ierge remote-tracking branch 'origin' into docs

jjjermiah · Feb 12, 2024 · ad0ec3a · ad0ec3a
2 parents 7625694 + d10a38d
commit ad0ec3a
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -36,6 +36,8 @@ jobs:
           poetry run pytest -n 4 --cov --cov-report xml:coverage-report/coverage.xml
 
       - name: Upload coverage report artifact to be used by Codecov
+        # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
         uses: actions/upload-artifact@v2
         with:
           name: coverage-report

diff --git a/README.md b/README.md
@@ -55,7 +55,7 @@ For quick access to the NBIA, the toolkit also provides a command line interface
 /_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/  
 
 
-Version: 0.28.0
+Version: 0.29.0
 
 Available CLI tools: 
 

diff --git a/docs/markdowns/CHANGELOG.md b/docs/markdowns/CHANGELOG.md
@@ -2,10 +2,75 @@
 
 
 
+## v0.29.0 (2024-02-12)
+
+### Build
+
+* build: Add conditional upload of coverage report artifact ([`972c785`](https://github.com/jjjermiah/nbia-toolkit/commit/972c785b9ffef735ab9544819917d0a23b0d909f))
+
+### Chore
+
+* chore: Update README: 0.28.0 ([`92ff4eb`](https://github.com/jjjermiah/nbia-toolkit/commit/92ff4ebe8420bd3f63011424ec3bb44ebe286f4c))
+
+### Feature
+
+* feat: Add getDICOMTags method to NBIAClient class ([`18b6625`](https://github.com/jjjermiah/nbia-toolkit/commit/18b6625df5a1d435aaad37d4d920b5198e0e58d3))
+
+### Fix
+
+* fix: remove err ([`58a9ada`](https://github.com/jjjermiah/nbia-toolkit/commit/58a9ada2bdfc0ec126ff80ce3adff4608562001b))
+
+* fix: remove extra files ([`91b277b`](https://github.com/jjjermiah/nbia-toolkit/commit/91b277ba1a09f491bf8c8943dc4cf6f940f523d0))
+
+* fix: Update pydicom version to 2.4.0 ([`b78edd8`](https://github.com/jjjermiah/nbia-toolkit/commit/b78edd842f230b75d54e11d91a91c9979a2b8380))
+
+* fix: merge ([`544c682`](https://github.com/jjjermiah/nbia-toolkit/commit/544c682d9300aae80def16a22e379602ef5a8370))
+
+* fix: Fix encryption key in OAuth2 class ([`1082e47`](https://github.com/jjjermiah/nbia-toolkit/commit/1082e476f9f00bd4e45df2f9262b344718a83ee6))
+
+### Refactor
+
+* refactor: clean, lint ([`688a1a6`](https://github.com/jjjermiah/nbia-toolkit/commit/688a1a6de485c14a9e20150fc1335635f3221f01))
+
+### Unknown
+
+* Merge pull request #104 from jjjermiah/dicomtags
+
+feat: Dicomtags ([`25760ef`](https://github.com/jjjermiah/nbia-toolkit/commit/25760ef89c94dce23c4bf4ba8e5ba00fabe32c29))
+
+* Merge pull request #103 from jjjermiah/devel
+
+refactor: clean, lint ([`f9ab11e`](https://github.com/jjjermiah/nbia-toolkit/commit/f9ab11e6980cd95b7b661465a0cc4796d8e8df66))
+
+* remove unused lines ([`c1dc231`](https://github.com/jjjermiah/nbia-toolkit/commit/c1dc23113340d358cd201c36f2e1e9b1505644cc))
+
+* Merge pull request #102 from jjjermiah/19-authpy-logout-functionality
+
+19 authpy logout functionality ([`fee4ee0`](https://github.com/jjjermiah/nbia-toolkit/commit/fee4ee0c870a178a459db9e15d8f521456daa170))
+
+* tests: remove main code in md5 ([`2972b5f`](https://github.com/jjjermiah/nbia-toolkit/commit/2972b5fc9b7bb37dea525abeb9a1e8f1748bc072))
+
+* tests: add more coverage for logger ([`b90c74c`](https://github.com/jjjermiah/nbia-toolkit/commit/b90c74c0bd7af5940e72401d17a5e41982466897))
+
+* Merge pull request #101 from jjjermiah/19-authpy-logout-functionality
+
+19 authpy logout functionality ([`a6f40cc`](https://github.com/jjjermiah/nbia-toolkit/commit/a6f40cc506ce035e2a6568e1af546ded37b34677))
+
+* tests: fix small error ([`977df6c`](https://github.com/jjjermiah/nbia-toolkit/commit/977df6c1ae29262f45963cb929d70fb446f5768a))
+
+* Merge pull request #100 from jjjermiah/main
+
+merge ([`d2a6f55`](https://github.com/jjjermiah/nbia-toolkit/commit/d2a6f55cd6df0e98a122f8f94cb6512c8f3da65a))
+
+* tests:  add tests and Update user authentication logic ([`bf4b8d8`](https://github.com/jjjermiah/nbia-toolkit/commit/bf4b8d8737a5621c778c07c52d517a379741139a))
+
+
 ## v0.28.0 (2024-02-05)
 
 ### Chore
 
+* chore(sem-ver): 0.28.0 ([`4f78b7a`](https://github.com/jjjermiah/nbia-toolkit/commit/4f78b7a01e3d58d60ad83b039079198c0181324d))
+
 * chore: Update README: 0.27.0 ([`79f7eda`](https://github.com/jjjermiah/nbia-toolkit/commit/79f7edafff8bf0ada9f0ea14909c9fe45f628a69))
 
 ### Feature

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "nbiatoolkit"
-version = "0.28.0"
+version = "0.29.0"
 description = "A python package to query the National Biomedical Imaging Archive (NBIA) database."
 authors = ["Jermiah Joseph"]
 license = "MIT"
@@ -21,7 +21,7 @@ downloadSingleSeries = "nbiatoolkit.nbia_cli:downloadSingleSeries_cli"
 [tool.poetry.dependencies]
 python = ">=3.10 || 3.12"
 requests = "2.31.0"
-pydicom = "^2.4.3"
+pydicom = "^2.4.0"
 tqdm = "^4.66.1"
 pyfiglet = "^1.0"
 beautifulsoup4 = "^4.12.3"

diff --git a/setup.py b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup
 
-__version__ = "0.28.0"
+__version__ = "0.29.0"
 
 setup(
     name="nbiatoolkit",

diff --git a/src/nbiatoolkit/auth.py b/src/nbiatoolkit/auth.py
@@ -141,6 +141,7 @@ def __init__(
         self.username, self.password = encrypt_credentials(
             key=self.fernet_key, username=username, password=password
         )
+        self.username, self.password = encrypt_credentials(key=self._fernet_key, username=username, password=password)
 
         if isinstance(base_url, NBIA_ENDPOINTS):
             self.base_url = base_url.value
@@ -153,6 +154,7 @@ def __init__(
         self.refresh_token = ""  # Fix: Assign an empty string instead of None
         self.scope = None
 
+
     @property
     def fernet_key(self) -> bytes:
         return self._fernet_key

diff --git a/src/nbiatoolkit/dicomsort/crawl.py b/src/nbiatoolkit/dicomsort/crawl.py
diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py
@@ -20,7 +20,7 @@
 from datetime import datetime
 
 # set __version__ variable
-__version__ = "0.28.0"
+__version__ = "0.29.0"
 
 
 class NBIAClient:
@@ -432,6 +432,24 @@ def getNewSeries(
 
         return response
 
+    def getDICOMTags(
+        self,
+        SeriesInstanceUID: str,
+    ) -> Union[list[dict], None]:
+        assert SeriesInstanceUID is not None and isinstance(SeriesInstanceUID, str), \
+            "SeriesInstanceUID must be a string"
+
+        PARAMS = self.parsePARAMS({"SeriesUID": SeriesInstanceUID})
+
+        response = self.query_api(endpoint=NBIA_ENDPOINTS.GET_DICOM_TAGS, params=PARAMS)
+
+        if not isinstance(response, list):
+            self._log.error("Expected list, but received: %s", type(response))
+            return None
+
+        return response
+
+
     def downloadSeries(
         self,
         SeriesInstanceUID: Union[str, list],