From 99c5777e58e6d94ff3199f7f8062523c97dc42a7 Mon Sep 17 00:00:00 2001
From: Jermiah Joseph <jermiahjoseph98@gmail.com>
Date: Sun, 4 Feb 2024 11:50:42 -0500
Subject: [PATCH] feat: add getStudies and getNewSeries CLI tools

---
 pyproject.toml              | 10 ++++---
 src/nbiatoolkit/nbia_cli.py | 54 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 59 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1835bf2..aaf79cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,11 +10,13 @@ readme = "README.md"
 dicomsort = "nbiatoolkit.nbia_cli:DICOMSorter_cli"
 NBIAToolkit = "nbiatoolkit:version"
 getCollections = "nbiatoolkit.nbia_cli:getCollections_cli"
-getPatients = "nbiatoolkit.nbia_cli:getPatients_cli"
 getBodyPartCounts = "nbiatoolkit.nbia_cli:getBodyPartCounts_cli"
-downloadSingleSeries = "nbiatoolkit.nbia_cli:downloadSingleSeries_cli"
-getSeries = "nbiatoolkit.nbia_cli:getSeries_cli"
+getPatients = "nbiatoolkit.nbia_cli:getPatients_cli"
 getNewPatients = "nbiatoolkit.nbia_cli:getNewPatients_cli"
+getStudies = "nbiatoolkit.nbia_cli:getStudies_cli"
+getSeries = "nbiatoolkit.nbia_cli:getSeries_cli"
+getNewSeries = "nbiatoolkit.nbia_cli:getNewSeries_cli"
+downloadSingleSeries = "nbiatoolkit.nbia_cli:downloadSingleSeries_cli"
 
 [tool.poetry.dependencies]
 python = ">=3.10 || 3.12"
@@ -54,7 +56,7 @@ dist_path = "dist/"
 upload_to_release = true
 upload_to_pypi = false
 remove_dist = false
-commit_message = "chore(release): {version}"
+commit_message = "chore(sem-ver): {version}"
 patch_without_tag = true
 
 [tool.semantic_release.commit_parser_options]
diff --git a/src/nbiatoolkit/nbia_cli.py b/src/nbiatoolkit/nbia_cli.py
index 39c35f2..6b80010 100644
--- a/src/nbiatoolkit/nbia_cli.py
+++ b/src/nbiatoolkit/nbia_cli.py
@@ -28,10 +28,12 @@ def version():
     # run each command with -h to see the available options
     commands = [
         "getCollections",
+        "getBodyPartCounts",
         "getPatients",
         "getNewPatients",
-        "getBodyPartCounts",
+        "getStudies",
         "getSeries",
+        "getNewSeries",
         "downloadSingleSeries",
         "dicomsort"
     ]
@@ -278,6 +280,40 @@ def getBodyPartCounts_cli() -> None:
         func=NBIAClient(args.username, args.password).getBodyPartCounts, Collection=args.collection
     )
 
+def getStudies_cli() -> None:
+    global query
+    query = f"getStudies"
+    p = _initialize_parser(description=f"NBIAToolkit: {query}. Get studies from a collection.")
+
+    p.add_argument(
+        "-c",
+        "--collection",
+        action="store",
+        required=True,
+        type=str,
+    )
+
+    p.add_argument(
+        "-p",
+        "--patientID",
+        action="store",
+        default="",
+        type=str,
+    )
+
+    p.add_argument(
+        "-s", "--studyInstanceUID",
+        action="store",
+        default="",
+        type=str,
+    )
+
+    args = _add_extra_args(p)
+
+    return getResults_cli(func=NBIAClient(args.username, args.password).getStudies, Collection=args.collection, PatientID=args.patientID, StudyInstanceUID=args.studyInstanceUID)
+
+
+
 
 def getSeries_cli() -> None:
     global query
@@ -367,6 +403,22 @@ def getSeries_cli() -> None:
         Manufacturer=args.manufacturer,
     )
 
+def getNewSeries_cli() -> None:
+    global query
+    query = f"newSeries"
+    p = _initialize_parser(description=f"NBIAToolkit: {query}. Get new series from a collection since a given date.")
+
+    p.add_argument(
+        "-d", "--date",
+        action="store",
+        required=True,
+        type=str,
+        help="The date to filter by, i.e '2021-01-01' or '2019/12/31",
+    )
+
+    args = _add_extra_args(p)
+
+    return getResults_cli(func=NBIAClient(args.username, args.password).getNewSeries, Date=args.date)
 
 def downloadSingleSeries_cli() -> None:
     global query