geoseeq 0.7.3.dev1__tar.gz → 0.7.3.dev2__tar.gz

{geoseeq-0.7.3.dev1 → geoseeq-0.7.3.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geoseeq
-Version: 0.7.3.dev1
+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.dev1 → geoseeq-0.7.3.dev2}/docs/examples/simple_python_example/sample_dashboard_example.py

@@ -1,3 +1,4 @@
+import os
 from geoseeq import Knex
 from geoseeq.dashboard.dashboard import SampleDashboard
 from geoseeq.id_constructors.from_uuids import (
@@ -6,8 +7,8 @@ from geoseeq.id_constructors.from_uuids import (
 )
 
 
-endpoint = ""
-token = ""
+endpoint = os.environ.get("GEOSEEQ_ENDPOINT", "")
+token = os.environ.get("GEOSEEQ_API_TOKEN", "")
 sample_id = ""
 file_id = ""
 file2_id = ""

{geoseeq-0.7.3.dev1 → 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.dev1 → geoseeq-0.7.3.dev2}/geoseeq/dashboard/dashboard.py

@@ -5,6 +5,7 @@ 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")
 
@@ -13,17 +14,22 @@ class Dashboard(RemoteObject):
     parent_field = "project"
     remote_fields = ["is_default"]
 
-    def __init__(self, knex, project, name="Default dashboard", is_default=False):
+    def __init__(
+        self, knex, project, title="Default dashboard", default=False, tiles=[]
+    ):
         super().__init__(self)
         self.knex = knex
         self.project = project
-        self._name = name
-        self.tiles = []
-        self.is_default = is_default
+        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")
-        blob = blob["dashboard_data"][self.name]
+        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)
@@ -31,56 +37,62 @@ class Dashboard(RemoteObject):
         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]}
-        blob = self.knex.post(
-            f"sample_groups/{self.project.uuid}/dashboard/{self.name}/tiles",
+        self.knex.post(
+            f"sample_groups/{self.project.uuid}/dashboard/{self._original_title}/tiles",
             json=post_data,
             json_response=False,
         )
-        print(blob)
 
     def _create(self):
-        post_data = {"name": self.name, "is_default": self.is_default}
-        blob = self.knex.post(
-            f"sample_groups/{self.project.uuid}/dashboard", json=post_data
+        post_data = {"name": self.title, "is_default": self.default}
+        self.knex.post(
+            f"sample_groups/{self.project.uuid}/dashboard-list", json=post_data
         )
-        self.load_blob(blob)
 
-    def tile(
+    def add_tile(
         self,
-        title,
         result_file,
-        style: Literal["col-span-1", "col-span-2"] = "col-span-1",
+        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
-        return tile
-
-    def add_tile(self, tile):
-        self.tiles.append(tile)
-        self._modified = True
 
-    @property
-    def name(self):
-        return self._name
+    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.name}"/>'
+        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.name}"'
+        return f'grn:dashboard:{self.project.uuid}:"{self._original_title}"'
 
     def pre_hash(self):
-        return "DASH" + self.project.uuid + self.name
+        return "DASH" + self.project.uuid + self._original_title
 
 
 class DashboardTile:

{geoseeq-0.7.3.dev1 → geoseeq-0.7.3.dev2}/geoseeq/project.py

@@ -3,6 +3,7 @@ import urllib
 
 import pandas as pd
 
+
 from .pipeline import Pipeline
 from .remote_object import RemoteObject
 from .result import ProjectResultFolder
@@ -59,11 +60,23 @@ class Project(RemoteObject):
         self._modified = True
 
     def get_post_data(self):
-        data = {field: getattr(self, field) for field in self.remote_fields if hasattr(self, field)}
+        data = {
+            field: getattr(self, field)
+            for field in self.remote_fields
+            if hasattr(self, field)
+        }
         data["organization"] = self.org.uuid
-        data['description'] = self.description if hasattr(self, 'description') and self.description else self.name
-        data['privacy_level'] = self.privacy_level if hasattr(self, 'privacy_level') and self.privacy_level else 'private'
-        data['storage_provider_name'] = self.storage_provider
+        data["description"] = (
+            self.description
+            if hasattr(self, "description") and self.description
+            else self.name
+        )
+        data["privacy_level"] = (
+            self.privacy_level
+            if hasattr(self, "privacy_level") and self.privacy_level
+            else "private"
+        )
+        data["storage_provider_name"] = self.storage_provider
         if self.new_org:
             if isinstance(self.new_org, RemoteObject):
                 data["organization"] = self.new_org.uuid
@@ -90,7 +103,9 @@ class Project(RemoteObject):
             url = f"sample_groups/{self.uuid}/samples"
             chunk_size = 100
             for i in range(0, len(sample_uuids), chunk_size):
-                self.knex.post(url, json={"sample_uuids": sample_uuids[i : i + chunk_size]})
+                self.knex.post(
+                    url, json={"sample_uuids": sample_uuids[i : i + chunk_size]}
+                )
         self._sample_cache = []
 
     def _delete_sample_list(self):
@@ -126,7 +141,7 @@ class Project(RemoteObject):
             json=post_data,
         )
         self.load_blob(blob)
-    
+
     def add_sample_uuids(self, sample_uuids):
         """Return this group and add a sample to this group.
 
@@ -166,7 +181,7 @@ class Project(RemoteObject):
 
     def analysis_result(self, *args, **kwargs):
         """Return a ProjectResultFolder object for this project.
-        
+
         Alias for result_folder."""
         return self.result_folder(*args, **kwargs)
 
@@ -177,7 +192,9 @@ class Project(RemoteObject):
                 yield sample
             return
         url = f"sample_groups/{self.uuid}/samples-list?page=1&page_size=100"
-        for sample_blob in paginated_iterator(self.knex, url, error_handler=error_handler):
+        for sample_blob in paginated_iterator(
+            self.knex, url, error_handler=error_handler
+        ):
             sample = self.sample(sample_blob["name"])
             sample.uuid = sample_blob["uuid"]
             sample.metadata = sample_blob["metadata"]
@@ -199,12 +216,16 @@ class Project(RemoteObject):
                 yield sample.uuid
             return
         url = f"sample_groups/{self.uuid}/samples-list?page=1"
-        for sample_blob in paginated_iterator(self.knex, url, error_handler=error_handler):
-            yield sample_blob['uuid']
+        for sample_blob in paginated_iterator(
+            self.knex, url, error_handler=error_handler
+        ):
+            yield sample_blob["uuid"]
 
     def _batch_sample_uuids(self, batch_size, input_sample_uuids=[]):
         """Yield batches of sample uuids."""
-        uuids_to_batch = input_sample_uuids if input_sample_uuids else self.get_sample_uuids()
+        uuids_to_batch = (
+            input_sample_uuids if input_sample_uuids else self.get_sample_uuids()
+        )
         sample_uuids = []
         for sample_uuid in uuids_to_batch:
             sample_uuids.append(sample_uuid)
@@ -216,7 +237,7 @@ class Project(RemoteObject):
 
     def get_analysis_results(self, cache=True):
         """Yield ProjectResultFolder objects for this project fetched from the server.
-        
+
         Alias for get_result_folders."""
         return self.get_result_folders(cache=cache)
 
@@ -262,24 +283,25 @@ class Project(RemoteObject):
             rows.extend(blob["results"])
             url = blob["next"]
         return pd.DataFrame(rows)
-    
-    
+
     @property
     def n_samples(self):
         """Return the number of samples in this project."""
-        if hasattr(self, 'samples_count') and self.samples_count is not None:
+        if hasattr(self, "samples_count") and self.samples_count is not None:
             return self.samples_count
         return len(list(self.get_sample_uuids()))
-    
-    def bulk_find_files(self,
-                        sample_uuids=[],
-                        sample_name_includes=[],
-                        folder_types="all",
-                        folder_names=[],
-                        file_names=[],
-                        extensions=[],
-                        with_versions=False,
-                        use_batches_cutoff=500):
+
+    def bulk_find_files(
+        self,
+        sample_uuids=[],
+        sample_name_includes=[],
+        folder_types="all",
+        folder_names=[],
+        file_names=[],
+        extensions=[],
+        with_versions=False,
+        use_batches_cutoff=500,
+    ):
         """Return a dict with links to download files that match the given criteria.
 
         Options:
@@ -291,36 +313,48 @@ class Project(RemoteObject):
         - extensions: list of strings; finds files with these file extensions
         - with_versions: bool; if True, include all versions of files in results
         """
+
         def _my_bulk_find(sample_uuids=None):  # curry to save typing
-            return self._bulk_find_files_batch(sample_uuids=sample_uuids or [],
-                                             sample_name_includes=sample_name_includes,
-                                             folder_types=folder_types,
-                                             folder_names=folder_names,
-                                             file_names=file_names,
-                                             extensions=extensions,
-                                             with_versions=with_versions)
+            return self._bulk_find_files_batch(
+                sample_uuids=sample_uuids or [],
+                sample_name_includes=sample_name_includes,
+                folder_types=folder_types,
+                folder_names=folder_names,
+                file_names=file_names,
+                extensions=extensions,
+                with_versions=with_versions,
+            )
+
         n_samples = len(sample_uuids) if sample_uuids else self.n_samples
         if n_samples < use_batches_cutoff:
             logger.debug(f"Using single batch bulk_find for {n_samples} samples")
             return _my_bulk_find(sample_uuids=sample_uuids)
         else:
             logger.debug(f"Using multi batch bulk_find for {n_samples} samples")
-            merged_response = {'file_size_bytes': 0, 'links': {}, 'no_size_info_count': 0}
-            for batch in self._batch_sample_uuids(use_batches_cutoff - 1, input_sample_uuids=sample_uuids):
+            merged_response = {
+                "file_size_bytes": 0,
+                "links": {},
+                "no_size_info_count": 0,
+            }
+            for batch in self._batch_sample_uuids(
+                use_batches_cutoff - 1, input_sample_uuids=sample_uuids
+            ):
                 response = _my_bulk_find(sample_uuids=batch)
-                merged_response['file_size_bytes'] += response['file_size_bytes']
-                merged_response['links'].update(response['links'])
-                merged_response['no_size_info_count'] += response['no_size_info_count']
+                merged_response["file_size_bytes"] += response["file_size_bytes"]
+                merged_response["links"].update(response["links"])
+                merged_response["no_size_info_count"] += response["no_size_info_count"]
             return merged_response
-                
-    def _bulk_find_files_batch(self,
-                               sample_uuids=None,
-                               sample_name_includes=None,
-                               folder_types=None,
-                               folder_names=None,
-                               file_names=None,
-                               extensions=None,
-                               with_versions=False):
+
+    def _bulk_find_files_batch(
+        self,
+        sample_uuids=None,
+        sample_name_includes=None,
+        folder_types=None,
+        folder_names=None,
+        file_names=None,
+        extensions=None,
+        with_versions=False,
+    ):
         data = {
             "sample_uuids": sample_uuids or [],
             "sample_names": sample_name_includes or [],
@@ -328,22 +362,105 @@ class Project(RemoteObject):
             "folder_names": folder_names or [],
             "file_names": file_names or [],
             "extensions": extensions or [],
-            "with_versions": with_versions
+            "with_versions": with_versions,
         }
         url = f"sample_groups/{self.uuid}/download"
         response = self.knex.post(url, data)
         return response
-    
+
     def run_app(self, app: Pipeline, input_parameters=None):
         """Run an app on this group."""
         if not input_parameters:
             input_parameters = app.get_input_parameters()
         params = {
-            'pipeline_id': app.uuid,
-            'sample_uuids': list(self.get_sample_uuids()),
-            'input_parameters': input_parameters,
+            "pipeline_id": app.uuid,
+            "sample_uuids": list(self.get_sample_uuids()),
+            "input_parameters": input_parameters,
         }
-        self.knex.post(f"sample_groups/{self.uuid}/run_app", json=params, json_response=False)
+        self.knex.post(
+            f"sample_groups/{self.uuid}/run_app", json=params, json_response=False
+        )
+
+    def create_dashboard(self, title="Default dashboard", default=False):
+        """Create a dashboard for this project."""
+        from geoseeq.dashboard.dashboard import Dashboard
+
+        post_data = {"name": title, "is_default": default}
+        self.knex.post(f"sample_groups/{self.uuid}/dashboard-list", json=post_data)
+
+        return Dashboard(knex=self.knex, project=self, title=title, default=default)
+
+    def get_default_dashbaord(self):
+        """Get the default dashboard for this project."""
+        from geoseeq.dashboard.dashboard import Dashboard, DashboardTile
+
+        resp = self.knex.get(f"sample_groups/{self.uuid}/dashboard-list")
+        try:
+            dashboard_name = [
+                name
+                for name, data in resp["dashboard_data"].items()
+                if data["is_default"] == True
+            ][0]
+            blob = resp["dashboard_data"][dashboard_name]
+            tiles = []
+            for tile_blob in blob["tiles"]:
+                tile = DashboardTile.from_blob(self, tile_blob)
+                tiles.append(tile)
+            dashboard = Dashboard(
+                self.knex,
+                project=self,
+                title=dashboard_name,
+                default=blob["is_default"],
+                tiles=tiles,
+            )
+            return dashboard
+        except IndexError:
+            logger.warning("Default dashboard not found.")
+            pass
+        return None
+
+    def get_or_create_default_dashbaord(self):
+        """Get the default dashboard for this project or create it if does not exist."""
+        default_dashboard = self.get_default_dashbaord()
+        if default_dashboard:
+            return default_dashboard
+        else:
+            return self.create_dashboard(default=True)
+
+    def get_dashbaord_by_title(self, title):
+        """Get dashboard for this project by the title of the dashboard."""
+        from geoseeq.dashboard.dashboard import Dashboard, DashboardTile
+
+        resp = self.knex.get(f"sample_groups/{self.uuid}/dashboard-list")
+        try:
+            dashboard_name = [
+                name for name in resp["dashboard_data"].keys() if name == title
+            ][0]
+            blob = resp["dashboard_data"][dashboard_name]
+            tiles = []
+            for tile_blob in blob["tiles"]:
+                tile = DashboardTile.from_blob(self, tile_blob)
+                tiles.append(tile)
+            dashboard = Dashboard(
+                knex=self.knex,
+                project=self,
+                title=dashboard_name,
+                default=blob["is_default"],
+                tiles=tiles,
+            )
+            return dashboard
+        except IndexError:
+            logger.warning(f"Dashboard {title} not found.")
+            pass
+        return None
+
+    def get_or_create_dashbaord_by_title(self, title: str):
+        """Get dashboard by title for this project or create it if does not exist."""
+        default_dashboard = self.get_dashbaord_by_title(title)
+        if default_dashboard:
+            return default_dashboard
+        else:
+            return self.create_dashboard(title=title, default=False)
 
     def __str__(self):
         return f"<Geoseeq::Project {self.name} {self.uuid} />"
@@ -353,7 +470,7 @@ class Project(RemoteObject):
 
     def pre_hash(self):
         return "PROJ" + self.name + self.org.pre_hash()
-    
+
     @property
     def grn(self):
         return f"grn::project:{self.uuid}"
@@ -363,4 +480,5 @@ class Project(RemoteObject):
         self._modified = True
         return self
 
-SampleGroup = Project  # alias for backwards compatibility
+
+SampleGroup = Project  # alias for backwards compatibility

{geoseeq-0.7.3.dev1 → geoseeq-0.7.3.dev2}/geoseeq/sample.py

@@ -233,6 +233,7 @@ class Sample(RemoteObject):
         return file, blob["read_type"]
 
     def create_dashboard(self, title="Default dashboard", default=False):
+        "Create a new dashboard for the sample"
         from geoseeq.dashboard.dashboard import SampleDashboard
 
         post_data = {
@@ -249,6 +250,7 @@ class Sample(RemoteObject):
         return dashboard
 
     def get_default_dashbaord(self):
+        """Get the default dashboard for this sample."""
         from geoseeq.dashboard.dashboard import SampleDashboard
 
         dashboard_resp = self.knex.get(f"samples/{self.uuid}/dashboards")
@@ -266,6 +268,7 @@ class Sample(RemoteObject):
         return None
 
     def get_or_create_default_dashbaord(self):
+        """Get the default dashboard for this sample or create it if does not exist."""
         default_dashboard = self.get_default_dashbaord()
         if default_dashboard:
             return default_dashboard
@@ -273,6 +276,7 @@ class Sample(RemoteObject):
             return self.create_dashboard(default=True)
 
     def get_dashbaord_by_title(self, title):
+        """Get dashboard by title for this sample."""
         from geoseeq.dashboard.dashboard import SampleDashboard
 
         dashboard_resp = self.knex.get(f"samples/{self.uuid}/dashboards")
@@ -290,6 +294,7 @@ class Sample(RemoteObject):
         return None
 
     def get_or_create_dashbaord_by_title(self, title):
+        """Get dashboard by title for this sample or create it if does not exist."""
         default_dashboard = self.get_dashbaord_by_title(title)
         if default_dashboard:
             return default_dashboard

{geoseeq-0.7.3.dev1 → geoseeq-0.7.3.dev2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "geoseeq"
-version = "0.7.3dev1"
+version = "0.7.3dev2"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]