skip WaveformArray.java, add fake array inserts (#41)

* skip WaveformArray.java, add fake array inserts

* bump lint

* fix typo and bump versions

* another typo

* unpin superlinter

* superlinter

* bump more versions

* bump minimum version of python

Author: t-young31

.github/workflows/lint.yml

@@ -33,23 +33,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
         with:
           # Full git history is needed to get a proper list of
           # changed files within `super-linter`
           fetch-depth: 0
           persist-credentials: false
 
       - name: Setup Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
 
       - name: Run pre-commit
-        uses: pre-commit/action@v3.0.0
+        uses: pre-commit/action@v3.0.1
         with:
           extra_args: --all-files
 
       - name: Lint code base
-        uses: github/super-linter/slim@v4.9.7
+        uses: super-linter/super-linter/slim@v8
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: main

.github/workflows/test.yml

@@ -30,10 +30,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Install Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
 
       - name: Install Python dependencies
         run: |

.gitignore

@@ -6,3 +6,5 @@ satellite.egg-info/
 .mypy_cache/
 .pytest_cache/
 .DS_Store
+.vscode
+tmp*

.pre-commit-config.yaml

@@ -16,19 +16,19 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.12.0
+    rev: 26.1.0
     hooks:
       - id: black
         args: [--diff, --check]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.19.1
     hooks:
       - id: mypy
         args: [--ignore-missing-imports]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.3.0
     hooks:
       - id: flake8
 

Dockerfile

@@ -11,7 +11,7 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 # limitations under the License.
-FROM postgres:15.0-bullseye
+FROM postgres:17
 
 # User definable arguments
 ARG POSTGRES_USER=postgres
@@ -32,7 +32,7 @@ ARG DEBIAN_FRONTEND=noninteractive
 # OS setup
 RUN apt-get update && \
     apt-get install --yes --no-install-recommends \
-    procps ca-certificates locales python3.9-dev python3-pip git && \
+    procps ca-certificates locales pipx git && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* && \
     sed -i '/en_GB.UTF-8/s/^# //g' /etc/locale.gen && locale-gen
@@ -46,11 +46,11 @@ RUN if [ -d "/Satellite/satellite" ] ; then \
       echo "Cloning Satellite repo on: $TAG" && \
       rm -rf /Satellite && \
       git clone --depth 1 --branch ${TAG} https://github.com/SAFEHR-data/Satellite.git ;\
-    fi && \
-    pip install --no-cache-dir --upgrade pip==22.3.1
+    fi
 
+ENV PATH="$PATH:/root/.local/bin"
 WORKDIR /Satellite
-RUN pip install --no-cache-dir . && \
+RUN pipx install . && \
     satellite print-db-create-command > /docker-entrypoint-initdb.d/create.sql && \
     satellite print-create-command >> /docker-entrypoint-initdb.d/create.sql
 

pyproject.toml

@@ -1,12 +1,12 @@
 [project]
 name = "satellite"
-version = "0.1.2"
+version = "0.2.0"
 authors = [
   { name="Tom Young" },
 ]
 description = "Create, update and delete rows in a synthetic EMAP star schema"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 classifiers = [
     "Programming Language :: Python :: 3"
@@ -17,7 +17,7 @@ dependencies = [
     "coloredlogs==15.0.*",
     "networkx==2.8.*",
     "click==8.1.*",
-    "black==22.12.*",
+    "black==26.1.*",
     "psycopg2-binary==2.9.*",
     "pytest==7.2.*"
 ]

satellite/_column.py

@@ -11,13 +11,12 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 # limitations under the License.
-from typing import Optional, Callable, TYPE_CHECKING
+from typing import Optional, Callable, Any, TYPE_CHECKING
 from dataclasses import dataclass
 
 from satellite._log import logger
 from satellite._fake import fake
 
-
 if TYPE_CHECKING:
     from satellite._tables import Table
 
@@ -54,6 +53,7 @@ def sql_type(self) -> str:
             "double": "real",
             "localdate": "date",
             "byte[]": "bytea",
+            "double[]": "real[]",
         }
 
         if self.java_type.lower() in java_to_sql_type_map:
@@ -65,16 +65,17 @@ def sql_type(self) -> str:
             )
             return "text"
 
-    @property
-    def format_specifier(self) -> str:
+    def sql_marshal(self, value: Any) -> str:
         if self.sql_type == "text":
-            return "'%s'"
+            return f"'{value}'"
         elif self.sql_type == "timestamptz" or self.sql_type == "date":
-            return "timestamp '%s'"
+            return f"timestamp '{value}'"
         elif self.sql_type == "bytea":
-            return "E'%s'"
+            return f"E'{value}'"
+        elif self.sql_type == "real[]":
+            return f"ARRAY {str(value)}"
 
-        return "%s"
+        return str(value)
 
     @property
     def is_foreign_key(self) -> bool:
@@ -114,5 +115,5 @@ def faker_method(self) -> Callable:
             return getattr(fake, self.sql_type)
 
         else:
-            logger.error(f"Have no provider for {self.sql_type}")
+            logger.error(f"Have no provider for {self.sql_type} in column {self.name}")
             return fake.default

satellite/_fake.py

@@ -128,6 +128,9 @@ def standardised_code() -> None:
     def standardised_vocabulary() -> None:
         return None
 
+    def values_array(self) -> list[float]:
+        return [self.real() for _ in range(10)]
+
 
 class _StarPersonProvider(PersonProvider, _StarBaseProvider):
     def firstname(self) -> str:

satellite/_schema.py

@@ -89,14 +89,14 @@ def _try_and_connect(self) -> None:
 
     def empty_table_create_command_for(self, table: Table) -> str:
         """Create a table for a set of data. Drop it if it exists"""
-
-        columns_name_and_type = ", ".join(
-            [col.definition_in_schema(self._name) for col in table.non_pk_columns]
-        )
+        non_pk_columns = ""
+        if len(table.non_pk_columns) > 0:
+            non_pk_columns += ", " + ", ".join(
+                [col.definition_in_schema(self._name) for col in table.non_pk_columns]
+            )
         return (
-            f"CREATE TABLE {self.schema_name}.{table.name} "
-            f"({table.primary_key_name} serial PRIMARY KEY, "
-            f"{columns_name_and_type});"
+            f"CREATE TABLE {self.schema_name}.{table.name}"
+            f"({table.primary_key_name} serial PRIMARY KEY{non_pk_columns});"
         )
 
     @staticmethod
@@ -118,9 +118,11 @@ def add_data_command_for(self, table: Table) -> str:
 
         for i in range(table.n_rows):
             values = ",".join(
-                column.format_specifier % self._decode_if_bytes(table[column][i])
-                if table[column][i] is not None
-                else "null"
+                (
+                    column.sql_marshal(self._decode_if_bytes(table[column][i]))
+                    if table[column][i] is not None
+                    else "null"
+                )
                 for column in table.non_pk_columns
             )
             string += f"  ({values}),\n"

satellite/_settings.py

@@ -15,7 +15,6 @@
 
 from typing import Any
 
-
 _default_values = {
     "STAR_SCHEMA_NAME": "star",
     "FAKER_SEED": "0",