Merge pull request #86 from pepkit/dev

V0.4.2

docs/changelog.md

@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.4.2] -- 2023-06-27
+- Added validation of question mark in name and tag
+- Fixed description and name in config file
+- Fixed preserving order of columns in database
+
 ## [0.4.1] -- 2023-06-09
 - Fixed project.update function
 

manual_tests.py

@@ -58,8 +58,13 @@ def upload_sample_pep_to_db(connection: pepdbagent.PEPDatabaseAgent):
 prj = peppy.Project(
     "/home/bnt4me/virginia/repos/pepdbagent/tests/data/namespace1/basic/project_config.yaml"
 )
+fgf = prj.to_dict()
+rr = prj.to_dict(extended=True)
 con.project.create(project=prj, namespace="dog_namespace", name="testttt", tag="test1", overwrite=True)
 
+
+pr = con.project.get(namespace="dog_namespace", name="testttt", tag="test1", raw=True)
+pr
 con.project.exists(namespace="dog_namespace", name="testttt", tag="test1")
 
 
@@ -114,4 +119,7 @@ def upload_sample_pep_to_db(connection: pepdbagent.PEPDatabaseAgent):
 
 con.project.update(update_dict={"is_private": False}, namespace="dog_namespace", name="testttt", tag="test1")
 
-dell = con.project.delete(namespace="dog_namespace", name="testttt", tag="test1")
+dell = con.project.delete(namespace="dog_namespace", name="testttt", tag="test1")
+
+
+from pydantic import BaseModel

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.4.1"
+__version__ = "0.4.2"

pepdbagent/db_utils.py

@@ -13,7 +13,7 @@
     select,
     TIMESTAMP,
 )
-from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.dialects.postgresql import JSON
 from sqlalchemy.engine import URL, create_engine
 from sqlalchemy.exc import ProgrammingError
 from sqlalchemy.ext.compiler import compiles
@@ -39,9 +39,9 @@ def compile_bigserial_pg(type_, compiler, **kw):
     return "BIGSERIAL"
 
 
-@compiles(JSONB, POSTGRES_DIALECT)
+@compiles(JSON, POSTGRES_DIALECT)
 def compile_jsonb_pg(type_, compiler, **kw):
-    return "JSONB"
+    return "JSON"
 
 
 class Base(DeclarativeBase):
@@ -67,7 +67,7 @@ class Projects(Base):
     name: Mapped[str] = mapped_column(primary_key=True)
     tag: Mapped[str] = mapped_column(primary_key=True)
     digest: Mapped[str] = mapped_column(String(32))
-    project_value: Mapped[dict] = mapped_column(JSONB, server_default=FetchedValue())
+    project_value: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
     private: Mapped[bool]
     number_of_samples: Mapped[int]
     submission_date: Mapped[datetime.datetime]

pepdbagent/models.py

@@ -110,6 +110,12 @@ def value_must_be_lowercase(cls, v):
             return v.lower()
         return v
 
+    @validator("tag", "name")
+    def value_should_not_contain_question(cls, v):
+        if "?" in v:
+            return ValueError("Question mark (?) is prohibited in name and tag.")
+        return v
+
     class Config:
         extra = Extra.forbid
         allow_population_by_field_name = True

pepdbagent/modules/project.py

@@ -190,12 +190,14 @@ def create(
         :return: None
         """
         proj_dict = project.to_dict(extended=True)
+        proj_dict["_config"]["description"] = project.description
 
         namespace = namespace.lower()
         if name:
             name = name.lower()
             proj_name = name
             proj_dict["name"] = name
+            proj_dict["_config"]["name"] = project.name
         elif proj_dict["name"]:
             proj_name = proj_dict["name"].lower()
         else:
@@ -381,8 +383,11 @@ def __create_update_dict(update_values: UpdateItems) -> dict:
         update_final = UpdateModel()
 
         if update_values.project_value is not None:
+            proj_dict = update_values.project_value.to_dict(extended=True)
+            proj_dict["_config"]["description"] = proj_dict["description"]
+            proj_dict["_config"]["name"] = proj_dict["name"]
             update_final = UpdateModel(
-                project_value=update_values.project_value.to_dict(extended=True),
+                project_value=proj_dict,
                 name=update_values.project_value.name,
                 digest=create_digest(update_values.project_value.to_dict(extended=True)),
                 last_update_date=datetime.datetime.now(datetime.timezone.utc),