas.
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/FieldSchemasResponse'
+        '400':
+          description: missing application context
+        '5XX':
+          description: Unexpected error
 components:
   schemas:
     AssayTypePropertyInfo:
@@ -1077,4 +1203,165 @@ components:
               name:
                 type: string
                 description: Name (preferred term) for organ in source
-                example: heart
\ No newline at end of file
+                example: heart
+    FieldDescriptionsResponse:
+      type: object
+      description: Descriptions ingest metadata fields from legacy field_descriptions.yaml
+      properties:
+        fields:
+          type: array
+          description: array of fields and their descriptions
+          items:
+            type: object
+            properties:
+              codeID:
+                type: string
+                description: Code in the HMFIELD ontology
+                example: HMFIELD:1001
+              identifier:
+                type: string
+                description: identifier for metadata field
+                example: ablation_distance_between_shots_x_units
+              description:
+                type: string
+                description: description of field
+                example: Units of x resolution distance between laser ablation shots.
+    FieldTypesResponse:
+      type: object
+      description: Associations between metadata field and data type ingest metadata fields from legacy field_types.yaml
+      properties:
+        fields:
+          type: array
+          description: array of fields and their data types
+          items:
+            type: object
+            properties:
+              codeID:
+                type: string
+                description: Code in the HMFIELD ontology
+                example: HMFIELD:1001
+              identifier:
+                type: string
+                description: identifier for metadata field
+                example: ablation_distance_between_shots_x_units
+              type:
+                type: object
+                properties:
+                  XSDCode:
+                    type: string
+                    description: Code in XSD
+                    example: xsd:string
+                  name:
+                    type: string
+                    description: name for type
+                    example: string
+    FieldEntitiesResponse:
+      type: object
+      description: Associations between fields and provenance entities for ingest metadata fields from legacy field_types.yaml
+      properties:
+        fields:
+          type: array
+          description: array of fields, each with its associated provenance entities
+          items:
+            type: object
+            properties:
+              codeID:
+                type: string
+                description: Code in the HMFIELD ontology
+                example: HMFIELD:1001
+              identifier:
+                type: string
+                description: identifier for metadata field
+                example: ablation_distance_between_shots_x_units
+              entities:
+                type: array
+                description: array of provenance entities associated with the field
+                items:
+                  type: object
+                  properties:
+                    code:
+                      type: string
+                      description: Code in application ontology
+                      example: HUBMAP:C040001
+                    name:
+                      type: string
+                      description: name
+                      example: dataset
+    FieldAssaysResponse:
+      type: object
+      description: Associations between fields and "assays" (dataset types) for ingest metadata fields from legacy field_assays.yaml
+      properties:
+        fields:
+          type: array
+          description: array of fields, each with its associated assays/dataset types
+          items:
+            type: object
+            properties:
+              codeID:
+                type: string
+                description: Code in the HMFIELD ontology
+                example: HMFIELD:1001
+              identifier:
+                type: string
+                description: identifier for metadata field
+                example: ablation_distance_between_shots_x_units
+              assays:
+                type: array
+                description: array of "assays" (dataset types) associated with the field
+                items:
+                  type: object
+                  properties:
+                    data_type:
+                      type: object
+                      description: The data_type for the assay/dataset type--i.e., the key for ingest workflows
+                      properties:
+                        code:
+                          type: string
+                          description: Code in application ontology
+                          example: HUBMAP:C006904
+                        name:
+                          type: string
+                          description: the data_type string used in ingest workflows
+                          example: IMC
+                    display_name:
+                      type: string
+                      description: The display name for the assay/dataset type in the Portal UI
+                      example: Imaging Mass Cytometry (2D)
+                    alt-names:
+                      type: array
+                      description: The set of alt-names (synonyms for data_type) for the assay/dataset type
+                      items:
+                        type: string
+                        example: [Imaging Mass Cytometry,2D-IMC,IMC]
+    FieldSchemasResponse:
+      type: object
+      description: Associations between fields and metadata schemas for ingest metadata fields from legacy field_schemas.yaml
+      properties:
+        fields:
+          type: array
+          description: array of fields, each with its associated schemas
+          items:
+            type: object
+            properties:
+              codeID:
+                type: string
+                description: Code in the HMFIELD ontology
+                example: HMFIELD:1001
+              identifier:
+                type: string
+                description: identifier for metadata field
+                example: ablation_distance_between_shots_x_units
+              schemas:
+                type: array
+                description: array of metadata schemas associated with the field
+                items:
+                  type: object
+                  properties:
+                    code:
+                      type: string
+                      description: Code in HMFIELD ontology
+                      example: HMFIELD:1001
+                    name:
+                      type: string
+                      description: name
+                      example: imc3d
\ No newline at end of file

From 78b86e4c21598300e3581e9615d19721e39458d7 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 7 Nov 2023 17:27:37 -0600
Subject: [PATCH 05/11] Refactored controllers and Blueprints to reflect
 requested change in names of routes--i.e., genes and genes-info.

---
 .../routes/{genedetail => genes}/__init__.py        |  0
 .../genes_controller.py}                            | 13 ++++---------
 .../routes/{geneslist => genesinfo}/__init__.py     |  0
 .../genesinfo_controller.py}                        |  4 ++--
 src/main.py                                         |  8 ++++----
 5 files changed, 10 insertions(+), 15 deletions(-)
 rename src/hs_ontology_api/routes/{genedetail => genes}/__init__.py (100%)
 rename src/hs_ontology_api/routes/{genedetail/genedetail_controller.py => genes/genes_controller.py} (67%)
 rename src/hs_ontology_api/routes/{geneslist => genesinfo}/__init__.py (100%)
 rename src/hs_ontology_api/routes/{geneslist/geneslist_controller.py => genesinfo/genesinfo_controller.py} (95%)

diff --git a/src/hs_ontology_api/routes/genedetail/__init__.py b/src/hs_ontology_api/routes/genes/__init__.py
similarity index 100%
rename from src/hs_ontology_api/routes/genedetail/__init__.py
rename to src/hs_ontology_api/routes/genes/__init__.py
diff --git a/src/hs_ontology_api/routes/genedetail/genedetail_controller.py b/src/hs_ontology_api/routes/genes/genes_controller.py
similarity index 67%
rename from src/hs_ontology_api/routes/genedetail/genedetail_controller.py
rename to src/hs_ontology_api/routes/genes/genes_controller.py
index d96947f..857028c 100644
--- a/src/hs_ontology_api/routes/genedetail/genedetail_controller.py
+++ b/src/hs_ontology_api/routes/genes/genes_controller.py
@@ -4,15 +4,10 @@
 from ..neo4j_logic import genedetail_get_logic
 
 
-genedetail_blueprint = Blueprint('genedetail', __name__, url_prefix='/gene')
+genes_blueprint = Blueprint('genes', __name__, url_prefix='/genes')
 
-@genedetail_blueprint.route('', methods=['GET'])
-def genedetail_expand_get():
-    return make_response('The /gene endpoint should specify a single HGNC gene identifier--e.g., /gene/MMRN1.', 400)
-
-
-@genedetail_blueprint.route('/<id>', methods=['GET'])
-def genedetail_id_expand_get(id=None):
+@genes_blueprint.route('/<id>', methods=['GET'])
+def genes_id_expand_get(id=None):
     """Returns detailed information on a single gene.
 
     :rtype: Union[List[GeneDetail]]
@@ -30,7 +25,7 @@ def genedetail_id_expand_get(id=None):
 
     if id =='' or id is None:
         # Missing ID parameter in URL
-        return make_response('The /gene endpoint must specify a HGNC gene identifier--e.g., /gene/MMRN1.',400)
+        return make_response('The /genes endpoint must specify a HGNC gene identifier--e.g., /genes/MMRN1.',400)
 
     neo4j_instance = current_app.neo4jConnectionHelper.instance()
     result = genedetail_get_logic(neo4j_instance, id)
diff --git a/src/hs_ontology_api/routes/geneslist/__init__.py b/src/hs_ontology_api/routes/genesinfo/__init__.py
similarity index 100%
rename from src/hs_ontology_api/routes/geneslist/__init__.py
rename to src/hs_ontology_api/routes/genesinfo/__init__.py
diff --git a/src/hs_ontology_api/routes/geneslist/geneslist_controller.py b/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
similarity index 95%
rename from src/hs_ontology_api/routes/geneslist/geneslist_controller.py
rename to src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
index f1a40e8..93da0d5 100644
--- a/src/hs_ontology_api/routes/geneslist/geneslist_controller.py
+++ b/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
@@ -4,9 +4,9 @@
 from ..neo4j_logic import genelist_get_logic,genelist_count_get_logic
 import math
 
-geneslist_blueprint = Blueprint('geneslist', __name__, url_prefix='/genes')
+genesinfo_blueprint = Blueprint('genes-info', __name__, url_prefix='/genes-info')
 
-@geneslist_blueprint.route('', methods=['GET'])
+@genesinfo_blueprint.route('', methods=['GET'])
 def geneslist() -> list[str]:
 
     neo4j_instance = current_app.neo4jConnectionHelper.instance()
diff --git a/src/main.py b/src/main.py
index d48a00a..cf6deec 100755
--- a/src/main.py
+++ b/src/main.py
@@ -10,8 +10,8 @@
 from hs_ontology_api.routes.relationships.relationships_controller import relationships_blueprint
 from hs_ontology_api.routes.valueset.valueset_controller import valueset_blueprint
 # JAS September 2023
-from hs_ontology_api.routes.genedetail.genedetail_controller import genedetail_blueprint
-from hs_ontology_api.routes.geneslist.geneslist_controller import geneslist_blueprint
+from hs_ontology_api.routes.genes.genes_controller import genes_blueprint
+from hs_ontology_api.routes.genesinfo.genesinfo_controller import genesinfo_blueprint
 
 # Cells API client
 from hs_ontology_api.routes.cellsclient import OntologyCellsClient
@@ -32,8 +32,8 @@ def make_flask_config():
 app.register_blueprint(relationships_blueprint)
 app.register_blueprint(valueset_blueprint)
 # JAS Sept 2023
-app.register_blueprint(genedetail_blueprint)
-app.register_blueprint(geneslist_blueprint)
+app.register_blueprint(genes_blueprint)
+app.register_blueprint(genesinfo_blueprint)
 
 # Instantiate a Cells API client.
 cellsurl = make_flask_config().get('CELLSURL')

From a891665d48f14026fe49914fc44e6db1f6c7b4f1 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 7 Nov 2023 20:30:58 -0600
Subject: [PATCH 06/11] Refactored to move neo4j_logic.py, cellsclient.py to
 utils directory. Moved loadquerystring function into neo4j_logic.py.

---
 src/hs_ontology_api/cypher/util_query.py      |  22 --
 src/hs_ontology_api/models/genelist.py        | 164 +++------------
 src/hs_ontology_api/models/pagination.py      | 188 ++++++++++++++++++
 .../routes/assayname/assayname_controller.py  |   2 +-
 .../routes/assaytype/assaytype_controller.py  |   2 +-
 .../routes/datasets/datasets_controller.py    |   2 +-
 .../routes/genes/genes_controller.py          |   4 +-
 .../routes/genesinfo/genesinfo_controller.py  |  26 +--
 .../routes/organs/organs_controller.py        |   2 +-
 .../relationships/relationships_controller.py |   2 +-
 .../routes/valueset/valueset_controller.py    |   2 +-
 src/hs_ontology_api/utils/README.md           |   9 +
 src/hs_ontology_api/utils/__init__.py         |   0
 .../{routes => utils}/cellsclient.py          |   2 +-
 .../{routes => utils}/neo4j_logic.py          |  47 +++--
 src/main.py                                   |   2 +-
 16 files changed, 283 insertions(+), 193 deletions(-)
 delete mode 100644 src/hs_ontology_api/cypher/util_query.py
 create mode 100644 src/hs_ontology_api/models/pagination.py
 create mode 100644 src/hs_ontology_api/utils/README.md
 create mode 100644 src/hs_ontology_api/utils/__init__.py
 rename src/hs_ontology_api/{routes => utils}/cellsclient.py (97%)
 rename src/hs_ontology_api/{routes => utils}/neo4j_logic.py (96%)

diff --git a/src/hs_ontology_api/cypher/util_query.py b/src/hs_ontology_api/cypher/util_query.py
deleted file mode 100644
index 402c47e..0000000
--- a/src/hs_ontology_api/cypher/util_query.py
+++ /dev/null
@@ -1,22 +0,0 @@
-# coding: utf-8
-
-# JAS September 2023
-
-# Utilities to load large Cypher query strings.
-
-import os
-
-def loadquerystring(filename: str) ->str:
-
-    # Load a query string from a file.
-    # filename: filename, without path.
-
-    # Assumes that the file is in the cypher directory.
-
-    fpath = os.path.dirname(os.getcwd())
-    fpath = os.path.join(fpath,'src/hs_ontology_api/cypher',filename)
-
-    f = open(fpath, "r")
-    query = f.read()
-    f.close()
-    return query
diff --git a/src/hs_ontology_api/models/genelist.py b/src/hs_ontology_api/models/genelist.py
index 3811c27..4dccf5f 100644
--- a/src/hs_ontology_api/models/genelist.py
+++ b/src/hs_ontology_api/models/genelist.py
@@ -2,7 +2,7 @@
 
 # JAS October 2023
 # GeneList model class
-# Used by the geneslist endpoint.
+# Used by the genes-info endpoints.
 # Provides information on genes identified by either the UBKG or the Cells API--i.e., that have relevance to HuBMAP/SenNet.
 
 from __future__ import absolute_import
@@ -13,64 +13,50 @@
 # Sub-object models
 # Array of gene detail objects
 from hs_ontology_api.models.genelist_detail import GeneListDetail
+from hs_ontology_api.models.pagination import Pagination
 
 class GeneList():
-    def __init__(self, page=None, total_pages=None, genesperpage=None, genes=None, starts_with=None, gene_count=None):
+    def __init__(self, page=None, totalpages=None, genesperpage=None, genes=None, startswith=None, genecount=None):
         """GeneList - a model defined in OpenAPI
 
-                    :param page: Relative "page" (block of genes)
+                    :param page: Requested relative "page" (block of genes)
                     :type page: str
-                    :param total_pages: Total number of "pages" (blocks of genes)
-                    :type total_pages: str
-                    :param genes: List of genes in page
+                    :param totalpages: Calculated total number of "pages" (blocks of genes)
+                    :type totalpages: str
+                    :param genes: List of gene objects for an array
                     :type genes: List[GeneListDetail]
-                    :param genesperpage: Number of genes in each "page" (block)
-                    :type genes: str
-                    :starts_with: Search string for type ahead
-                    :type starts_with: str
-                    :gene_count: Count of (filtered) genes
-                    :type gene_count: str
-
+                    :param genesperpage: Requested number of genes in each "page" (block)
+                    :type genesperpage: str
+                    :startswith: Optional search string for type ahead
+                    :type startswith: str
+                    :genecount: Calculated count of genes that satisfied the search criteria
+                    :type genecount: str
 
                 """
 
-        # Parameters other than page will be used to build nested GeneListDetail objects.
+        # The page, totalpages, genesperpage, startswith, and genecount parameters will be used to build a
+        # Pagination object.
+        # The genes parameter will be used to build an array of GeneListDetail objects.
 
         # Types for JSON objects
         self.openapi_types = {
-            'page': int,
-            'total_pages': int,
-            'genes_per_page': int,
+            'pagination': Pagination,
             'genes': List[GeneListDetail],
-            'starts_with': str,
-            'gene_count': int
         }
         # Attribute mappings used by the base Model class to assert key/value pairs.
         self.attribute_map = {
-            'page': 'page',
-            'total_pages': 'total_pages',
-            'genes_per_page': 'genes_per_page',
+            'pagination': 'pagination',
             'genes': 'genes',
-            'starts_with': 'starts_with',
-            'gene_count': 'gene_count'
         }
         # Property assignments
-        self._page = int(page)
-        self._total_pages = int(total_pages)
-        self._genes_per_page = int(genesperpage)
         self._genes = genes
-        self._starts_with = starts_with
-        self._gene_count = gene_count
+        self._pagination = Pagination(page, totalpages, genesperpage, startswith, genecount).serialize()
 
     def serialize(self):
         # Key/value format of response.
         return {
-            "page": self._page,
-            "total_pages": self._total_pages,
-            "genes_per_page": self._genes_per_page,
+            "pagination": self._pagination,
             "genes": self._genes,
-            "starts_with": self._starts_with,
-            "gene_count": self._gene_count
         }
 
     @classmethod
@@ -85,26 +71,25 @@ def from_dict(cls, dikt) -> 'GeneList':
         return util.deserialize_model(dikt, cls)
 
     @property
-    def page(self):
-        """Gets the page of this GeneList.
+    def pagination(self):
+        """Gets the pagination of this GeneList.
 
-        'Page' or relative block of genes.
-        :return: The page of this GeneList.
+        Pagination statistics
+        :return: The pagination of this GeneList.
         :rtype: str
         """
-        return self._page
-
-    @page.setter
-    def page(self, page):
-        """Sets the page of this GeneList.
+        return self._pagination
 
-        'Page' or relative block of genes.
+    @pagination.setter
+    def pagination(self, pagination):
+        """Sets the pagination of this GeneList.
 
-        :param page: The page of this GeneList
-        :type page: str
+        Pagination statistics
+        :param pagination: The pagination of this GeneList
+        :type pagination: str
         """
 
-        self._page = page
+        self._pagination = pagination
 
     @property
     def genes(self):
@@ -128,88 +113,3 @@ def genes(self, genes):
 
         self._genes = genes
 
-    @property
-    def total_pages(self):
-        """Gets the total_pages of this GeneList.
-
-        Total number of "pages" (blocks of genes)
-        :return: The total_pages of this GeneList.
-        :rtype: int
-        """
-        return self._total_pages
-
-    @total_pages.setter
-    def total_pages(self, total_pages):
-        """Sets the total_pages of this GeneList.
-
-        Total number of "pages" (blocks of genes)
-
-        :param total_pages: The genes of this GeneList
-        :type genes: int
-        """
-
-        self._total_pages = total_pages
-
-    @property
-    def genes_per_page(self):
-        """Gets the genes_per_page of this GeneList.
-
-        Number of genes per "page" or block of returns
-        :return: The total_pages of this GeneList.
-        :rtype: int
-        """
-        return self._total_pages
-
-    @genes_per_page.setter
-    def genes_per_page(self, genes_per_page):
-        """Sets the genes_per_page of this GeneList.
-
-        Number of genes per "page" or block of returns
-
-        :param genes_per_page: The genes_per_page of this GeneList
-        :type genes_per_page: int
-        """
-
-        self._genes_per_page = genes_per_page
-    @property
-    def starts_with(self):
-        """Gets the starts_with of this GeneList.
-
-        Optional type-ahead search string
-        :return: The starts_with of this GeneList.
-        :rtype: str
-        """
-        return self._starts_with
-
-    @starts_with.setter
-    def starts_with(self, starts_with):
-        """Sets the starts_with of this GeneList.
-
-        Optional type-ahead search string
-
-        :param starts_with: The genes_per_page of this GeneList
-        :type starts_with: int
-        """
-
-        self._starts_with = starts_with
-    @property
-    def gene_count(self):
-        """Gets the gene_count of this GeneList.
-
-        Count of genes
-        :return: The gene_count of this GeneList.
-        :rtype: str
-        """
-        return self._gene_count
-
-    @gene_count.setter
-    def gene_count(self, gene_count):
-        """Sets the gene_count of this GeneList.
-
-        Count of genes
-
-        :param gene_count: The gene_count of this GeneList
-        :type gene_count: int
-        """
-
-        self._gene_count = gene_count
diff --git a/src/hs_ontology_api/models/pagination.py b/src/hs_ontology_api/models/pagination.py
new file mode 100644
index 0000000..289b742
--- /dev/null
+++ b/src/hs_ontology_api/models/pagination.py
@@ -0,0 +1,188 @@
+# coding: utf-8
+
+# JAS November 2023
+# Pagination model class
+# Used by the *s-info endpoints--e.g., genes-info, proteins-info
+
+from __future__ import absolute_import
+from typing import List
+from ubkg_api.models.base_model_ import Model
+from ubkg_api.models import util
+
+class Pagination():
+
+    def __init__(self, page=None, totalpages=None, itemsperpage=None, startswith=None, itemcount=None):
+        """Pagination - a model defined in OpenAPI
+
+        :param page: Relative "page" (block of items)
+        :param totalpages: Total number of "pages" (blocks of items)
+        :param itemsperpage: Number of items in each "page" (block)
+        :param startswith: Optional search string for type ahead
+        :param itemcount: Count of items, optionally filtered by startswith
+
+        """
+
+        # Types for JSON objects
+        self.openapi_types = {
+            'page': int,
+            'totalpages': int,
+            'itemsperpage': int,
+            'startswith': str,
+            'itemcount': int
+        }
+
+        # Attribute mappings used by the base Model class to assert key/value pairs.
+        self.attribute_map = {
+            'page': 'page',
+            'totalpages': 'totalpages',
+            'itemsperpage': 'itemsperpage',
+            'startswith': 'startswith',
+            'itemcount': 'itemcount'
+        }
+        # Property assignments
+        self._page = int(page)
+        self._totalpages = int(totalpages)
+        self._itemsperpage = int(itemsperpage)
+        self._startswith = startswith
+        self._itemcount = itemcount
+
+    def serialize(self):
+        # Key/value format of response.
+        return {
+            "page": self._page,
+            "totalpages": self._totalpages,
+            "genes_per_page": self._itemsperpage,
+            "startswith": self._startswith,
+            "itemcount": self._itemcount
+        }
+
+    @classmethod
+    def from_dict(cls, dikt) -> 'Pagination':
+        """Returns the dict as a model
+
+        :param dikt: A dict.
+        :type: dict
+        :return: The class
+        :rtype: GeneDetail
+        """
+        return util.deserialize_model(dikt, cls)
+
+    def serialize(self):
+        # Key/value format of response.
+        return {
+            "page": self._page,
+            "totalpages": self._totalpages,
+            "itemsperpage": self._itemsperpage,
+            "startswith": self._startswith,
+            "itemcount": self._itemcount
+        }
+
+    @property
+    def page(self):
+        """Gets the page of this Pagination.
+
+        'Page' or relative block of items.
+        :return: The page of this Pagination.
+        :rtype: str
+        """
+        return self._page
+
+    @page.setter
+    def page(self, page):
+        """Sets the page of this Pagination.
+
+        'Page' or relative block of items.
+
+        :param page: The page of this Pagination
+        :type page: str
+        """
+
+        self._page = page
+
+    @property
+    def totalpages(self):
+        """Gets the total_pages of this Pagination.
+
+        Total number of "pages" (blocks of items)
+        :return: The total_pages of this Pagination.
+        :rtype: int
+        """
+        return self._totalpages
+
+    @totalpages.setter
+    def total_pages(self, totalpages):
+        """Sets the total_pages of this Pagination.
+
+        Total number of "pages" (blocks of items)
+
+        :param totalpages: The number of itmes in this Pagination
+        :type genes: int
+        """
+
+        self._totalpages = totalpages
+
+    @property
+    def itemsperpage(self):
+        """Gets the itemsperpage of this Pagination.
+
+        Number of items per "page" or block of returns
+        :return: The itemsperpage of this Pagination.
+        :rtype: int
+        """
+        return self._itemsperpage
+
+    @itemsperpage.setter
+    def genes_per_page(self, itemsperpage):
+        """Sets the itemsperpage of this Pagination.
+
+        Number of items per "page" or block of returns
+
+        :param itemsperpage: The itemsperpage of this Pagination
+        :type itemsperpage: int
+        """
+
+        self._itemsperpage = itemsperpage
+
+    @property
+    def startswith(self):
+        """Gets the startswith of this Pagination.
+
+        Optional type-ahead search string
+        :return: The startswith of this Pagination.
+        :rtype: str
+        """
+        return self._startswith
+
+    @startswith.setter
+    def startswith(self, startswith):
+        """Sets the startswith of this Pagination.
+
+        Optional type-ahead search string
+
+        :param starts_with: The startswith of this Pagination
+        :type startswith: int
+        """
+
+        self._startswith = startswith
+
+    @property
+    def itemcount(self):
+        """Gets the itemcount of this Pagination.
+
+        Count of items, optionally filtered by startswith.
+        :return: The itemcount of this Pagination.
+        :rtype: str
+        """
+        return self._itemcount
+
+    @itemcount.setter
+    def itemcount(self, itemcount):
+        """Sets the itemcount of this Pagination.
+
+        Count of items, optionally filtered by startswith
+
+        :param itemcount: The itemcount of this Pagination
+        :type itemcount: int
+        """
+
+        self._itemcount = itemcount
\ No newline at end of file
diff --git a/src/hs_ontology_api/routes/assayname/assayname_controller.py b/src/hs_ontology_api/routes/assayname/assayname_controller.py
index 92ae027..65b3199 100644
--- a/src/hs_ontology_api/routes/assayname/assayname_controller.py
+++ b/src/hs_ontology_api/routes/assayname/assayname_controller.py
@@ -1,6 +1,6 @@
 from flask import Blueprint, jsonify, current_app, request, make_response
 
-from hs_ontology_api.routes.neo4j_logic import assaytype_name_get_logic
+from hs_ontology_api.utils.neo4j_logic import assaytype_name_get_logic
 
 assayname_blueprint = Blueprint('assayname', __name__, url_prefix='/assayname')
 
diff --git a/src/hs_ontology_api/routes/assaytype/assaytype_controller.py b/src/hs_ontology_api/routes/assaytype/assaytype_controller.py
index c99de88..4ca052f 100644
--- a/src/hs_ontology_api/routes/assaytype/assaytype_controller.py
+++ b/src/hs_ontology_api/routes/assaytype/assaytype_controller.py
@@ -2,7 +2,7 @@
 
 from ubkg_api.common_routes.validate import validate_application_context
 
-from hs_ontology_api.routes.neo4j_logic import assaytype_get_logic, assaytype_name_get_logic
+from hs_ontology_api.utils.neo4j_logic import assaytype_get_logic, assaytype_name_get_logic
 
 assaytype_blueprint = Blueprint('assaytype', __name__, url_prefix='/assaytype')
 
diff --git a/src/hs_ontology_api/routes/datasets/datasets_controller.py b/src/hs_ontology_api/routes/datasets/datasets_controller.py
index 6185f74..a227a04 100644
--- a/src/hs_ontology_api/routes/datasets/datasets_controller.py
+++ b/src/hs_ontology_api/routes/datasets/datasets_controller.py
@@ -2,7 +2,7 @@
 
 from ubkg_api.common_routes.validate import validate_application_context
 
-from ..neo4j_logic import dataset_get_logic
+from hs_ontology_api.utils.neo4j_logic import dataset_get_logic
 
 datasets_blueprint = Blueprint('datasets_hs', __name__, url_prefix='/datasets')
 
diff --git a/src/hs_ontology_api/routes/genes/genes_controller.py b/src/hs_ontology_api/routes/genes/genes_controller.py
index 857028c..2955f6a 100644
--- a/src/hs_ontology_api/routes/genes/genes_controller.py
+++ b/src/hs_ontology_api/routes/genes/genes_controller.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # JAS September 2023
-from flask import Blueprint, jsonify, current_app, request, make_response
-from ..neo4j_logic import genedetail_get_logic
+from flask import Blueprint, jsonify, current_app, make_response
+from hs_ontology_api.utils.neo4j_logic import genedetail_get_logic
 
 
 genes_blueprint = Blueprint('genes', __name__, url_prefix='/genes')
diff --git a/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py b/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
index 93da0d5..a4c8623 100644
--- a/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
+++ b/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # JAS October 2023
 from flask import Blueprint, jsonify, current_app, request, make_response
-from ..neo4j_logic import genelist_get_logic,genelist_count_get_logic
+from hs_ontology_api.utils.neo4j_logic import genelist_get_logic,genelist_count_get_logic
 import math
 
 genesinfo_blueprint = Blueprint('genes-info', __name__, url_prefix='/genes-info')
@@ -18,9 +18,9 @@ def geneslist() -> list[str]:
     # Obtain parameters.
     page = request.args.get('page')
     genesperpage = request.args.get('genesperpage')
-    starts_with = request.args.get('starts_with')
-    if starts_with is None:
-        starts_with = ''
+    startswith = request.args.get('startswith')
+    if startswith is None:
+        startswith = ''
 
     # Validate and set defaults for genesperpage.
     if genesperpage is None:
@@ -31,9 +31,9 @@ def geneslist() -> list[str]:
         return (make_response(f'The value for parameter genesperpage ({genesperpage}) must be greater than zero.', 400))
 
     # Obtain the total count of genes, considering the filter starts_with.
-    gene_count = genelist_count_get_logic(neo4j_instance, starts_with)
-    if gene_count == 0:
-        return make_response(f'There are no genes with HGNC symbols that start with \'{starts_with}\'.', 404)
+    genecount = genelist_count_get_logic(neo4j_instance, startswith)
+    if genecount == 0:
+        return make_response(f'There are no genes with HGNC symbols that start with \'{startswith}\'.', 404)
 
     # Default values for page.
     # Case: No parameter specified.
@@ -45,12 +45,12 @@ def geneslist() -> list[str]:
         page = '1'
 
     # Calculate the total number of (filtered) pages.
-    total_pages = str(math.ceil(int(gene_count) / int(genesperpage)))
+    totalpages = str(math.ceil(int(genecount) / int(genesperpage)))
 
     # Translation for cases "last" or "first"
-    print(f'total_pages={total_pages}')
+    print(f'total_pages={totalpages}')
     if page == 'last':
-        page = str(int(total_pages))
+        page = str(int(totalpages))
     if page == 'first':
         page = '1'
 
@@ -60,9 +60,9 @@ def geneslist() -> list[str]:
     if int(page) < 0:
         return make_response(f'The value for parameter page ({page}) must be >= 0', 400)
 
-    if int(page) > int(total_pages):
-        page = str(int(total_pages))
+    if int(page) > int(totalpages):
+        page = str(int(totalpages))
 
     # Obtain results.
     neo4j_instance = current_app.neo4jConnectionHelper.instance()
-    return jsonify(genelist_get_logic(neo4j_instance, page=page, total_pages=total_pages, genesperpage=genesperpage, starts_with=starts_with, gene_count=gene_count))
\ No newline at end of file
+    return jsonify(genelist_get_logic(neo4j_instance, page=page, totalpages=totalpages, genesperpage=genesperpage, startswith=startswith, genecount=genecount))
\ No newline at end of file
diff --git a/src/hs_ontology_api/routes/organs/organs_controller.py b/src/hs_ontology_api/routes/organs/organs_controller.py
index 9e23825..affd8ad 100644
--- a/src/hs_ontology_api/routes/organs/organs_controller.py
+++ b/src/hs_ontology_api/routes/organs/organs_controller.py
@@ -2,7 +2,7 @@
 
 from ubkg_api.common_routes.validate import validate_application_context
 
-from ..neo4j_logic import get_organ_types_logic
+from hs_ontology_api.utils.neo4j_logic import get_organ_types_logic
 
 organs_blueprint = Blueprint('organs_hs', __name__, url_prefix='/organs')
 
diff --git a/src/hs_ontology_api/routes/relationships/relationships_controller.py b/src/hs_ontology_api/routes/relationships/relationships_controller.py
index 05e0d29..540f96b 100644
--- a/src/hs_ontology_api/routes/relationships/relationships_controller.py
+++ b/src/hs_ontology_api/routes/relationships/relationships_controller.py
@@ -1,6 +1,6 @@
 from flask import Blueprint, jsonify, current_app, make_response
 
-from ..neo4j_logic import relationships_for_gene_target_symbol_get_logic
+from hs_ontology_api.utils.neo4j_logic import relationships_for_gene_target_symbol_get_logic
 
 
 relationships_blueprint = Blueprint('relationships', __name__, url_prefix='/relationships')
diff --git a/src/hs_ontology_api/routes/valueset/valueset_controller.py b/src/hs_ontology_api/routes/valueset/valueset_controller.py
index 12ed3b8..6c8c9db 100644
--- a/src/hs_ontology_api/routes/valueset/valueset_controller.py
+++ b/src/hs_ontology_api/routes/valueset/valueset_controller.py
@@ -1,6 +1,6 @@
 from flask import Blueprint, jsonify, current_app, request
 
-from ..neo4j_logic import valueset_get_logic
+from hs_ontology_api.utils.neo4j_logic import valueset_get_logic
 
 valueset_blueprint = Blueprint('valueset_hs', __name__, url_prefix='/valueset')
 
diff --git a/src/hs_ontology_api/utils/README.md b/src/hs_ontology_api/utils/README.md
new file mode 100644
index 0000000..8b4dd21
--- /dev/null
+++ b/src/hs_ontology_api/utils/README.md
@@ -0,0 +1,9 @@
+# hs-ontology-api
+# Utility scripts
+
+## neo4j_logic.py
+Scripts that execute queries against the UBKG instance and return JSON to endpoints.
+
+## cellsclient.py
+A wrapper class around the Cells API python client.
+
diff --git a/src/hs_ontology_api/utils/__init__.py b/src/hs_ontology_api/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/hs_ontology_api/routes/cellsclient.py b/src/hs_ontology_api/utils/cellsclient.py
similarity index 97%
rename from src/hs_ontology_api/routes/cellsclient.py
rename to src/hs_ontology_api/utils/cellsclient.py
index 1cf53d2..4b3f531 100644
--- a/src/hs_ontology_api/routes/cellsclient.py
+++ b/src/hs_ontology_api/utils/cellsclient.py
@@ -8,7 +8,7 @@
 from hubmap_api_py_client.errors import ClientError
 
 # Array of cell type objects
-from ..models.genedetail_celltype import GeneDetailCellType
+from hs_ontology_api.models.genedetail_celltype import GeneDetailCellType
 
 import pandas as pd
 import os
diff --git a/src/hs_ontology_api/routes/neo4j_logic.py b/src/hs_ontology_api/utils/neo4j_logic.py
similarity index 96%
rename from src/hs_ontology_api/routes/neo4j_logic.py
rename to src/hs_ontology_api/utils/neo4j_logic.py
index c3a93ba..296c7b5 100644
--- a/src/hs_ontology_api/routes/neo4j_logic.py
+++ b/src/hs_ontology_api/utils/neo4j_logic.py
@@ -2,6 +2,7 @@
 import neo4j
 from typing import List
 import pandas as pd
+import os
 
 from flask import current_app
 
@@ -17,13 +18,28 @@
 from hs_ontology_api.models.genelist_detail import GeneListDetail
 
 # Query utilities
-from hs_ontology_api.cypher.util_query import loadquerystring
+# from hs_ontology_api.cypher.util_query import loadquerystring
 
 logging.basicConfig(format='[%(asctime)s] %(levelname)s in %(module)s:%(lineno)d: %(message)s',
                     datefmt='%Y-%m-%d %H:%M:%S',
                     level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+def loadquerystring(filename: str) ->str:
+
+    # Load a query string from a file.
+    # filename: filename, without path.
+
+    # Assumes that the file is in the cypher directory.
+
+    fpath = os.path.dirname(os.getcwd())
+    fpath = os.path.join(fpath,'src/hs_ontology_api/cypher',filename)
+
+    f = open(fpath, "r")
+    query = f.read()
+    f.close()
+    return query
+
 def make_assaytype_property_info(record):
     return AssayTypePropertyInfo(
         record['data_type'],
@@ -664,7 +680,7 @@ def genedetail_get_logic(neo4j_instance, gene_id: str) -> List[GeneDetail]:
 
     return genedetails
 
-def genelist_get_logic(neo4j_instance, page:str, total_pages:str, genesperpage:str, starts_with:str, gene_count:str) -> List[GeneList]:
+def genelist_get_logic(neo4j_instance, page:str, totalpages:str, genesperpage:str, startswith:str, genecount:str) -> List[GeneList]:
 
     """
     Returns information on HGNC genes.
@@ -672,13 +688,12 @@ def genelist_get_logic(neo4j_instance, page:str, total_pages:str, genesperpage:s
     list with pagination features.
 
     :param neo4j_instance:  neo4j client
-    :page: Zero-based number of pages with rows=pagesize to skip in neo4j query
-    :genesperpage: number of rows to limit in neo4j query
+    :param page: Zero-based number of pages with rows=pagesize to skip in neo4j query
+    :param totalpages: Calculated number of pages of genes
+    :param genesperpage: number of rows to limit in neo4j query
+    :param startswith: string for type-ahead (starts with) searches
+    :param genecount: Calculated total count of genes, optionally filtered with startswith
     :return: List[GeneList]
-    :starts_with: string for type-ahead (starts with) searches
-    :return: str
-    :gene_count: filtered count of genes
-    :return: str
 
     """
 
@@ -702,8 +717,8 @@ def genelist_get_logic(neo4j_instance, page:str, total_pages:str, genesperpage:s
     skiprows = intpage * int(genesperpage)
 
     starts_with_clause = ''
-    if starts_with != '':
-        starts_with_clause = f'AND map[\'approved_symbol\'][0] STARTS WITH \'{starts_with}\''
+    if startswith != '':
+        starts_with_clause = f'AND map[\'approved_symbol\'][0] STARTS WITH \'{startswith}\''
     query = query.replace('$starts_with_clause',starts_with_clause)
     query = query.replace('$skiprows', str(skiprows))
     query = query.replace('$limitrows', str(genesperpage))
@@ -722,16 +737,16 @@ def genelist_get_logic(neo4j_instance, page:str, total_pages:str, genesperpage:s
             except KeyError:
                 pass
         # Use the list of gene details with the page to build a genelist object.
-        genelist: GeneList = GeneList(page, total_pages, genesperpage, genes, starts_with, gene_count).serialize()
+        genelist: GeneList = GeneList(page, totalpages, genesperpage, genes, startswith, genecount).serialize()
     return genelist
 
-def genelist_count_get_logic(neo4j_instance, starts_with: str) -> int:
+def genelist_count_get_logic(neo4j_instance, startswith: str) -> int:
     """
         Returns the count of HGNC genes in the UBKG.
-        If starts_with is non-null, returns the count of HGNC genes with approved symbol
+        If startswith is non-null, returns the count of HGNC genes with approved symbol
         that starts with the parameter value.
         :param neo4j_instance:  neo4j client
-        :param starts_with: filtering string for STARTS WITH queries
+        :param startswith: filtering string for STARTS WITH queries
         :return: integer count
     """
     #
@@ -740,8 +755,8 @@ def genelist_count_get_logic(neo4j_instance, starts_with: str) -> int:
     queryfile = 'geneslist_count.cypher'
     query = loadquerystring(queryfile)
     starts_with_clause = ''
-    if starts_with != '':
-        starts_with_clause = f'AND tGene.name STARTS WITH \'{starts_with}\''
+    if startswith != '':
+        starts_with_clause = f'AND tGene.name STARTS WITH \'{startswith}\''
     query = query.replace('$starts_with_clause', starts_with_clause)
 
     with neo4j_instance.driver.session() as session:
diff --git a/src/main.py b/src/main.py
index cf6deec..100d470 100755
--- a/src/main.py
+++ b/src/main.py
@@ -14,7 +14,7 @@
 from hs_ontology_api.routes.genesinfo.genesinfo_controller import genesinfo_blueprint
 
 # Cells API client
-from hs_ontology_api.routes.cellsclient import OntologyCellsClient
+from hs_ontology_api.utils.cellsclient import OntologyCellsClient
 
 def make_flask_config():
     temp_flask_app = Flask(__name__,

From 05c6aa1f389921f6d0bdac10e7e4f2548cb52ace Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 7 Nov 2023 20:34:01 -0600
Subject: [PATCH 07/11] Updated test script for renamed genes endpoints.

---
 test_api.sh | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/test_api.sh b/test_api.sh
index e7e51b0..e7ab62c 100755
--- a/test_api.sh
+++ b/test_api.sh
@@ -116,27 +116,27 @@ curl --request GET \
 echo
 
 # Test for gene_list endpoint
-echo "genes GET"
+echo "genes-info GET"
 curl --request GET \
- --url "${UBKG_URL}/genes?page=1&genesperpage=3" \
+ --url "${UBKG_URL}/genes-info?page=1&genesperpage=3" \
  --header "Content-Type: application/json"
 echo
-echo "genes GET last page"
+echo "genes-info GET last page"
 curl --request GET \
- --url "${UBKG_URL}/genes?page=last&genesperpage=3" \
+ --url "${UBKG_URL}/genes-info?page=last&genesperpage=3" \
  --header "Content-Type: application/json"
 echo
 
-echo "genes GET starts_with B"
+echo "genes-info GET starts_with B"
 curl --request GET \
- --url "${UBKG_URL}/genes?genesperpage=3&starts_with=B" \
+ --url "${UBKG_URL}/genes-info?genesperpage=3&starts_with=B" \
  --header "Content-Type: application/json"
 echo
 
 # Test for gene endpoint.
-echo "gene GET for MMRN1"
+echo "genes GET for MMRN1"
 curl --request GET \
- --url "${UBKG_URL}/gene/MMRN1" \
+ --url "${UBKG_URL}/genes/MMRN1" \
  --header "Content-Type: application/json"
 echo
 

From 80126f87603e0b08188df4aec2fcb4357c902344 Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Tue, 7 Nov 2023 21:00:20 -0600
Subject: [PATCH 08/11] Updated SmartAPI YAML for genes-info/genes,
 proteins-info/proteins, and celltypes-info/celltypes endpoints. Updated YAML
 for new pagination object in *-info endpoints.

---
 hs-ontology-api-spec.yaml | 176 ++++++++++++++++++++------------------
 1 file changed, 94 insertions(+), 82 deletions(-)

diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
index 562c2e7..b062b06 100644
--- a/hs-ontology-api-spec.yaml
+++ b/hs-ontology-api-spec.yaml
@@ -1,7 +1,7 @@
 openapi: 3.0.3
 info:
   title: HubMAP/SenNet Ontology API (hs-ontology-api)
-  description: The HuBMAP/SenNet Ontology API contains endpoints for querying a UBKG(https://ubkg.docs.xconsortia.org/) instance with content from the HuBMAP/SenNet context (https://ubkg.docs.xconsortia.org/contexts/#hubmapsennet-context). The hs-ontology-api imports the [ubkg-api](https://github.com/x-atlas-consortia/ubkg-api), which encapsulates both basic connectivity to a UBKG instance and generic endpoint code. This specification describes endpoints of both hs-ontology-api and ubkg-api.
+  description: The HuBMAP/SenNet Ontology API contains endpoints for querying a [UBKG](https://ubkg.docs.xconsortia.org/) instance with content from the [HuBMAP/SenNet context](https://ubkg.docs.xconsortia.org/contexts/#hubmapsennet-context). The hs-ontology-api imports the [ubkg-api](https://smart-api.info/ui/96e5b5c0b0efeef5b93ea98ac2794837), which encapsulates both basic connectivity to a UBKG instance and generic endpoint code.
   version: 1.3.1
   contact:
     name: GitHub repository
@@ -350,10 +350,10 @@ paths:
                 type: array
                 items:
                   $ref: '#/components/schemas/SabCodeTerm'
-  /genes:
+  /genes-info:
     get:
-      operationId: gene_list_get
-      summary: Return high-level information on a set of genes specified by pagination parameters.
+      operationId: genes_info_get
+      summary: Return high-level information on a set of genes specified by pagination request parameters.
       parameters:
         - name: page
           in: query
@@ -370,7 +370,7 @@ paths:
           schema:
             type: string
             default: 10
-        - name: starts_with
+        - name: startswith
           in: query
           required: false
           description: Optional string by which to filter by gene symbol.
@@ -389,12 +389,12 @@ paths:
         '400':
           description: Invalid parameter--e.g., *genesperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
         '404':
-          description: No genes that satisfied the criteria were found. This usually means that there are no genes with HGNC approved symbols that start with the string specified in the *starts_with* parameter.
+          description: No genes that satisfied the criteria were found. This usually means that there are no genes with HGNC approved symbols that start with the string specified in the *startswith* parameter.
         '5XX':
           description: Unexpected error
-  /gene/{id}:
+  /genes/{id}:
     get:
-      operationId: gene_detail_get
+      operationId: genes_get
       summary: Return detailed information on a gene specified by a HGNC identifier.
       parameters:
         - name: id
@@ -417,10 +417,10 @@ paths:
           description: No information for gene with HGNC identifier *id*.
         '5XX':
           description: Unexpected error
-  /proteins:
+  /proteins-info:
     get:
-      operationId: protein_list_get
-      summary: Return high-level information on a set of proteins specified by pagination parameters.
+      operationId: protein_info_get
+      summary: Return high-level information on a set of proteins specified by pagination request parameters.
       parameters:
         - name: page
           in: query
@@ -437,7 +437,7 @@ paths:
           schema:
             type: string
             default: 10
-        - name: starts_with
+        - name: startswith
           in: query
           required: false
           description: Optional *case-insensitive* string by which to filter by UniProtKB protein name.
@@ -456,12 +456,12 @@ paths:
         '400':
           description: Invalid parameter--e.g., *proteinsperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
         '404':
-          description: No proteins that satisfied the criteria were found. This usually means that there are no proteins with UniprotKB names that start with the string specified in the *starts_with* parameter.
+          description: No proteins that satisfied the criteria were found. This usually means that there are no proteins with UniprotKB names that start with the string specified in the *startswith* parameter.
         '5XX':
           description: Unexpected error
-  /protein/{id}:
+  /proteins/{id}:
     get:
-      operationId: protein_detail_get
+      operationId: proteins_get
       summary: Return detailed information on a protein specified by a UniProtKB identifier.
       parameters:
         - name: id
@@ -484,10 +484,10 @@ paths:
           description: No information for protein with UniProtKB identifier *id*.
         '5XX':
           description: Unexpected error
-  /celltypes:
+  /celltypes-info:
     get:
-      operationId: celltype_list_get
-      summary: Return high-level information on a set of cell types specified by pagination parameters.
+      operationId: celltypes_info_get
+      summary: Return high-level information on a set of cell types specified by pagination request parameters.
       parameters:
         - name: page
           in: query
@@ -504,7 +504,7 @@ paths:
           schema:
             type: string
             default: 10
-        - name: starts_with
+        - name: startswith
           in: query
           required: false
           description: Optional *case-insensitive* string by which to filter by cell type name.
@@ -523,12 +523,12 @@ paths:
         '400':
           description: Invalid parameter--e.g., *celltypesperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
         '404':
-          description: No cell types that satisfied the criteria were found. This usually means that there are no cell types with names that start with the string specified in the *starts_with* parameter.
+          description: No cell types that satisfied the criteria were found. This usually means that there are no cell types with names that start with the string specified in the *startswith* parameter.
         '5XX':
           description: Unexpected error
-  /celltype/{id}:
+  /celltypes/{id}:
     get:
-      operationId: celltype_detail_get
+      operationId: celltypes_get
       summary: Return detailed information on a cell type specified by a name.
       parameters:
         - name: id
@@ -870,26 +870,30 @@ components:
                 type: string
                 description: RefSeq summary for the gene
                 example: Multimerin is a massive, soluble protein found in....
-        genes_per_page:
-          type: number
-          description: value of genesperpage parameter from the gene_list endpoint
-          example: 3
-        page:
-          type: number
-          description: value of page parameter from the gene_list endpoint
-          example: 1
-        total_pages:
-          type: number
-          description: total number of "pages" based on the values of genesperpage and the total number of genes
-          example: 14381
-        starts_with:
-          type: string
-          description: value of starts_with from the gene_list endpoint
-          example: M
-        gene_count:
-          type: number
-          description: Count of genes. If starts_with is non-null, the count is that of the genes with approved HGNC symbols that start with the value of starts_with.
-          example: 500
+        pagination:
+          type: object
+          description: pagination statistics
+          properties:
+            itemsperpage:
+              type: number
+              description: original value of genesperpage request parameter
+              example: 3
+            page:
+              type: number
+              description: original value of page request parameter
+              example: 1
+            totalpages:
+              type: number
+              description: calculated total number of "pages" (blocks) based on the values of itemsperpage and the total number of items
+              example: 14381
+            startswith:
+              type: string
+              description: original value of startswith request parameter
+              example: M
+            itemcount:
+              type: number
+              description: Calculated count of items. If startswith is non-null, the count is that of the genes with approved HGNC symbols that start with the value of starts_with.
+              example: 500
     GeneDetailResponse: # JAS Sept 2023
       type: object
       description: Detailed information on a gene requested by the gene endpoint
@@ -1016,26 +1020,30 @@ components:
                 type: string
                 description: UniProtKB Recommended Name
                 example: multimerin-1
-        proteins_per_page:
-          type: number
-          description: value of proteinsperpage parameter from the proteins endpoint
-          example: 3
-        page:
-          type: number
-          description: value of page parameter from the proteins endpoint
-          example: 1
-        total_pages:
-          type: number
-          description: total number of "pages" based on the values of proteinsperpage and the total number of proteins
-          example: 14381
-        starts_with:
-          type: string
-          description: value of starts_with from the proteins endpoint
-          example: M
-        protein_count:
-          type: number
-          description: Count of proteins. If starts_with is non-null, the count is that of the proteins with names that start with the value of starts_with.
-          example: 500
+        pagination:
+          type: object
+          description: pagination statistics
+          properties:
+            itemsperpage:
+              type: number
+              description: original value of proteinsperpage request parameter
+              example: 3
+            page:
+              type: number
+              description: original value of page request parameter
+              example: 1
+            totalpages:
+              type: number
+              description: calculated total number of "pages" (blocks) based on the values of proteinsperpage and the total number of proteins
+              example: 14381
+            startswith:
+              type: string
+              description: original value of startswith request parameter
+              example: M
+            itemcount:
+              type: number
+              description: Count of proteins. If startswith is non-null, the count is that of the proteins with names that start with the value of startswith.
+              example: 500
     ProteinDetailResponse:
       type: object
       description: Detailed information on a protein requested by the protein endpoint
@@ -1110,26 +1118,30 @@ components:
                 type: string
                 description: Definition of the cell type from Cell Ontology
                 example: A endothelial cell of a lymphatic vessel. The border of…
-        celltypes_per_page:
-          type: number
-          description: value of celltypesperpage parameter from the celltypes endpoint
-          example: 3
-        page:
-          type: number
-          description: value of page parameter from the celltypes endpoint
-          example: 1
-        total_pages:
-          type: number
-          description: total number of "pages" based on the values of celltypesperpage and the total number of celltypes
-          example: 14381
-        starts_with:
-          type: string
-          description: value of starts_with from the celltypes endpoint
-          example: E
-        cell_type_count:
-          type: number
-          description: Count of cell types. If starts_with is non-null, the count is that of the cell types with names that start with the value of starts_with.
-          example: 500
+        pagination:
+          type: object
+          description: pagination statistics
+          properties:
+            itemsperpage:
+              type: number
+              description: original value of celltypesperpage request parameter
+              example: 3
+            page:
+              type: number
+              description: original value of page request parameter
+              example: 1
+            totalpages:
+              type: number
+              description: calculated total number of "pages" (blocks) based on the values of celltypesperpage and the total number of celltypes
+              example: 14381
+            startswith:
+              type: string
+              description: original value of startswith request parameter
+              example: E
+            itemcount:
+              type: number
+              description: calculated count of cell types. If startswith is non-null, the count is that of the cell types with names that start with the value of startswith.
+              example: 500
     CellTypeDetailResponse:
       type: object
       description: Detailed information on a cell type requested by the celltype endpoint

From b1faaee66555c1d690e70cadba0a10b2b61a43db Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Wed, 8 Nov 2023 11:18:55 -0600
Subject: [PATCH 09/11] Updated to change pagination-related parameters to use
 underscores (e.g. starts_with instead of startswith).

---
 hs-ontology-api-spec.yaml                     |  78 +++++------
 src/hs_ontology_api/models/genelist.py        |  22 +--
 src/hs_ontology_api/models/pagination.py      | 126 +++++++++---------
 .../routes/genesinfo/genesinfo_controller.py  |  41 +++---
 src/hs_ontology_api/utils/neo4j_logic.py      |  34 ++---
 test_api.sh                                   |   6 +-
 6 files changed, 154 insertions(+), 153 deletions(-)

diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
index b062b06..30f7b93 100644
--- a/hs-ontology-api-spec.yaml
+++ b/hs-ontology-api-spec.yaml
@@ -358,19 +358,19 @@ paths:
         - name: page
           in: query
           required: false
-          description: Offset set of genes of count=genesperpage. Can be a non-negative number or the words "first" or "last".
+          description: Offset set of genes of count=genes_per_page. Can be a non-negative number or the words "first" or "last".
           schema:
             type: string
             default: 1
           example: 1
-        - name: genesperpage
+        - name: genes_per_page
           in: query
           required: false
           description: Number of genes per "page" to return. Can be a nonzero number.
           schema:
             type: string
             default: 10
-        - name: startswith
+        - name: starts_with
           in: query
           required: false
           description: Optional string by which to filter by gene symbol.
@@ -387,9 +387,9 @@ paths:
                 items:
                   $ref: '#/components/schemas/GeneListResponse'
         '400':
-          description: Invalid parameter--e.g., *genesperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
+          description: Invalid parameter--e.g., *genes_per_page* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
         '404':
-          description: No genes that satisfied the criteria were found. This usually means that there are no genes with HGNC approved symbols that start with the string specified in the *startswith* parameter.
+          description: No genes that satisfied the criteria were found. This usually means that there are no genes with HGNC approved symbols that start with the string specified in the *starts_with* parameter.
         '5XX':
           description: Unexpected error
   /genes/{id}:
@@ -425,19 +425,19 @@ paths:
         - name: page
           in: query
           required: false
-          description: Offset set of proteins of count=proteinsperpage. Can be a non-negative number or the words "first" or "last".
+          description: Offset set of proteins of count=proteins_per_page. Can be a non-negative number or the words "first" or "last".
           schema:
             type: string
             default: 1
           example: 1
-        - name: proteinsperpage
+        - name: proteins_per_page
           in: query
           required: false
           description: Number of proteins per "page" to return. Can be a nonzero number.
           schema:
             type: string
             default: 10
-        - name: startswith
+        - name: starts_with
           in: query
           required: false
           description: Optional *case-insensitive* string by which to filter by UniProtKB protein name.
@@ -454,9 +454,9 @@ paths:
                 items:
                   $ref: '#/components/schemas/ProteinListResponse'
         '400':
-          description: Invalid parameter--e.g., *proteinsperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
+          description: Invalid parameter--e.g., *proteins_per_page* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
         '404':
-          description: No proteins that satisfied the criteria were found. This usually means that there are no proteins with UniprotKB names that start with the string specified in the *startswith* parameter.
+          description: No proteins that satisfied the criteria were found. This usually means that there are no proteins with UniprotKB names that start with the string specified in the *starts_with* parameter.
         '5XX':
           description: Unexpected error
   /proteins/{id}:
@@ -492,19 +492,19 @@ paths:
         - name: page
           in: query
           required: false
-          description: Offset set of genes of count=celltypesperpage. Can be a non-negative number or the words "first" or "last".
+          description: Offset set of genes of count=celltypes_per_page. Can be a non-negative number or the words "first" or "last".
           schema:
             type: string
             default: 1
           example: 1
-        - name: celltypesperpage
+        - name: celltypes_per_page
           in: query
           required: false
           description: Number of cell types per "page" to return. Can be a nonzero number.
           schema:
             type: string
             default: 10
-        - name: startswith
+        - name: starts_with
           in: query
           required: false
           description: Optional *case-insensitive* string by which to filter by cell type name.
@@ -521,9 +521,9 @@ paths:
                 items:
                   $ref: '#/components/schemas/CellTypeListResponse'
         '400':
-          description: Invalid parameter--e.g., *celltypesperpage* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
+          description: Invalid parameter--e.g., *celltypes_per_page* is either non-numeric or a negative number; *page* is something other than a non-negative number or the words 'first' or 'last'
         '404':
-          description: No cell types that satisfied the criteria were found. This usually means that there are no cell types with names that start with the string specified in the *startswith* parameter.
+          description: No cell types that satisfied the criteria were found. This usually means that there are no cell types with names that start with the string specified in the *starts_with* parameter.
         '5XX':
           description: Unexpected error
   /celltypes/{id}:
@@ -874,25 +874,25 @@ components:
           type: object
           description: pagination statistics
           properties:
-            itemsperpage:
+            items_per_page:
               type: number
-              description: original value of genesperpage request parameter
+              description: original value of genes_per_page request parameter
               example: 3
             page:
               type: number
               description: original value of page request parameter
               example: 1
-            totalpages:
+            total_pages:
               type: number
-              description: calculated total number of "pages" (blocks) based on the values of itemsperpage and the total number of items
+              description: calculated total number of "pages" (blocks) based on the values of items_per_page and the total number of items
               example: 14381
-            startswith:
+            starts_with:
               type: string
-              description: original value of startswith request parameter
+              description: original value of starts_with request parameter
               example: M
-            itemcount:
+            item_count:
               type: number
-              description: Calculated count of items. If startswith is non-null, the count is that of the genes with approved HGNC symbols that start with the value of starts_with.
+              description: Calculated count of items. If starts_with is non-null, the count is that of the genes with approved HGNC symbols that start with the value of starts_with.
               example: 500
     GeneDetailResponse: # JAS Sept 2023
       type: object
@@ -1024,25 +1024,25 @@ components:
           type: object
           description: pagination statistics
           properties:
-            itemsperpage:
+            items_per_page:
               type: number
-              description: original value of proteinsperpage request parameter
+              description: original value of proteins_per_page request parameter
               example: 3
             page:
               type: number
               description: original value of page request parameter
               example: 1
-            totalpages:
+            total_pages:
               type: number
-              description: calculated total number of "pages" (blocks) based on the values of proteinsperpage and the total number of proteins
+              description: calculated total number of "pages" (blocks) based on the values of proteins_per_page and the total number of proteins
               example: 14381
-            startswith:
+            starts_with:
               type: string
-              description: original value of startswith request parameter
+              description: original value of starts_with request parameter
               example: M
-            itemcount:
+            item_count:
               type: number
-              description: Count of proteins. If startswith is non-null, the count is that of the proteins with names that start with the value of startswith.
+              description: Count of proteins. If starts_with is non-null, the count is that of the proteins with names that start with the value of starts_with.
               example: 500
     ProteinDetailResponse:
       type: object
@@ -1122,25 +1122,25 @@ components:
           type: object
           description: pagination statistics
           properties:
-            itemsperpage:
+            items_per_page:
               type: number
-              description: original value of celltypesperpage request parameter
+              description: original value of celltypes_per_page request parameter
               example: 3
             page:
               type: number
               description: original value of page request parameter
               example: 1
-            totalpages:
+            total_pages:
               type: number
-              description: calculated total number of "pages" (blocks) based on the values of celltypesperpage and the total number of celltypes
+              description: calculated total number of "pages" (blocks) based on the values of celltypes_per_page and the total number of celltypes
               example: 14381
-            startswith:
+            starts_with:
               type: string
-              description: original value of startswith request parameter
+              description: original value of starts_with request parameter
               example: E
-            itemcount:
+            item_count:
               type: number
-              description: calculated count of cell types. If startswith is non-null, the count is that of the cell types with names that start with the value of startswith.
+              description: calculated count of cell types. If starts_with is non-null, the count is that of the cell types with names that start with the value of starts_with.
               example: 500
     CellTypeDetailResponse:
       type: object
diff --git a/src/hs_ontology_api/models/genelist.py b/src/hs_ontology_api/models/genelist.py
index 4dccf5f..62399ec 100644
--- a/src/hs_ontology_api/models/genelist.py
+++ b/src/hs_ontology_api/models/genelist.py
@@ -16,25 +16,25 @@
 from hs_ontology_api.models.pagination import Pagination
 
 class GeneList():
-    def __init__(self, page=None, totalpages=None, genesperpage=None, genes=None, startswith=None, genecount=None):
+    def __init__(self, page=None, total_pages=None, genes_per_page=None, genes=None, starts_with=None, gene_count=None):
         """GeneList - a model defined in OpenAPI
 
                     :param page: Requested relative "page" (block of genes)
                     :type page: str
-                    :param totalpages: Calculated total number of "pages" (blocks of genes)
-                    :type totalpages: str
+                    :param total_pages: Calculated total number of "pages" (blocks of genes)
+                    :type total_pages: str
                     :param genes: List of gene objects for an array
                     :type genes: List[GeneListDetail]
-                    :param genesperpage: Requested number of genes in each "page" (block)
-                    :type genesperpage: str
-                    :startswith: Optional search string for type ahead
-                    :type startswith: str
-                    :genecount: Calculated count of genes that satisfied the search criteria
-                    :type genecount: str
+                    :param genes_per_page: Requested number of genes in each "page" (block)
+                    :type genes_per_page: str
+                    :starts_with: Optional search string for type ahead
+                    :type starts_with: str
+                    :gene_count: Calculated count of genes that satisfied the search criteria
+                    :type gene_count: str
 
                 """
 
-        # The page, totalpages, genesperpage, startswith, and genecount parameters will be used to build a
+        # The page, total_pages, genes_per_page, starts_with, and gene_count parameters will be used to build a
         # Pagination object.
         # The genes parameter will be used to build an array of GeneListDetail objects.
 
@@ -50,7 +50,7 @@ def __init__(self, page=None, totalpages=None, genesperpage=None, genes=None, st
         }
         # Property assignments
         self._genes = genes
-        self._pagination = Pagination(page, totalpages, genesperpage, startswith, genecount).serialize()
+        self._pagination = Pagination(page, total_pages, genes_per_page, starts_with, gene_count).serialize()
 
     def serialize(self):
         # Key/value format of response.
diff --git a/src/hs_ontology_api/models/pagination.py b/src/hs_ontology_api/models/pagination.py
index 289b742..9bee031 100644
--- a/src/hs_ontology_api/models/pagination.py
+++ b/src/hs_ontology_api/models/pagination.py
@@ -11,49 +11,49 @@
 
 class Pagination():
 
-    def __init__(self, page=None, totalpages=None, itemsperpage=None, startswith=None, itemcount=None):
+    def __init__(self, page=None, total_pages=None, items_per_page=None, starts_with=None, item_count=None):
         """Pagination - a model defined in OpenAPI
 
         :param page: Relative "page" (block of items)
-        :param totalpages: Total number of "pages" (blocks of items)
-        :param itemsperpage: Number of items in each "page" (block)
-        :param startswith: Optional search string for type ahead
-        :param itemcount: Count of items, optionally filtered by startswith
+        :param total_pages: Total number of "pages" (blocks of items)
+        :param items_per_page: Number of items in each "page" (block)
+        :param starts_with: Optional search string for type ahead
+        :param item_count: Count of items, optionally filtered by starts_with
 
         """
 
         # Types for JSON objects
         self.openapi_types = {
             'page': int,
-            'totalpages': int,
-            'itemsperpage': int,
-            'startswith': str,
-            'itemcount': int
+            'total_pages': int,
+            'items_per_page': int,
+            'starts_with': str,
+            'item_count': int
         }
 
         # Attribute mappings used by the base Model class to assert key/value pairs.
         self.attribute_map = {
             'page': 'page',
-            'totalpages': 'totalpages',
-            'itemsperpage': 'itemsperpage',
-            'startswith': 'startswith',
-            'itemcount': 'itemcount'
+            'total_pages': 'total_pages',
+            'items_per_page': 'items_per_page',
+            'starts_with': 'starts_with',
+            'item_count': 'item_count'
         }
         # Property assignments
         self._page = int(page)
-        self._totalpages = int(totalpages)
-        self._itemsperpage = int(itemsperpage)
-        self._startswith = startswith
-        self._itemcount = itemcount
+        self._total_pages = int(total_pages)
+        self._items_per_page = int(items_per_page)
+        self._starts_with = starts_with
+        self._item_count = item_count
 
     def serialize(self):
         # Key/value format of response.
         return {
             "page": self._page,
-            "totalpages": self._totalpages,
-            "genes_per_page": self._itemsperpage,
-            "startswith": self._startswith,
-            "itemcount": self._itemcount
+            "total_pages": self._total_pages,
+            "genes_per_page": self._items_per_page,
+            "starts_with": self._starts_with,
+            "item_count": self._item_count
         }
 
     @classmethod
@@ -71,10 +71,10 @@ def serialize(self):
         # Key/value format of response.
         return {
             "page": self._page,
-            "totalpages": self._totalpages,
-            "itemsperpage": self._itemsperpage,
-            "startswith": self._startswith,
-            "itemcount": self._itemcount
+            "total_pages": self._total_pages,
+            "items_per_page": self._items_per_page,
+            "starts_with": self._starts_with,
+            "item_count": self._item_count
         }
 
     @property
@@ -100,89 +100,89 @@ def page(self, page):
         self._page = page
 
     @property
-    def totalpages(self):
+    def total_pages(self):
         """Gets the total_pages of this Pagination.
 
         Total number of "pages" (blocks of items)
         :return: The total_pages of this Pagination.
         :rtype: int
         """
-        return self._totalpages
+        return self._total_pages
 
-    @totalpages.setter
-    def total_pages(self, totalpages):
+    @total_pages.setter
+    def total_pages(self, total_pages):
         """Sets the total_pages of this Pagination.
 
         Total number of "pages" (blocks of items)
 
-        :param totalpages: The number of itmes in this Pagination
+        :param total_pages: The number of itmes in this Pagination
         :type genes: int
         """
 
-        self._totalpages = totalpages
+        self._total_pages = total_pages
 
     @property
-    def itemsperpage(self):
-        """Gets the itemsperpage of this Pagination.
+    def items_per_page(self):
+        """Gets the items_per_page of this Pagination.
 
         Number of items per "page" or block of returns
-        :return: The itemsperpage of this Pagination.
+        :return: The items_per_page of this Pagination.
         :rtype: int
         """
-        return self._itemsperpage
+        return self._items_per_page
 
-    @itemsperpage.setter
-    def genes_per_page(self, itemsperpage):
-        """Sets the itemsperpage of this Pagination.
+    @items_per_page.setter
+    def genes_per_page(self, items_per_page):
+        """Sets the items_per_page of this Pagination.
 
         Number of items per "page" or block of returns
 
-        :param itemsperpage: The itemsperpage of this Pagination
-        :type itemsperpage: int
+        :param items_per_page: The items_per_page of this Pagination
+        :type items_per_page: int
         """
 
-        self._itemsperpage = itemsperpage
+        self._items_per_page = items_per_page
 
     @property
-    def startswith(self):
-        """Gets the startswith of this Pagination.
+    def starts_with(self):
+        """Gets the starts_with of this Pagination.
 
         Optional type-ahead search string
-        :return: The startswith of this Pagination.
+        :return: The starts_with of this Pagination.
         :rtype: str
         """
-        return self._startswith
+        return self._starts_with
 
-    @startswith.setter
-    def startswith(self, startswith):
-        """Sets the startswith of this Pagination.
+    @starts_with.setter
+    def starts_with(self, starts_with):
+        """Sets the starts_with of this Pagination.
 
         Optional type-ahead search string
 
-        :param starts_with: The startswith of this Pagination
-        :type startswith: int
+        :param starts_with: The starts_with of this Pagination
+        :type starts_with: int
         """
 
-        self._startswith = startswith
+        self._starts_with = starts_with
 
     @property
-    def itemcount(self):
-        """Gets the itemcount of this Pagination.
+    def item_count(self):
+        """Gets the item_count of this Pagination.
 
-        Count of items, optionally filtered by startswith.
-        :return: The itemcount of this Pagination.
+        Count of items, optionally filtered by starts_with.
+        :return: The item_count of this Pagination.
         :rtype: str
         """
-        return self._itemcount
+        return self._item_count
 
-    @itemcount.setter
-    def itemcount(self, itemcount):
-        """Sets the itemcount of this Pagination.
+    @item_count.setter
+    def item_count(self, item_count):
+        """Sets the item_count of this Pagination.
 
-        Count of items, optionally filtered by startswith
+        Count of items, optionally filtered by starts_with
 
-        :param itemcount: The itemcount of this Pagination
-        :type itemcount: int
+        :param item_count: The item_count of this Pagination
+        :type item_count: int
         """
 
-        self._itemcount = itemcount
\ No newline at end of file
+        self._item_count = item_count
\ No newline at end of file
diff --git a/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py b/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
index a4c8623..78d7d43 100644
--- a/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
+++ b/src/hs_ontology_api/routes/genesinfo/genesinfo_controller.py
@@ -17,23 +17,23 @@ def geneslist() -> list[str]:
 
     # Obtain parameters.
     page = request.args.get('page')
-    genesperpage = request.args.get('genesperpage')
-    startswith = request.args.get('startswith')
-    if startswith is None:
-        startswith = ''
+    genes_per_page = request.args.get('genes_per_page')
+    starts_with = request.args.get('starts_with')
+    if starts_with is None:
+        starts_with = ''
 
-    # Validate and set defaults for genesperpage.
-    if genesperpage is None:
-        genesperpage = '10'
-    if not genesperpage.isnumeric():
-        return make_response(f'The value for parameter genesperpage ({genesperpage}) must be numeric.', 400)
-    if int(genesperpage) <= 0:
-        return (make_response(f'The value for parameter genesperpage ({genesperpage}) must be greater than zero.', 400))
+    # Validate and set defaults for genes_per_page.
+    if genes_per_page is None:
+        genes_per_page = '10'
+    if not genes_per_page.isnumeric():
+        return make_response(f'The value for parameter genes_per_page ({genes_per_page}) must be numeric.', 400)
+    if int(genes_per_page) <= 0:
+        return (make_response(f'The value for parameter genes_per_page ({genes_per_page}) must be greater than zero.', 400))
 
     # Obtain the total count of genes, considering the filter starts_with.
-    genecount = genelist_count_get_logic(neo4j_instance, startswith)
-    if genecount == 0:
-        return make_response(f'There are no genes with HGNC symbols that start with \'{startswith}\'.', 404)
+    gene_count = genelist_count_get_logic(neo4j_instance, starts_with)
+    if gene_count == 0:
+        return make_response(f'There are no genes with HGNC symbols that start with \'{starts_with}\'.', 404)
 
     # Default values for page.
     # Case: No parameter specified.
@@ -45,12 +45,12 @@ def geneslist() -> list[str]:
         page = '1'
 
     # Calculate the total number of (filtered) pages.
-    totalpages = str(math.ceil(int(genecount) / int(genesperpage)))
+    total_pages = str(math.ceil(int(gene_count) / int(genes_per_page)))
 
     # Translation for cases "last" or "first"
-    print(f'total_pages={totalpages}')
+    print(f'total_pages={total_pages}')
     if page == 'last':
-        page = str(int(totalpages))
+        page = str(int(total_pages))
     if page == 'first':
         page = '1'
 
@@ -60,9 +60,10 @@ def geneslist() -> list[str]:
     if int(page) < 0:
         return make_response(f'The value for parameter page ({page}) must be >= 0', 400)
 
-    if int(page) > int(totalpages):
-        page = str(int(totalpages))
+    if int(page) > int(total_pages):
+        page = str(int(total_pages))
 
     # Obtain results.
     neo4j_instance = current_app.neo4jConnectionHelper.instance()
-    return jsonify(genelist_get_logic(neo4j_instance, page=page, totalpages=totalpages, genesperpage=genesperpage, startswith=startswith, genecount=genecount))
\ No newline at end of file
+    return jsonify(genelist_get_logic(neo4j_instance, page=page, total_pages=total_pages, genes_per_page=genes_per_page,
+                                      starts_with=starts_with, gene_count=gene_count))
\ No newline at end of file
diff --git a/src/hs_ontology_api/utils/neo4j_logic.py b/src/hs_ontology_api/utils/neo4j_logic.py
index 296c7b5..9fc7794 100644
--- a/src/hs_ontology_api/utils/neo4j_logic.py
+++ b/src/hs_ontology_api/utils/neo4j_logic.py
@@ -680,7 +680,7 @@ def genedetail_get_logic(neo4j_instance, gene_id: str) -> List[GeneDetail]:
 
     return genedetails
 
-def genelist_get_logic(neo4j_instance, page:str, totalpages:str, genesperpage:str, startswith:str, genecount:str) -> List[GeneList]:
+def genelist_get_logic(neo4j_instance, page:str, total_pages:str, genes_per_page:str, starts_with:str, gene_count:str) -> List[GeneList]:
 
     """
     Returns information on HGNC genes.
@@ -689,10 +689,10 @@ def genelist_get_logic(neo4j_instance, page:str, totalpages:str, genesperpage:st
 
     :param neo4j_instance:  neo4j client
     :param page: Zero-based number of pages with rows=pagesize to skip in neo4j query
-    :param totalpages: Calculated number of pages of genes
-    :param genesperpage: number of rows to limit in neo4j query
-    :param startswith: string for type-ahead (starts with) searches
-    :param genecount: Calculated total count of genes, optionally filtered with startswith
+    :param total_pages: Calculated number of pages of genes
+    :param genes_per_page: number of rows to limit in neo4j query
+    :param starts_with: string for type-ahead (starts with) searches
+    :param gene_count: Calculated total count of genes, optionally filtered with starts_with
     :return: List[GeneList]
 
     """
@@ -714,14 +714,14 @@ def genelist_get_logic(neo4j_instance, page:str, totalpages:str, genesperpage:st
     # Convert to 1-based.
     intpage = int(page)-1
 
-    skiprows = intpage * int(genesperpage)
+    skiprows = intpage * int(genes_per_page)
 
     starts_with_clause = ''
-    if startswith != '':
-        starts_with_clause = f'AND map[\'approved_symbol\'][0] STARTS WITH \'{startswith}\''
+    if starts_with != '':
+        starts_with_clause = f'AND map[\'approved_symbol\'][0] STARTS WITH \'{starts_with}\''
     query = query.replace('$starts_with_clause',starts_with_clause)
     query = query.replace('$skiprows', str(skiprows))
-    query = query.replace('$limitrows', str(genesperpage))
+    query = query.replace('$limitrows', str(genes_per_page))
 
     with neo4j_instance.driver.session() as session:
         # Execute Cypher query.
@@ -737,16 +737,16 @@ def genelist_get_logic(neo4j_instance, page:str, totalpages:str, genesperpage:st
             except KeyError:
                 pass
         # Use the list of gene details with the page to build a genelist object.
-        genelist: GeneList = GeneList(page, totalpages, genesperpage, genes, startswith, genecount).serialize()
+        genelist: GeneList = GeneList(page, total_pages, genes_per_page, genes, starts_with, gene_count).serialize()
     return genelist
 
-def genelist_count_get_logic(neo4j_instance, startswith: str) -> int:
+def genelist_count_get_logic(neo4j_instance, starts_with: str) -> int:
     """
         Returns the count of HGNC genes in the UBKG.
-        If startswith is non-null, returns the count of HGNC genes with approved symbol
+        If starts_with is non-null, returns the count of HGNC genes with approved symbol
         that starts with the parameter value.
         :param neo4j_instance:  neo4j client
-        :param startswith: filtering string for STARTS WITH queries
+        :param starts_with: filtering string for STARTS WITH queries
         :return: integer count
     """
     #
@@ -755,8 +755,8 @@ def genelist_count_get_logic(neo4j_instance, startswith: str) -> int:
     queryfile = 'geneslist_count.cypher'
     query = loadquerystring(queryfile)
     starts_with_clause = ''
-    if startswith != '':
-        starts_with_clause = f'AND tGene.name STARTS WITH \'{startswith}\''
+    if starts_with != '':
+        starts_with_clause = f'AND tGene.name STARTS WITH \'{starts_with}\''
     query = query.replace('$starts_with_clause', starts_with_clause)
 
     with neo4j_instance.driver.session() as session:
@@ -765,8 +765,8 @@ def genelist_count_get_logic(neo4j_instance, startswith: str) -> int:
 
         for record in recds:
             try:
-                genecount = record.get('genelistcount')
+                gene_count = record.get('genelistcount')
             except KeyError:
                 pass
-    return genecount
+    return gene_count
 
diff --git a/test_api.sh b/test_api.sh
index e7ab62c..e24c28c 100755
--- a/test_api.sh
+++ b/test_api.sh
@@ -118,18 +118,18 @@ echo
 # Test for gene_list endpoint
 echo "genes-info GET"
 curl --request GET \
- --url "${UBKG_URL}/genes-info?page=1&genesperpage=3" \
+ --url "${UBKG_URL}/genes-info?page=1&genes_per_page=3" \
  --header "Content-Type: application/json"
 echo
 echo "genes-info GET last page"
 curl --request GET \
- --url "${UBKG_URL}/genes-info?page=last&genesperpage=3" \
+ --url "${UBKG_URL}/genes-info?page=last&genes_per_page=3" \
  --header "Content-Type: application/json"
 echo
 
 echo "genes-info GET starts_with B"
 curl --request GET \
- --url "${UBKG_URL}/genes-info?genesperpage=3&starts_with=B" \
+ --url "${UBKG_URL}/genes-info?genes_per_page=3&starts_with=B" \
  --header "Content-Type: application/json"
 echo
 

From 7618426ffe540ea0d35c6e2f44eef6f84817813d Mon Sep 17 00:00:00 2001
From: yuanzhou <zhy19@pitt.edu>
Date: Wed, 8 Nov 2023 15:48:51 -0500
Subject: [PATCH 10/11] Correct version of yaml

---
 hs-ontology-api-spec.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
index 30f7b93..1c22a0b 100644
--- a/hs-ontology-api-spec.yaml
+++ b/hs-ontology-api-spec.yaml
@@ -2,7 +2,7 @@ openapi: 3.0.3
 info:
   title: HubMAP/SenNet Ontology API (hs-ontology-api)
   description: The HuBMAP/SenNet Ontology API contains endpoints for querying a [UBKG](https://ubkg.docs.xconsortia.org/) instance with content from the [HuBMAP/SenNet context](https://ubkg.docs.xconsortia.org/contexts/#hubmapsennet-context). The hs-ontology-api imports the [ubkg-api](https://smart-api.info/ui/96e5b5c0b0efeef5b93ea98ac2794837), which encapsulates both basic connectivity to a UBKG instance and generic endpoint code.
-  version: 1.3.1
+  version: 1.4.4
   contact:
     name: GitHub repository
     url: https://github.com/x-atlas-consortia/hs-ontology-api

From ad1d466640a15c16b35c15bdf95f588b82a5170c Mon Sep 17 00:00:00 2001
From: AlanSimmons <jas971@pitt.edu>
Date: Wed, 8 Nov 2023 15:25:11 -0600
Subject: [PATCH 11/11] Changed underscores to dashes in proposed endpoints:
 field-descriptions field-types field-entities field-assays field-schemas

Also changed underscores to dashes in route summary fields to reflect the names of the legacy YAML files.
---
 hs-ontology-api-spec.yaml | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/hs-ontology-api-spec.yaml b/hs-ontology-api-spec.yaml
index 1c22a0b..808b002 100644
--- a/hs-ontology-api-spec.yaml
+++ b/hs-ontology-api-spec.yaml
@@ -551,10 +551,10 @@ paths:
           description: No information for cell type with identifier *id*.
         '5XX':
           description: Unexpected error
-  /field_descriptions:
+  /field-descriptions:
     get:
       operationId: field_descriptions_get
-      summary: Return descriptions for ingest metadata fields. Replacement for field_descriptions.yaml.
+      summary: Return descriptions for ingest metadata fields. Replacement for field-descriptions.yaml.
       responses:
         '200':
           description: Ingest metadata fields and descriptions
@@ -566,10 +566,10 @@ paths:
                   $ref: '#/components/schemas/FieldDescriptionsResponse'
         '5XX':
           description: Unexpected error
-  /field_types:
+  /field-types:
     get:
       operationId: field_types_get
-      summary: Return data types for ingest metadata fields. Replacement for field_types.yaml.
+      summary: Return data types for ingest metadata fields. Replacement for field-types.yaml.
       responses:
         '200':
           description: Ingest metadata fields mapped to XSD data types.
@@ -581,10 +581,10 @@ paths:
                   $ref: '#/components/schemas/FieldTypesResponse'
         '5XX':
           description: Unexpected error
-  /field_entities:
+  /field-entities:
     get:
       operationId: field_entities_get
-      summary: Return associations between ingest metadata fields and the provenance entities of an application. Replacement for field_types.yaml.
+      summary: Return associations between ingest metadata fields and the provenance entities of an application. Replacement for field-types.yaml.
       parameters:
         - name: application_context
           in: query
@@ -613,10 +613,10 @@ paths:
           description: missing application context
         '5XX':
           description: Unexpected error
-  /field_assays:
+  /field-assays:
     get:
       operationId: field_assays_get
-      summary: Return associations between ingest metadata fields and the "assays" (dataset data types) for an application. Replacement for field_assays.yaml.
+      summary: Return associations between ingest metadata fields and the "assays" (dataset data types) for an application. Replacement for field-assays.yaml.
       parameters:
         - name: application_context
           in: query
@@ -645,10 +645,10 @@ paths:
           description: missing application context
         '5XX':
           description: Unexpected error
-  /field_schemas:
+  /field-schemas:
     get:
       operationId: field_schemas_get
-      summary: Return associations between ingest metadata fields and metadata schemas for an application. Replacement for field_schemas.yaml.
+      summary: Return associations between ingest metadata fields and metadata schemas for an application. Replacement for field-schemas.yaml.
       parameters:
         - name: application_context
           in: query
@@ -1218,7 +1218,7 @@ components:
                 example: heart
     FieldDescriptionsResponse:
       type: object
-      description: Descriptions ingest metadata fields from legacy field_descriptions.yaml
+      description: Descriptions ingest metadata fields from legacy field-descriptions.yaml
       properties:
         fields:
           type: array
@@ -1240,7 +1240,7 @@ components:
                 example: Units of x resolution distance between laser ablation shots.
     FieldTypesResponse:
       type: object
-      description: Associations between metadata field and data type ingest metadata fields from legacy field_types.yaml
+      description: Associations between metadata field and data type ingest metadata fields from legacy field-types.yaml
       properties:
         fields:
           type: array
@@ -1269,7 +1269,7 @@ components:
                     example: string
     FieldEntitiesResponse:
       type: object
-      description: Associations between fields and provenance entities for ingest metadata fields from legacy field_types.yaml
+      description: Associations between fields and provenance entities for ingest metadata fields from legacy field-types.yaml
       properties:
         fields:
           type: array
@@ -1301,7 +1301,7 @@ components:
                       example: dataset
     FieldAssaysResponse:
       type: object
-      description: Associations between fields and "assays" (dataset types) for ingest metadata fields from legacy field_assays.yaml
+      description: Associations between fields and "assays" (dataset types) for ingest metadata fields from legacy field-assays.yaml
       properties:
         fields:
           type: array
@@ -1347,7 +1347,7 @@ components:
                         example: [Imaging Mass Cytometry,2D-IMC,IMC]
     FieldSchemasResponse:
       type: object
-      description: Associations between fields and metadata schemas for ingest metadata fields from legacy field_schemas.yaml
+      description: Associations between fields and metadata schemas for ingest metadata fields from legacy field-schemas.yaml
       properties:
         fields:
           type: array