geoseeq 0.7.1__py3-none-any.whl → 0.7.3.dev0__py3-none-any.whl

geoseeq/cli/main.py

@@ -1,35 +1,33 @@
-
 import logging
 
 import click
 
+from geoseeq.knex import DEFAULT_ENDPOINT
+from geoseeq.utils import set_profile
 
 from .copy import cli_copy
-from .manage import cli_manage
+from .detail import cli_detail
 from .download import cli_download
+from .find_grn import cli_find_grn
+from .get_eula import cli_eula
+from .manage import cli_manage
+from .run import cli_app
+from .search import cli_search
+from .shared_params.opts_and_args import overwrite_option, yes_option
 from .upload import cli_upload, cli_upload_advanced
 from .user import cli_user
 from .view import cli_view
-from .search import cli_search
-
-from geoseeq.knex import DEFAULT_ENDPOINT
-from geoseeq.utils import set_profile
-from .shared_params.opts_and_args import overwrite_option, yes_option
-from .detail import cli_detail
-from .run import cli_app
-from .get_eula import cli_eula
-from .find_grn import cli_find_grn
 
-logger = logging.getLogger('geoseeq_api')
+logger = logging.getLogger("geoseeq_api")
 handler = logging.StreamHandler()
-handler.setFormatter(logging.Formatter('[%(levelname)s] %(name)s :: %(message)s'))
+handler.setFormatter(logging.Formatter("[%(levelname)s] %(name)s :: %(message)s"))
 logger.addHandler(handler)
 
 
-@click.group(context_settings={'show_default': True})
+@click.group(context_settings={"show_default": True})
 def main():
     """Command line interface for the GeoSeeq API.
-    
+
     ---
 
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
@@ -37,6 +35,7 @@ def main():
     """
     pass
 
+
 main.add_command(cli_download)
 main.add_command(cli_upload)
 main.add_command(cli_manage)
@@ -46,86 +45,105 @@ main.add_command(cli_app)
 main.add_command(cli_eula)
 main.add_command(cli_find_grn)
 
+
 @main.command()
 def version():
     """Print the version of the Geoseeq API being used.
 
     ---
-    
+
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo('0.7.1')  # remember to update pyproject.toml
+    click.echo("0.7.3dev0")  # remember to update pyproject.toml
 
 
-@main.group('advanced')
+@main.group("advanced")
 def cli_advanced():
     """Advanced commands."""
     pass
 
+
 cli_advanced.add_command(cli_copy)
 cli_advanced.add_command(cli_user)
 cli_advanced.add_command(cli_detail)
 cli_advanced.add_command(cli_upload_advanced)
 
-@cli_advanced.group('experimental')
+
+@cli_advanced.group("experimental")
 def cli_experimental():
     """Experimental commands."""
     pass
 
 
-
 try:
     from geoseeq.vc.cli import cli_vc
+
     from .project import cli_project
+
     cli_experimental.add_command(cli_vc)
     cli_advanced.add_command(cli_project)
 
 except (ModuleNotFoundError, ImportError):
     pass
 
-@main.command('config')
+
+@main.command("config")
 @yes_option
-@click.option('--api-token', default=None, help='The API token to use.')
-@click.option('--endpoint', default=None, help='The endpoint to use.')
-@click.option('-p', '--profile', default=None, help='The profile name to use.')
+@click.option("--api-token", default=None, help="The API token to use.")
+@click.option("--endpoint", default=None, help="The endpoint to use.")
+@click.option("-p", "--profile", default=None, help="The profile name to use.")
 @overwrite_option
 def cli_config(yes, api_token, endpoint, profile, overwrite):
     """Configure the GeoSeeq API.
 
     ---
-    
+
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
     if not profile and not yes:
-        profile = click.prompt(f'Set custom profile name? (Leave blank for default)', default="").strip(' \"\'')
+        profile = click.prompt(
+            f"Set custom profile name? (Leave blank for default)", default=""
+        ).strip(" \"'")
     if not endpoint:
         endpoint = DEFAULT_ENDPOINT
         if not yes:
-            endpoint = click.prompt(f'Enter the URL to use for GeoSeeq (Most users can use the default)', default=DEFAULT_ENDPOINT).strip(' \"\'')
+            endpoint = click.prompt(
+                f"Enter the URL to use for GeoSeeq (Most users can use the default)",
+                default=DEFAULT_ENDPOINT,
+            ).strip(" \"'")
     if not api_token:
-        api_token = click.prompt(f'Enter your GeoSeeq API token', hide_input=True).strip(' \"\'')
+        api_token = click.prompt(
+            f"Enter your GeoSeeq API token", hide_input=True
+        ).strip(" \"'")
     if not yes:
-        eula_accepted = click.confirm(f'Have you read and accepted the GeoSeeq End User License Agreement? Use `geoseeq eula show` to view the EULA.')
+        eula_accepted = click.confirm(
+            (
+                "Have you read and accepted the GeoSeeq End User License "
+                "Agreement? Use `geoseeq eula show` to view the EULA."
+            )
+        )
         if not eula_accepted:
-            click.echo('You must accept the EULA to use the GeoSeeq API.')
+            click.echo("You must accept the EULA to use the GeoSeeq API.")
             return
     set_profile(api_token, endpoint=endpoint, profile=profile, overwrite=overwrite)
-    click.echo(f'Profile configured.')
+    click.echo(f"Profile configured.")
 
 
-@main.command('clear-cache')
+@main.command("clear-cache")
 @yes_option
 def cli_clear_cache(yes):
     """Clear the local cache.
 
     ---
-    
+
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    from geoseeq.file_system_cache import GEOSEEQ_CACHE_DIR
     import shutil
-    if yes or click.confirm('Are you sure you want to clear the cache?'):
-        shutil.rmtree(GEOSEEQ_CACHE_DIR, ignore_errors=True)
+
+    from geoseeq.file_system_cache import GEOSEEQ_CACHE_DIR
+
+    if yes or click.confirm("Are you sure you want to clear the cache?"):
+        shutil.rmtree(GEOSEEQ_CACHE_DIR, ignore_errors=True)

geoseeq/cli/upload/upload.py

@@ -128,9 +128,9 @@ def cli_upload_file(state, cores, threads_per_upload, num_retries, chunk_size_mb
     )
     for geoseeq_file_name, file_path in name_pairs:
         if isfile(file_path):
-            upload_manager.add_local_file_to_result_folder(result_folder, file_path)
+            upload_manager.add_local_file_to_result_folder(result_folder, file_path, geoseeq_file_name=geoseeq_file_name)
         elif isdir(file_path) and recursive:
-            upload_manager.add_local_folder_to_result_folder(result_folder, file_path, recursive=recursive, hidden_files=hidden, prefix=file_path)
+            upload_manager.add_local_folder_to_result_folder(result_folder, file_path, recursive=recursive, hidden_files=hidden, prefix=file_path, geoseeq_file_name=geoseeq_file_name)
         elif isdir(file_path) and not recursive:
             raise click.UsageError('Cannot upload a folder without --recursive')
     click.echo(upload_manager.get_preview_string(), err=True)

geoseeq/dashboard/dashboard.py

@@ -1,10 +1,9 @@
-
 import logging
-import json
 from typing import Literal
-from geoseeq.remote_object import RemoteObject
-from geoseeq.id_constructors import result_file_from_blob
+
 from geoseeq import ProjectResultFile
+from geoseeq.id_constructors import result_file_from_blob
+from geoseeq.remote_object import RemoteObject
 
 logger = logging.getLogger("geoseeq_api")
 
@@ -32,18 +31,29 @@ class Dashboard(RemoteObject):
 
     def _save(self):
         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", json=post_data, json_response=False)
+        blob = self.knex.post(
+            f"sample_groups/{self.project.uuid}/dashboard/{self.name}/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)
+        blob = self.knex.post(
+            f"sample_groups/{self.project.uuid}/dashboard", json=post_data
+        )
         self.load_blob(blob)
-    
-    def tile(self, title, result_file, style: Literal["col-span-1", "col-span-2"]="col-span-1"):
+
+    def tile(
+        self,
+        title,
+        result_file,
+        style: Literal["col-span-1", "col-span-2"] = "col-span-1",
+    ):
         result_file.get()
         tile = DashboardTile(self.knex, self, title, result_file, style=style)
         self.tiles.append(tile)
@@ -59,19 +69,92 @@ class Dashboard(RemoteObject):
         return self._name
 
     def __str__(self):
-        return f"<Geoseeq Dashboard: {self.project.grn} \"{self.name}\"/>"
-    
+        return f'<Geoseeq Dashboard: {self.project.grn} "{self.name}"/>'
+
     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.name}"'
+
     def pre_hash(self):
         return "DASH" + self.project.uuid + self.name
 
 
+class SampleDashboard(RemoteObject):
+    """Dashboard client for a single sample."""
+
+    parent_field = "sample"
+    remote_fields = ["is_default"]
+
+    def __init__(self, knex, sample, name="Default dashboard", is_default=False):
+        super().__init__(self)
+        self.knex = knex
+        self.sample = sample
+        self._name = name
+        self.tiles = []
+        self.is_default = is_default
+
+    def _get(self, allow_overwrite=False):
+        blob = self.knex.get(f"samples/{self.sample.uuid}/dashboard-list")
+        blob = blob["dashboard_data"][self.name]
+        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):
+        self.save_tiles()
+
+    def save_tiles(self):
+        post_data = {"tiles": [tile._get_post_data() for tile in self.tiles]}
+        self.knex.post(
+            f"samples/{self.sample.uuid}/dashboard/{self.name}/tiles",
+            json=post_data,
+            json_response=False,
+        )
+
+    def _create(self):
+        post_data = {"name": self.name, "is_default": self.is_default}
+        blob = self.knex.post(f"samples/{self.sample.uuid}/dashboard", json=post_data)
+        self.load_blob(blob)
+
+    def tile(
+        self,
+        title,
+        result_file,
+        style: Literal["col-span-1", "col-span-2"] = "col-span-1",
+    ):
+        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 __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 DashboardTile:
 
     def __init__(self, knex, dashboard, title, result_file, style="col-span-1"):
@@ -82,9 +165,11 @@ class DashboardTile:
         self.result_file = result_file
 
     def _get_post_data(self):
-        out =  {
+        out = {
             "field_uuid": self.result_file.uuid,
-            "field_type": "group" if isinstance(self.result_file, ProjectResultFile) else "sample",
+            "field_type": (
+                "group" if isinstance(self.result_file, ProjectResultFile) else "sample"
+            ),
             "style": self.style,
             "title": self.title,
             "has_related_field": False,
@@ -93,11 +178,13 @@ class DashboardTile:
 
     @classmethod
     def from_blob(cls, dashboard, blob):
-        result_file = result_file_from_blob(blob["viz_field"])
-        return cls(dashboard.knex, dashboard, blob["title"], result_file, style=blob["style"])
-    
+        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}\" />"
-    
+        return f'<Geoseeq DashboardTile: {self.dashboard.grn} "{self.title}" />'
+
     def __repr__(self) -> str:
-        return str(self)
+        return str(self)

geoseeq/project.py

@@ -358,4 +358,9 @@ class Project(RemoteObject):
     def grn(self):
         return f"grn::project:{self.uuid}"
 
+    def set_description(self, description):
+        self.description = description
+        self._modified = True
+        return self
+
 SampleGroup = Project  # alias for backwards compatibility

{geoseeq-0.7.1.dist-info → geoseeq-0.7.3.dev0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: geoseeq
-Version: 0.7.1
+Version: 0.7.3.dev0
 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
@@ -15,6 +15,11 @@ Requires-Dist: click
 Requires-Dist: pandas
 Requires-Dist: requests
 Requires-Dist: tqdm
+Provides-Extra: test
+Requires-Dist: pytest-cov>=4.0; extra == 'test'
+Requires-Dist: pytest-mock>=3.10; extra == 'test'
+Requires-Dist: pytest>=7.0; extra == 'test'
+Requires-Dist: requests-mock>=1.11; extra == 'test'
 Description-Content-Type: text/markdown
 
 # Geoseeq API Client
@@ -39,7 +44,7 @@ Download this directory and run `python setup.py install`
 
 ---
 
-## Using the Command Line 
+## Using the Command Line
 
 Run the command line by typing `geoseeq` into a terminal prompt. See available options by adding `--help`
 
@@ -55,7 +60,7 @@ Once you have a token you will need to configure GeoSeeq to use it. Run `geoseeq
 
 ```
 $ geoseeq config
-Set custom profile name? (Leave blank for default) []: 
+Set custom profile name? (Leave blank for default) []:
 Enter the URL to use for GeoSeeq (Most users can use the default) [https://backend.geoseeq.com]:
 Enter your GeoSeeq API token:
 Profile configured.
@@ -77,11 +82,11 @@ $ geoseeq download files --extension fastq.gz "GeoSeeq/Example CLI Project"
 
 #### Uploading sequencing data
 
-GeoSeeq can automatically group fastq files into samples according to their 
+GeoSeeq can automatically group fastq files into samples according to their
 sample name, read number, and lane number. It supports paired end, single end,
 and nanopore reads.
 
-Assume you have data from a single ended sequencing run stored as fastq files: 
+Assume you have data from a single ended sequencing run stored as fastq files:
  - Sample1_L1_R1.fastq.gz
  - Sample1_L1_R2.fastq.gz
  - Sample1_L2_R1.fastq.gz
@@ -114,8 +119,13 @@ Note: You will need to have an API token set to use this command (see above)
 
 ## Using the Python API in a program
 
+
 Please see `geoseeq_api/cli/download.py` for examples of how to download data using the Python API directly.
 
+## Development in GitHub Codespaces
+
+This repository includes a `.devcontainer` configuration so it can be opened directly in [GitHub Codespaces](https://docs.github.com/codespaces). When the codespace is created the development dependencies are installed and `pre-commit` hooks are set up automatically.
+
 ---
 
 ## Notes

{geoseeq-0.7.1.dist-info → geoseeq-0.7.3.dev0.dist-info}/RECORD

@@ -7,7 +7,7 @@ geoseeq/file_system_cache.py,sha256=HzVZWtwLD2fjWWSo_UfWmGeBltm9He4lP_OqzKwNGWg,
 geoseeq/knex.py,sha256=zcjafsmUn9SC3LlRnvvaXpr-pHYZ0IXk7LpzuUoE3MI,8312
 geoseeq/organization.py,sha256=bJkYL8_D-k6IYAaii2ZbxjwYnXy6lvu6iLXscxKlA3w,2542
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
-geoseeq/project.py,sha256=Ba3yvrSyPVnEM5_VGSQu6YPH3CTwE3fHs4JjAepEK7g,13880
+geoseeq/project.py,sha256=_8uttLKc6yVGDdJhPRmQOzzPeMYmUg0zBBPOAJc3yyo,14014
 geoseeq/remote_object.py,sha256=GYN6PKU7Zz3htIdpFjfZiFejzGqqJHbJyKlefM1Eixk,7151
 geoseeq/sample.py,sha256=HAfMiDPHp1UJgIA2lI6oGnNit4YKyj7nx9X07CCN98U,8316
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
@@ -25,7 +25,7 @@ geoseeq/cli/download.py,sha256=Znjuc9IFOcIa5_Od9mFXHJdYAJtgw9Bc_wPPcOVXn7s,21298
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/find_grn.py,sha256=oMDxkzGQBQb2_cCuvmwoeHOsFHqyO9RLeJzrB6bAe5M,439
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=jN3ar-CL5glFnlJhelXliESoP_W2QMrVKkHPQtvhU54,3982
+geoseeq/cli/main.py,sha256=_P_pp_ohm0Pq390FgWjNw-oQA06KGbQPAGbvgY-iL6U,4137
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/project.py,sha256=V5SdXm2Hwo2lxrkpwRDedw-mAE4XnM2uwT-Gj1D90VQ,3030
@@ -42,7 +42,7 @@ geoseeq/cli/shared_params/id_handlers.py,sha256=KtzflnplYVkXsyqI5Ej6r-_BwQnuXVHP
 geoseeq/cli/shared_params/obj_getters.py,sha256=ZSkt6LnDkVFlNVYKgLrjzg60-6BthZMr3eeD3HNqzac,2741
 geoseeq/cli/shared_params/opts_and_args.py,sha256=_DcJ-TqgrbBaeDd-kuHEx2gLZPQN6EHZYWh8Ag-d8Vg,2091
 geoseeq/cli/upload/__init__.py,sha256=tRrljqG7uBM6zVBKpDw1zevHz6Vy418HuIYZKwByyWg,862
-geoseeq/cli/upload/upload.py,sha256=U9w18sG6dZ0uJoAMcQDLdrEtgmRaSaPS7-8KM5LkVd4,14220
+geoseeq/cli/upload/upload.py,sha256=tBga8TW_5qXM4avXH5BAfLrYNms_5eqdyJZex47hZ90,14294
 geoseeq/cli/upload/upload_advanced.py,sha256=1pjtbe8EidIo4eR1_oVD00rPCTxYj8CRqB8D9buA62M,12432
 geoseeq/cli/upload/upload_reads.py,sha256=dZK_Mh3a3NdC4zVB4Yyfz-NViCK9_rROQbmLWTrh8Pc,11642
 geoseeq/contrib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -52,7 +52,7 @@ geoseeq/contrib/ncbi/api.py,sha256=WQeLoGA_-Zha-QeSO8_i7HpvXyD8UkV0qc5okm11KiA,1
 geoseeq/contrib/ncbi/bioproject.py,sha256=_oThTd_iLDOC8cLOlJKAatSr362OBYZCEV3YrqodhFg,4341
 geoseeq/contrib/ncbi/cli.py,sha256=j9zEcaZPTryK3a4xluRxigcJKDhRpRxbp3KZSx-Bfhk,2400
 geoseeq/contrib/ncbi/setup_logging.py,sha256=Tp1bY1U0f-o739aHpvVYriG2qdd1lFvCYBXZeXQgt-w,175
-geoseeq/dashboard/dashboard.py,sha256=HOUJoQcFGLc3JL5UVIYETq6CkQEMP2I4WaPr2u9YV3Q,3297
+geoseeq/dashboard/dashboard.py,sha256=0ISzcTby35oJVsOCeg4b_7Em6hRsh3QzsnbChf946Eo,5564
 geoseeq/file_system/filesystem_download.py,sha256=8bcnxjWltekmCvb5N0b1guBIjLp4-CL2VtsEok-snv4,16963
 geoseeq/file_system/main.py,sha256=4HgYGq7WhlF96JlVIf16iFBTDujlBpxImmtoh4VCzDA,3627
 geoseeq/id_constructors/__init__.py,sha256=w5E0PNQ9UuAxBeZbDI7KBnUoERd85gGz3nScz45bd2o,126
@@ -92,8 +92,8 @@ geoseeq/vc/vc_cache.py,sha256=P4LXTbq2zOIv1OhP7Iw5MmypR2vXuy29Pq5K6gRvi-M,730
 geoseeq/vc/vc_dir.py,sha256=A9CLTh2wWCRzZjiLyqXD1vhtsWZGD3OjaMT5KqlfAXI,457
 geoseeq/vc/vc_sample.py,sha256=qZeioWydXvfu4rGMs20nICfNcp46y_XkND-bHdV6P5M,3850
 geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
-geoseeq-0.7.1.dist-info/METADATA,sha256=7muy1ekQlBoXXfeEAz6NeuvXHgNttqHKJkCVSIqxdIU,4892
-geoseeq-0.7.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-geoseeq-0.7.1.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.7.1.dist-info/licenses/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.7.1.dist-info/RECORD,,
+geoseeq-0.7.3.dev0.dist-info/METADATA,sha256=GqNnxtN09jNv5HRMkxGp5D8ZfrJUyJdxlzL5-6N2Ogw,5415
+geoseeq-0.7.3.dev0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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