Rename endpoints and names (#17)

* Rename endpoints and names - Change to *IPD-IMGT/HLA* - Change endpoint to `ipd-imgt-hla-versions` * Upgrade Docker python to 3.10 * Fix quotes * Fix quotes * Bump version: 0.0.1 → 1.0.0 * Bump version: 1.0.0 → 2.0.0 * Fix name * Fix keyname * Fix package copy
nmdp-bioinformatics · Aug 29, 2023 · 60fc027 · 60fc027
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diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -38,8 +38,8 @@ and "help wanted" is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-My Project Template could always use more documentation, whether as part of the
-official My Project Template docs, in docstrings, or even on the web in blog posts,
+GFE Service could always use more documentation, whether as part of the
+official GFE Service docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
 Submit Feedback

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.8-slim-buster
+FROM python:3.10-slim-buster
 
 LABEL MAINTAINER="Pradeep Bashyal"
 
@@ -13,7 +13,7 @@ RUN pip install --no-cache-dir -r requirements-deploy.txt
 COPY api-spec.yaml /app/
 COPY app.py /app/
 COPY api.py /app/
-COPY query.py /app/
+COPY gfe_service /app/gfe_service/
 COPY neo4j.yaml /app/
 
 CMD ["gunicorn"  , "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm", "app:app"]
diff --git a/HEADER.txt b/HEADER.txt
@@ -1,5 +1,5 @@
 #
-#    gfe_service My Project Template.
+#    gfe_service GFE Service.
 #    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
 #
 #    This library is free software; you can redistribute it and/or modify it

diff --git a/api-spec.yaml b/api-spec.yaml
@@ -13,30 +13,30 @@ servers:
     -   url: 'http://localhost:8080'
 tags:
     -   name: IMGT
-        description: "Available IMGT DB releases"
+        description: "Available IPD-IMGT/HLA Database releases"
     -   name: GFE
         description: Create and Retrieve GFE
     -   name: "Sequence Annotation"
         description: Annotation by sequence (Coming Soon)
 paths:
-    /imgt-versions:
+    /ipd-imgt-hla-versions:
         get:
-            summary: IMGT DB versions in the DB
+            summary: IPD-IMGT/HLA Database versions in the GFE-DB
             tags:
                 - IMGT
             operationId: api.imgt_versions
-            description: Versions of IMGT DB Alleles in GFE DB
+            description: Versions of IPD-IMGT/HLA Database Alleles in GFE DB
 
             responses:
                 200:
-                    description: Version Numbers of Available IMGT DB
+                    description: Version Numbers of Available IPD-IMGT/HLA Database
                     content:
                         application/json:
                             schema:
                                 type: object
                                 properties:
                                     imgt_versions:
-                                        description: IMGT DB Versions
+                                        description: IPD-IMGT/HLA Database Versions
                                         type: array
                                         items:
                                             type: string
@@ -56,25 +56,25 @@ paths:
                                         type: string
                                         example: "Database Unreachable"
 
-    /who/{who_name}:
+    /ipd/{ipd_name}:
         get:
-            summary: Get GFE for a WHO name
+            summary: Get GFE for a IPD-IMGT/HLA HLA name
             tags:
                 - GFE
-            operationId: api.gfe_from_who
-            description: For a given WHO Allele name, return the corresponding GFE
+            operationId: api.gfe_from_ipd
+            description: For a given IPD-IMGT/HLA Allele name, return the corresponding GFE
             parameters:
-                -   name: who_name
+                -   name: ipd_name
                     in: path
-                    description: WHO Allele name
+                    description: IPD-IMGT/HLA Database Allele name
                     required: true
                     schema:
                         type: string
                     style: simple
                     example: "HLA-A*01:01:01:08"
             responses:
                 200:
-                    description: GFE from WHO allele name
+                    description: GFE from IPD-IMGT/HLA allele name
                     content:
                         application/json:
                             schema:
@@ -88,12 +88,12 @@ paths:
                                         description: GFE Name
                                         type: string
                                         example: "HLA-Aw878-8-363-912-830-2901-1044-581-151-324-198-9-316-80-508-43-151"
-                                    who:
-                                        description: WHO Name
+                                    allele:
+                                        description: IPD-IMGT/HLA Allele Name
                                         type: string
                                         example: "HLA-A*01:01:01:08"
                                     imgt_versions:
-                                        description: IMGT Versions
+                                        description: IPD-IMGT/HLA Database Versions
                                         type: array
                                         items:
                                             type: string
@@ -103,23 +103,23 @@ paths:
 
     /gfe/locus/{gene}:
         get:
-            summary: GFEs and WHO Names for a gene
+            summary: GFEs and IPD Allele Names for a gene
             tags:
                 - GFE
             operationId: api.all_locus_gfe
-            description: Get all GFEs and WHO Names for a gene
+            description: Get all GFEs and IPD Allele Names for a gene
             parameters:
                 -   name: gene
                     in: path
-                    description: WHO Gene Name
+                    description: IPD Allele Gene Name
                     required: true
                     schema:
                         type: string
                     style: simple
                     example: "HLA-A"
             responses:
                 200:
-                    description: List of WHO allele names and their corresponding GFEs
+                    description: List of IPD Allele names and their corresponding GFEs
                     content:
                         application/json:
                             schema:
@@ -130,7 +130,7 @@ paths:
                                         type: string
                                         example: "HLA-A"
                                     GFEs:
-                                        description: List of WHO alleles and GFE
+                                        description: List of IPD Alleles and GFE
                                         type: array
                                         items:
                                             type: object
@@ -140,7 +140,7 @@ paths:
                                                     type: string
                                                     example: "HLA-Aw878-8-363-912-830-2901-1044-581-151-324-198-9-316-80-508-43-151"
                                                 who:
-                                                    description: WHO Allele Name
+                                                    description: IPD Allele Name
                                                     type: string
                                                     example: "HLA-A*01:01:01:08"
 

diff --git a/api.py b/api.py
@@ -1,7 +1,7 @@
 import yaml
 from py2neo import Graph
 
-import query
+from gfe_service import query
 
 with open("neo4j.yaml", "r") as neo4j_file:
     neo_dict = yaml.safe_load(neo4j_file)
@@ -20,14 +20,14 @@ def imgt_versions():
     return {"imgt_versions": dbs}, 200
 
 
-def gfe_from_who(who_name: str):
-    cypher = query.gfe_from_who()
-    response = graph.run(cypher, {"who_name": who_name})
+def gfe_from_ipd(ipd_name: str):
+    cypher = query.gfe_from_ipd()
+    response = graph.run(cypher, {"ipd_name": ipd_name})
     result = response.next()
     return {
         "locus": result["locus"],
         "gfe": result["gfe"],
-        "who": result["who"],
+        "allele": result["allele"],
         "imgt_versions": result["imgt_versions"],
     }, 200
 
@@ -37,7 +37,7 @@ def all_locus_gfe(gene: str):
     response = graph.run(cypher, {"locus": gene})
     allele_gfe_list = []
     for result in response:
-        allele_gfe_list.append({"allele": result["who"], "GFE": result["gfe"]})
+        allele_gfe_list.append({"allele": result["allele"], "GFE": result["gfe"]})
     return {"gene": gene, "GFEs": allele_gfe_list}
 
 

diff --git a/gfe_service/__init__.py b/gfe_service/__init__.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    gfe_service My Project Template.
+#    gfe_service GFE Service.
 #    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
 #
 #    This library is free software; you can redistribute it and/or modify it
@@ -23,7 +23,7 @@
 #
 
 
-"""Top-level package for My Project Template."""
+"""Top-level package for gfe-service."""
 
 __organization__ = "NMDP/CIBMTR Bioinformatics"
-__version__ = "2.0.1"
+__version__ = "2.0.0"
diff --git a/gfe_service/gfe_service.py b/gfe_service/gfe_service.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    gfe_service My Project Template.
+#    gfe_service GFE Service.
 #    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
 #
 #    This library is free software; you can redistribute it and/or modify it

diff --git a/query.py → gfe_service/query.py b/query.py → gfe_service/query.py
@@ -1,6 +1,6 @@
 def imgt_db_versions():
     query = """
-    MATCH (g:GFE)-[e:HAS_WHO]-(w:WHO)
+    MATCH (g:GFE)-[e:HAS_IPD_Allele]-(a:IPD_Allele)
         WITH COLLECT(DISTINCT e.releases) AS releases
         UNWIND REDUCE(output=[], r IN releases| output + r) as dbs
         RETURN COLLECT(DISTINCT dbs) as HLA_DB_VERSIONS
@@ -9,20 +9,20 @@ def imgt_db_versions():
     return query
 
 
-def gfe_from_who():
+def gfe_from_ipd():
     query = """
-    MATCH (g:GFE)-[r:HAS_WHO]-(w:WHO)
-        WHERE w.name = $who_name
-        RETURN g.locus AS locus, g.gfe_name AS gfe, w.name AS who, r.releases AS imgt_versions
+    MATCH (g:GFE)-[r:HAS_IPD_Allele]-(a:IPD_Allele)
+        WHERE a.name = $allele
+        RETURN g.locus AS locus, g.gfe_name AS gfe, a.name AS allele, r.releases AS imgt_versions
     """
     return query
 
 
 def all_gfe_from_locus():
     query = """
-    MATCH (g:GFE)-[:HAS_WHO]-(w:WHO)
+    MATCH (g:GFE)-[:HAS_IPD_Allele]-(a:IPD_Allele)
     WHERE g.locus = $locus
-    RETURN g.gfe_name AS gfe, w.name AS who
+    RETURN g.gfe_name AS gfe, a.name AS allele
     limit 100
     """
     return query
@@ -31,6 +31,6 @@ def all_gfe_from_locus():
 def sequence_from_gfe():
     query = """
     MATCH (g:GFE)-[:HAS_SEQUENCE]-(s:Sequence)
-    WHERE g.gfe_name = $gfe return s.sequence as sequence;
+    WHERE g.name = $gfe return s.sequence as sequence;
     """
     return query
diff --git a/neo4j.yaml b/neo4j.yaml
@@ -1,5 +1,4 @@
 ---
   user: "neo4j"
   password: "gfedb"
-#  neo4j_url: "http://0.0.0.0:7474"
-  neo4j_url: "http://dev-gfedb.b12x.org:7474"
+  neo4j_url: "http://workshop-gfedb.b12x.org:7474"
diff --git a/requirements-tests.txt b/requirements-tests.txt
@@ -1,3 +1,3 @@
-pytest==6.2.5
+pytest==7.1.2
 behave==1.2.6
-PyHamcrest==2.0.2
+PyHamcrest==2.0.3
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1 @@
+py2neo==2021.2.3
diff --git a/setup.cfg b/setup.cfg
@@ -1,15 +1,15 @@
 [bumpversion]
-current_version = 0.0.1
+current_version = 2.0.0
 commit = True
 tag = True
 
 [bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
+search = version="{current_version}"
+replace = version="{new_version}"
 
-[bumpversion:file:my_project_template/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
+[bumpversion:file:gfe_service/__init__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
 
 [bdist_wheel]
 universal = 1
@@ -18,5 +18,4 @@ universal = 1
 exclude = docs
 
 [aliases]
-# Define setup.py command aliases here
 test = pytest
diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    gfe_service My Project Template.
+#    gfe_service GFE Service.
 #    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
 #
 #    This library is free software; you can redistribute it and/or modify it
@@ -57,12 +57,12 @@
     license="LGPL 3.0",
     long_description=readme + "\n\n" + history,
     include_package_data=True,
-    keywords="gfe_service",
+    keywords="GFE,HLA",
     name="gfe_service",
     packages=find_packages(include=["gfe_service"]),
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/nmdp-bioinformatics/my_project_template",
-    version="0.0.1",
+    version="2.0.0",
     zip_safe=False,
 )
diff --git a/tests/unit/test_sample.py b/tests/unit/test_sample.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 #
-#    gfe_service My Project Template.
+#    gfe_service GFE Service.
 #    Copyright (c) 2021 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
 #
 #    This library is free software; you can redistribute it and/or modify it