Merge pull request #118 from jverswijver/add_components

Add components

Author: guzman-raphael

CHANGELOG.md

@@ -2,6 +2,15 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.4.0] - 2022-03-18
+### Fixed
+- Bug with `order_by` not applying from fetch args PR #117
+
+### Added
+- Support for new `slider` and `dropdown-query` components PR #118
+- Numpy parser for `component_interface.py` to remove numpy types for json serialization PR #118
+- Support for loginless mode PR #118
+
 ## [0.3.0] - 2022-01-21
 ### Changed
 - Hot-reload mechanism to use `otumat watch` PR #116
@@ -102,6 +111,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 - Support for DataJoint attribute types: `varchar`, `int`, `float`, `datetime`, `date`, `time`, `decimal`, `uuid`.
 - Check dependency utility to determine child table references.
 
+[0.4.0]: https://github.com/datajoint/pharus/compare/0.3.0...0.4.0
 [0.3.0]: https://github.com/datajoint/pharus/compare/0.2.3...0.3.0
 [0.2.3]: https://github.com/datajoint/pharus/compare/0.2.2...0.2.3
 [0.2.2]: https://github.com/datajoint/pharus/compare/0.2.1...0.2.2

pharus/component_interface.py

@@ -4,13 +4,44 @@
 import datajoint as dj
 import re
 import inspect
-from datetime import datetime
+from datetime import date, datetime
 from flask import request, send_file
 from .interface import _DJConnector
 import os
 from pathlib import Path
 import types
 import io
+import numpy as np
+
+
+class NumpyEncoder(json.JSONEncoder):
+    """teach json to dump datetimes, etc"""
+
+    npmap = {
+        np.bool_: bool,
+        np.uint8: int,
+        np.uint16: int,
+        np.uint32: int,
+        np.uint64: int,
+        np.int8: int,
+        np.int16: int,
+        np.int32: int,
+        np.int64: int,
+        np.float32: float,
+        np.float64: float,
+        np.ndarray: list,
+    }
+
+    def default(self, o):
+        if type(o) in self.npmap:
+            return self.npmap[type(o)](o)
+        if type(o) in (datetime, date):
+            return o.isoformat()
+        return json.JSONEncoder.default(self, o)
+
+    @classmethod
+    def dumps(cls, obj):
+        return json.dumps(obj, cls=cls)
 
 
 class QueryComponent:
@@ -70,9 +101,9 @@ def restriction(self):
                 self.dj_restriction(),
                 {
                     k: (
-                        datetime.fromtimestamp(float(v))
+                        datetime.fromtimestamp(float(v)).isoformat()
                         if re.match(
-                            r"^datetime.*$",
+                            r"^date.*$",
                             self.fetch_metadata["query"].heading.attributes[k].type,
                         )
                         else v
@@ -226,8 +257,42 @@ def __init__(self, *args, **kwargs):
 
     def dj_query_route(self):
         fetch_metadata = self.fetch_metadata
-        return (fetch_metadata["query"] & self.restriction).fetch1(
-            *fetch_metadata["fetch_args"]
+        return NumpyEncoder.dumps(
+            (fetch_metadata["query"] & self.restriction).fetch1(
+                *fetch_metadata["fetch_args"]
+            )
+        )
+
+
+class BasicQuery(QueryComponent):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.frontend_map = {
+            "source": "sci-viz/src/Components/Plots/FullPlotly.tsx",
+            "target": "FullPlotly",
+        }
+        self.response_examples = {
+            "dj_query_route": {
+                "recordHeader": ["subject_uuid", "session_start_time", "session_uuid"],
+                "records": [
+                    [
+                        "00778394-c956-408d-8a6c-ca3b05a611d5",
+                        1565436299.0,
+                        "fb9bdf18-76be-452b-ac4e-21d5de3a6f9f",
+                    ]
+                ],
+                "totalCount": 1,
+            },
+        }
+
+    def dj_query_route(self):
+        fetch_metadata = self.fetch_metadata
+        record_header, table_records, total_count = _DJConnector._fetch_records(
+            query=fetch_metadata["query"] & self.restriction,
+            fetch_args=fetch_metadata["fetch_args"],
+        )
+        return dict(
+            recordHeader=record_header, records=table_records, totalCount=total_count
         )
 
 
@@ -254,8 +319,11 @@ def dj_query_route(self):
 
 
 type_map = {
+    "basicquery": BasicQuery,
     "plot:plotly:stored_json": PlotPlotlyStoredjsonComponent,
     "table": TableComponent,
     "metadata": MetadataComponent,
     "file:image:attach": FileImageAttachComponent,
+    "slider": BasicQuery,
+    "dropdown-query": BasicQuery,
 }

pharus/dynamic_api_gen.py

@@ -16,6 +16,7 @@ def populate_api():
 from datetime import datetime
 import inspect
 import traceback
+import os
 try:
     from .component_interface_override import type_map
 except (ModuleNotFoundError, ImportError):
@@ -37,13 +38,35 @@ def {method_name}(jwt_payload: dict) -> dict:
         except Exception as e:
             return traceback.format_exc(), 500
 """
+    route_template_nologin = """
+
+@app.route('{route}', methods=['GET'])
+def {method_name}() -> dict:
+    if request.method in {{'GET'}}:
+        jwt_payload = dict(
+            databaseAddress=os.environ["PHARUS_HOST"],
+            username=os.environ["PHARUS_USER"],
+            password=os.environ["PHARUS_PASSWORD"],
+        )
+        try:
+            component_instance = type_map['{component_type}'](name='{component_name}',
+                                                              component_config={component},
+                                                              static_config={static_config},
+                                                              jwt_payload=jwt_payload)
+            return component_instance.{method_name_type}()
+        except Exception as e:
+            return traceback.format_exc(), 500
+"""
 
     pharus_root = f"{pkg_resources.get_distribution('pharus').module_path}/pharus"
     api_path = f"{pharus_root}/dynamic_api.py"
     spec_path = os.environ.get("PHARUS_SPEC_PATH")
     values_yaml = EnvYAML(Path(spec_path))
     with open(Path(api_path), "w") as f:
         f.write(header_template)
+        active_route_template = (
+            route_template if values_yaml["SciViz"]["auth"] else route_template_nologin
+        )
         if (
             "component_interface" in values_yaml["SciViz"]
             and "override" in values_yaml["SciViz"]["component_interface"]
@@ -74,10 +97,10 @@ def {method_name}(jwt_payload: dict) -> dict:
             for grid in page["grids"].values():
                 if grid["type"] == "dynamic":
                     f.write(
-                        route_template.format(
+                        (active_route_template).format(
                             route=grid["route"],
                             method_name=grid["route"].replace("/", ""),
-                            component_type="table",
+                            component_type="basicquery",
                             component_name="dynamicgrid",
                             component=json.dumps(grid),
                             static_config=static_config,
@@ -90,9 +113,12 @@ def {method_name}(jwt_payload: dict) -> dict:
                     if "component_templates" in grid
                     else grid["components"]
                 ).items():
-                    if re.match(r"^(table|metadata|plot|file).*$", comp["type"]):
+                    if re.match(
+                        r"^(table|metadata|plot|file|slider|dropdown-query).*$",
+                        comp["type"],
+                    ):
                         f.write(
-                            route_template.format(
+                            (active_route_template).format(
                                 route=comp["route"],
                                 method_name=comp["route"].replace("/", ""),
                                 component_type=comp["type"],
@@ -107,7 +133,7 @@ def {method_name}(jwt_payload: dict) -> dict:
                                 comp["type"]
                             ].attributes_route_format.format(route=comp["route"])
                             f.write(
-                                route_template.format(
+                                (active_route_template).format(
                                     route=attributes_route,
                                     method_name=attributes_route.replace("/", ""),
                                     component_type=comp["type"],

pharus/interface.py

@@ -113,7 +113,7 @@ def _fetch_records(
         restriction: list = [],
         limit: int = 1000,
         page: int = 1,
-        order=["KEY ASC"],
+        order=None,
         fetch_blobs=False,
         fetch_args=[],
     ) -> tuple:
@@ -150,19 +150,25 @@ def _fetch_records(
             ]
         )
 
+        order_by = (
+            fetch_args.pop("order_by") if "order_by" in fetch_args else ["KEY ASC"]
+        )
+        order_by = order if order else order_by
+
+        limit = fetch_args.pop("limit") if "limit" in fetch_args else limit
+
         if fetch_blobs and not fetch_args:
             fetch_args = [*query.heading.attributes]
         elif not fetch_args:
             fetch_args = query.heading.non_blobs
         else:
             attributes = {k: v for k, v in attributes.items() if k in fetch_args}
-
         non_blobs_rows = query_restricted.fetch(
             *fetch_args,
             as_dict=True,
             limit=limit,
             offset=(page - 1) * limit,
-            order_by=order,
+            order_by=order_by,
         )
 
         # Buffer list to be return

pharus/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.3.0"
+__version__ = "0.4.0"

requirements.txt

@@ -6,3 +6,4 @@ datajoint_connection_hub
 pyyaml
 envyaml
 otumat
+numpy