Merge pull request #89 from pepkit/new_desc_column

v0.4.3

docs/changelog.md

@@ -2,6 +2,12 @@
 
 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.
 
+## [0.4.3] -- 2023-06-30
+- Changed the orientation of the raw project dictionary to "records" and updated peppy version to 0.35.6.
+- Added description column
+- Added sql description search
+- Deleted unused files
+
 ## [0.4.2] -- 2023-06-27
 - Added validation of question mark in name and tag
 - Fixed description and name in config file

manual_tests.py

@@ -59,7 +59,7 @@ def upload_sample_pep_to_db(connection: pepdbagent.PEPDatabaseAgent):
     "/home/bnt4me/virginia/repos/pepdbagent/tests/data/namespace1/basic/project_config.yaml"
 )
 fgf = prj.to_dict()
-rr = prj.to_dict(extended=True)
+rr = prj.to_dict(extended=True, orient="records")
 con.project.create(project=prj, namespace="dog_namespace", name="testttt", tag="test1", overwrite=True)
 
 

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.4.2"
+__version__ = "0.4.3"

pepdbagent/const.py

@@ -5,7 +5,7 @@
 
 DESCRIPTION_KEY = "description"
 
-from peppy.const import SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_DICT_KEY
+from peppy.const import SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_LIST_KEY
 
 DEFAULT_OFFSET = 0
 DEFAULT_LIMIT = 100

pepdbagent/db_utils.py

@@ -59,6 +59,13 @@ def receive_after_create(target, connection, tables, **kw):
         _LOGGER.info("A table was not created")
 
 
+def deliver_description(context):
+    try:
+        return context.get_current_parameters()["project_value"]["_config"]["description"]
+    except KeyError:
+        return ""
+
+
 class Projects(Base):
     __tablename__ = "projects"
 
@@ -67,6 +74,9 @@ 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))
+    description: Mapped[Optional[str]] = mapped_column(
+        default=deliver_description, onupdate=deliver_description
+    )
     project_value: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
     private: Mapped[bool]
     number_of_samples: Mapped[int]

pepdbagent/models.py

@@ -97,6 +97,7 @@ class UpdateModel(BaseModel):
     last_update_date: Optional[datetime.datetime]
     number_of_samples: Optional[int]
     pep_schema: Optional[str]
+    description: Optional[str]
 
     @validator("tag", "name")
     def value_must_not_be_empty(cls, v):

pepdbagent/modules/annotation.py

@@ -158,7 +158,7 @@ def _get_single_annotation(
             Projects.name,
             Projects.tag,
             Projects.private,
-            Projects.project_value["description"].astext.label("description"),
+            Projects.description,
             Projects.number_of_samples,
             Projects.submission_date,
             Projects.last_update_date,
@@ -256,7 +256,7 @@ def _get_projects(
             Projects.name,
             Projects.tag,
             Projects.private,
-            Projects.project_value["description"].astext.label("description"),
+            Projects.description,
             Projects.number_of_samples,
             Projects.submission_date,
             Projects.last_update_date,
@@ -349,6 +349,7 @@ def _add_condition(
             search_query = or_(
                 Projects.name.ilike(sql_search_str),
                 Projects.tag.ilike(sql_search_str),
+                Projects.description.ilike(sql_search_str),
             )
             statement = statement.where(search_query)
         if namespace:

pepdbagent/modules/project.py

@@ -168,6 +168,7 @@ def create(
         namespace: str,
         name: str = None,
         tag: str = DEFAULT_TAG,
+        description: str = None,
         is_private: bool = False,
         pep_schema: str = None,
         overwrite: bool = False,
@@ -187,19 +188,21 @@ def create(
         :param overwrite: if project exists overwrite the project, otherwise upload it.
             [Default: False - project won't be overwritten if it exists in db]
         :param update_only: if project exists overwrite it, otherwise do nothing.  [Default: False]
+        :param description: description of the project
         :return: None
         """
-        proj_dict = project.to_dict(extended=True)
-        proj_dict["_config"]["description"] = project.description
+        proj_dict = project.to_dict(extended=True, orient="records")
+        if not description:
+            description = project.description
+        proj_dict["_config"]["description"] = 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()
+        elif proj_dict["_config"]["name"]:
+            proj_name = proj_dict["_config"]["name"].lower()
         else:
             raise ValueError(f"Name of the project wasn't provided. Project will not be uploaded.")
 
@@ -336,7 +339,6 @@ def update(
                     tag: Optional[str]
                     name: Optional[str]
             }
-            *project_value should contain name and description
         :param namespace: project namespace
         :param name: project name
         :param tag: project tag
@@ -383,13 +385,13 @@ 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"]
+            proj_dict = update_values.project_value.to_dict(extended=True, orient="records")
             update_final = UpdateModel(
                 project_value=proj_dict,
                 name=update_values.project_value.name,
-                digest=create_digest(update_values.project_value.to_dict(extended=True)),
+                digest=create_digest(
+                    update_values.project_value.to_dict(extended=True, orient="records")
+                ),
                 last_update_date=datetime.datetime.now(datetime.timezone.utc),
                 number_of_samples=len(update_values.project_value.samples),
             )

requirements/requirements-all.txt

@@ -1,8 +1,8 @@
 sqlalchemy>=2.0.0
 logmuse
-peppy>=0.35.5
+peppy>=0.35.6
 ubiquerg>=0.6.2
 coloredlogs>=15.0.1
 pytest-mock
-pydantic
+pydantic<2.0
 psycopg2