Merge pull request #2582 from chaoss/dev

UPdate dependabot branch with updates to dev

augur/api/view/routes.py

@@ -74,17 +74,15 @@ def repo_table_view():
     pagination_offset = config.get_value("frontend", "pagination_offset")
 
     if current_user.is_authenticated:
-        data = load_repos_test(user = current_user, search = query, page = page, sort = sorting, direction = direction, source = "user")
-        page_count = load_repos_test(user = current_user, search = query, count = True, source = "user")
-        # data = current_user.get_repos(page = page, sort = sorting, direction = direction, search=query)[0]
-        # page_count = (current_user.get_repo_count(search = query)[0] or 0) // pagination_offset
+        data = current_user.get_repos(page = page, sort = sorting, direction = direction, search=query)[0]
+        repos_count = (current_user.get_repo_count(search = query)[0] or 0)
     else:
-        data = load_repos_test(search = query, page = page, sort = sorting, direction = direction)
-        page_count = load_repos_test(search = query, count = True)
-        # data = get_all_repos(page = page, sort = sorting, direction = direction, search=query)[0]
-        # page_count = (get_all_repos_count(search = query)[0] or 0) // pagination_offset
+        data = get_all_repos(page = page, sort = sorting, direction = direction, search=query)[0]
+        repos_count = (get_all_repos_count(search = query)[0] or 0)
+
+    page_count = math.ceil(repos_count / pagination_offset) - 1
 
-    if not data.count():
+    if not data:
         data = None
 
 

augur/api/view/utils.py

@@ -9,11 +9,13 @@
 from augur.application.db.session import DatabaseSession
 from augur.application.db.engine import DatabaseEngine
 from augur.application.db.models import User, Repo, RepoGroup, UserGroup, UserRepo
-from sqlalchemy import Column, Table, Integer, MetaData, or_, Label
+from sqlalchemy import Column, Table, Integer, MetaData, or_
 from sqlalchemy.sql.operators import ilike_op, distinct_op
 from sqlalchemy.sql.functions import coalesce
 from augur.application.db.models.base import Base
 
+from sqlalchemy.orm import Query
+
 init_logging()
 
 from .init import logger
@@ -310,66 +312,4 @@ def render_module(module, **args):
     return render_template('index.j2', **args)
 
 """ ----------------------------------------------------------------
-    No longer used
 """
-# My attempt at a loading page
-def renderLoading(dest, query, request):
-    cache_files_requested.append(request)
-    return render_template('index.j2', body="loading", title="Loading", d=dest, query_key=query, api_url=getSetting('serving'))
-
-with DatabaseEngine() as engine:
-    augur_data_schema = MetaData(schema = "augur_data")
-    augur_data_schema.reflect(bind = engine, views = True)
-
-    commits_materialized_view: Table = augur_data_schema.tables["augur_data.api_get_all_repos_commits"]
-    issues_materialized_view: Table = augur_data_schema.tables["augur_data.api_get_all_repos_issues"]
-
-""" ----------------------------------------------------------------
-"""
-def load_repos_test(count = False, source = None, **kwargs):
-    columns: list[Label] = [
-        Repo.repo_id.distinct().label("repo_id"),
-        Repo.description.label("description"),
-        Repo.repo_git.label("url"),
-        coalesce(commits_materialized_view.columns.commits_all_time, 0).label("commits_all_time"),
-        coalesce(issues_materialized_view.columns.issues_all_time, 0).label("issues_all_time"),
-        RepoGroup.rg_name.label("rg_name"),
-        Repo.repo_git.regexp_replace('.*github\.com\/[A-Za-z0-9 \- _]+\/([A-Za-z0-9 \- _ .]+)$', "\\1").label("repo_name"),
-        Repo.repo_git.regexp_replace('.*github\.com\/([A-Za-z0-9 \- _]+)\/[A-Za-z0-9 \- _ .]+$', "\\1").label("repo_owner"),
-        RepoGroup.repo_group_id.label("repo_group_id")
-    ]
-
-    def get_colum_by_label(label: str)-> Label:
-        for column in columns:
-            if column.name == label:
-                return column
-
-    repos = db_session.query(*columns)\
-        .outerjoin(commits_materialized_view, Repo.repo_id == commits_materialized_view.columns.repo_id)\
-        .outerjoin(issues_materialized_view, Repo.repo_id == issues_materialized_view.columns.repo_id)\
-        .join(RepoGroup, Repo.repo_group_id == RepoGroup.repo_group_id)
-
-    user: User = kwargs.get("user")
-    if user:
-        repos = repos.join(UserRepo, Repo.repo_id == UserRepo.repo_id)\
-            .join(UserGroup, UserGroup.group_id == UserRepo.group_id)\
-            .filter(UserGroup.user_id == user.user_id)
-
-    search = kwargs.get("search")
-    qkey = kwargs.get("query_key") or ["repo_name", "repo_owner"]
-    if search:
-        if isinstance(qkey, list) and len(qkey) > 0:
-            repos = repos.filter(or_(ilike_op(get_colum_by_label(filter_column), f"%{search}%") for filter_column in qkey))
-        else:
-            repos = repos.filter(ilike_op(get_colum_by_label(qkey), f"%{search}%"))
-
-    page_size: int = kwargs.get("page_size") or 25
-    if count:
-        c = repos.count()
-        return math.ceil(c / page_size) - 1
-
-    page: int = kwargs.get("page") or 0
-    offset = page * page_size
-
-    return repos.slice(offset, offset + page_size)
-

augur/application/db/models/augur_data.py

@@ -564,6 +564,8 @@ class RepoGroup(Base):
     data_source = Column(String)
     data_collection_date = Column(TIMESTAMP(precision=0))
 
+    repo = relationship("Repo", back_populates="repo_group")
+
     @staticmethod
     def is_valid_repo_group_id(session, repo_group_id: int) -> bool:
         """Deterime is repo_group_id exists.
@@ -866,8 +868,8 @@ class Repo(Base):
         TIMESTAMP(precision=0), server_default=text("CURRENT_TIMESTAMP")
     )
 
-    repo_group = relationship("RepoGroup")
-    user_repo = relationship("UserRepo")
+    repo_group = relationship("RepoGroup", back_populates="repo")
+    user_repo = relationship("UserRepo", back_populates="repo")
     collection_status = relationship("CollectionStatus", back_populates="repo")
     issues = relationship("Issue", back_populates="repo")
     prs = relationship("PullRequest", back_populates="repo")
@@ -1208,10 +1210,6 @@ class Commit(Base):
         primaryjoin="Commit.cmt_author_platform_username == Contributor.cntrb_login",
         back_populates="commits"
     )
-    contributor1 = relationship(
-        "Contributor",
-        primaryjoin="Commit.cmt_author_platform_username == Contributor.cntrb_login",
-    )
     repo = relationship("Repo", back_populates="commits")
     message_ref = relationship("CommitCommentRef", back_populates="cmt")
 

augur/application/db/models/augur_operations.py

@@ -271,9 +271,9 @@ class User(Base):
         {"schema": "augur_operations"}
     )
 
-    groups = relationship("UserGroup")
-    tokens = relationship("UserSessionToken")
-    applications = relationship("ClientApplication")
+    groups = relationship("UserGroup", back_populates="user")
+    tokens = relationship("UserSessionToken", back_populates="user")
+    applications = relationship("ClientApplication", back_populates="user")
 
     _is_authenticated = False
     _is_active = True
@@ -628,8 +628,8 @@ class UserGroup(Base):
         {"schema": "augur_operations"}
     )
 
-    user = relationship("User")
-    repos = relationship("UserRepo")
+    user = relationship("User", back_populates="groups")
+    user_repos = relationship("UserRepo", back_populates="group")
 
     @staticmethod
     def insert(session, user_id:int, group_name:str) -> dict:
@@ -739,8 +739,8 @@ class UserRepo(Base):
         ForeignKey("augur_data.repo.repo_id", name="user_repo_user_id_fkey"), primary_key=True, nullable=False
     )
 
-    repo = relationship("Repo")
-    group = relationship("UserGroup")
+    repo = relationship("Repo", back_populates="user_repo")
+    group = relationship("UserGroup", back_populates="user_repos")
 
     @staticmethod
     def insert(session, repo_id: int, group_id:int = 1) -> bool:
@@ -949,9 +949,9 @@ class UserSessionToken(Base):
     application_id = Column(ForeignKey("augur_operations.client_applications.id", name="user_session_token_application_id_fkey"), nullable=False)
     created_at = Column(BigInteger)
 
-    user = relationship("User")
-    application = relationship("ClientApplication")
-    refresh_tokens = relationship("RefreshToken")
+    user = relationship("User", back_populates="tokens")
+    application = relationship("ClientApplication", back_populates="sessions")
+    refresh_tokens = relationship("RefreshToken", back_populates="user_session")
 
     @staticmethod
     def create(session, user_id, application_id, seconds_to_expire=86400):
@@ -991,9 +991,9 @@ class ClientApplication(Base):
     redirect_url = Column(String, nullable=False)
     api_key = Column(String, nullable=False)
 
-    user = relationship("User")
+    user = relationship("User", back_populates="applications")
     sessions = relationship("UserSessionToken")
-    subscriptions = relationship("Subscription")
+    subscriptions = relationship("Subscription", back_populates="application")
 
     def __eq__(self, other):
         return isinstance(other, ClientApplication) and str(self.id) == str(other.id)
@@ -1013,8 +1013,8 @@ class Subscription(Base):
     application_id = Column(ForeignKey("augur_operations.client_applications.id", name="subscriptions_application_id_fkey"), primary_key=True)
     type_id = Column(ForeignKey("augur_operations.subscription_types.id", name="subscriptions_type_id_fkey"), primary_key=True)
 
-    application = relationship("ClientApplication")
-    type = relationship("SubscriptionType")
+    application = relationship("ClientApplication", back_populates="subscriptions")
+    type = relationship("SubscriptionType", back_populates="subscriptions")
 
 class SubscriptionType(Base):
     __tablename__ = "subscription_types"
@@ -1027,7 +1027,7 @@ class SubscriptionType(Base):
     id = Column(BigInteger, primary_key=True)
     name = Column(String, nullable=False)
 
-    subscriptions = relationship("Subscription")
+    subscriptions = relationship("Subscription", back_populates="type")
 
 
 class RefreshToken(Base):
@@ -1040,7 +1040,7 @@ class RefreshToken(Base):
     id = Column(String, primary_key=True)
     user_session_token = Column(ForeignKey("augur_operations.user_session_tokens.token", name="refresh_token_session_token_id_fkey"), nullable=False)
 
-    user_session = relationship("UserSessionToken")
+    user_session = relationship("UserSessionToken", back_populates="refresh_tokens")
 
     @staticmethod
     def create(session, user_session_token_id):