added functionality to remove participants from dpr

scripts/remove_slide.py

@@ -1,92 +1,153 @@
-import sys
 from pymongo import MongoClient
 import os
+import argparse
 
 
-def remove_links(slide_id):
-    targets = [
-        f'/data/deepZoomImages/{slide_id}_files',
-        f'/data/deepZoomImages/{slide_id}.dzi',
-        f'/data/deepZoomImages/tn_{slide_id}.jpeg'
-    ]
-    for target in targets:
-        if os.path.islink(target) or os.path.exists(target):
-            try:
-                os.remove(target)
-                print(f"Removed link or file: {target}")
-            except Exception as e:
-                print(f"Failed to remove {target}: {e}")
+class Main:
+    def __init__(self):
+        self.client, self.collection = self.create_connection()
+        self.remove_if_block_from_linksh = self.remove_if_block_from_linksh
+        self.remove_links = self.remove_links
+        self.remove_slide = self.remove_slide
+        self.remove_participant = self.remove_participant
 
-def remove_if_block_from_linksh(slide_id, link_sh_path):
-    if not os.path.exists(link_sh_path):
-        print(f"link.sh not found at {link_sh_path}")
-        return
-    with open(link_sh_path, "r") as f:
-        lines = f.readlines()
+    def create_connection(self):
+        uri = "mongodb://localhost:27017"
+        db_name = "knowledgeEnvironment"
+        collection_name = "patients"
+
+        client = MongoClient(uri)
+        db = client[db_name]
+        collection = db[collection_name]
+
+        return client, collection
 
-    new_lines = []
-    inside_if = False
-    block_buffer = []
+    def remove_links(self, slide_id):
+        targets = [
+            f'/data/deepZoomImages/{slide_id}_files',
+            f'/data/deepZoomImages/{slide_id}.dzi',
+            f'/data/deepZoomImages/tn_{slide_id}.jpeg'
+        ]
+        for target in targets:
+            if os.path.islink(target) or os.path.exists(target):
+                try:
+                    os.remove(target)
+                    print(f"Removed link or file: {target}")
+                except Exception as e:
+                    print(f"Failed to remove {target}: {e}")
 
-    for line in lines:
-        if line.strip().startswith("if ! [ -L "):
-            inside_if = True
-            block_buffer = [line]
-            continue
-        if inside_if:
-            block_buffer.append(line)
-            if line.strip() == "fi":
-                block_str = "".join(block_buffer)
-                if slide_id in block_str:
-                    inside_if = False
-                    block_buffer = []
-                    continue
-                else:
-                    new_lines.extend(block_buffer)
-                    inside_if = False
-                    block_buffer = []
-            continue
-        new_lines.append(line)
+    def remove_if_block_from_linksh(self, slide_id, link_sh_path):
+        if not os.path.exists(link_sh_path):
+            print(f"link.sh not found at {link_sh_path}")
+            return
+        with open(link_sh_path, "r") as f:
+            lines = f.readlines()
 
-    with open(link_sh_path, "w") as f:
-        f.writelines(new_lines)
-    print(f"Removed if block containing slide id '{slide_id}' from {link_sh_path}")
-
+        new_lines = []
+        inside_if = False
+        block_buffer = []
 
-if len(sys.argv) < 2:
-    print("Usage: python removeSlide.py <slideName>")
-    sys.exit(1)
+        for line in lines:
+            if line.strip().startswith("if ! [ -L "):
+                inside_if = True
+                block_buffer = [line]
+                continue
+            if inside_if:
+                block_buffer.append(line)
+                if line.strip() == "fi":
+                    block_str = "".join(block_buffer)
+                    if slide_id in block_str:
+                        inside_if = False
+                        block_buffer = []
+                        continue
+                    else:
+                        new_lines.extend(block_buffer)
+                        inside_if = False
+                        block_buffer = []
+                continue
+            new_lines.append(line)
 
-slide_name = sys.argv[1]
-uri = "mongodb://localhost:27017"
-db_name = "knowledgeEnvironment"
-collection_name = "patients"
-link_sh_path = "/data/deepZoomImages/link.sh"
+        with open(link_sh_path, "w") as f:
+            f.writelines(new_lines)
+        print(f"Removed if block containing slide id '{slide_id}' from {link_sh_path}")
 
-client = MongoClient(uri)
-db = client[db_name]
-collection = db[collection_name]
+    def remove_slide(self, slide_name):
+        link_sh_path = "/data/deepZoomImages/link.sh"
+        client, collection = self.create_connection()
 
-query = {"slides.slideName": slide_name}
-found_docs = list(collection.find(query))
+        query = {"slides.slideName": slide_name}
+        found_docs = list(collection.find(query))
 
-if len(found_docs) == 1:
-    for doc in found_docs:
-        kpmp_id = doc.get("kpmp_id")
-        slides = doc.get("slides", [])
-        for slide in slides:
-            if slide.get("slideName") == slide_name:
-                slide_id = slide.get("_id")
-                if kpmp_id and slide_id:
-                    remove_links(slide_id)
-                    remove_if_block_from_linksh(slide_id, link_sh_path)
+        if len(found_docs) == 1:
+            for doc in found_docs:
+                kpmp_id = doc.get("kpmp_id")
+                slides = doc.get("slides", [])
+                for slide in slides:
+                    if slide.get("slideName") == slide_name:
+                        slide_id = slide.get("_id")
+                        if kpmp_id and slide_id:
+                            self.remove_links(slide_id)
+                            self.remove_if_block_from_linksh(slide_id, link_sh_path)
 
-                    update = {"$pull": {"slides": {"slideName": slide_name}}}
-                    result = collection.update_many(query, update)
-                    print(f"\nRemoved slide '{slide_name}' from {result.modified_count} document(s).")
-elif len(found_docs) > 1:
-    print(f"Error: Found multiple documents with slide name '{slide_name}'.")
-else:
-    print(f"No documents found with slide name '{slide_name}'.")
-
-client.close()
+                            update = {"$pull": {"slides": {"slideName": slide_name}}}
+                            result = collection.update_many(query, update)
+                            print(f"\nRemoved slide '{slide_name}' from {result.modified_count} document(s).")
+        elif len(found_docs) > 1:
+            print(f"Error: Found multiple documents with slide name '{slide_name}'.")
+        else:
+            print(f"No documents found with slide name '{slide_name}'.")
+
+        client.close()
+
+    def remove_participant(self, participant_id):
+        link_sh_path = "/data/deepZoomImages/link.sh"
+        client, collection = self.create_connection()
+        query = {"kpmp_id": participant_id}
+        found_docs = list(collection.find(query))
+        if len(found_docs) == 1:
+            for doc in found_docs:
+                    slides = doc.get("slides", [])
+                    for slide in slides:
+                        slide_id = slide.get("_id")
+                        self.remove_links(slide_id)
+                        self.remove_if_block_from_linksh(slide_id, link_sh_path)
+            result = collection.delete_one(query)
+            if result.deleted_count > 0:
+                 print(f"Removed participant with kpmp_id '{participant_id}'.")
+            else:
+                print(f"Failed to remove participant from patients collection with kpmp_id '{participant_id}'.")
+        elif len(found_docs) > 1:
+            print(f"Error: Found multiple participants with kpmp_id '{participant_id}'.")
+
+        elif len(found_docs) == 0:
+            print(f"No participant found with kpmp_id '{participant_id}'.")
+        client.close()
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-s",
+        "--slide_name",
+        type=str,
+        help="Name of the slide to remove without an extension (e.g., 'sample-id_HE_1of2' )",
+    )
+    parser.add_argument(
+        "-a",
+        "--action",
+        choices=['remove-slide', 'remove-participant'],
+        required=True,
+        help="remove-slide: Remove a slide from the database and filesystem."
+             "remove-participant: Remove a participant from the database.",
+    )
+    parser.add_argument(
+        "-p",
+        "--participant_id",
+        type=str,
+        help="kpmp_id of the participant to remove from the database.",
+    )
+    args = parser.parse_args()
+    main = Main()
+    if args.action == 'remove-slide':
+        result = main.remove_slide(args.slide_name)
+    elif args.action == 'remove-participant':
+        result = main.remove_participant(args.participant_id)