Merge pull request #116 from jjjermiah/main

merge w main
jjjermiah · Feb 19, 2024 · 4f79f98 · 4f79f98
2 parents 7cf41c4 + f053d10
commit 4f79f98
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -67,7 +67,6 @@ jobs:
 
   Build-Documentation:
     runs-on: ubuntu-latest
-    if: github.ref == 'refs/heads/docs'
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
@@ -362,33 +361,3 @@ jobs:
               # No changes
               echo "No changes found. Nothing to commit or push."
           fi
-
-
-
-  #         # git add README.md
-
-  #         # git commit -m "Update README with latest version"
-  #         # git push
-
-
-# #!/bin/bash
-
-# # Check for changes
-# if [[ $(git status --porcelain) ]]; then
-#     # Changes are present
-#     echo "Changes found. Committing and pushing..."
-
-#     # Add all changes
-#     git add .
-
-#     # Commit with a timestamp
-#     git commit -m "Auto commit: $(date)"
-
-#     # Push changes to the remote repository
-#     git push origin <your-branch-name>
-
-#     echo "Changes committed and pushed successfully."
-# else
-#     # No changes
-#     echo "No changes found. Nothing to commit or push."
-# fi
diff --git a/Dockerfile b/Dockerfile
@@ -14,9 +14,15 @@ LABEL license="MIT"
 LABEL usage="docker run -it --rm <image_name> NBIAToolkit --help"
 LABEL org.opencontainers.image.source="github.com/jjjermiah/nbiatoolkit"
 
-# install the dependencies
+# copy current directory to /nbiatoolkit
+COPY . /nbiatoolkit
+
+# set working directory
+WORKDIR /nbiatoolkit
+
+# install nbiatoolkit
 RUN pip install --upgrade pip
-RUN python -m pip install nbiatoolkit
+RUN pip install .
 
 RUN NBIAToolkit --help
 

diff --git a/README.md b/README.md
@@ -49,16 +49,16 @@ For quick access to the NBIA, the toolkit also provides a command line interface
 
 ``` bash NBIAToolkit-Output
 > NBIAToolkit --version
-    _   ______  _______  ______            ____   _ __
+    _   ______  _______  ______            ____   _ __ 
    / | / / __ )/  _/   |/_  __/___  ____  / / /__(_) /_
   /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/
- / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
-/_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/
+ / /|  / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_  
+/_/ |_/_____/___/_/  |_/_/  \____/\____/_/_/|_/_/\__/  
+
 
+Version: 0.32.0
 
-Version: 0.29.2
-
-Available CLI tools:
+Available CLI tools: 
 
 getCollections [-h] [-u USERNAME] [-pw PASSWORD] [-p PREFIX]
                [-o OUTPUTFILE] [--version]

diff --git a/docs/markdowns/CHANGELOG.md b/docs/markdowns/CHANGELOG.md
@@ -2,10 +2,65 @@
 
 
 
+## v0.32.0 (2024-02-18)
+
+### Chore
+
+* chore: Update README: 0.31.0 ([`799667e`](https://github.com/jjjermiah/nbia-toolkit/commit/799667ed8eaad93dafe751ab170a2f4f96a4dc36))
+
+### Feature
+
+* feat: Refactor workflows and update test case ([`e111fb2`](https://github.com/jjjermiah/nbia-toolkit/commit/e111fb28e35084891f5551f264e0ab707441fd88))
+
+* feat: refactor return_type test ([`f2058e8`](https://github.com/jjjermiah/nbia-toolkit/commit/f2058e8f259ed5e2250f20ca08b556883449f399))
+
+
+## v0.31.0 (2024-02-18)
+
+### Build
+
+* build: docker build ([`fc6fd28`](https://github.com/jjjermiah/nbia-toolkit/commit/fc6fd28ad815b904648dbcd7ddc8bba4cc15e4eb))
+
+### Chore
+
+* chore(sem-ver): 0.31.0 ([`f8b2253`](https://github.com/jjjermiah/nbia-toolkit/commit/f8b2253d948a9bdc4f42a94e38b7751ba37d4b5d))
+
+* chore: Update README: 0.30.1 ([`ec7c9d3`](https://github.com/jjjermiah/nbia-toolkit/commit/ec7c9d38eeb602353c83c54664b0e60baef55d22))
+
+### Feature
+
+* feat: Update version to 0.31.1 and upgrade pip ([`12c5018`](https://github.com/jjjermiah/nbia-toolkit/commit/12c501883b91a2ef26b12866c75a6047c53e2103))
+
+### Fix
+
+* fix: ci ([`2f52670`](https://github.com/jjjermiah/nbia-toolkit/commit/2f526705a2814f26fb73f38f80cdf76e8838c28f))
+
+
+## v0.30.1 (2024-02-18)
+
+### Chore
+
+* chore(sem-ver): 0.30.1 ([`b4ef0c7`](https://github.com/jjjermiah/nbia-toolkit/commit/b4ef0c7b096fb1953cd683381fa490a5fdf6cba3))
+
+### Fix
+
+* fix: Fix import statements in nbia.py and nbia_cli.py ([`14816f1`](https://github.com/jjjermiah/nbia-toolkit/commit/14816f162ba309de82daacb2c0a765d6fb753c99))
+
+### Unknown
+
+* Merge pull request #111 from jjjermiah/development
+
+fix cli ([`b044404`](https://github.com/jjjermiah/nbia-toolkit/commit/b04440409480749f45522f57274baf4cd0da6205))
+
+* Merge remote-tracking branch &#39;origin&#39; into development ([`7cf41c4`](https://github.com/jjjermiah/nbia-toolkit/commit/7cf41c4d41fedf3cd5d37e9e5ef952a80bbe9e36))
+
+
 ## v0.30.0 (2024-02-18)
 
 ### Chore
 
+* chore(sem-ver): 0.30.0 ([`aae2d61`](https://github.com/jjjermiah/nbia-toolkit/commit/aae2d6197b1f6e7ded7413814788a4bd109584f1))
+
 * chore: Update README: 0.29.2 ([`c7d69ec`](https://github.com/jjjermiah/nbia-toolkit/commit/c7d69ec58df0faf15b8645a74d6332848c2356f5))
 
 ### Ci

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "nbiatoolkit"
-version = "0.30.0"
+version = "0.32.0"
 description = "A python package to query the National Biomedical Imaging Archive (NBIA) database."
 authors = ["Jermiah Joseph"]
 license = "MIT"

diff --git a/src/nbiatoolkit/__init__.py b/src/nbiatoolkit/__init__.py
@@ -22,4 +22,5 @@
     "NBIA_ENDPOINTS",
     "version",
     "__version__",
+    "downloadSingleSeries",
 ]
diff --git a/src/nbiatoolkit/dicomsort/__init__.py b/src/nbiatoolkit/dicomsort/__init__.py
@@ -5,6 +5,7 @@
 #     "setup_logger",
 #     "NBIA_ENDPOINTS",
 #     "validateMD5"
+
 # ]
 
 from .dicomsort import DICOMSorter

diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py
@@ -33,7 +33,7 @@
 from datetime import datetime
 
 # set __version__ variable
-__version__ = "0.30.0"
+__version__ = "0.32.0"
 
 
 # function that takes a list of dictionaries and returns either a list or a dataframe

diff --git a/tests/test_downloadSeries.py b/tests/test_downloadSeries.py
@@ -1,5 +1,6 @@
 import pytest
-from src.nbiatoolkit import NBIAClient
+from sqlalchemy import over
+from src.nbiatoolkit import NBIAClient, downloadSingleSeries
 from tempfile import TemporaryDirectory
 import os
 
@@ -9,8 +10,13 @@ def nbia_client():
     return NBIAClient()
 
 
-def test_downloadSeries(nbia_client):
-    seriesList = nbia_client.getSeries(Collection="NSCLC-Radiomics")
+@pytest.fixture
+def series_list(nbia_client):
+    return nbia_client.getSeries(Collection="NSCLC-Radiomics")
+
+
+def test_downloadSeries(nbia_client, series_list):
+    seriesList = series_list
     filePattern = (
         "%PatientID/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm"
     )
@@ -32,3 +38,32 @@ def test_downloadSeries(nbia_client):
         assert len(modality_dir) == 1
         assert modality_dir[0].startswith("CT")
         assert os.path.isdir(os.path.join(tempdir, dir[0], modality_dir[0]))
+
+
+def test_downloadSingleSeries(nbia_client, series_list):
+    seriesList = series_list
+    filePattern = (
+        "%PatientID/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm"
+    )
+    # create a temporary directory
+
+    with TemporaryDirectory() as tempdir:
+
+        downloadSingleSeries(
+            SeriesInstanceUID=seriesList[0]["SeriesInstanceUID"],
+            downloadDir=tempdir,
+            filePattern=filePattern,
+            overwrite=True,
+            api_headers=nbia_client.headers,
+            base_url=nbia_client.base_url,
+            log=nbia_client.logger,
+        )
+        dir = os.listdir(tempdir)
+
+        assert len(dir) == 1
+        assert os.path.isdir(os.path.join(tempdir, dir[0]))
+
+        modality_dir = os.listdir(os.path.join(tempdir, dir[0]))
+        assert len(modality_dir) == 1
+        assert modality_dir[0].startswith("CT")
+        assert os.path.isdir(os.path.join(tempdir, dir[0], modality_dir[0]))
diff --git a/tests/test_new_query_functionality.py b/tests/test_new_query_functionality.py
@@ -3,6 +3,7 @@
 from src.nbiatoolkit import NBIAClient
 from src.nbiatoolkit.auth import OAuth2
 from src.nbiatoolkit.utils import *
+from src.nbiatoolkit.logger import setup_logger
 import pandas as pd
 
 
@@ -12,6 +13,12 @@ def nbia_client():
     return nbia_client
 
 
+@pytest.fixture(scope="session")
+def nbia_client2():
+    nbia_client = NBIAClient(log_level="DEBUG")
+    return nbia_client
+
+
 @pytest.fixture(scope="session")
 def tcga_patients(nbia_client):
 
@@ -20,7 +27,8 @@ def tcga_patients(nbia_client):
     return tcga_patients
 
 
-def test_nbia_properties(nbia_client):
+def test_nbia_properties(nbia_client2):
+    nbia_client = nbia_client2
     assert isinstance(nbia_client.OAuth_client, OAuth2)
     assert isinstance(nbia_client.headers, dict)
     assert "Authorization" in nbia_client.headers.keys()
@@ -31,6 +39,13 @@ def test_nbia_properties(nbia_client):
 
     assert nbia_client.logger is not None
 
+    nbia_client.logger = setup_logger(
+        name="NBIAClient", log_level="INFO", console_logging=True, log_file=None
+    )
+
+    assert nbia_client.return_type == "list"
+    nbia_client.return_type = "dataframe"
+
 
 def test_tcga_collection_description(nbia_client: NBIAClient):
     tcga_collection_description_df = nbia_client.getCollectionDescriptions(