Merge pull request #82 from jjjermiah/70-feat-implement-user-and-pass…

…word-for-clie

70 feat implement user and password for cli

README.md

@@ -54,24 +54,21 @@ Version: 0.21.1
 
 Available CLI tools: 
 
-getCollections [-h] [-p PREFIX] [-o OUTPUTFILE] [--version]
+getPatients [-h] [-u USERNAME] [-p PASSWORD] -c COLLECTION
+            [-o OUTPUTFILE] [--version]
 
-getPatients [-h] -c COLLECTION [-o OUTPUTFILE] [--version]
+getNewPatients [-h] [-u USERNAME] [-p PASSWORD] -c COLLECTION -d DATE
+               [-o OUTPUTFILE] [--version]
 
-getBodyPartCounts [-h] [-c COLLECTION] [-o OUTPUTFILE] [--version]
+getBodyPartCounts [-h] [-u USERNAME] [-p PASSWORD] [-c COLLECTION]
+                  [-o OUTPUTFILE] [--version]
 
-getSeries [-h] [-c COLLECTION] [-p PATIENTID] [-m MODALITY]
-          [-study STUDYINSTANCEUID]
-          [--seriesInstanceUID SERIESINSTANCEUID]
-          [--bodyPartExamined BODYPARTEXAMINED]
-          [--manufacturerModelName MANUFACTURERMODELNAME]
-          [--manufacturer MANUFACTURER] [-o OUTPUTFILE] [--version]
+downloadSingleSeries [-h] [-u USERNAME] [-p PASSWORD] --seriesUID
+                     SERIESUID --downloadDir DOWNLOADDIR
+                     [--filePattern FILEPATTERN] [--overwrite]
 
-downloadSingleSeries [-h] --seriesUID SERIESUID --downloadDir
-                     DOWNLOADDIR [--filePattern FILEPATTERN]
-                     [--overwrite]
-
-dicomsort [-h] [--targetPattern TARGETPATTERN] [--truncateUID]
+dicomsort [-h] [-u USERNAME] [-p PASSWORD]
+          [--targetPattern TARGETPATTERN] [--truncateUID]
           [--sanitizeFilename] [--overwrite] [--nParallel NPARALLEL]
           sourceDir destinationDir
 

pyproject.toml

@@ -14,6 +14,7 @@ getPatients = "nbiatoolkit.nbia_cli:getPatients_cli"
 getBodyPartCounts = "nbiatoolkit.nbia_cli:getBodyPartCounts_cli"
 downloadSingleSeries = "nbiatoolkit.nbia_cli:downloadSingleSeries_cli"
 getSeries = "nbiatoolkit.nbia_cli:getSeries_cli"
+getNewPatients = "nbiatoolkit.nbia_cli:getNewPatients_cli"
 
 [tool.poetry.dependencies]
 python = ">=3.10 || 3.12"

src/nbiatoolkit/nbia_cli.py

@@ -29,6 +29,7 @@ def version():
     commands = [
         "getCollections",
         "getPatients",
+        "getNewPatients",
         "getBodyPartCounts",
         "getSeries",
         "downloadSingleSeries",
@@ -45,8 +46,30 @@ def version():
 
     return
 
+def _initialize_parser(description: str) -> argparse.ArgumentParser:
+    p = argparse.ArgumentParser(description=description)
+
+    # create an argparse group called "Credentials" to hold the username and password arguments
+    credentials = p.add_argument_group(
+        title="authentication parameters",
+        description="The username and password for the NBIA API if querying restricted datasets, defaults to the NBIA Guest Account")
+
+    credentials.add_argument(
+        "-u",  "--username", action="store", type=str, default= "nbia_guest", #help="Username for the NBIA API (default: nbia_guest)"
+    )
+
+    credentials.add_argument(
+        "-p", "--password", action="store", type=str, default= "", #help="Password for the NBIA API (default: '')"
+    )
+
+    # make the credentials group show up first
+    p._action_groups.insert(0, p._action_groups.pop())
+
+    return p
+
+def _add_extra_args(parser: argparse.ArgumentParser) -> argparse.Namespace:
+
 
-def general_parser(parser: argparse.ArgumentParser) -> argparse.Namespace:
     parser.add_argument(
         "-o",
         "--output",
@@ -175,7 +198,7 @@ def cli_wrapper(func, **kwargs) -> List[str] | None:
 def getPatients_cli() -> None:
     global query
     query = "patients"
-    p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
+    p = _initialize_parser(description=f"NBIAToolkit: {query} ")
 
     p.add_argument(
         "-c",
@@ -185,15 +208,15 @@ def getPatients_cli() -> None:
         type=str,
     )
 
-    args = general_parser(p)
+    args = _add_extra_args(p)
 
-    return getResults_cli(func=NBIAClient().getPatients, Collection=args.collection)
+    return getResults_cli(func=NBIAClient(args.username, args.password).getPatients, Collection=args.collection)
 
 
 def getCollections_cli() -> None:
     global query
     query = "collections"
-    p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
+    p = _initialize_parser(description=f"NBIAToolkit: {query} ")
 
     p.add_argument(
         "-p",
@@ -204,17 +227,41 @@ def getCollections_cli() -> None:
         help="The prefix to filter collections by, i.e 'TCGA', 'LIDC', 'NSCLC'",
     )
 
-    args = general_parser(p)
+    args = _add_extra_args(p)
+
+    return getResults_cli(func=NBIAClient(args.username, args.password).getCollections, prefix=args.prefix)
+
+def getNewPatients_cli() -> None:
+    global query
+    query = "newPatients"
+    p = _initialize_parser(description=f"NBIAToolkit: {query}. Get new patients from a collection since a given date.")
+
+    p.add_argument(
+        "-c",
+        "--collection",
+        action="store",
+        required=True,
+        type=str,
+    )
+
+    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",
+    )
 
-    return getResults_cli(func=NBIAClient().getCollections, prefix=args.prefix)
+    args = _add_extra_args(p)
 
+    return getResults_cli(func=NBIAClient(args.username, args.password).getNewPatients, Collection=args.collection, Date=args.date)
 
 def getBodyPartCounts_cli() -> None:
     global query
     global output
     query = f"BodyPartCounts"
 
-    p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
+    p = _initialize_parser(description=f"NBIAToolkit: {query} ")
 
     p.add_argument(
         "-c",
@@ -225,10 +272,10 @@ def getBodyPartCounts_cli() -> None:
         type=str,
     )
 
-    args = general_parser(p)
+    args = _add_extra_args(p)
 
     return getResults_cli(
-        func=NBIAClient().getBodyPartCounts, Collection=args.collection
+        func=NBIAClient(args.username, args.password).getBodyPartCounts, Collection=args.collection
     )
 
 
@@ -237,7 +284,7 @@ def getSeries_cli() -> None:
     global output
     query = f"series"
 
-    p = argparse.ArgumentParser(description=f"NBIAToolkit: {query} ")
+    p = _initialize_parser(description=f"NBIAToolkit: {query} ")
 
     p.add_argument(
         "-c",
@@ -307,9 +354,9 @@ def getSeries_cli() -> None:
         type=str,
     )
 
-    args = general_parser(p)
+    args = _add_extra_args(p)
     return getResults_cli(
-        func=NBIAClient().getSeries,
+        func=NBIAClient(args.username, args.password).getSeries,
         Collection=args.collection,
         PatientID=args.patientID,
         StudyInstanceUID=args.studyInstanceUID,
@@ -326,7 +373,7 @@ def downloadSingleSeries_cli() -> None:
     query = f"series"
     # use the NBIAClient._downloadSingleSeries function to download a single series
 
-    p = argparse.ArgumentParser(description="NBIAToolkit: download a single series")
+    p = _initialize_parser(description="NBIAToolkit: download a single series")
 
     p.add_argument(
         "--seriesUID",
@@ -364,7 +411,7 @@ def downloadSingleSeries_cli() -> None:
     args = p.parse_args()
 
     return getResults_cli(
-        func=NBIAClient()._downloadSingleSeries,
+        func=NBIAClient(args.username, args.password)._downloadSingleSeries,
         SeriesInstanceUID=args.seriesUID,
         downloadDir=args.downloadDir,
         filePattern=args.filePattern,
@@ -379,7 +426,7 @@ def downloadSingleSeries_cli() -> None:
 
 
 def DICOMSorter_cli():
-    parser = argparse.ArgumentParser(
+    parser = _initialize_parser(
         description="NBIAToolkit: Sort DICOM files into destination directory according to target pattern."
     )