geoseeq 0.7.3.dev0__tar.gz → 0.7.3.dev2__tar.gz

{geoseeq-0.7.3.dev0 → geoseeq-0.7.3.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geoseeq
-Version: 0.7.3.dev0
+Version: 0.7.3.dev2
 Summary: GeoSeeq command line tools and python API
 Project-URL: Homepage, https://github.com/biotia/geoseeq_api_client
 Project-URL: Issues, https://github.com/biotia/geoseeq_api_client/issues

geoseeq-0.7.3.dev2/docs/examples/simple_python_example/project_dashboard_example.py

@@ -0,0 +1,61 @@
+import os
+from geoseeq import Knex
+from geoseeq.dashboard.dashboard import Dashboard
+from geoseeq.id_constructors.from_uuids import (
+    project_from_uuid,
+    sample_group_ar_field_from_uuid,
+)
+
+
+endpoint = os.environ.get("GEOSEEQ_ENDPOINT", "")
+token = os.environ.get("GEOSEEQ_API_TOKEN", "")
+project_id = ""
+file_id = ""
+file2_id = ""
+
+
+knex = Knex(endpoint)
+knex.add_api_token(token)
+
+
+project = project_from_uuid(knex, project_id)
+dashboard = project.get_or_create_default_dashbaord()
+
+# Rename dashboard
+dashboard.title = "My default dashboard"
+
+# Add tile
+file = sample_group_ar_field_from_uuid(knex, file_id)
+dashboard.add_tile(file, title="Tile title", width="full")
+dashboard.save()
+
+# Remove tiles
+dashboard.tiles = []
+dashboard.save()
+
+# Add multiple tiles
+file = sample_group_ar_field_from_uuid(knex, file_id)
+dashboard.add_tile(file, title="Tile title", width="full")
+file2 = sample_group_ar_field_from_uuid(knex, file2_id)
+dashboard.add_tile(file2, title="Tile title 2", width="half")
+dashboard.save()
+
+
+dashboard2 = project.get_or_create_dashbaord_by_title(title="Dashboard Dix")
+dashboard2.title = "Renamed dashboard"
+
+# Set dashboard to default
+dashboard2.default = True
+dashboard2.add_tile(file, title="Best tile", width="half")
+dashboard2.save()
+
+# Delete dashboard
+# dashboard2.delete()
+
+# Using the constructors
+dashboard3 = Dashboard(knex=knex, project=project, title="Third dashboard")
+dashboard3.create()
+
+dashboard2 = Dashboard(knex=knex, project=project, title="Renamed dashboard")
+dashboard2.get()  # Load tiles
+print(dashboard.tiles)

geoseeq-0.7.3.dev2/docs/examples/simple_python_example/sample_dashboard_example.py

@@ -0,0 +1,44 @@
+import os
+from geoseeq import Knex
+from geoseeq.dashboard.dashboard import SampleDashboard
+from geoseeq.id_constructors.from_uuids import (
+    sample_from_uuid,
+    sample_result_file_from_uuid,
+)
+
+
+endpoint = os.environ.get("GEOSEEQ_ENDPOINT", "")
+token = os.environ.get("GEOSEEQ_API_TOKEN", "")
+sample_id = ""
+file_id = ""
+file2_id = ""
+
+
+knex = Knex(endpoint)
+knex.add_api_token(token)
+
+
+sample = sample_from_uuid(knex, sample_id)
+dashboard = sample.get_or_create_default_dashbaord()
+
+# Add tiles
+file = sample_result_file_from_uuid(knex, file_id)
+dashboard.add_tile(file, title="Tile title", width="full", order=2)
+file2 = sample_result_file_from_uuid(knex, file2_id)
+dashboard.add_tile(file2, title="Tile title 2", width="half", order=1)
+dashboard.save()
+
+
+dashboard2 = sample.get_or_create_dashbaord_by_title(title="BDX Dashboard")
+
+# Rename dahboard
+# dashboard2.title = "Another title"
+
+# Remove existing tiles
+dashboard2.tiles = []
+
+dashboard2.add_tile(file, title="Tile title 2", width="half")
+dashboard2.save()
+
+# Delete dashboard
+# dashboard2.delete()

{geoseeq-0.7.3.dev0 → geoseeq-0.7.3.dev2}/docs/examples/simple_python_example/smart_table_example.py

@@ -1,3 +1,4 @@
+import os
 import pandas as pd
 
 from geoseeq import Knex
@@ -7,8 +8,8 @@ from geoseeq.id_constructors.from_uuids import (
 )
 from geoseeq.smart_table import SmartTable
 
-endpoint = "https://backend.geoseeq.com"
-token = ""
+endpoint = os.environ.get("GEOSEEQ_ENDPOINT", "")
+token = os.environ.get("GEOSEEQ_API_TOKEN", "")
 folder_id = ""
 
 knex = Knex(endpoint)

geoseeq-0.7.3.dev2/geoseeq/dashboard/dashboard.py

@@ -0,0 +1,273 @@
+import logging
+from typing import Literal
+
+from geoseeq import ProjectResultFile
+from geoseeq.id_constructors import result_file_from_blob
+from geoseeq.id_constructors.from_ids import result_file_from_id
+from geoseeq.remote_object import RemoteObject
+from geoseeq import GeoseeqNotFoundError
+
+logger = logging.getLogger("geoseeq_api")
+
+
+class Dashboard(RemoteObject):
+    parent_field = "project"
+    remote_fields = ["is_default"]
+
+    def __init__(
+        self, knex, project, title="Default dashboard", default=False, tiles=[]
+    ):
+        super().__init__(self)
+        self.knex = knex
+        self.project = project
+        self.title = title
+        self._original_title = title
+        self.tiles = tiles
+        self.default = default
+
+    def _get(self, allow_overwrite=False):
+        blob = self.knex.get(f"sample_groups/{self.project.uuid}/dashboard-list")
+        if self.title not in blob["dashboard_data"].keys():
+            raise GeoseeqNotFoundError(f"Dashboard '{self.title}' not found.")
+        blob = blob["dashboard_data"][self.title]
+        for tile_blob in blob["tiles"]:
+            tile = DashboardTile.from_blob(self, tile_blob)
+            self.tiles.append(tile)
+        blob.pop("tiles")
+        self.load_blob(blob, allow_overwrite=allow_overwrite)
+
+    def save(self):
+        put_data = {
+            "name": self._original_title,
+            "is_default": self.default,
+            "new_name": self.title,
+        }
+        self.knex.put(
+            f"sample_groups/{self.project.uuid}/dashboard-list",
+            json=put_data,
+            json_response=False,
+        )
+        self._original_title = self.title
+        self.save_tiles()
+
+    def save_tiles(self):
+        post_data = {"tiles": [tile._get_post_data() for tile in self.tiles]}
+        self.knex.post(
+            f"sample_groups/{self.project.uuid}/dashboard/{self._original_title}/tiles",
+            json=post_data,
+            json_response=False,
+        )
+
+    def _create(self):
+        post_data = {"name": self.title, "is_default": self.default}
+        self.knex.post(
+            f"sample_groups/{self.project.uuid}/dashboard-list", json=post_data
+        )
+
+    def add_tile(
+        self,
+        result_file,
+        title,
+        width: Literal["hafl", "full"] = "half",
+    ):
+        style = "col-span-1" if width == "half" else "col-span-2"
+        result_file.get()
+        tile = DashboardTile(self.knex, self, title, result_file, style=style)
+        self.tiles.append(tile)
+        self._modified = True
+
+    def delete(self):
+        self.knex.delete(
+            f"sample_groups/{self.project.uuid}/dashboard-list?name={self._original_title}"
+        )
+
+    def __str__(self):
+        return f'<Geoseeq Dashboard: {self.project.grn} "{self._original_title}"/>'
+
+    def __repr__(self):
+        return str(self)
+
+    @property
+    def grn(self):
+        return f'grn:dashboard:{self.project.uuid}:"{self._original_title}"'
+
+    def pre_hash(self):
+        return "DASH" + self.project.uuid + self._original_title
+
+
+class DashboardTile:
+    def __init__(self, knex, dashboard, title, result_file, style="col-span-1"):
+        self.knex = knex
+        self.dashboard = dashboard
+        self.title = title
+        self.style = style
+        self.result_file = result_file
+
+    def _get_post_data(self):
+        out = {
+            "field_uuid": self.result_file.uuid,
+            "field_type": (
+                "group" if isinstance(self.result_file, ProjectResultFile) else "sample"
+            ),
+            "style": self.style,
+            "title": self.title,
+            "has_related_field": False,
+        }
+        return out
+
+    @classmethod
+    def from_blob(cls, dashboard, blob):
+        result_file = result_file_from_blob(dashboard.knex, blob["viz_field"])
+        return cls(
+            dashboard.knex, dashboard, blob["title"], result_file, style=blob["style"]
+        )
+
+    def __str__(self) -> str:
+        return f'<Geoseeq DashboardTile: {self.dashboard.grn} "{self.title}" />'
+
+    def __repr__(self) -> str:
+        return str(self)
+
+
+class SampleDashboard(RemoteObject):
+    """Dashboard client for a single sample."""
+
+    parent_field = "sample"
+    remote_fields = ["uuid", "title", "default", "created_at", "updated_at"]
+
+    def __init__(self, knex, sample, title="Default dashboard", default=False):
+        super().__init__(self)
+        self.knex = knex
+        self.sample = sample
+        self.title = title
+        self.tiles = []
+        self.default = default
+
+    def _get(self, allow_overwrite=False):
+        blob = self.knex.get(f"samples/{self.sample.uuid}/dashboards")
+        try:
+            blob = [
+                dashboard_blob
+                for dashboard_blob in blob["results"]
+                if dashboard_blob["title"] == self.title
+            ][0]
+        except IndexError:
+            raise ValueError(f"There is no existing dashboard with title {self.title}")
+
+        self.load_blob(blob, allow_overwrite=allow_overwrite)
+
+        # Load tiles
+        tiles_res = self.knex.get(f"samples/dashboards/{self.uuid}/tiles")
+        for tile_blob in tiles_res["results"]:
+            tile = SampleDashboardTile.from_blob(self, tile_blob)
+            self.tiles.append(tile)
+
+    def save(self):
+        data = self._get_post_data()
+        url = f"samples/{self.sample.uuid}/dashboards/{self.uuid}"
+        self.knex.put(url, json=data)
+        self.save_tiles()
+
+    def save_tiles(self):
+        post_data = {"tiles": [tile._get_post_data() for tile in self.tiles]}
+        self.knex.put(
+            f"samples/dashboards/{self.uuid}/tiles",
+            json=post_data,
+            json_response=False,
+        )
+
+    def delete(self):
+        self.knex.delete(f"samples/{self.sample.uuid}/dashboards/{self.uuid}")
+        self._already_fetched = False
+        self._deleted = True
+
+    def _create(self):
+        post_data = {
+            "title": self.title,
+            "sample": self.sample.uuid,
+            "default": self.default,
+        }
+        blob = self.knex.post(f"samples/{self.sample.uuid}/dashboards", json=post_data)
+        self.load_blob(blob)
+
+    def _get_post_data(self):
+        out = {
+            "sample": self.sample.uuid,
+            "title": self.title,
+            "default": self.default,
+        }
+        return out
+
+    def add_tile(self, result_file, title, width="half", order=None):
+        result_file.get()
+        tile = SampleDashboardTile(
+            self.knex, self, title, result_file, width=width, order=order
+        )
+        self.tiles.append(tile)
+        self._modified = True
+
+    @classmethod
+    def from_blob(cls, sample, blob):
+        instance = cls(
+            sample.knex,
+            sample,
+            blob["title"],
+            blob["default"],
+        )
+        instance.uuid = blob["uuid"]
+        return instance
+
+    @property
+    def name(self):
+        return self.title
+
+    def __str__(self):
+        return f'<Geoseeq SampleDashboard: {self.sample.brn} "{self.name}"/>'
+
+    def __repr__(self):
+        return str(self)
+
+    @property
+    def grn(self):
+        return f'grn:dashboard:{self.sample.uuid}:"{self.name}"'
+
+    def pre_hash(self):
+        return "DASH" + self.sample.uuid + self.name
+
+
+class SampleDashboardTile:
+    def __init__(self, knex, dashboard, title, result_file, width="half", order=None):
+        self.knex = knex
+        self.dashboard = dashboard
+        self.title = title
+        self.width = width
+        self.result_file = result_file
+        self.order = order
+
+    def _get_post_data(self):
+        out = {
+            "field": self.result_file.uuid,
+            "dashboard": self.dashboard.uuid,
+            "width": self.width,
+            "title": self.title,
+            "order": self.order,
+        }
+        return out
+
+    @classmethod
+    def from_blob(cls, dashboard, blob):
+        result_file = result_file_from_id(dashboard.knex, blob["field_obj"]["uuid"])
+        return cls(
+            dashboard.knex,
+            dashboard,
+            blob["title"],
+            result_file,
+            width=blob["width"],
+            order=blob["order"],
+        )
+
+    def __str__(self) -> str:
+        return f'<Geoseeq DashboardTile: {self.dashboard.grn} "{self.title}" />'
+
+    def __repr__(self) -> str:
+        return str(self)