From f47668501b21163049d02dd186522e680e464bb8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:49:58 -0600 Subject: [PATCH 01/46] Bump the gha-dependencies group with 3 updates (#422) --- .github/workflows/integration-test.yml | 2 +- .github/workflows/static-analysis.yml | 2 +- .github/workflows/test-mindeps.yml | 4 ++-- .github/workflows/test.yml | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index d416449e..436abdde 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -21,7 +21,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Get full python version diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml index 826982aa..ec51cacb 100644 --- a/.github/workflows/static-analysis.yml +++ b/.github/workflows/static-analysis.yml @@ -9,7 +9,7 @@ jobs: - uses: actions/checkout@v4 - name: Install Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.x diff --git a/.github/workflows/test-mindeps.yml b/.github/workflows/test-mindeps.yml index 21035cf6..c3663d33 100644 --- a/.github/workflows/test-mindeps.yml +++ b/.github/workflows/test-mindeps.yml @@ -26,7 +26,7 @@ jobs: - name: Checkout source uses: actions/checkout@v4.1.1 - name: Setup Conda Environment - uses: conda-incubator/setup-miniconda@v2.2.0 + uses: conda-incubator/setup-miniconda@v3.0.1 with: miniforge-variant: Mambaforge miniforge-version: latest @@ -46,4 +46,4 @@ jobs: run: bash scripts/test.sh - name: Upload coverage - uses: codecov/codecov-action@v1 + uses: codecov/codecov-action@v3 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9f94ad85..f393ac66 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -16,7 +16,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Get full python version From 42a9acdcda6142d5423702c82a4cce359d89203b Mon Sep 17 00:00:00 2001 From: Aimee Barciauskas Date: Tue, 16 Jan 2024 14:32:30 -0800 Subject: [PATCH 02/46] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bd64f264..67c325ef 100644 --- a/README.md +++ b/README.md @@ -99,7 +99,7 @@ Once you are authenticated with NASA EDL you can: ### **Searching for data** Once we have selected our dataset we can search for the data granules using *doi*, *short_name* or *concept_id*. -If we are not sure or we don't know how to search for a particular dataset, we can start with the ["Introducing NASA earthaccess"](https://nsidc.github.io/earthaccess/tutorials/demo/#querying-for-datasets) tutorial or through the [NASA Earthdata Search portal](https://search.earthdata.nasa.gov/). For a complete list of search parameters we can use visit the extended [API documentation](https://nsidc.github.io/earthaccess/user-reference/api/api/). +If we are not sure or we don't know how to search for a particular dataset, we can start with the ["Introducing NASA earthaccess"](https://nsidc.github.io/earthaccess/tutorials/demo/#querying-for-datasets) tutorial or through the [NASA Earthdata Search portal](https://search.earthdata.nasa.gov/). For a complete list of search parameters we can use visit the extended [API documentation](https://earthaccess.readthedocs.io/en/latest/user-reference/api/api/). ```python From e97e6f09fc50d9e46dc8609ab79f74a96cf2786d Mon Sep 17 00:00:00 2001 From: betolink Date: Thu, 1 Feb 2024 11:14:06 -0600 Subject: [PATCH 03/46] refactoring auth to allow other trusted domains besides NASA's URS --- binder/environment-dev.yml | 2 +- earthaccess/auth.py | 19 +- earthaccess/results.py | 4 +- earthaccess/search.py | 43 +- poetry.lock | 1950 ++++++++++++++++++------------------ 5 files changed, 1054 insertions(+), 964 deletions(-) diff --git a/binder/environment-dev.yml b/binder/environment-dev.yml index 202d825b..e59cedf7 100644 --- a/binder/environment-dev.yml +++ b/binder/environment-dev.yml @@ -4,7 +4,7 @@ channels: dependencies: # This environment bootstraps poetry, the actual dev environment # is installed and managed with poetry - - python=3.9 + - python=3.10 - jupyterlab=3 - xarray>=0.19 - ipyleaflet>=0.13 diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 9a3b22cb..63e36941 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -18,10 +18,13 @@ class SessionWithHeaderRedirection(requests.Session): """ Requests removes auth headers if the redirect happens outside the original req domain. - This is taken from https://wiki.earthdata.nasa.gov/display/EL/How+To+Access+Data+With+Python """ - AUTH_HOST = "urs.earthdata.nasa.gov" + AUTH_HOSTS: List[str] = [ + "urs.earthdata.nasa.gov", + "cumulus.asf.alaska.edu", + "datapool.asf.alaska.edu", + ] def __init__( self, username: Optional[str] = None, password: Optional[str] = None @@ -39,11 +42,13 @@ def rebuild_auth(self, prepared_request: Any, response: Any) -> None: if "Authorization" in headers: original_parsed = urlparse(response.request.url) redirect_parsed = urlparse(url) - if ( - (original_parsed.hostname != redirect_parsed.hostname) - and redirect_parsed.hostname != self.AUTH_HOST - and original_parsed.hostname != self.AUTH_HOST + if (original_parsed.hostname != redirect_parsed.hostname) and ( + redirect_parsed.hostname not in self.AUTH_HOSTS + or original_parsed.hostname not in self.AUTH_HOSTS ): + logger.debug( + f"Deleting Auth Headers: {original_parsed.hostname} -> {redirect_parsed.hostname}" + ) del headers["Authorization"] return @@ -210,7 +215,7 @@ def get_session(self, bearer_token: bool = True) -> requests.Session: Returns: class Session instance with Auth and bearer token headers """ - session = requests.Session() + session = SessionWithHeaderRedirection() if bearer_token and self.authenticated: # This will avoid the use of the netrc after we are logged in session.trust_env = False diff --git a/earthaccess/results.py b/earthaccess/results.py index a466e1c3..f0bb2167 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -228,7 +228,9 @@ def __repr__(self) -> str: Temporal coverage: {self['umm']['TemporalExtent']} Size(MB): {self.size()} Data: {data_links}\n\n - """.strip().replace(" ", "") + """.strip().replace( + " ", "" + ) return rep_str def _repr_html_(self) -> str: diff --git a/earthaccess/search.py b/earthaccess/search.py index 8392ca51..fda9732f 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -60,7 +60,16 @@ def hits(self) -> int: Returns: number of results reported by CMR """ - return super().hits() + url = self._build_url() + + response = self.session.get(url, headers=self.headers, params={"page_size": 0}) + + try: + response.raise_for_status() + except exceptions.HTTPError as ex: + raise RuntimeError(ex.response.text) + + return int(response.headers["CMR-Hits"]) def concept_id(self, IDs: List[str]) -> Type[CollectionQuery]: """Filter by concept ID (ex: C1299783579-LPDAAC_ECS or G1327299284-LPDAAC_ECS, S12345678-LPDAAC_ECS) @@ -106,6 +115,38 @@ def doi(self, doi: str) -> Type[CollectionQuery]: self.params["doi"] = doi return self + def instrument(self, instrument: str) -> Type[CollectionQuery]: + """Searh datasets by instrument + + ???+ Tip + Not all datasets have an associated instrument. This works + only at the dataset level but not the granule (data) level. + + Parameters: + instrument (String): instrument of a datasets, e.g. instrument=GEDI + """ + if not isinstance(instrument, str): + raise TypeError("instrument must be of type str") + + self.params["instrument"] = instrument + return self + + def project(self, project: str) -> Type[CollectionQuery]: + """Searh datasets by associated project + + ???+ Tip + Not all datasets have an associated instrument. This works + only at the dataset level but not the granule (data) level. + + Parameters: + project (String): associated project of a datasets, e.g. project=EMIT + """ + if not isinstance(project, str): + raise TypeError("project must be of type str") + + self.params["project"] = project + return self + def parameters(self, **kwargs: Any) -> Type[CollectionQuery]: """Provide query parameters as keyword arguments. 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"sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"}, + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, ] [[package]] From 073e4ac3c1808ef530ea726db30fca79d834b471 Mon Sep 17 00:00:00 2001 From: betolink Date: Thu, 1 Feb 2024 11:22:43 -0600 Subject: [PATCH 04/46] updated changelog and readme --- CHANGELOG.md | 10 +++++++++- README.md | 2 -- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3b83fcdc..b4e21691 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog +## [Unreleased] + +* Bug fixes: + * fixed #439 by implementing more trusted domains in the SessionWithRedirection + * fixed #438 by using an authenticated session for hits() +* Enhancements: + * addressing #427 by adding parameters to collection query + ## [v0.8.2] 2023-12-06 * Bug fixes: * Enable AWS check with IMDSv2 @@ -167,7 +175,7 @@ - Add basic classes to interact with NASA CMR, EDL and cloud access. - Basic object formatting. -[Unreleased]: https://github.com/nsidc/earthaccess/compare/v0.5.2...HEAD +[Unreleased]: https://github.com/nsidc/earthaccess/compare/v0.8.2...HEAD [v0.5.2]: https://github.com/nsidc/earthaccess/releases/tag/v0.5.2 [v0.5.1]: https://github.com/nsidc/earthaccess/releases/tag/v0.5.1 [v0.5.0]: https://github.com/nsidc/earthaccess/releases/tag/v0.4.0 diff --git a/README.md b/README.md index 67c325ef..657ca4c7 100644 --- a/README.md +++ b/README.md @@ -65,8 +65,6 @@ With *earthaccess* we can login, search and download data with a few lines of co The only requirement to use this library is to open a free account with NASA [EDL](https://urs.earthdata.nasa.gov). - - ### **Authentication** From acade7096b6238320b181205407c243cc2866a77 Mon Sep 17 00:00:00 2001 From: betolink Date: Thu, 1 Feb 2024 11:44:58 -0600 Subject: [PATCH 05/46] fix docstring --- earthaccess/search.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/earthaccess/search.py b/earthaccess/search.py index fda9732f..1d3e429f 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -135,8 +135,9 @@ def project(self, project: str) -> Type[CollectionQuery]: """Searh datasets by associated project ???+ Tip - Not all datasets have an associated instrument. This works + Not all datasets have an associated project. This works only at the dataset level but not the granule (data) level. + Will bring datasets across DAACs matching the project. Parameters: project (String): associated project of a datasets, e.g. project=EMIT From 429324a5945cb380a76686d199fee945bef1fd1a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luis=20L=C3=B3pez?= Date: Thu, 1 Feb 2024 22:35:21 -0600 Subject: [PATCH 06/46] Update earthaccess/auth.py adding Sentinel 1, (I though Sentinel was working before.) Co-authored-by: Joseph H Kennedy --- earthaccess/auth.py | 1 + 1 file changed, 1 insertion(+) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 63e36941..53850a83 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -23,6 +23,7 @@ class SessionWithHeaderRedirection(requests.Session): AUTH_HOSTS: List[str] = [ "urs.earthdata.nasa.gov", "cumulus.asf.alaska.edu", + "sentinel1.asf.alaska.edu", "datapool.asf.alaska.edu", ] From b3206523e4f7a1ff417f15116449ddfcc4c9b031 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luis=20L=C3=B3pez?= Date: Thu, 1 Feb 2024 22:35:29 -0600 Subject: [PATCH 07/46] Update earthaccess/search.py Co-authored-by: Joseph H Kennedy --- earthaccess/search.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/earthaccess/search.py b/earthaccess/search.py index 1d3e429f..bd9f1196 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -137,7 +137,7 @@ def project(self, project: str) -> Type[CollectionQuery]: ???+ Tip Not all datasets have an associated project. This works only at the dataset level but not the granule (data) level. - Will bring datasets across DAACs matching the project. + Will return datasets across DAACs matching the project. Parameters: project (String): associated project of a datasets, e.g. project=EMIT From 0ead9dbed9b69dce1b3d4be1475c8d9aab11a7e0 Mon Sep 17 00:00:00 2001 From: betolink Date: Thu, 1 Feb 2024 22:40:09 -0600 Subject: [PATCH 08/46] making ruff happy --- earthaccess/results.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/earthaccess/results.py b/earthaccess/results.py index f0bb2167..a466e1c3 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -228,9 +228,7 @@ def __repr__(self) -> str: Temporal coverage: {self['umm']['TemporalExtent']} Size(MB): {self.size()} Data: {data_links}\n\n - """.strip().replace( - " ", "" - ) + """.strip().replace(" ", "") return rep_str def _repr_html_(self) -> str: From c692069dd91891d421b1b2c947140a5877d8ed06 Mon Sep 17 00:00:00 2001 From: betolink Date: Fri, 2 Feb 2024 19:52:20 -0600 Subject: [PATCH 09/46] using user-agent to start tracing client usage --- earthaccess/auth.py | 12 ++++++++++++ tests/unit/test_auth.py | 6 ++++++ 2 files changed, 18 insertions(+) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 53850a83..11b57dfe 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -6,11 +6,20 @@ from typing import Any, Dict, List, Optional from urllib.parse import urlparse + import requests # type: ignore from tinynetrc import Netrc from .daac import DAACS +import importlib.metadata + +try: + user_agent = f"earthaccess v{importlib.metadata.version('earthacess')}" +except importlib.metadata.PackageNotFoundError: + user_agent = "earthaccess" + + logger = logging.getLogger(__name__) @@ -31,6 +40,9 @@ def __init__( self, username: Optional[str] = None, password: Optional[str] = None ) -> None: super().__init__() + self.headers.update({"User-Agent": user_agent}) + + if username and password: self.auth = (username, password) diff --git a/tests/unit/test_auth.py b/tests/unit/test_auth.py index 510278bb..0c59fc86 100644 --- a/tests/unit/test_auth.py +++ b/tests/unit/test_auth.py @@ -39,11 +39,17 @@ def test_auth_gets_proper_credentials(self, user_input, user_password) -> bool: # Test auth = Auth() + session = auth.get_session() + headers = session.headers self.assertEqual(auth.authenticated, False) auth.login(strategy="interactive") self.assertEqual(auth.authenticated, True) self.assertTrue(auth.token in json_response) + # test that we are creaintg a session with the proper headers + self.assertTrue("User-Agent" in headers) + self.assertTrue("earthaccess" in headers["User-Agent"]) + @responses.activate @mock.patch("getpass.getpass") @mock.patch("builtins.input") From b94897eb40a43ae47786db0889aa52948449e971 Mon Sep 17 00:00:00 2001 From: betolink Date: Fri, 2 Feb 2024 19:53:48 -0600 Subject: [PATCH 10/46] fix lintint --- earthaccess/auth.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 11b57dfe..dbf20463 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -18,7 +18,7 @@ user_agent = f"earthaccess v{importlib.metadata.version('earthacess')}" except importlib.metadata.PackageNotFoundError: user_agent = "earthaccess" - + logger = logging.getLogger(__name__) @@ -42,7 +42,6 @@ def __init__( super().__init__() self.headers.update({"User-Agent": user_agent}) - if username and password: self.auth = (username, password) From 11686dd4e95eeefb4cdd3e1fffd3016fd4155296 Mon Sep 17 00:00:00 2001 From: betolink Date: Fri, 2 Feb 2024 19:55:51 -0600 Subject: [PATCH 11/46] fix lintint --- earthaccess/auth.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index dbf20463..3455a286 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -1,4 +1,5 @@ import getpass +import importlib.metadata import logging import os from netrc import NetrcParseError @@ -6,14 +7,11 @@ from typing import Any, Dict, List, Optional from urllib.parse import urlparse - import requests # type: ignore from tinynetrc import Netrc from .daac import DAACS -import importlib.metadata - try: user_agent = f"earthaccess v{importlib.metadata.version('earthacess')}" except importlib.metadata.PackageNotFoundError: From 6892007a0b91b33280398f0a47eaadc81d3abc72 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 6 Feb 2024 12:49:14 -0700 Subject: [PATCH 12/46] Clarify that temporal and bbox args must be tuples in docstrings Addresses #279, but does not resolve it. --- earthaccess/api.py | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 8e518912..500a2be4 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -50,14 +50,19 @@ def search_datasets( * **provider**: particular to each DAAC, e.g. POCLOUD, LPDAAC etc. - * **temporal**: ("yyyy-mm-dd", "yyyy-mm-dd") + * **temporal**: a tuple representing temporal bounds in the form + ("yyyy-mm-dd", "yyyy-mm-dd") + + * **bounding_box**: a tuple representing spatial bounds in the form + (lower_left_lon, lower_left_lat , upper_right_lon, upper_right_lat) - * **bounding_box**: (lower_left_lon, lower_left_lat , - upper_right_lon, upper_right_lat) Returns: - an list of DataCollection results that can be used to get + + a list of DataCollection results that can be used to get information such as concept_id, doi, etc. about a dataset. + Examples: + ```python datasets = earthaccess.search_datasets( keyword="sea surface anomaly", @@ -103,14 +108,19 @@ def search_data( * **provider**: particular to each DAAC, e.g. POCLOUD, LPDAAC etc. - * **temporal**: ("yyyy-mm-dd", "yyyy-mm-dd") + * **temporal**: a tuple representing temporal bounds in the form + ("yyyy-mm-dd", "yyyy-mm-dd") + + * **bounding_box**: a tuple representing spatial bounds in the form + (lower_left_lon, lower_left_lat , upper_right_lon, upper_right_lat) - * **bounding_box**: (lower_left_lon, lower_left_lat , - upper_right_lon, upper_right_lat) Returns: + Granules: a list of DataGranules that can be used to access - the granule files by using `download()` or `open()`. + the granule files by using `download()` or `open()`. + Examples: + ```python datasets = earthaccess.search_data( doi="10.5067/SLREF-CDRV2", From 14cbfefd2e03ad45516e57542e92be6f05fe94aa Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 6 Feb 2024 14:04:36 -0700 Subject: [PATCH 13/46] Move shebang to first line --- scripts/docs-live.sh | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/scripts/docs-live.sh b/scripts/docs-live.sh index 286f2a7c..6ed6a4be 100755 --- a/scripts/docs-live.sh +++ b/scripts/docs-live.sh @@ -1,7 +1,4 @@ - #!/usr/bin/env bash - -set -e -set -x +set -ex mkdocs serve --dev-addr 0.0.0.0:8008 --dirtyreload From 29ad00e13e2b80e1cdef0d2368778958d3ace8e0 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 6 Feb 2024 14:09:03 -0700 Subject: [PATCH 14/46] Fixup docstring formatting issues --- earthaccess/api.py | 71 ++++++++++++++++------------------------------ 1 file changed, 25 insertions(+), 46 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 500a2be4..077a6ced 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -31,38 +31,30 @@ def _normalize_location(location: Union[str, None]) -> Union[str, None]: def search_datasets( count: int = -1, **kwargs: Any ) -> List[earthaccess.results.DataCollection]: - """Search datasets using NASA's CMR + """Search datasets using NASA's CMR. [https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html) Parameters: - count (Integer): Number of records to get, -1 = all - kwargs (Dict): arguments to CMR: + kwargs (Dict): + arguments to CMR: * **keyword**: case insensitive and support wild cards ? and *, - * **short_name**: e.g. ATL08 - * **doi**: DOI for a dataset - * **daac**: e.g. NSIDC or PODAAC - * **provider**: particular to each DAAC, e.g. POCLOUD, LPDAAC etc. - * **temporal**: a tuple representing temporal bounds in the form - ("yyyy-mm-dd", "yyyy-mm-dd") - + `("yyyy-mm-dd", "yyyy-mm-dd")` * **bounding_box**: a tuple representing spatial bounds in the form - (lower_left_lon, lower_left_lat , upper_right_lon, upper_right_lat) + `(lower_left_lon, lower_left_lat, upper_right_lon, upper_right_lat)` Returns: - - a list of DataCollection results that can be used to get - information such as concept_id, doi, etc. about a dataset. + a list of DataCollection results that can be used to get information about a + dataset, e.g. concept_id, doi, etc. Examples: - ```python datasets = earthaccess.search_datasets( keyword="sea surface anomaly", @@ -94,33 +86,25 @@ def search_data( [https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html) Parameters: - count (Integer): Number of records to get, -1 = all - kwargs (Dict): arguments to CMR: + kwargs (Dict): + arguments to CMR: * **short_name**: dataset short name e.g. ATL08 - * **version**: dataset version - * **doi**: DOI for a dataset - * **daac**: e.g. NSIDC or PODAAC - * **provider**: particular to each DAAC, e.g. POCLOUD, LPDAAC etc. - * **temporal**: a tuple representing temporal bounds in the form - ("yyyy-mm-dd", "yyyy-mm-dd") - + `("yyyy-mm-dd", "yyyy-mm-dd")` * **bounding_box**: a tuple representing spatial bounds in the form - (lower_left_lon, lower_left_lat , upper_right_lon, upper_right_lat) + `(lower_left_lon, lower_left_lat, upper_right_lon, upper_right_lat)` Returns: - - Granules: a list of DataGranules that can be used to access - the granule files by using `download()` or `open()`. + a list of DataGranules that can be used to access the granule files by using + `download()` or `open()`. Examples: - ```python datasets = earthaccess.search_data( doi="10.5067/SLREF-CDRV2", @@ -144,17 +128,15 @@ def login(strategy: str = "all", persist: bool = False) -> Auth: """Authenticate with Earthdata login (https://urs.earthdata.nasa.gov/) Parameters: + strategy (String): + authentication method. - strategy (String): authentication method. - - "all": (default) try all methods until one works - - "interactive": enter username and password. - - "netrc": retrieve username and password from ~/.netrc. - - "environment": retrieve username and password from $EARTHDATA_USERNAME and $EARTHDATA_PASSWORD. + * **"all"**: (default) try all methods until one works + * **"interactive"**: enter username and password. + * **"netrc"**: retrieve username and password from ~/.netrc. + * **"environment"**: retrieve username and password from `$EARTHDATA_USERNAME` and `$EARTHDATA_PASSWORD`. persist (Boolean): will persist credentials in a .netrc file + Returns: an instance of Auth. """ @@ -218,8 +200,10 @@ def open( hosted on S3 or HTTPS by third party libraries like xarray. Parameters: - granules: a list of granule instances **or** list of URLs, e.g. s3://some-granule, - if a list of URLs is passed we need to specify the data provider e.g. POCLOUD, NSIDC_CPRD etc. + granules: a list of granule instances **or** list of URLs, e.g. + `s3://some-granule`, if a list of URLs is passed we need to specify the data + provider e.g. POCLOUD, NSIDC_CPRD etc. + Returns: a list of s3fs "file pointers" to s3 files. """ @@ -242,6 +226,7 @@ def get_s3_credentials( daac (String): a DAAC short_name like NSIDC or PODAAC etc provider (String: if we know the provider for the DAAC e.g. POCLOUD, LPCLOUD etc. results (list[earthaccess.results.DataGranule]): List of results from search_data() + Returns: a dictionary with S3 credentials for the DAAC or provider """ @@ -256,8 +241,6 @@ def get_s3_credentials( def collection_query() -> Type[CollectionQuery]: """Returns a query builder instance for NASA collections (datasets) - Parameters: - cloud_hosted (Boolean): initializes the query builder for cloud hosted collections. Returns: class earthaccess.DataCollections: a query builder instance for data collections. """ @@ -271,9 +254,6 @@ class earthaccess.DataCollections: a query builder instance for data collections def granule_query() -> Type[GranuleQuery]: """Returns a query builder instance for data granules - Parameters: - cloud_hosted (Boolean): initializes the query builder for a particular DOI - if we have it. Returns: class earthaccess.DataGranules: a query builder instance for data granules. """ @@ -359,7 +339,6 @@ def get_edl_token() -> str: Returns: str: EDL token - """ token = earthaccess.__auth__.token return token From fc2a379beb99d030885a314e241c421def83aa81 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 6 Feb 2024 14:09:16 -0700 Subject: [PATCH 15/46] Enable building docs with dev conda env --- binder/environment-dev.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/binder/environment-dev.yml b/binder/environment-dev.yml index 202d825b..6783a808 100644 --- a/binder/environment-dev.yml +++ b/binder/environment-dev.yml @@ -10,6 +10,16 @@ dependencies: - ipyleaflet>=0.13 - h5netcdf>=0.11 - cartopy + + - mkdocs>=1.2 + - mkdocs-material>=7.1,<9.0 + - markdown-include>=0.6 + - mkdocstrings>=0.19.0 + - mkdocstrings-python + - mkdocs-jupyter>=0.19.0 + - pymdown-extensions>=9.2 + - pip - pip: - poetry + - markdown-callouts>=0.2.0 From 71fb424eef7b6bf8cfc10c3b130ce1a4a35d24ec Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 6 Feb 2024 14:17:47 -0700 Subject: [PATCH 16/46] Remove redundant docstring type info --- earthaccess/api.py | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 077a6ced..21845d7d 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -36,7 +36,7 @@ def search_datasets( [https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html) Parameters: - count (Integer): Number of records to get, -1 = all + count: Number of records to get, -1 = all kwargs (Dict): arguments to CMR: @@ -86,7 +86,7 @@ def search_data( [https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html](https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html) Parameters: - count (Integer): Number of records to get, -1 = all + count: Number of records to get, -1 = all kwargs (Dict): arguments to CMR: @@ -128,14 +128,14 @@ def login(strategy: str = "all", persist: bool = False) -> Auth: """Authenticate with Earthdata login (https://urs.earthdata.nasa.gov/) Parameters: - strategy (String): + strategy: authentication method. * **"all"**: (default) try all methods until one works * **"interactive"**: enter username and password. * **"netrc"**: retrieve username and password from ~/.netrc. * **"environment"**: retrieve username and password from `$EARTHDATA_USERNAME` and `$EARTHDATA_PASSWORD`. - persist (Boolean): will persist credentials in a .netrc file + persist: will persist credentials in a .netrc file Returns: an instance of Auth. @@ -223,9 +223,9 @@ def get_s3_credentials( this is useful for missions that do not use the same endpoint as their DAACs e.g. SWOT Parameters: - daac (String): a DAAC short_name like NSIDC or PODAAC etc - provider (String: if we know the provider for the DAAC e.g. POCLOUD, LPCLOUD etc. - results (list[earthaccess.results.DataGranule]): List of results from search_data() + daac: a DAAC short_name like NSIDC or PODAAC etc + provider: if we know the provider for the DAAC e.g. POCLOUD, LPCLOUD etc. + results: List of results from search_data() Returns: a dictionary with S3 credentials for the DAAC or provider @@ -242,7 +242,7 @@ def collection_query() -> Type[CollectionQuery]: """Returns a query builder instance for NASA collections (datasets) Returns: - class earthaccess.DataCollections: a query builder instance for data collections. + a query builder instance for data collections. """ if earthaccess.__auth__.authenticated: query_builder = DataCollections(earthaccess.__auth__) @@ -255,7 +255,7 @@ def granule_query() -> Type[GranuleQuery]: """Returns a query builder instance for data granules Returns: - class earthaccess.DataGranules: a query builder instance for data granules. + a query builder instance for data granules. """ if earthaccess.__auth__.authenticated: query_builder = DataGranules(earthaccess.__auth__) @@ -268,7 +268,7 @@ def get_fsspec_https_session() -> AbstractFileSystem: """Returns a fsspec session that can be used to access datafiles across many different DAACs Returns: - class AbstractFileSystem: an fsspec instance able to access data across DAACs + an fsspec instance able to access data across DAACs Examples: ```python @@ -291,7 +291,7 @@ def get_requests_https_session() -> requests.Session: require authentication with NASA EDL. Returns: - class requests.Session: an authenticated requests Session instance. + an authenticated requests Session instance. Examples: ```python @@ -316,12 +316,12 @@ def get_s3fs_session( """Returns a fsspec s3fs file session for direct access when we are in us-west-2 Parameters: - daac (String): Any DAAC short name e.g. NSIDC, GES_DISC - provider (String): Each DAAC can have a cloud provider, if the DAAC is specified, there is no need to use provider - results (list[class earthaccess.results.DataGranule]): A list of results from search_data(), earthaccess will use the metadata form CMR to obtain the S3 Endpoint + daac: Any DAAC short name e.g. NSIDC, GES_DISC + provider: Each DAAC can have a cloud provider, if the DAAC is specified, there is no need to use provider + results: A list of results from search_data(), earthaccess will use the metadata form CMR to obtain the S3 Endpoint Returns: - class s3fs.S3FileSystem: an authenticated s3fs session valid for 1 hour + an authenticated s3fs session valid for 1 hour """ daac = _normalize_location(daac) provider = _normalize_location(provider) @@ -338,7 +338,7 @@ def get_edl_token() -> str: """Returns the current token used for EDL Returns: - str: EDL token + EDL token """ token = earthaccess.__auth__.token return token From 48c88703be1b57dfa6a1b97f0c7458f36f66d1e4 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 6 Feb 2024 14:21:14 -0700 Subject: [PATCH 17/46] Prefer Optional over Union with None for consistency in docs --- earthaccess/api.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 21845d7d..ed858ac7 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -13,7 +13,7 @@ from .utils import _validation as validate -def _normalize_location(location: Union[str, None]) -> Union[str, None]: +def _normalize_location(location: Optional[str]) -> Optional[str]: """Handle user-provided `daac` and `provider` values These values must have a capital letter as the first character @@ -160,7 +160,7 @@ def login(strategy: str = "all", persist: bool = False) -> Auth: def download( granules: Union[DataGranule, List[DataGranule], str, List[str]], - local_path: Union[str, None], + local_path: Optional[str], provider: Optional[str] = None, threads: int = 8, ) -> List[str]: From dd25609048f059f82c3302acae721d0e8a124a4f Mon Sep 17 00:00:00 2001 From: vincentsarago Date: Wed, 7 Feb 2024 11:33:02 +0100 Subject: [PATCH 18/46] allow datetime object to be provided for temporal queries --- earthaccess/search.py | 47 +++++++++++++++------------ tests/unit/test_collection_queries.py | 31 ++++++++++++++++++ tests/unit/test_granule_queries.py | 2 ++ 3 files changed, 60 insertions(+), 20 deletions(-) diff --git a/earthaccess/search.py b/earthaccess/search.py index 8392ca51..a0231b8d 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -1,6 +1,6 @@ import datetime as dt from inspect import getmembers, ismethod -from typing import Any, Dict, List, Optional, Tuple, Type +from typing import Any, Dict, List, Optional, Tuple, Type, Union import dateutil.parser as parser # type: ignore from cmr import CollectionQuery, GranuleQuery # type: ignore @@ -262,31 +262,36 @@ def get(self, limit: int = 2000) -> list: return results def temporal( - self, date_from: str, date_to: str, exclude_boundary: bool = False + self, + date_from: Optional[Union[str, dt.datetime]] = None, + date_to: Optional[Union[str, dt.datetime]] = None, + exclude_boundary: bool = False, ) -> Type[CollectionQuery]: """Filter by an open or closed date range. Dates can be provided as datetime objects or ISO 8601 formatted strings. Multiple ranges can be provided by successive calls. to this method before calling execute(). Parameters: - date_from (String): earliest date of temporal range - date_to (string): latest date of temporal range + date_from (String or Datetime object): earliest date of temporal range + date_to (String or Datetime object): latest date of temporal range exclude_boundary (Boolean): whether or not to exclude the date_from/to in the matched range """ DEFAULT = dt.datetime(1979, 1, 1) - if date_from is not None: + if date_from is not None and not isinstance(date_from, dt.datetime): try: - parsed_from = parser.parse(date_from, default=DEFAULT).isoformat() + "Z" + date_from = parser.parse(date_from, default=DEFAULT).isoformat() + "Z" except Exception: print("The provided start date was not recognized") - parsed_from = "" - if date_to is not None: + date_from = "" + + if date_to is not None and not isinstance(date_to, dt.datetime): try: - parsed_to = parser.parse(date_to, default=DEFAULT).isoformat() + "Z" + date_to = parser.parse(date_to, default=DEFAULT).isoformat() + "Z" except Exception: print("The provided end date was not recognized") - parsed_to = "" - super().temporal(parsed_from, parsed_to, exclude_boundary) + date_to = "" + + super().temporal(date_from, date_to, exclude_boundary) return self @@ -614,8 +619,8 @@ def debug(self, debug: bool = True) -> Type[GranuleQuery]: def temporal( self, - date_from: Optional[str] = None, - date_to: Optional[str] = None, + date_from: Optional[Union[str, dt.datetime]] = None, + date_to: Optional[Union[str, dt.datetime]] = None, exclude_boundary: bool = False, ) -> Type[GranuleQuery]: """Filter by an open or closed date range. @@ -628,19 +633,21 @@ def temporal( exclude_boundary (Boolean): whether or not to exclude the date_from/to in the matched range """ DEFAULT = dt.datetime(1979, 1, 1) - if date_from is not None: + if date_from is not None and not isinstance(date_from, dt.datetime): try: - parsed_from = parser.parse(date_from, default=DEFAULT).isoformat() + "Z" + date_from = parser.parse(date_from, default=DEFAULT).isoformat() + "Z" except Exception: print("The provided start date was not recognized") - parsed_from = "" - if date_to is not None: + date_from = "" + + if date_to is not None and not isinstance(date_to, dt.datetime): try: - parsed_to = parser.parse(date_to, default=DEFAULT).isoformat() + "Z" + date_to = parser.parse(date_to, default=DEFAULT).isoformat() + "Z" except Exception: print("The provided end date was not recognized") - parsed_to = "" - super().temporal(parsed_from, parsed_to, exclude_boundary) + date_to = "" + + super().temporal(date_from, date_to, exclude_boundary) return self def version(self, version: str = "") -> Type[GranuleQuery]: diff --git a/tests/unit/test_collection_queries.py b/tests/unit/test_collection_queries.py index b050d42e..bc152b63 100644 --- a/tests/unit/test_collection_queries.py +++ b/tests/unit/test_collection_queries.py @@ -1,7 +1,22 @@ # package imports +import datetime as dt +import pytest from earthaccess.search import DataCollections +valid_single_dates = [ + ("2001-12-12", "2001-12-21", "2001-12-12T00:00:00Z,2001-12-21T00:00:00Z"), + ("2021-02-01", "", "2021-02-01T00:00:00Z,"), + ("1999-02-01 06:00", "2009-01-01", "1999-02-01T06:00:00Z,2009-01-01T00:00:00Z"), + (dt.datetime(2021, 2, 1), dt.datetime(2021, 2, 2), "2021-02-01T00:00:00Z,2021-02-02T00:00:00Z") +] + +invalid_single_dates = [ + ("2001-12-45", "2001-12-21", None), + ("2021w1", "", None), + ("2999-02-01", "2009-01-01", None), +] + def test_query_can_find_cloud_provider(): query = DataCollections().daac("PODAAC").cloud_hosted(True) assert query.params["provider"] == "POCLOUD" @@ -18,3 +33,19 @@ def test_querybuilder_can_handle_doi(): assert query.params["doi"] == doi query = DataCollections().cloud_hosted(True).daac("PODAAC").doi(doi) assert query.params["doi"] == doi + + +@pytest.mark.parametrize("start,end,expected", valid_single_dates) +def test_query_can_parse_single_dates(start, end, expected): + query = DataCollections().temporal(start, end) + assert query.params["temporal"][0] == expected + + +@pytest.mark.parametrize("start,end,expected", invalid_single_dates) +def test_query_can_handle_invalid_dates(start, end, expected): + query = DataCollections() + try: + query = query.temporal(start, end) + except Exception as e: + assert isinstance(e, ValueError) + assert "temporal" not in query.params diff --git a/tests/unit/test_granule_queries.py b/tests/unit/test_granule_queries.py index f16f2ee8..fa05fcd8 100644 --- a/tests/unit/test_granule_queries.py +++ b/tests/unit/test_granule_queries.py @@ -1,4 +1,5 @@ # package imports +import datetime as dt import pytest from earthaccess.search import DataGranules @@ -6,6 +7,7 @@ ("2001-12-12", "2001-12-21", "2001-12-12T00:00:00Z,2001-12-21T00:00:00Z"), ("2021-02-01", "", "2021-02-01T00:00:00Z,"), ("1999-02-01 06:00", "2009-01-01", "1999-02-01T06:00:00Z,2009-01-01T00:00:00Z"), + (dt.datetime(2021, 2, 1), dt.datetime(2021, 2, 2), "2021-02-01T00:00:00Z,2021-02-02T00:00:00Z") ] invalid_single_dates = [ From 9fd6fb4881e0f8b9f3df4f301aa00c8a3edfd0ba Mon Sep 17 00:00:00 2001 From: vincentsarago Date: Wed, 7 Feb 2024 11:51:21 +0100 Subject: [PATCH 19/46] lint --- tests/unit/test_collection_queries.py | 9 +++++++-- tests/unit/test_granule_queries.py | 7 ++++++- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/tests/unit/test_collection_queries.py b/tests/unit/test_collection_queries.py index bc152b63..f2c42a38 100644 --- a/tests/unit/test_collection_queries.py +++ b/tests/unit/test_collection_queries.py @@ -1,14 +1,18 @@ # package imports import datetime as dt + import pytest from earthaccess.search import DataCollections - valid_single_dates = [ ("2001-12-12", "2001-12-21", "2001-12-12T00:00:00Z,2001-12-21T00:00:00Z"), ("2021-02-01", "", "2021-02-01T00:00:00Z,"), ("1999-02-01 06:00", "2009-01-01", "1999-02-01T06:00:00Z,2009-01-01T00:00:00Z"), - (dt.datetime(2021, 2, 1), dt.datetime(2021, 2, 2), "2021-02-01T00:00:00Z,2021-02-02T00:00:00Z") + ( + dt.datetime(2021, 2, 1), + dt.datetime(2021, 2, 2), + "2021-02-01T00:00:00Z,2021-02-02T00:00:00Z", + ), ] invalid_single_dates = [ @@ -17,6 +21,7 @@ ("2999-02-01", "2009-01-01", None), ] + def test_query_can_find_cloud_provider(): query = DataCollections().daac("PODAAC").cloud_hosted(True) assert query.params["provider"] == "POCLOUD" diff --git a/tests/unit/test_granule_queries.py b/tests/unit/test_granule_queries.py index fa05fcd8..33280810 100644 --- a/tests/unit/test_granule_queries.py +++ b/tests/unit/test_granule_queries.py @@ -1,5 +1,6 @@ # package imports import datetime as dt + import pytest from earthaccess.search import DataGranules @@ -7,7 +8,11 @@ ("2001-12-12", "2001-12-21", "2001-12-12T00:00:00Z,2001-12-21T00:00:00Z"), ("2021-02-01", "", "2021-02-01T00:00:00Z,"), ("1999-02-01 06:00", "2009-01-01", "1999-02-01T06:00:00Z,2009-01-01T00:00:00Z"), - (dt.datetime(2021, 2, 1), dt.datetime(2021, 2, 2), "2021-02-01T00:00:00Z,2021-02-02T00:00:00Z") + ( + dt.datetime(2021, 2, 1), + dt.datetime(2021, 2, 2), + "2021-02-01T00:00:00Z,2021-02-02T00:00:00Z", + ), ] invalid_single_dates = [ From 898f0cd5ad4946642fb374ad393208a2157e1861 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 12:26:15 -0500 Subject: [PATCH 20/46] docstring cleanup --- earthaccess/results.py | 52 ++++++++++++++++++++++-------------------- 1 file changed, 27 insertions(+), 25 deletions(-) diff --git a/earthaccess/results.py b/earthaccess/results.py index a466e1c3..5569f670 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -56,9 +56,7 @@ def _filter_related_links(self, filter: str) -> List[str]: class DataCollection(CustomDict): - """ - Dictionary-like object to represent a data collection from CMR - """ + """Dictionary-like object to represent a data collection from CMR.""" _basic_meta_fields_ = [ "concept-id", @@ -78,10 +76,10 @@ class DataCollection(CustomDict): ] def summary(self) -> Dict[str, Any]: - """Summary containing short_name, concept-id, file-type, and cloud-info if the dataset is cloud hosted. + """Summary containing short_name, concept-id, file-type, and cloud-info (if cloud-hosted). Returns: - Returns a sumary of the collection metadata + A summary of the collection metadata. """ # we can print only the concept-id @@ -101,6 +99,7 @@ def get_umm(self, umm_field: str) -> Union[str, Dict[str, Any]]: """ Parameters: umm_field: Valid UMM item, i.e. `TemporalExtent` + Returns: Returns the value of a given field inside the UMM (Unified Metadata Model) """ @@ -111,14 +110,15 @@ def get_umm(self, umm_field: str) -> Union[str, Dict[str, Any]]: def concept_id(self) -> str: """ Returns: - Retrurns a collection's `concept_id`, this id is the most relevant search field on granule queries. + A collection's `concept_id`. + This id is the most relevant search field on granule queries. """ return self["meta"]["concept-id"] def data_type(self) -> str: """ Returns: - If available, it returns the collection data type, i.e. HDF5, CSV etc + The collection data type, i.e. HDF5, CSV etc., if available. """ if "ArchiveAndDistributionInformation" in self["umm"]: return str( @@ -131,7 +131,7 @@ def data_type(self) -> str: def version(self) -> str: """ Returns: - returns the collection's version. + The collection's version. """ if "Version" in self["umm"]: return self["umm"]["Version"] @@ -140,7 +140,7 @@ def version(self) -> str: def abstract(self) -> str: """ Returns: - Returns the abstract of a collection + The abstract of a collection """ if "Abstract" in self["umm"]: return self["umm"]["Abstract"] @@ -149,7 +149,7 @@ def abstract(self) -> str: def landing_page(self) -> str: """ Returns: - if available it returns the first landing page for the collection, can be many. + The first landing page for the collection (can be many), if available. """ links = self._filter_related_links("LANDING PAGE") if len(links) > 0: @@ -159,7 +159,7 @@ def landing_page(self) -> str: def get_data(self) -> List[str]: """ Returns: - Returns the GET DATA links, usually a link to a landing page, a DAAC portal or an FTP location. + The GET DATA links (usually a landing page link, a DAAC portal, or an FTP location). """ links = self._filter_related_links("GET DATA") return links @@ -167,7 +167,8 @@ def get_data(self) -> List[str]: def s3_bucket(self) -> Dict[str, Any]: """ Returns: - Returns the S3 bucket information if the collection has it (**cloud hosted collections only**) + The S3 bucket information if the collection has it. + (**cloud hosted collections only**) """ if "DirectDistributionInformation" in self["umm"]: return self["umm"]["DirectDistributionInformation"] @@ -180,9 +181,7 @@ def __repr__(self) -> str: class DataGranule(CustomDict): - """ - Dictionary-like object to represent a granule from CMR - """ + """Dictionary-like object to represent a granule from CMR.""" _basic_meta_fields_ = [ "concept-id", @@ -219,7 +218,7 @@ def __init__( def __repr__(self) -> str: """ Returns: - returns a basic representation of a data granule + A basic representation of a data granule. """ data_links = [link for link in self.data_links()] rep_str = f""" @@ -234,7 +233,7 @@ def __repr__(self) -> str: def _repr_html_(self) -> str: """ Returns: - Returns a rich representation for a data granule if we are in a Jupyter notebook. + A rich representation for a data granule if we are in a Jupyter notebook. """ granule_html_repr = _repr_granule_html(self) return granule_html_repr @@ -248,7 +247,7 @@ def get_s3_credentials_endpoint(self) -> Union[str, None]: def size(self) -> float: """ Returns: - Returns the total size for the granule in MB + The total size for the granule in MB. """ try: data_granule = self["umm"]["DataGranule"] @@ -290,17 +289,20 @@ def data_links( """Returns the data links form a granule Parameters: - access: direct or external, direct means in-region access for cloud hosted collections. - in_region: if we are running in us-west-2, meant for the store class, default is False + access: direct or external. + direct means in-region access for cloud-hosted collections. + in_region: True if we are running in us-west-2. + It is meant for the store class. + Returns: - the data link for the requested access type + The data link for the requested access type. """ https_links = self._filter_related_links("GET DATA") s3_links = self._filter_related_links("GET DATA VIA DIRECT ACCESS") if in_region: # we are in us-west-2 if self.cloud_hosted and access in (None, "direct"): - # this is a cloud collection and we didn't specify the access type + # this is a cloud collection, and we didn't specify the access type # default to S3 links if len(s3_links) == 0 and len(https_links) > 0: # This is guessing the S3 links for some cloud collections that for @@ -310,14 +312,14 @@ def data_links( # we have the s3 links so we return those return s3_links else: - # Even though we are in us-west-2 the user wants the HTTPS links + # Even though we are in us-west-2, the user wants the HTTPS links # used in region they are S3 signed links from TEA # https://github.com/asfadmin/thin-egress-app return https_links else: # we are not in region if access == "direct": - # maybe the user wants to collect S3 links ans use them later + # maybe the user wants to collect S3 links and use them later # from the cloud return s3_links else: @@ -327,7 +329,7 @@ def data_links( def dataviz_links(self) -> List[str]: """ Returns: - Returns the data visualization links, usually the browse images. + The data visualization links, usually the browse images. """ links = self._filter_related_links("GET RELATED VISUALIZATION") return links From ec33f43fb19b5ad89c2d5d5774c5a7be2181393b Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 14:04:07 -0500 Subject: [PATCH 21/46] more docstring cleanup in search.py --- earthaccess/api.py | 2 +- earthaccess/search.py | 125 +++++++++++++++++++++++------------------- 2 files changed, 71 insertions(+), 56 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index ed858ac7..81e3c377 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -201,7 +201,7 @@ def open( Parameters: granules: a list of granule instances **or** list of URLs, e.g. - `s3://some-granule`, if a list of URLs is passed we need to specify the data + `s3://some-granule`, if a list of URLs is passed, we need to specify the data provider e.g. POCLOUD, NSIDC_CPRD etc. Returns: diff --git a/earthaccess/search.py b/earthaccess/search.py index 8392ca51..22a26923 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -15,7 +15,7 @@ class DataCollections(CollectionQuery): """ ???+ Info The DataCollection class queries against https://cmr.earthdata.nasa.gov/search/collections.umm_json, - the response has to be in umm_json in order to use the result classes. + the response has to be in umm_json to use the result classes. """ _fields = None @@ -37,13 +37,13 @@ def __init__(self, auth: Optional[Auth] = None, *args: Any, **kwargs: Any) -> No """Builds an instance of DataCollections to query CMR Parameters: - auth (Auth): An authenticated `Auth` instance, this is an optional parameter - for queries that need authentication e.g. restricted datasets + auth: An authenticated `Auth` instance. This is an optional parameter + for queries that need authentication, e.g. restricted datasets. """ super().__init__(*args, **kwargs) self.session = session() if auth is not None and auth.authenticated: - # To search we need the new bearer tokens from NASA Earthdata + # To search, we need the new bearer tokens from NASA Earthdata self.session = auth.get_session(bearer_token=True) self._debug = False @@ -54,16 +54,17 @@ def __init__(self, auth: Optional[Auth] = None, *args: Any, **kwargs: Any) -> No def hits(self) -> int: """Returns the number of hits the current query will return. This is done by making a lightweight query to CMR and inspecting the returned headers. - Restricted datasets will always return 0 results even if there are results. + Restricted datasets will always return zero results even if there are results. Returns: - number of results reported by CMR + The number of results reported by CMR. """ return super().hits() def concept_id(self, IDs: List[str]) -> Type[CollectionQuery]: - """Filter by concept ID (ex: C1299783579-LPDAAC_ECS or G1327299284-LPDAAC_ECS, S12345678-LPDAAC_ECS) + """Filter by concept ID. + For example: C1299783579-LPDAAC_ECS or G1327299284-LPDAAC_ECS, S12345678-LPDAAC_ECS Collections, granules, tools, services are uniquely identified with this ID. > @@ -73,24 +74,24 @@ def concept_id(self, IDs: List[str]) -> Type[CollectionQuery]: * If providing a service's concept ID here, it will uniquely identify those services. Parameters: - IDs (String, List): ID(s) to search by. Can be provided as a string or list of strings. + IDs: ID(s) to search by. Can be provided as a string or list of strings. """ super().concept_id(IDs) return self def keyword(self, text: str) -> Type[CollectionQuery]: - """Case insentive and wildcard (*) search through over two dozen fields in + """Case-insensitive and wildcard (*) search through over two dozen fields in a CMR collection record. This allows for searching against fields like summary and science keywords. Parameters: - text (String): text to search for + text: text to search for """ super().keyword(text) return self def doi(self, doi: str) -> Type[CollectionQuery]: - """Searh datasets by DOI + """Search datasets by DOI. ???+ Tip Not all datasets have an associated DOI, also DOI search works @@ -98,7 +99,7 @@ def doi(self, doi: str) -> Type[CollectionQuery]: We need to search by DOI, grab the concept_id and then get the data. Parameters: - doi (String): DOI of a datasets, e.g. 10.5067/AQR50-3Q7CS + doi: DOI of a datasets, e.g. 10.5067/AQR50-3Q7CS """ if not isinstance(doi, str): raise TypeError("doi must be of type str") @@ -137,13 +138,14 @@ def parameters(self, **kwargs: Any) -> Type[CollectionQuery]: return self def print_help(self, method: str = "fields") -> None: - """Prints the help information for a given method""" + """Prints the help information for a given method.""" print("Class components: \n") print([method for method in dir(self) if method.startswith("_") is False]) help(getattr(self, method)) def fields(self, fields: Optional[List[str]] = None) -> Type[CollectionQuery]: - """Masks the response by only showing the fields included in this list + """Masks the response by only showing the fields included in this list. + Parameters: fields (List): list of fields to show, these fields come from the UMM model e.g. Abstract, Title """ @@ -152,6 +154,7 @@ def fields(self, fields: Optional[List[str]] = None) -> Type[CollectionQuery]: def debug(self, debug: bool = True) -> Type[CollectionQuery]: """If True, prints the actual query to CMR, notice that the pagination happens in the headers. + Parameters: debug (Boolean): Print CMR query. """ @@ -166,7 +169,7 @@ def cloud_hosted(self, cloud_hosted: bool = True) -> Type[CollectionQuery]: Restricted collections will not be matched using this parameter Parameters: - cloud_hosted (Boolean): True to require granules only be online + cloud_hosted: True to require granules only be online """ if not isinstance(cloud_hosted, bool): raise TypeError("cloud_hosted must be of type bool") @@ -178,27 +181,31 @@ def cloud_hosted(self, cloud_hosted: bool = True) -> Type[CollectionQuery]: return self def provider(self, provider: str = "") -> Type[CollectionQuery]: - """Only match collections from a given provider, a NASA datacenter or DAAC can have 1 or more providers - i.e. PODAAC is a data center or DAAC, PODAAC is the default provider for on prem data, POCLOUD is - the PODAAC provider for their data in the cloud. + """Only match collections from a given provider. + + A NASA datacenter or DAAC can have one or more providers. + E.g., PODAAC is a data center or DAAC; PODAAC is the default provider for on-premises data, + POCLOUD is the PODAAC provider for their data in the cloud. Parameters: - provider (String): a provider code for any DAAC. e.g. POCLOUD, NSIDC_CPRD, etc. + provider: a provider code for any DAAC, e.g. POCLOUD, NSIDC_CPRD, etc. """ self.params["provider"] = provider return self def data_center(self, data_center_name: str = "") -> Type[CollectionQuery]: - """An alias name for `daac()` + """An alias name for `daac()`. + Parameters: - data_center_name (String): DAAC shortname, e.g. NSIDC, PODAAC, GESDISC + data_center_name: DAAC shortname, e.g. NSIDC, PODAAC, GESDISC """ return self.daac(data_center_name) def daac(self, daac_short_name: str = "") -> Type[CollectionQuery]: - """Only match collections for a given DAAC, by default the on-prem collections for the DAAC + """Only match collections for a given DAAC, by default the on-prem collections for the DAAC. + Parameters: - daac_short_name (String): a DAAC shortname, e.g. NSIDC, PODAAC, GESDISC + daac_short_name: a DAAC shortname, e.g. NSIDC, PODAAC, GESDISC """ if "cloud_hosted" in self.params: cloud_hosted = self.params["cloud_hosted"] @@ -218,7 +225,8 @@ def get(self, limit: int = 2000) -> list: they can be potentially millions of them. Parameters: - limit (Integer): The number of results to return + limit: The number of results to return + Returns: query results as a list of `DataCollection` instances. """ @@ -269,9 +277,9 @@ def temporal( to this method before calling execute(). Parameters: - date_from (String): earliest date of temporal range - date_to (string): latest date of temporal range - exclude_boundary (Boolean): whether or not to exclude the date_from/to in the matched range + date_from: earliest date of temporal range + date_to: latest date of temporal range + exclude_boundary: whether to exclude the date_from/to in the matched range """ DEFAULT = dt.datetime(1979, 1, 1) if date_from is not None: @@ -291,8 +299,7 @@ def temporal( class DataGranules(GranuleQuery): - """ - A Granule oriented client for NASA CMR + """A Granule oriented client for NASA CMR. API: https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html """ @@ -316,17 +323,17 @@ def __init__(self, auth: Any = None, *args: Any, **kwargs: Any) -> None: super().__init__(*args, **kwargs) self.session = session() if auth is not None and auth.authenticated: - # To search we need the new bearer tokens from NASA Earthdata + # To search, we need the new bearer tokens from NASA Earthdata self.session = auth.get_session(bearer_token=True) self._debug = False def hits(self) -> int: - """ - Returns the number of hits the current query will return. This is done by - making a lightweight query to CMR and inspecting the returned headers. + """Returns the number of hits the current query will return. + This is done by making a lightweight query to CMR and inspecting the returned headers. - :returns: number of results reported by CMR + Returns: + The number of results reported by CMR. """ url = self._build_url() @@ -353,6 +360,7 @@ def parameters(self, **kwargs: Any) -> Type[CollectionQuery]: temporal=("2015-01","2015-02"), point=(42.5, -101.25)) ``` + Returns: Query instance """ @@ -379,22 +387,24 @@ def provider(self, provider: str = "") -> Type[CollectionQuery]: the PODAAC provider for their data in the cloud. Parameters: - provider (String): a provider code for any DAAC. e.g. POCLOUD, NSIDC_CPRD, etc. + provider: a provider code for any DAAC. e.g. POCLOUD, NSIDC_CPRD, etc. """ self.params["provider"] = provider return self def data_center(self, data_center_name: str = "") -> Type[CollectionQuery]: - """An alias name for `daac()` + """An alias name for `daac()`. + Parameters: data_center_name (String): DAAC shortname, e.g. NSIDC, PODAAC, GESDISC """ return self.daac(data_center_name) def daac(self, daac_short_name: str = "") -> Type[CollectionQuery]: - """Only match collections for a given DAAC, by default the on-prem collections for the DAAC + """Only match collections for a given DAAC. Default to on-prem collections for the DAAC. + Parameters: - daac_short_name (String): a DAAC shortname, e.g. NSIDC, PODAAC, GESDISC + daac_short_name: a DAAC shortname, e.g. NSIDC, PODAAC, GESDISC """ if "cloud_hosted" in self.params: cloud_hosted = self.params["cloud_hosted"] @@ -446,7 +456,7 @@ def granule_name(self, granule_name: str) -> Type[CollectionQuery]: i.e. MODGRNLD.*.daily.* Parameters: - granule_name (String): granule name (accepts wildcards) + granule_name: granule name (accepts wildcards) """ if not isinstance(granule_name, str): raise TypeError("granule_name must be of type string") @@ -477,7 +487,7 @@ def instrument(self, instrument: str = "") -> Type[GranuleQuery]: """Filter by the instrument associated with the granule. Parameters: - instrument (str): name of the instrument + instrument: name of the instrument """ super().instrument(instrument) return self @@ -497,8 +507,8 @@ def cloud_cover( """Filter by the percentage of cloud cover present in the granule. Parameters: - min_cover (int): minimum percentage of cloud cover - max_cover (int): maximum percentage of cloud cover + min_cover: minimum percentage of cloud cover + max_cover: maximum percentage of cloud cover """ super().cloud_cover(min_cover, max_cover) return self @@ -527,10 +537,13 @@ def _is_cloud_hosted(self, granule: Any) -> bool: return False def short_name(self, short_name: str = "") -> Type[GranuleQuery]: - """ - Filter by short name (aka product or collection name). - :param short_name: name of collection - :returns: Query instance + """Filter by short name (aka product or collection name). + + Parameters: + short_name: name of a collection + + Returns: + Query instance """ super().short_name(short_name) return self @@ -545,7 +558,8 @@ def get(self, limit: int = 2000) -> list: they can be potentially millions of them. Parameters: - limit (Integer): The number of results to return + limit: The number of results to return + Returns: query results as a list of `DataCollection` instances. """ @@ -606,8 +620,9 @@ def get(self, limit: int = 2000) -> list: def debug(self, debug: bool = True) -> Type[GranuleQuery]: """If True, prints the actual query to CMR, notice that the pagination happens in the headers. + Parameters: - debug (Boolean): Print CMR query. + debug: Print CMR query. """ self._debug = True return self @@ -623,9 +638,9 @@ def temporal( ranges can be provided by successive calls to this method before calling execute(). Parameters: - date_from (Date, String): earliest date of temporal range - date_to (Date, String): latest date of temporal range - exclude_boundary (Boolean): whether or not to exclude the date_from/to in the matched range + date_from: earliest date of temporal range + date_to: latest date of temporal range + exclude_boundary: whether to exclude the date_from/to in the matched range """ DEFAULT = dt.datetime(1979, 1, 1) if date_from is not None: @@ -668,7 +683,7 @@ def polygon(self, coordinates: List[Tuple[str, str]]) -> Type[GranuleQuery]: collection filtering parameter such as short_name or entry_title. Parameters: - coordinates (List): list of (lon, lat) tuples + coordinates: list of (lon, lat) tuples """ super().polygon(coordinates) return self @@ -699,7 +714,7 @@ def line(self, coordinates: List[Tuple[str, str]]) -> Type[GranuleQuery]: with a collection filtering parameter such as short_name or entry_title. Parameters: - coordinates (List): a list of (lon, lat) tuples + coordinates: a list of (lon, lat) tuples """ super().line(coordinates) return self @@ -715,14 +730,14 @@ def downloadable(self, downloadable: bool = True) -> Type[GranuleQuery]: return self def doi(self, doi: str) -> Type[GranuleQuery]: - """Searh data granules by DOI + """Search data granules by DOI ???+ Tip Not all datasets have an associated DOI, internally if a DOI is found earthaccess will grab the concept_id for the query to CMR. Parameters: - doi (String): DOI of a datasets, e.g. 10.5067/AQR50-3Q7CS + doi: DOI of a datasets, e.g. 10.5067/AQR50-3Q7CS """ collection = DataCollections().doi(doi).get() if len(collection) > 0: From 5a6bd14e33a00505cba8d7b129d2ae2c5b5e0f40 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 14:14:00 -0500 Subject: [PATCH 22/46] more docstring cleanup in store.py --- earthaccess/store.py | 86 +++++++++++++++++++++++++------------------- 1 file changed, 49 insertions(+), 37 deletions(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index 645721ad..27ee8814 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -79,7 +79,7 @@ def make_instance( def _get_url_granule_mapping( granules: List[DataGranule], access: str ) -> Mapping[str, DataGranule]: - """Construct a mapping between file urls and granules""" + """Construct a mapping between file urls and granules.""" url_mapping = {} for granule in granules: for url in granule.data_links(access=access): @@ -88,15 +88,13 @@ def _get_url_granule_mapping( class Store(object): - """ - Store class to access granules on-prem or in the cloud. - """ + """Store class to access granules on-prem or in the cloud.""" def __init__(self, auth: Any, pre_authorize: bool = False) -> None: - """Store is the class to access data + """Store is the class to access data. Parameters: - auth (Auth): Required, Auth instance to download and access data. + auth: Auth instance to download and access data. """ if auth.authenticated is True: self.auth = auth @@ -169,9 +167,9 @@ def set_requests_session( This HTTPS session can be used to download granules if we want to use a direct, lower level API Parameters: - url (String): used to test the credentials and populate the class auth cookies - method (String): HTTP method to test. default: "GET" - bearer_token (Boolean): if true will be used for authenticated queries on CMR + url: used to test the credentials and populate the class auth cookies + method: HTTP method to test. default: "GET" + bearer_token: if true will be used for authenticated queries on CMR Returns: fsspec HTTPFileSystem (aiohttp client session) @@ -202,13 +200,13 @@ def get_s3fs_session( provider: Optional[str] = None, endpoint: Optional[str] = None, ) -> s3fs.S3FileSystem: - """ - Returns a s3fs instance for a given cloud provider / DAAC + """Returns a s3fs instance for a given cloud provider / DAAC. Parameters: daac: any of the DAACs e.g. NSIDC, PODAAC - provider: a data provider if we know them, e.g PODAAC -> POCLOUD + provider: a data provider if we know them, e.g. PODAAC -> POCLOUD endpoint: pass the URL for the credentials directly + Returns: a s3fs file instance """ @@ -284,7 +282,7 @@ def get_requests_session(self, bearer_token: bool = True) -> requests.Session: This HTTPS session can be used to download granules if we want to use a direct, lower level API Parameters: - bearer_token (Boolean): if true will be used for authenticated queries on CMR + bearer_token: if true will be used for authenticated queries on CMR Returns: requests Session @@ -300,7 +298,9 @@ def open( hosted on S3 or HTTPS by third party libraries like xarray. Parameters: - granules (List): a list of granules(DataGranule) instances or list of URLs, e.g. s3://some-granule + granules: a list of granules(DataGranule) instances or list of URLs, + e.g. s3://some-granule + Returns: a list of s3fs "file pointers" to s3 files. """ @@ -318,7 +318,8 @@ def _open( hosted on S3 or HTTPS by third party libraries like xarray. Parameters: - granules (List): a list of granules(DataGranule) instances or list of URLs, e.g. s3://some-granule + granules: a list of granules(DataGranule) instances or list of URLs, e.g. s3://some-granule + Returns: a list of s3fs "file pointers" to s3 files. """ @@ -442,17 +443,19 @@ def get( ) -> List[str]: """Retrieves data granules from a remote storage system. - * If we run this in the cloud we are moving data from S3 to a cloud compute instance (EC2, AWS Lambda) + * If we run this in the cloud, + we are moving data from S3 to a cloud compute instance (EC2, AWS Lambda). * If we run it outside the us-west-2 region and the data granules are part of a cloud-based - collection the method will not get any files. - * If we requests data granules from an on-prem collection the data will be effectively downloaded - to a local directory. + collection, the method will not get any files. + * If we request data granules from an on-prem collection, + the data will be effectively downloaded to a local directory. Parameters: granules: a list of granules(DataGranule) instances or a list of granule links (HTTP) local_path: local directory to store the remote data granules access: direct or on_prem, if set it will use it for the access method. - threads: parallel number of threads to use to download the files, adjust as necessary, default = 8 + threads: parallel number of threads to use to download the files; + adjust as necessary, default = 8 Returns: List of downloaded files @@ -479,11 +482,12 @@ def _get( ) -> List[str]: """Retrieves data granules from a remote storage system. - * If we run this in the cloud we are moving data from S3 to a cloud compute instance (EC2, AWS Lambda) + * If we run this in the cloud, + we are moving data from S3 to a cloud compute instance (EC2, AWS Lambda). * If we run it outside the us-west-2 region and the data granules are part of a cloud-based - collection the method will not get any files. - * If we requests data granules from an on-prem collection the data will be effectively downloaded - to a local directory. + collection, the method will not get any files. + * If we request data granules from an on-prem collection, + the data will be effectively downloaded to a local directory. Parameters: granules: a list of granules(DataGranule) instances or a list of granule links (HTTP) @@ -568,15 +572,19 @@ def _get_granules( downloaded_files.append(file_name) return downloaded_files else: - # if the data is cloud based bu we are not in AWS it will be downloaded as if it was on prem + # if the data are cloud-based, but we are not in AWS, + # it will be downloaded as if it was on prem return self._download_onprem_granules(data_links, local_path, threads) def _download_file(self, url: str, directory: str) -> str: - """ - download a single file from an on-prem location, a DAAC data center. - :param url: the granule url - :param directory: local directory - :returns: local filepath or an exception + """Download a single file from an on-prem location, a DAAC data center. + + Parameters: + url: the granule url + directory: local directory + + Returns: + a local filepath or an exception """ # If the get data link is an Opendap location if "opendap" in url and url.endswith(".html"): @@ -595,7 +603,7 @@ def _download_file(self, url: str, directory: str) -> str: r.raise_for_status() with open(local_path, "wb") as f: # This is to cap memory usage for large files at 1MB per write to disk per thread - # https://docs.python-requests.org/en/master/user/quickstart/#raw-response-content + # https://docs.python-requests.org/en/latest/user/quickstart/#raw-response-content shutil.copyfileobj(r.raw, f, length=1024 * 1024) except Exception: print(f"Error while downloading the file {local_filename}") @@ -608,12 +616,16 @@ def _download_file(self, url: str, directory: str) -> str: def _download_onprem_granules( self, urls: List[str], directory: str, threads: int = 8 ) -> List[Any]: - """ - downloads a list of URLS into the data directory. - :param urls: list of granule URLs from an on-prem collection - :param directory: local directory to store the files - :param threads: parallel number of threads to use to download the files, adjust as necessary, default = 8 - :returns: None + """Downloads a list of URLS into the data directory. + + Parameters: + urls: list of granule URLs from an on-prem collection + directory: local directory to store the downloaded files + threads: parallel number of threads to use to download the files; + adjust as necessary, default = 8 + + Returns: + a list of local filepaths to which the files were downloaded """ if urls is None: raise ValueError("The granules didn't provide a valid GET DATA link") From 8b540d6096bc8e41122f643a9d702febab8ff571 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 14:34:49 -0500 Subject: [PATCH 23/46] further docstring cleanup --- earthaccess/api.py | 6 +++--- earthaccess/auth.py | 28 ++++++++++++++-------------- earthaccess/search.py | 3 ++- earthaccess/store.py | 9 ++++++--- 4 files changed, 25 insertions(+), 21 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 81e3c377..c8140770 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -200,9 +200,9 @@ def open( hosted on S3 or HTTPS by third party libraries like xarray. Parameters: - granules: a list of granule instances **or** list of URLs, e.g. - `s3://some-granule`, if a list of URLs is passed, we need to specify the data - provider e.g. POCLOUD, NSIDC_CPRD etc. + granules: a list of granule instances **or** list of URLs, e.g. `s3://some-granule`. + If a list of URLs is passed, we need to specify the data provider. + provider: e.g. POCLOUD, NSIDC_CPRD etc. Returns: a list of s3fs "file pointers" to s3 files. diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 9a3b22cb..90e72c82 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -49,9 +49,7 @@ def rebuild_auth(self, prepared_request: Any, response: Any) -> None: class Auth(object): - """ - Authentication class for operations that require Earthdata login (EDL) - """ + """Authentication class for operations that require Earthdata login (EDL).""" def __init__(self) -> None: # Maybe all these predefined URLs should be in a constants.py file @@ -63,18 +61,18 @@ def __init__(self) -> None: self.EDL_REVOKE_TOKEN = "https://urs.earthdata.nasa.gov/api/users/revoke_token" def login(self, strategy: str = "netrc", persist: bool = False) -> Any: - """Authenticate with Earthdata login + """Authenticate with Earthdata login. Parameters: - - strategy (String): authentication method. + strategy: authentication method. "interactive": enter username and password. "netrc": (default) retrieve username and password from ~/.netrc. "environment": retrieve username and password from $EARTHDATA_USERNAME and $EARTHDATA_PASSWORD. - persist (Boolean): will persist credentials in a .netrc file + persist: will persist credentials in a .netrc file + Returns: an instance of Auth. """ @@ -90,8 +88,9 @@ def login(self, strategy: str = "netrc", persist: bool = False) -> Any: return self def refresh_tokens(self) -> bool: - """Refresh CMR tokens - Tokens are used to do authenticated queries on CMR for restricted and early access datastes + """Refresh CMR tokens. + + Tokens are used to do authenticated queries on CMR for restricted and early access datasets. This method renews the tokens to make sure we can query the collections allowed to our EDL user. """ if len(self.tokens) == 0: @@ -146,7 +145,7 @@ def get_s3_credentials( provider: Optional[str] = None, endpoint: Optional[str] = None, ) -> Dict[str, str]: - """Gets AWS S3 credentials for a given NASA cloud provider, the + """Gets AWS S3 credentials for a given NASA cloud provider. The easier way is to use the DAAC short name. provider is optional if we know it. Parameters: @@ -154,7 +153,7 @@ def get_s3_credentials( daac: the name of a NASA DAAC, i.e. NSIDC or PODAAC endpoint: getting the credentials directly from the S3Credentials URL - Rreturns: + Returns: A Python dictionary with the temporary AWS S3 credentials """ @@ -199,14 +198,15 @@ def get_s3_credentials( print(f"Credentials for the cloud provider {daac} are not available") return {} else: - print("We need to auhtenticate with EDL first") + print("We need to authenticate with EDL first") return {} def get_session(self, bearer_token: bool = True) -> requests.Session: - """Returns a new request session instance + """Returns a new request session instance. Parameters: - bearer_token (Boolean): boolean, include bearer token + bearer_token: boolean, include bearer token + Returns: class Session instance with Auth and bearer token headers """ diff --git a/earthaccess/search.py b/earthaccess/search.py index 22a26923..15f0b49f 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -468,8 +468,9 @@ def granule_name(self, granule_name: str) -> Type[CollectionQuery]: def online_only(self, online_only: bool = True) -> Type[GranuleQuery]: """Only match granules that are listed online and not available for download. The opposite of this method is downloadable(). + Parameters: - online_only (Boolean): True to require granules only be online + online_only: True to require granules only be online """ super().online_only(online_only) return self diff --git a/earthaccess/store.py b/earthaccess/store.py index 27ee8814..1a615631 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -270,7 +270,7 @@ def get_fsspec_session(self) -> fsspec.AbstractFileSystem: token = self.auth.token["access_token"] client_kwargs = { "headers": {"Authorization": f"Bearer {token}"}, - # This is important! if we trust the env end send a bearer token + # This is important! If we trust the env and send a bearer token, # auth will fail! "trust_env": False, } @@ -282,7 +282,7 @@ def get_requests_session(self, bearer_token: bool = True) -> requests.Session: This HTTPS session can be used to download granules if we want to use a direct, lower level API Parameters: - bearer_token: if true will be used for authenticated queries on CMR + bearer_token: if true, will be used for authenticated queries on CMR Returns: requests Session @@ -300,6 +300,7 @@ def open( Parameters: granules: a list of granules(DataGranule) instances or list of URLs, e.g. s3://some-granule + provider: an option Returns: a list of s3fs "file pointers" to s3 files. @@ -318,7 +319,9 @@ def _open( hosted on S3 or HTTPS by third party libraries like xarray. Parameters: - granules: a list of granules(DataGranule) instances or list of URLs, e.g. s3://some-granule + granules: a list of granules(DataGranule) instances or list of URLs, + e.g. s3://some-granule + provider: an option Returns: a list of s3fs "file pointers" to s3 files. From 6ec1081413ffd27ab5a2593ffe991608ddd3a289 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 14:36:01 -0500 Subject: [PATCH 24/46] typo --- earthaccess/auth.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 90e72c82..4d9eb921 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -228,13 +228,13 @@ def get_user_profile(self) -> Dict[str, Any]: else: return {} - def _interactive(self, presist_credentials: bool = False) -> bool: + def _interactive(self, persist_credentials: bool = False) -> bool: username = input("Enter your Earthdata Login username: ") password = getpass.getpass(prompt="Enter your Earthdata password: ") authenticated = self._get_credentials(username, password) if authenticated: logger.debug("Using user provided credentials for EDL") - if presist_credentials: + if persist_credentials: print("Persisting credentials to .netrc") self._persist_user_credentials(username, password) return authenticated From f35c4ea9d3aa166be42f35ede0d2cc839fc41788 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 14:38:11 -0500 Subject: [PATCH 25/46] add indentation --- earthaccess/results.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/earthaccess/results.py b/earthaccess/results.py index 5569f670..ecfbc606 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -111,7 +111,7 @@ def concept_id(self) -> str: """ Returns: A collection's `concept_id`. - This id is the most relevant search field on granule queries. + This id is the most relevant search field on granule queries. """ return self["meta"]["concept-id"] @@ -168,7 +168,7 @@ def s3_bucket(self) -> Dict[str, Any]: """ Returns: The S3 bucket information if the collection has it. - (**cloud hosted collections only**) + (**cloud hosted collections only**) """ if "DirectDistributionInformation" in self["umm"]: return self["umm"]["DirectDistributionInformation"] From 2e57d2fbc8749e46b72d32c0e556288cacf52abf Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 14:44:55 -0500 Subject: [PATCH 26/46] further docstring cleanup in results.py --- earthaccess/results.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/earthaccess/results.py b/earthaccess/results.py index ecfbc606..4861f781 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -44,9 +44,7 @@ def _filter_fields_(self, fields: List[str]) -> Dict[str, Any]: return basic_dict def _filter_related_links(self, filter: str) -> List[str]: - """ - Filter RelatedUrls from the UMM fields on CMR - """ + """Filter RelatedUrls from the UMM fields on CMR.""" matched_links: List = [] if "RelatedUrls" in self["umm"]: for link in self["umm"]["RelatedUrls"]: @@ -101,7 +99,7 @@ def get_umm(self, umm_field: str) -> Union[str, Dict[str, Any]]: umm_field: Valid UMM item, i.e. `TemporalExtent` Returns: - Returns the value of a given field inside the UMM (Unified Metadata Model) + The value of a given field inside the UMM (Unified Metadata Model). """ if umm_field in self["umm"]: return self["umm"][umm_field] @@ -290,12 +288,12 @@ def data_links( Parameters: access: direct or external. - direct means in-region access for cloud-hosted collections. + direct means in-region access for cloud-hosted collections. in_region: True if we are running in us-west-2. - It is meant for the store class. + It is meant for the store class. Returns: - The data link for the requested access type. + The data links for the requested access type. """ https_links = self._filter_related_links("GET DATA") s3_links = self._filter_related_links("GET DATA VIA DIRECT ACCESS") From 8b6e58b1b89b02d37b67d60d044cb1a4bc966eab Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 15:33:59 -0500 Subject: [PATCH 27/46] further docstring cleanup in api.py and auth.py --- earthaccess/api.py | 35 ++++++++++++++++++----------------- earthaccess/auth.py | 17 +++++++---------- 2 files changed, 25 insertions(+), 27 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index c8140770..9177b37c 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -14,7 +14,7 @@ def _normalize_location(location: Optional[str]) -> Optional[str]: - """Handle user-provided `daac` and `provider` values + """Handle user-provided `daac` and `provider` values. These values must have a capital letter as the first character followed by capital letters, numbers, or an underscore. Here we @@ -40,7 +40,7 @@ def search_datasets( kwargs (Dict): arguments to CMR: - * **keyword**: case insensitive and support wild cards ? and *, + * **keyword**: case-insensitive and support wildcards ? and *, * **short_name**: e.g. ATL08 * **doi**: DOI for a dataset * **daac**: e.g. NSIDC or PODAAC @@ -125,7 +125,7 @@ def search_data( def login(strategy: str = "all", persist: bool = False) -> Auth: - """Authenticate with Earthdata login (https://urs.earthdata.nasa.gov/) + """Authenticate with Earthdata login (https://urs.earthdata.nasa.gov/). Parameters: strategy: @@ -202,7 +202,7 @@ def open( Parameters: granules: a list of granule instances **or** list of URLs, e.g. `s3://some-granule`. If a list of URLs is passed, we need to specify the data provider. - provider: e.g. POCLOUD, NSIDC_CPRD etc. + provider: e.g. POCLOUD, NSIDC_CPRD, etc. Returns: a list of s3fs "file pointers" to s3 files. @@ -217,14 +217,14 @@ def get_s3_credentials( provider: Optional[str] = None, results: Optional[List[earthaccess.results.DataGranule]] = None, ) -> Dict[str, Any]: - """Returns temporary (1 hour) credentials for direct access to NASA S3 buckets, we can - use the daac name, the provider or a list of results from earthaccess.search_data() - if we use results earthaccess will use the metadata on the response to get the credentials, - this is useful for missions that do not use the same endpoint as their DAACs e.g. SWOT + """Returns temporary (1 hour) credentials for direct access to NASA S3 buckets. We can + use the daac name, the provider, or a list of results from earthaccess.search_data(). + If we use results, earthaccess will use the metadata on the response to get the credentials, + which is useful for missions that do not use the same endpoint as their DAACs, e.g. SWOT. Parameters: - daac: a DAAC short_name like NSIDC or PODAAC etc - provider: if we know the provider for the DAAC e.g. POCLOUD, LPCLOUD etc. + daac: a DAAC short_name like NSIDC or PODAAC, etc. + provider: if we know the provider for the DAAC, e.g. POCLOUD, LPCLOUD etc. results: List of results from search_data() Returns: @@ -239,7 +239,7 @@ def get_s3_credentials( def collection_query() -> Type[CollectionQuery]: - """Returns a query builder instance for NASA collections (datasets) + """Returns a query builder instance for NASA collections (datasets). Returns: a query builder instance for data collections. @@ -265,7 +265,7 @@ def granule_query() -> Type[GranuleQuery]: def get_fsspec_https_session() -> AbstractFileSystem: - """Returns a fsspec session that can be used to access datafiles across many different DAACs + """Returns a fsspec session that can be used to access datafiles across many different DAACs. Returns: an fsspec instance able to access data across DAACs @@ -286,8 +286,8 @@ def get_fsspec_https_session() -> AbstractFileSystem: def get_requests_https_session() -> requests.Session: - """Returns a requests Session instance with an authorized bearer token - this is useful to make requests to restricted URLs like data granules or services that + """Returns a requests Session instance with an authorized bearer token. + This is useful to make requests to restricted URLs like data granules or services that require authentication with NASA EDL. Returns: @@ -313,11 +313,12 @@ def get_s3fs_session( provider: Optional[str] = None, results: Optional[earthaccess.results.DataGranule] = None, ) -> s3fs.S3FileSystem: - """Returns a fsspec s3fs file session for direct access when we are in us-west-2 + """Returns a fsspec s3fs file session for direct access when we are in us-west-2. Parameters: daac: Any DAAC short name e.g. NSIDC, GES_DISC - provider: Each DAAC can have a cloud provider, if the DAAC is specified, there is no need to use provider + provider: Each DAAC can have a cloud provider. + If the DAAC is specified, there is no need to use provider. results: A list of results from search_data(), earthaccess will use the metadata form CMR to obtain the S3 Endpoint Returns: @@ -335,7 +336,7 @@ def get_s3fs_session( def get_edl_token() -> str: - """Returns the current token used for EDL + """Returns the current token used for EDL. Returns: EDL token diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 4d9eb921..9b94e8d5 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -64,13 +64,12 @@ def login(self, strategy: str = "netrc", persist: bool = False) -> Any: """Authenticate with Earthdata login. Parameters: - strategy: authentication method. + strategy: + authentication method. - "interactive": enter username and password. - - "netrc": (default) retrieve username and password from ~/.netrc. - - "environment": retrieve username and password from $EARTHDATA_USERNAME and $EARTHDATA_PASSWORD. + * **"interactive"**: enter username and password. + * **"netrc"**: (default) retrieve username and password from ~/.netrc. + * **"environment"**: retrieve username and password from $EARTHDATA_USERNAME and $EARTHDATA_PASSWORD. persist: will persist credentials in a .netrc file Returns: @@ -89,7 +88,6 @@ def login(self, strategy: str = "netrc", persist: bool = False) -> Any: def refresh_tokens(self) -> bool: """Refresh CMR tokens. - Tokens are used to do authenticated queries on CMR for restricted and early access datasets. This method renews the tokens to make sure we can query the collections allowed to our EDL user. """ @@ -149,13 +147,12 @@ def get_s3_credentials( easier way is to use the DAAC short name. provider is optional if we know it. Parameters: - provider: A valid cloud provider, each DAAC has a provider code for their cloud distributions daac: the name of a NASA DAAC, i.e. NSIDC or PODAAC + provider: A valid cloud provider. Each DAAC has a provider code for their cloud distributions. endpoint: getting the credentials directly from the S3Credentials URL Returns: A Python dictionary with the temporary AWS S3 credentials - """ if self.authenticated: session = SessionWithHeaderRedirection(self.username, self.password) @@ -205,7 +202,7 @@ def get_session(self, bearer_token: bool = True) -> requests.Session: """Returns a new request session instance. Parameters: - bearer_token: boolean, include bearer token + bearer_token: whether to include bearer token Returns: class Session instance with Auth and bearer token headers From 9aea057578f6051e2f266ea50e3b7691a3a9e4ad Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 15:55:04 -0500 Subject: [PATCH 28/46] further docstring cleanup --- earthaccess/api.py | 12 +++++++----- earthaccess/auth.py | 23 ++++++++++++----------- earthaccess/daac.py | 2 +- earthaccess/kerchunk.py | 12 ++++++------ earthaccess/results.py | 4 ++-- earthaccess/search.py | 14 ++++++++------ earthaccess/store.py | 6 +++--- tests/integration/test_kerchunk.py | 20 ++++++++++---------- 8 files changed, 49 insertions(+), 44 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 9177b37c..9a6422a8 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -129,7 +129,7 @@ def login(strategy: str = "all", persist: bool = False) -> Auth: Parameters: strategy: - authentication method. + An authentication method. * **"all"**: (default) try all methods until one works * **"interactive"**: enter username and password. @@ -138,7 +138,7 @@ def login(strategy: str = "all", persist: bool = False) -> Auth: persist: will persist credentials in a .netrc file Returns: - an instance of Auth. + An instance of Auth. """ if strategy == "all": for strategy in ["environment", "netrc", "interactive"]: @@ -166,8 +166,9 @@ def download( ) -> List[str]: """Retrieves data granules from a remote storage system. - * If we run this in the cloud, we will be using S3 to move data to `local_path` - * If we run it outside AWS (us-west-2 region) and the dataset is cloud hostes we'll use HTTP links + * If we run this in the cloud, we will be using S3 to move data to `local_path`. + * If we run it outside AWS (us-west-2 region) and the dataset is cloud hosted, + we'll use HTTP links. Parameters: granules: a granule, list of granules, a granule link (HTTP), or a list of granule links (HTTP) @@ -319,7 +320,8 @@ def get_s3fs_session( daac: Any DAAC short name e.g. NSIDC, GES_DISC provider: Each DAAC can have a cloud provider. If the DAAC is specified, there is no need to use provider. - results: A list of results from search_data(), earthaccess will use the metadata form CMR to obtain the S3 Endpoint + results: A list of results from search_data(). + `earthaccess` will use the metadata from CMR to obtain the S3 Endpoint. Returns: an authenticated s3fs session valid for 1 hour diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 9b94e8d5..004efa7c 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -65,15 +65,16 @@ def login(self, strategy: str = "netrc", persist: bool = False) -> Any: Parameters: strategy: - authentication method. + The authentication method. - * **"interactive"**: enter username and password. - * **"netrc"**: (default) retrieve username and password from ~/.netrc. - * **"environment"**: retrieve username and password from $EARTHDATA_USERNAME and $EARTHDATA_PASSWORD. - persist: will persist credentials in a .netrc file + * **"interactive"**: Enter a username and password. + * **"netrc"**: (default) Retrieve a username and password from ~/.netrc. + * **"environment"**: + Retrieve a username and password from $EARTHDATA_USERNAME and $EARTHDATA_PASSWORD. + persist: Will persist credentials in a `.netrc` file. Returns: - an instance of Auth. + An instance of Auth. """ if self.authenticated: logger.debug("We are already authenticated with NASA EDL") @@ -143,16 +144,16 @@ def get_s3_credentials( provider: Optional[str] = None, endpoint: Optional[str] = None, ) -> Dict[str, str]: - """Gets AWS S3 credentials for a given NASA cloud provider. The - easier way is to use the DAAC short name. provider is optional if we know it. + """Gets AWS S3 credentials for a given NASA cloud provider. + The easier way is to use the DAAC short name; provider is optional if we know it. Parameters: - daac: the name of a NASA DAAC, i.e. NSIDC or PODAAC + daac: The name of a NASA DAAC, e.g. NSIDC or PODAAC. provider: A valid cloud provider. Each DAAC has a provider code for their cloud distributions. - endpoint: getting the credentials directly from the S3Credentials URL + endpoint: Getting the credentials directly from the S3Credentials URL. Returns: - A Python dictionary with the temporary AWS S3 credentials + A Python dictionary with the temporary AWS S3 credentials. """ if self.authenticated: session = SessionWithHeaderRedirection(self.username, self.password) diff --git a/earthaccess/daac.py b/earthaccess/daac.py index a15972c1..4f0e99f3 100644 --- a/earthaccess/daac.py +++ b/earthaccess/daac.py @@ -128,7 +128,7 @@ def find_provider( if len(daac["cloud-providers"]) > 0: return daac["cloud-providers"][0] else: - # We found the DAAC but it does not have cloud data + # We found the DAAC, but it does not have cloud data return daac["on-prem-providers"][0] else: # return on prem provider code diff --git a/earthaccess/kerchunk.py b/earthaccess/kerchunk.py index eb3f4cae..02533a0e 100644 --- a/earthaccess/kerchunk.py +++ b/earthaccess/kerchunk.py @@ -7,14 +7,14 @@ def _get_chunk_metadata( - granuale: earthaccess.results.DataGranule, + granule: earthaccess.results.DataGranule, fs: fsspec.AbstractFileSystem | s3fs.S3FileSystem, ) -> list[dict]: from kerchunk.hdf import SingleHdf5ToZarr metadata = [] access = "direct" if isinstance(fs, s3fs.S3FileSystem) else "indirect" - for url in granuale.data_links(access=access): + for url in granule.data_links(access=access): with fs.open(url) as inf: h5chunks = SingleHdf5ToZarr(inf, url) m = h5chunks.translate() @@ -23,7 +23,7 @@ def _get_chunk_metadata( def consolidate_metadata( - granuales: list[earthaccess.results.DataGranule], + granules: list[earthaccess.results.DataGranule], kerchunk_options: dict | None = None, access: str = "direct", outfile: str | None = None, @@ -39,13 +39,13 @@ def consolidate_metadata( ) from e if access == "direct": - fs = earthaccess.get_s3fs_session(provider=granuales[0]["meta"]["provider-id"]) + fs = earthaccess.get_s3fs_session(provider=granules[0]["meta"]["provider-id"]) else: fs = earthaccess.get_fsspec_https_session() - # Get metadata for each granuale + # Get metadata for each granule get_chunk_metadata = dask.delayed(_get_chunk_metadata) - chunks = dask.compute(*[get_chunk_metadata(g, fs) for g in granuales]) + chunks = dask.compute(*[get_chunk_metadata(g, fs) for g in granules]) chunks = sum(chunks, start=[]) # Get combined metadata object diff --git a/earthaccess/results.py b/earthaccess/results.py index 4861f781..3faaf8fc 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -284,11 +284,11 @@ def _derive_s3_link(self, links: List[str]) -> List[str]: def data_links( self, access: Optional[str] = None, in_region: bool = False ) -> List[str]: - """Returns the data links form a granule + """Returns the data links from a granule. Parameters: access: direct or external. - direct means in-region access for cloud-hosted collections. + Direct means in-region access for cloud-hosted collections. in_region: True if we are running in us-west-2. It is meant for the store class. diff --git a/earthaccess/search.py b/earthaccess/search.py index 15f0b49f..e8074368 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -273,7 +273,7 @@ def temporal( self, date_from: str, date_to: str, exclude_boundary: bool = False ) -> Type[CollectionQuery]: """Filter by an open or closed date range. Dates can be provided as datetime objects - or ISO 8601 formatted strings. Multiple ranges can be provided by successive calls. + or ISO 8601 formatted strings. Multiple ranges can be provided by successive calls to this method before calling execute(). Parameters: @@ -382,12 +382,14 @@ def parameters(self, **kwargs: Any) -> Type[CollectionQuery]: return self def provider(self, provider: str = "") -> Type[CollectionQuery]: - """Only match collections from a given provider, a NASA datacenter or DAAC can have 1 or more providers - i.e. PODAAC is a data center or DAAC, PODAAC is the default provider for on prem data, POCLOUD is + """Only match collections from a given provider. + A NASA datacenter or DAAC can have one or more providers. + For example, PODAAC is a data center or DAAC, + PODAAC is the default provider for on-prem data, and POCLOUD is the PODAAC provider for their data in the cloud. Parameters: - provider: a provider code for any DAAC. e.g. POCLOUD, NSIDC_CPRD, etc. + provider: a provider code for any DAAC, e.g. POCLOUD, NSIDC_CPRD, etc. """ self.params["provider"] = provider return self @@ -452,8 +454,8 @@ def granule_name(self, granule_name: str) -> Type[CollectionQuery]: queries using the readable_granule_name metadata field. ???+ Tip - We can use wirldcards on a granule name to further refine our search - i.e. MODGRNLD.*.daily.* + We can use wildcards on a granule name to further refine our search, + e.g. MODGRNLD.*.daily.* Parameters: granule_name: granule name (accepts wildcards) diff --git a/earthaccess/store.py b/earthaccess/store.py index 1a615631..e20ef10e 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -106,7 +106,7 @@ def __init__(self, auth: Any, pre_authorize: bool = False) -> None: self._requests_cookies: Dict[str, Any] = {} self.set_requests_session(oauth_profile) if pre_authorize: - # collect cookies from other daacs + # collect cookies from other DAACs for url in DAAC_TEST_URLS: self.set_requests_session(url) @@ -348,7 +348,7 @@ def _open_granules( if granules[0].cloud_hosted: access = "direct" provider = granules[0]["meta"]["provider-id"] - # if the data has its own S3 credentials endpoint we'll use it + # if the data has its own S3 credentials endpoint, we will use it endpoint = self._own_s3_credentials(granules[0]["umm"]["RelatedUrls"]) if endpoint is not None: print(f"using endpoint: {endpoint}") @@ -473,7 +473,7 @@ def get( files = self._get(granules, local_path, provider, threads) return files else: - raise ValueError("List of URLs or DataGranule isntances expected") + raise ValueError("List of URLs or DataGranule instances expected") @singledispatchmethod def _get( diff --git a/tests/integration/test_kerchunk.py b/tests/integration/test_kerchunk.py index 39c95e99..58f93077 100644 --- a/tests/integration/test_kerchunk.py +++ b/tests/integration/test_kerchunk.py @@ -20,21 +20,21 @@ @pytest.fixture(scope="module") -def granuales(): - granuales = earthaccess.search_data( +def granules(): + granules = earthaccess.search_data( count=2, short_name="SEA_SURFACE_HEIGHT_ALT_GRIDS_L4_2SATS_5DAY_6THDEG_V_JPL2205", cloud_hosted=True, ) - return granuales + return granules @pytest.mark.parametrize("protocol", ["", "file://"]) -def test_consolidate_metadata_outfile(tmp_path, granuales, protocol): +def test_consolidate_metadata_outfile(tmp_path, granules, protocol): outfile = f"{protocol}{tmp_path / 'metadata.json'}" assert not os.path.exists(outfile) result = earthaccess.consolidate_metadata( - granuales, + granules, outfile=outfile, access="indirect", kerchunk_options={"concat_dims": "Time"}, @@ -43,9 +43,9 @@ def test_consolidate_metadata_outfile(tmp_path, granuales, protocol): assert result == outfile -def test_consolidate_metadata_memory(tmp_path, granuales): +def test_consolidate_metadata_memory(tmp_path, granules): result = earthaccess.consolidate_metadata( - granuales, + granules, access="indirect", kerchunk_options={"concat_dims": "Time"}, ) @@ -54,10 +54,10 @@ def test_consolidate_metadata_memory(tmp_path, granuales): @pytest.mark.parametrize("output", ["file", "memory"]) -def test_consolidate_metadata(tmp_path, granuales, output): +def test_consolidate_metadata(tmp_path, granules, output): xr = pytest.importorskip("xarray") # Open directly with `earthaccess.open` - expected = xr.open_mfdataset(earthaccess.open(granuales)) + expected = xr.open_mfdataset(earthaccess.open(granules)) # Open with kerchunk consolidated metadata file if output == "file": @@ -65,7 +65,7 @@ def test_consolidate_metadata(tmp_path, granuales, output): else: kwargs = {} metadata = earthaccess.consolidate_metadata( - granuales, access="indirect", kerchunk_options={"concat_dims": "Time"}, **kwargs + granules, access="indirect", kerchunk_options={"concat_dims": "Time"}, **kwargs ) fs = earthaccess.get_fsspec_https_session() From ebb15a16cb66d4503465ef6e2f3e83cadcf88a80 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 7 Feb 2024 16:23:33 -0500 Subject: [PATCH 29/46] further docstring cleanup, grammar --- earthaccess/api.py | 17 ++++++++-------- earthaccess/results.py | 8 ++++---- earthaccess/search.py | 13 ++++++------ earthaccess/store.py | 46 ++++++++++++++++++++++-------------------- 4 files changed, 43 insertions(+), 41 deletions(-) diff --git a/earthaccess/api.py b/earthaccess/api.py index 9a6422a8..a7d35fb0 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -40,7 +40,7 @@ def search_datasets( kwargs (Dict): arguments to CMR: - * **keyword**: case-insensitive and support wildcards ? and *, + * **keyword**: case-insensitive and supports wildcards ? and * * **short_name**: e.g. ATL08 * **doi**: DOI for a dataset * **daac**: e.g. NSIDC or PODAAC @@ -51,7 +51,7 @@ def search_datasets( `(lower_left_lon, lower_left_lat, upper_right_lon, upper_right_lat)` Returns: - a list of DataCollection results that can be used to get information about a + A list of DataCollection results that can be used to get information about a dataset, e.g. concept_id, doi, etc. Examples: @@ -90,7 +90,7 @@ def search_data( kwargs (Dict): arguments to CMR: - * **short_name**: dataset short name e.g. ATL08 + * **short_name**: dataset short name, e.g. ATL08 * **version**: dataset version * **doi**: DOI for a dataset * **daac**: e.g. NSIDC or PODAAC @@ -173,7 +173,7 @@ def download( Parameters: granules: a granule, list of granules, a granule link (HTTP), or a list of granule links (HTTP) local_path: local directory to store the remote data granules - provider: if we download a list of URLs we need to specify the provider. + provider: if we download a list of URLs, we need to specify the provider. threads: parallel number of threads to use to download the files, adjust as necessary, default = 8 Returns: @@ -269,7 +269,7 @@ def get_fsspec_https_session() -> AbstractFileSystem: """Returns a fsspec session that can be used to access datafiles across many different DAACs. Returns: - an fsspec instance able to access data across DAACs + An fsspec instance able to access data across DAACs. Examples: ```python @@ -280,7 +280,6 @@ def get_fsspec_https_session() -> AbstractFileSystem: with fs.open(DAAC_GRANULE) as f: f.read(10) ``` - """ session = earthaccess.__store__.get_fsspec_session() return session @@ -288,11 +287,11 @@ def get_fsspec_https_session() -> AbstractFileSystem: def get_requests_https_session() -> requests.Session: """Returns a requests Session instance with an authorized bearer token. - This is useful to make requests to restricted URLs like data granules or services that + This is useful for making requests to restricted URLs, such as data granules or services that require authentication with NASA EDL. Returns: - an authenticated requests Session instance. + An authenticated requests Session instance. Examples: ```python @@ -324,7 +323,7 @@ def get_s3fs_session( `earthaccess` will use the metadata from CMR to obtain the S3 Endpoint. Returns: - an authenticated s3fs session valid for 1 hour + An authenticated s3fs session valid for 1 hour. """ daac = _normalize_location(daac) provider = _normalize_location(provider) diff --git a/earthaccess/results.py b/earthaccess/results.py index 3faaf8fc..6d91ca7e 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -310,12 +310,12 @@ def data_links( # we have the s3 links so we return those return s3_links else: - # Even though we are in us-west-2, the user wants the HTTPS links - # used in region they are S3 signed links from TEA - # https://github.com/asfadmin/thin-egress-app + # Even though we are in us-west-2, the user wants the HTTPS links used in-region. + # They are S3 signed links from TEA. + # return https_links else: - # we are not in region + # we are not in-region if access == "direct": # maybe the user wants to collect S3 links and use them later # from the cloud diff --git a/earthaccess/search.py b/earthaccess/search.py index e8074368..aa410985 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -428,15 +428,16 @@ def orbit_number(self, orbit1: int, orbit2: int) -> Type[GranuleQuery]: return self def cloud_hosted(self, cloud_hosted: bool = True) -> Type[CollectionQuery]: - """Only match granules that are hosted in the cloud. This is valid for public - collections and if we are using the short_name parameter. Concept-Id is unambiguous. + """Only match granules that are hosted in the cloud. + This is valid for public collections and when using the short_name parameter. + Concept-Id is unambiguous. ???+ Tip - Cloud hosted collections can be public or restricted. - Restricted collections will not be matched using this parameter + Cloud-hosted collections can be public or restricted. + Restricted collections will not be matched using this parameter. Parameters: - cloud_hosted (Boolean): True to require granules only be online + cloud_hosted: True to require granules only be online """ if not isinstance(cloud_hosted, bool): raise TypeError("cloud_hosted must be of type bool") @@ -455,7 +456,7 @@ def granule_name(self, granule_name: str) -> Type[CollectionQuery]: ???+ Tip We can use wildcards on a granule name to further refine our search, - e.g. MODGRNLD.*.daily.* + e.g. `MODGRNLD.*.daily.*`. Parameters: granule_name: granule name (accepts wildcards) diff --git a/earthaccess/store.py b/earthaccess/store.py index e20ef10e..4981fe50 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -155,7 +155,7 @@ def _running_in_us_west_2(self) -> bool: return False if resp.status_code == 200 and b"us-west-2" == resp.content: - # On AWS in region us-west-2 + # On AWS, in region us-west-2 return True return False @@ -163,13 +163,14 @@ def set_requests_session( self, url: str, method: str = "get", bearer_token: bool = False ) -> None: """Sets up a `requests` session with bearer tokens that are used by CMR. - Mainly used to get the authentication cookies from different DAACs and URS - This HTTPS session can be used to download granules if we want to use a direct, lower level API + Mainly used to get the authentication cookies from different DAACs and URS. + This HTTPS session can be used to download granules if we want to use a direct, + lower level API. Parameters: url: used to test the credentials and populate the class auth cookies - method: HTTP method to test. default: "GET" - bearer_token: if true will be used for authenticated queries on CMR + method: HTTP method to test, default: "GET" + bearer_token: if true, will be used for authenticated queries on CMR Returns: fsspec HTTPFileSystem (aiohttp client session) @@ -203,7 +204,7 @@ def get_s3fs_session( """Returns a s3fs instance for a given cloud provider / DAAC. Parameters: - daac: any of the DAACs e.g. NSIDC, PODAAC + daac: any of the DAACs, e.g. NSIDC, PODAAC provider: a data provider if we know them, e.g. PODAAC -> POCLOUD endpoint: pass the URL for the credentials directly @@ -262,7 +263,8 @@ def get_s3fs_session( @lru_cache def get_fsspec_session(self) -> fsspec.AbstractFileSystem: """Returns a fsspec HTTPS session with bearer tokens that are used by CMR. - This HTTPS session can be used to download granules if we want to use a direct, lower level API + This HTTPS session can be used to download granules if we want to use a direct, + lower level API. Returns: fsspec HTTPFileSystem (aiohttp client session) @@ -279,7 +281,8 @@ def get_fsspec_session(self) -> fsspec.AbstractFileSystem: def get_requests_session(self, bearer_token: bool = True) -> requests.Session: """Returns a requests HTTPS session with bearer tokens that are used by CMR. - This HTTPS session can be used to download granules if we want to use a direct, lower level API + This HTTPS session can be used to download granules if we want to use a direct, + lower level API. Parameters: bearer_token: if true, will be used for authenticated queries on CMR @@ -303,7 +306,7 @@ def open( provider: an option Returns: - a list of s3fs "file pointers" to s3 files. + A list of s3fs "file pointers" to s3 files. """ if len(granules): return self._open(granules, provider) @@ -324,7 +327,7 @@ def _open( provider: an option Returns: - a list of s3fs "file pointers" to s3 files. + A list of s3fs "file pointers" to s3 files. """ raise NotImplementedError("granules should be a list of DataGranule or URLs") @@ -454,11 +457,10 @@ def get( the data will be effectively downloaded to a local directory. Parameters: - granules: a list of granules(DataGranule) instances or a list of granule links (HTTP) - local_path: local directory to store the remote data granules - access: direct or on_prem, if set it will use it for the access method. - threads: parallel number of threads to use to download the files; - adjust as necessary, default = 8 + granules: A list of granules(DataGranule) instances or a list of granule links (HTTP). + local_path: Local directory to store the remote data granules. + threads: Parallel number of threads to use to download the files; + adjust as necessary, default = 8. Returns: List of downloaded files @@ -493,10 +495,10 @@ def _get( the data will be effectively downloaded to a local directory. Parameters: - granules: a list of granules(DataGranule) instances or a list of granule links (HTTP) - local_path: local directory to store the remote data granules - access: direct or on_prem, if set it will use it for the access method. - threads: parallel number of threads to use to download the files, adjust as necessary, default = 8 + granules: A list of granules (DataGranule) instances or a list of granule links (HTTP). + local_path: Local directory to store the remote data granules + threads: Parallel number of threads to use to download the files; + adjust as necessary, default = 8. Returns: None @@ -548,7 +550,7 @@ def _get_granules( cloud_hosted = granules[0].cloud_hosted access = "direct" if (cloud_hosted and self.in_region) else "external" data_links = list( - # we are not in region + # we are not in-region chain.from_iterable( granule.data_links(access=access, in_region=self.in_region) for granule in granules @@ -587,7 +589,7 @@ def _download_file(self, url: str, directory: str) -> str: directory: local directory Returns: - a local filepath or an exception + A local filepath or an exception. """ # If the get data link is an Opendap location if "opendap" in url and url.endswith(".html"): @@ -628,7 +630,7 @@ def _download_onprem_granules( adjust as necessary, default = 8 Returns: - a list of local filepaths to which the files were downloaded + A list of local filepaths to which the files were downloaded. """ if urls is None: raise ValueError("The granules didn't provide a valid GET DATA link") From 2b146097452eb9e31c137468a5bd01a2fab8cd3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luis=20L=C3=B3pez?= Date: Thu, 8 Feb 2024 10:03:20 -0600 Subject: [PATCH 30/46] Update earthaccess/auth.py Co-authored-by: Joseph H Kennedy --- earthaccess/auth.py | 1 + 1 file changed, 1 insertion(+) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 3455a286..f041b83a 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -31,6 +31,7 @@ class SessionWithHeaderRedirection(requests.Session): "urs.earthdata.nasa.gov", "cumulus.asf.alaska.edu", "sentinel1.asf.alaska.edu", + "nisar.asf.alaska.edu", "datapool.asf.alaska.edu", ] From 72539ddd90938466b22c07471dfb3d4ca74e9fd3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:05:01 +0000 Subject: [PATCH 31/46] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b4e21691..bd151d45 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ ## [Unreleased] * Bug fixes: - * fixed #439 by implementing more trusted domains in the SessionWithRedirection + * fixed #439 by implementing more trusted domains in the SessionWithRedirection * fixed #438 by using an authenticated session for hits() * Enhancements: * addressing #427 by adding parameters to collection query From 19b6be1c7218253203a868f5a8635d0154871f17 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luis=20L=C3=B3pez?= Date: Thu, 8 Feb 2024 16:43:20 -0600 Subject: [PATCH 32/46] Update earthaccess/auth.py Co-authored-by: Joseph H Kennedy --- earthaccess/auth.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index f041b83a..9f51ad92 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -13,7 +13,7 @@ from .daac import DAACS try: - user_agent = f"earthaccess v{importlib.metadata.version('earthacess')}" + user_agent = f"earthaccess v{earthaccess.__version__}" except importlib.metadata.PackageNotFoundError: user_agent = "earthaccess" From d20f713c8167d451a0bbe72ffc9c9c170296461c Mon Sep 17 00:00:00 2001 From: betolink Date: Thu, 8 Feb 2024 21:13:57 -0600 Subject: [PATCH 33/46] reverting last commit, avoid importing the library --- earthaccess/auth.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 9f51ad92..8f1cb3e5 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -13,7 +13,7 @@ from .daac import DAACS try: - user_agent = f"earthaccess v{earthaccess.__version__}" + user_agent = f"earthaccess v{importlib.metadata.version('earthaccess')}" except importlib.metadata.PackageNotFoundError: user_agent = "earthaccess" From 71219d7f68b3839ae1c5ca4668320647d092a3c0 Mon Sep 17 00:00:00 2001 From: karthik venkataramani Date: Mon, 12 Feb 2024 14:20:31 -0800 Subject: [PATCH 34/46] use pathlib.PurePath for file/folder operations --- earthaccess/store.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index 4981fe50..ee9b9033 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -1,5 +1,5 @@ import datetime -import os +from pathlib import Path import shutil import traceback from functools import lru_cache @@ -466,7 +466,7 @@ def get( List of downloaded files """ if local_path is None: - local_path = os.path.join( + local_path = Path( ".", "data", f"{datetime.datetime.today().strftime('%Y-%m-%d')}-{uuid4().hex[:6]}", @@ -526,7 +526,7 @@ def _get_urls( # TODO: make this parallel or concurrent for file in data_links: s3_fs.get(file, local_path) - file_name = os.path.join(local_path, os.path.basename(file)) + file_name = Path(local_path, Path(file).name) print(f"Downloaded: {file_name}") downloaded_files.append(file_name) return downloaded_files @@ -572,7 +572,7 @@ def _get_granules( # TODO: make this async for file in data_links: s3_fs.get(file, local_path) - file_name = os.path.join(local_path, os.path.basename(file)) + file_name = Path(local_path, Path(file).name) print(f"Downloaded: {file_name}") downloaded_files.append(file_name) return downloaded_files @@ -597,7 +597,7 @@ def _download_file(self, url: str, directory: str) -> str: local_filename = url.split("/")[-1] path = Path(directory) / Path(local_filename) local_path = str(path) - if not os.path.exists(local_path): + if not Path(local_path).exists(): try: session = self.auth.get_session() with session.get( @@ -638,8 +638,8 @@ def _download_onprem_granules( raise ValueError( "We need to be logged into NASA EDL in order to download data granules" ) - if not os.path.exists(directory): - os.makedirs(directory) + if not Path(directory).exists(): + Path(directory).mkdir(parents=True) arguments = [(url, directory) for url in urls] results = pqdm( From 2f39a736c6f778b3a2f363326e3055f9c33bcf90 Mon Sep 17 00:00:00 2001 From: karthik venkataramani Date: Mon, 12 Feb 2024 14:27:40 -0800 Subject: [PATCH 35/46] update to use pathlib --- earthaccess/auth.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index a8335f73..6308bf23 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -2,6 +2,7 @@ import importlib.metadata import logging import os +from pathlib import Path from netrc import NetrcParseError from pathlib import Path from typing import Any, Dict, List, Optional @@ -258,7 +259,7 @@ def _netrc(self) -> bool: my_netrc = Netrc() except FileNotFoundError as err: raise FileNotFoundError( - f"No .netrc found in {os.path.expanduser('~')}" + f"No .netrc found in {Path('~').expanduser()}" ) from err except NetrcParseError as err: raise NetrcParseError("Unable to parse .netrc") from err @@ -365,7 +366,7 @@ def _persist_user_credentials(self, username: str, password: str) -> bool: try: netrc_path = Path().home().joinpath(".netrc") netrc_path.touch(exist_ok=True) - os.chmod(netrc_path.absolute(), 0o600) + netrc_path.chmod(0o600) except Exception as e: print(e) return False From 1657e63aaa19c3e78d6ae61fec7d61cae4f01286 Mon Sep 17 00:00:00 2001 From: karthik venkataramani Date: Mon, 12 Feb 2024 22:06:07 -0800 Subject: [PATCH 36/46] update to use pathlib --- tests/integration/test_kerchunk.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tests/integration/test_kerchunk.py b/tests/integration/test_kerchunk.py index 58f93077..f15f5a1b 100644 --- a/tests/integration/test_kerchunk.py +++ b/tests/integration/test_kerchunk.py @@ -1,5 +1,6 @@ import logging import os +from pathlib import Path import unittest import earthaccess @@ -32,14 +33,14 @@ def granules(): @pytest.mark.parametrize("protocol", ["", "file://"]) def test_consolidate_metadata_outfile(tmp_path, granules, protocol): outfile = f"{protocol}{tmp_path / 'metadata.json'}" - assert not os.path.exists(outfile) + assert not Path(outfile).exists() result = earthaccess.consolidate_metadata( granules, outfile=outfile, access="indirect", kerchunk_options={"concat_dims": "Time"}, ) - assert os.path.exists(strip_protocol(outfile)) + assert Path(strip_protocol(outfile)).exists() assert result == outfile From 65320734bd5f02f43a9b3d7d7fd1c0a6691e2f87 Mon Sep 17 00:00:00 2001 From: karthik venkataramani Date: Mon, 12 Feb 2024 22:07:48 -0800 Subject: [PATCH 37/46] update to use pathlib --- tests/integration/test_api.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/integration/test_api.py b/tests/integration/test_api.py index 6fa1ccea..62cdb3e3 100644 --- a/tests/integration/test_api.py +++ b/tests/integration/test_api.py @@ -1,6 +1,7 @@ # package imports import logging import os +from pathlib import Path import unittest import earthaccess @@ -84,7 +85,7 @@ def test_download(tmp_path, selection, use_url): result = results[selection] files = earthaccess.download(result, str(tmp_path)) assertions.assertIsInstance(files, list) - assert all(os.path.exists(f) for f in files) + assert all(Path(f).exists() for f in files) def test_auth_environ(): From 9820912cb601f2d0eb19daabf9439c80b3aa2661 Mon Sep 17 00:00:00 2001 From: karthik venkataramani Date: Mon, 12 Feb 2024 22:11:21 -0800 Subject: [PATCH 38/46] update to use pathlib --- tests/integration/test_cloud_download.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/integration/test_cloud_download.py b/tests/integration/test_cloud_download.py index 63a05b93..07c13e99 100644 --- a/tests/integration/test_cloud_download.py +++ b/tests/integration/test_cloud_download.py @@ -1,6 +1,7 @@ # package imports import logging import os +from pathlib import Path import random import shutil import unittest @@ -166,4 +167,4 @@ def test_multi_file_granule(tmp_path): urls = granules[0].data_links() assert len(urls) > 1 files = earthaccess.download(granules, str(tmp_path)) - assert set(map(os.path.basename, urls)) == set(map(os.path.basename, files)) + assert set([Path(f).name for f in urls]) == set([Path(f).name for f in files]) From 7ea651f3d6b7660eba2626b1dcb349117bbb46cd Mon Sep 17 00:00:00 2001 From: Karthik Venkataramani Date: Tue, 13 Feb 2024 14:57:13 -0800 Subject: [PATCH 39/46] Update earthaccess/auth.py Co-authored-by: Joseph H Kennedy --- earthaccess/auth.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index 6308bf23..c6c830db 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -259,7 +259,7 @@ def _netrc(self) -> bool: my_netrc = Netrc() except FileNotFoundError as err: raise FileNotFoundError( - f"No .netrc found in {Path('~').expanduser()}" + f"No .netrc found in {Path.home()}" ) from err except NetrcParseError as err: raise NetrcParseError("Unable to parse .netrc") from err From 780c1f43f40be7637bdf47264dd1ffb12bd6308e Mon Sep 17 00:00:00 2001 From: Karthik Venkataramani Date: Tue, 13 Feb 2024 14:57:35 -0800 Subject: [PATCH 40/46] Update earthaccess/store.py Co-authored-by: Joseph H Kennedy --- earthaccess/store.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index ee9b9033..32dd2910 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -638,8 +638,7 @@ def _download_onprem_granules( raise ValueError( "We need to be logged into NASA EDL in order to download data granules" ) - if not Path(directory).exists(): - Path(directory).mkdir(parents=True) + Path(directory).mkdir(parents=True, exist_ok=True) arguments = [(url, directory) for url in urls] results = pqdm( From 9b7928ecf0e45254eb9b417b47ab1d2f48500272 Mon Sep 17 00:00:00 2001 From: Karthik Venkataramani Date: Tue, 13 Feb 2024 14:57:40 -0800 Subject: [PATCH 41/46] Update earthaccess/store.py Co-authored-by: Joseph H Kennedy --- earthaccess/store.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index 32dd2910..abe0c85c 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -572,7 +572,7 @@ def _get_granules( # TODO: make this async for file in data_links: s3_fs.get(file, local_path) - file_name = Path(local_path, Path(file).name) + file_name = Path(local_path) / Path(file).name print(f"Downloaded: {file_name}") downloaded_files.append(file_name) return downloaded_files From 6591ead54604bc58244c7301b0381af2ad236e1d Mon Sep 17 00:00:00 2001 From: Karthik Venkataramani Date: Tue, 13 Feb 2024 14:57:45 -0800 Subject: [PATCH 42/46] Update earthaccess/store.py Co-authored-by: Joseph H Kennedy --- earthaccess/store.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index abe0c85c..3cbb24d1 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -526,7 +526,7 @@ def _get_urls( # TODO: make this parallel or concurrent for file in data_links: s3_fs.get(file, local_path) - file_name = Path(local_path, Path(file).name) + file_name = Path(local_path) / Path(file).name print(f"Downloaded: {file_name}") downloaded_files.append(file_name) return downloaded_files From 95ce27f472d35b9b7afe4085d97657c1c89cad1f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Feb 2024 23:46:14 +0000 Subject: [PATCH 43/46] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- earthaccess/auth.py | 5 +---- earthaccess/store.py | 1 - tests/integration/test_api.py | 2 +- tests/integration/test_cloud_download.py | 1 - tests/integration/test_kerchunk.py | 2 +- 5 files changed, 3 insertions(+), 8 deletions(-) diff --git a/earthaccess/auth.py b/earthaccess/auth.py index c6c830db..2a820402 100644 --- a/earthaccess/auth.py +++ b/earthaccess/auth.py @@ -2,7 +2,6 @@ import importlib.metadata import logging import os -from pathlib import Path from netrc import NetrcParseError from pathlib import Path from typing import Any, Dict, List, Optional @@ -258,9 +257,7 @@ def _netrc(self) -> bool: try: my_netrc = Netrc() except FileNotFoundError as err: - raise FileNotFoundError( - f"No .netrc found in {Path.home()}" - ) from err + raise FileNotFoundError(f"No .netrc found in {Path.home()}") from err except NetrcParseError as err: raise NetrcParseError("Unable to parse .netrc") from err if my_netrc["urs.earthdata.nasa.gov"] is not None: diff --git a/earthaccess/store.py b/earthaccess/store.py index 3cbb24d1..9ec9c82c 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -1,5 +1,4 @@ import datetime -from pathlib import Path import shutil import traceback from functools import lru_cache diff --git a/tests/integration/test_api.py b/tests/integration/test_api.py index 62cdb3e3..8fd45489 100644 --- a/tests/integration/test_api.py +++ b/tests/integration/test_api.py @@ -1,8 +1,8 @@ # package imports import logging import os -from pathlib import Path import unittest +from pathlib import Path import earthaccess import pytest diff --git a/tests/integration/test_cloud_download.py b/tests/integration/test_cloud_download.py index 07c13e99..a9b9432c 100644 --- a/tests/integration/test_cloud_download.py +++ b/tests/integration/test_cloud_download.py @@ -1,7 +1,6 @@ # package imports import logging import os -from pathlib import Path import random import shutil import unittest diff --git a/tests/integration/test_kerchunk.py b/tests/integration/test_kerchunk.py index f15f5a1b..2e981cce 100644 --- a/tests/integration/test_kerchunk.py +++ b/tests/integration/test_kerchunk.py @@ -1,7 +1,7 @@ import logging import os -from pathlib import Path import unittest +from pathlib import Path import earthaccess import pytest From c68e63449b611476ac3492a94a85cce47fcb871c Mon Sep 17 00:00:00 2001 From: karthik venkataramani Date: Tue, 13 Feb 2024 16:57:38 -0800 Subject: [PATCH 44/46] update typehints and code for _get methods to use Path consistently --- earthaccess/store.py | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index 9ec9c82c..44853918 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -480,7 +480,7 @@ def get( def _get( self, granules: Union[List[DataGranule], List[str]], - local_path: str, + local_path: Path, provider: Optional[str] = None, threads: int = 8, ) -> List[str]: @@ -508,7 +508,7 @@ def _get( def _get_urls( self, granules: List[str], - local_path: str, + local_path: Path, provider: Optional[str] = None, threads: int = 8, ) -> List[str]: @@ -524,8 +524,8 @@ def _get_urls( s3_fs = self.get_s3fs_session(provider=provider) # TODO: make this parallel or concurrent for file in data_links: - s3_fs.get(file, local_path) - file_name = Path(local_path) / Path(file).name + s3_fs.get(file, str(local_path)) + file_name = local_path / Path(file).name print(f"Downloaded: {file_name}") downloaded_files.append(file_name) return downloaded_files @@ -538,7 +538,7 @@ def _get_urls( def _get_granules( self, granules: List[DataGranule], - local_path: str, + local_path: Path, provider: Optional[str] = None, threads: int = 8, ) -> List[str]: @@ -570,15 +570,15 @@ def _get_granules( s3_fs = self.get_s3fs_session(provider=provider) # TODO: make this async for file in data_links: - s3_fs.get(file, local_path) - file_name = Path(local_path) / Path(file).name + s3_fs.get(file, str(local_path)) + file_name = local_path / Path(file).name print(f"Downloaded: {file_name}") downloaded_files.append(file_name) return downloaded_files else: # if the data are cloud-based, but we are not in AWS, # it will be downloaded as if it was on prem - return self._download_onprem_granules(data_links, local_path, threads) + return self._download_onprem_granules(data_links, str(local_path), threads) def _download_file(self, url: str, directory: str) -> str: """Download a single file from an on-prem location, a DAAC data center. @@ -595,8 +595,7 @@ def _download_file(self, url: str, directory: str) -> str: url = url.replace(".html", "") local_filename = url.split("/")[-1] path = Path(directory) / Path(local_filename) - local_path = str(path) - if not Path(local_path).exists(): + if not path.exists(): try: session = self.auth.get_session() with session.get( @@ -605,7 +604,7 @@ def _download_file(self, url: str, directory: str) -> str: allow_redirects=True, ) as r: r.raise_for_status() - with open(local_path, "wb") as f: + with open(path, "wb") as f: # This is to cap memory usage for large files at 1MB per write to disk per thread # https://docs.python-requests.org/en/latest/user/quickstart/#raw-response-content shutil.copyfileobj(r.raw, f, length=1024 * 1024) @@ -615,7 +614,7 @@ def _download_file(self, url: str, directory: str) -> str: raise Exception else: print(f"File {local_filename} already downloaded") - return local_path + return str(path) def _download_onprem_granules( self, urls: List[str], directory: str, threads: int = 8 From b036811b4f1827c97c02e2af470117dcc996b659 Mon Sep 17 00:00:00 2001 From: Joseph H Kennedy Date: Fri, 16 Feb 2024 15:06:14 -0900 Subject: [PATCH 45/46] a little path vs str cleanup --- earthaccess/store.py | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/earthaccess/store.py b/earthaccess/store.py index 44853918..15ae4ef2 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -442,7 +442,7 @@ def _open_urls( def get( self, granules: Union[List[DataGranule], List[str]], - local_path: Optional[str] = None, + local_path: Optional[Path] = None, provider: Optional[str] = None, threads: int = 8, ) -> List[str]: @@ -465,11 +465,10 @@ def get( List of downloaded files """ if local_path is None: - local_path = Path( - ".", - "data", - f"{datetime.datetime.today().strftime('%Y-%m-%d')}-{uuid4().hex[:6]}", - ) + today = datetime.datetime.today().strftime("%Y-%m-%d") + uuid = uuid4().hex[:6] + local_path = Path.cwd() / "data" / f"{today}-{uuid}" + if len(granules): files = self._get(granules, local_path, provider, threads) return files @@ -578,9 +577,9 @@ def _get_granules( else: # if the data are cloud-based, but we are not in AWS, # it will be downloaded as if it was on prem - return self._download_onprem_granules(data_links, str(local_path), threads) + return self._download_onprem_granules(data_links, local_path, threads) - def _download_file(self, url: str, directory: str) -> str: + def _download_file(self, url: str, directory: Path) -> str: """Download a single file from an on-prem location, a DAAC data center. Parameters: @@ -594,7 +593,7 @@ def _download_file(self, url: str, directory: str) -> str: if "opendap" in url and url.endswith(".html"): url = url.replace(".html", "") local_filename = url.split("/")[-1] - path = Path(directory) / Path(local_filename) + path = directory / Path(local_filename) if not path.exists(): try: session = self.auth.get_session() @@ -617,7 +616,7 @@ def _download_file(self, url: str, directory: str) -> str: return str(path) def _download_onprem_granules( - self, urls: List[str], directory: str, threads: int = 8 + self, urls: List[str], directory: Path, threads: int = 8 ) -> List[Any]: """Downloads a list of URLS into the data directory. @@ -636,7 +635,7 @@ def _download_onprem_granules( raise ValueError( "We need to be logged into NASA EDL in order to download data granules" ) - Path(directory).mkdir(parents=True, exist_ok=True) + directory.mkdir(parents=True, exist_ok=True) arguments = [(url, directory) for url in urls] results = pqdm( From 453e7f968977936a4fa662d739a2ed0dab79dcb8 Mon Sep 17 00:00:00 2001 From: Joseph H Kennedy Date: Fri, 16 Feb 2024 15:13:35 -0900 Subject: [PATCH 46/46] one more os->pathlib --- tests/integration/test_auth.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integration/test_auth.py b/tests/integration/test_auth.py index d1bfae1e..a4879d12 100644 --- a/tests/integration/test_auth.py +++ b/tests/integration/test_auth.py @@ -30,7 +30,7 @@ def activate_netrc(): f.write( f"machine urs.earthdata.nasa.gov login {username} password {password}\n" ) - os.chmod(NETRC_PATH, 0o600) + NETRC_PATH.chmod(0o600) def delete_netrc():