fs issues

bloom_env.yaml

@@ -22,6 +22,7 @@ dependencies:
   - jq
   - fd-find
   - rclone
+  - gunicorn
   - pip:
     - zebra_day==0.3.4 
     - fedex_tracking_day==0.2.8

bloom_lims/bin/kill_proc_holding_port.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Function to kill processes by port
+kill_processes_by_port() {
+    local port=$1
+    local pids=$(lsof -t -i:$port)
+
+    if [ -z "$pids" ]; then
+        echo "No processes found running on port $port."
+        return
+    fi
+
+    echo "Found processes running on port $port: $pids"
+
+    echo "Sending SIGTERM to processes..."
+    for pid in $pids; do
+        sudo kill -TERM $pid
+    done
+
+    # Wait for a moment to ensure processes receive the signal
+    sleep 2
+
+    echo "Sending SIGKILL to processes..."
+    for pid in $pids; do
+        sudo kill -KILL $pid
+    done
+
+    # Wait for a moment to ensure processes are killed
+    sleep 2
+
+    echo "Using fuser to release port $port..."
+    sudo fuser -k $port/tcp
+
+    # Verify if any processes are still running on the port
+    remaining_pids=$(lsof -t -i:$port)
+    if [ -z "$remaining_pids" ]; then
+        echo "All processes on port $port have been terminated."
+    else
+        echo "Processes still running on port $port: $remaining_pids"
+        echo "Attempting to kill remaining processes with SIGKILL..."
+        for pid in $remaining_pids; do
+            sudo kill -KILL $pid
+        done
+    fi
+
+    # Final check
+    final_pids=$(lsof -t -i:$port)
+    if [ -z "$final_pids" ]; then
+        echo "All processes on port $port have been terminated."
+    else
+        echo "Failed to terminate processes: $final_pids"
+    fi
+}
+
+# Check if a port is provided
+if [ -z "$1" ]; then
+    echo "Usage: $0 <port>"
+    exit 1
+fi
+
+# Run the function to kill processes on the specified port
+kill_processes_by_port $1

bloom_lims/bobjs.py

@@ -701,9 +701,27 @@ def query_instance_by_component_v2(
 
 
     # should abstract to not assume properties key
-    def get_unique_property_values(self, property_key):
+    def get_unique_property_values(self, property_key, super_type=None, btype=None, b_sub_type=None, version=None):
+
         json_path = property_key.split("->")
+
+        # Start building the query with the base table
         query = self.session.query(
+            self.Base.classes.generic_instance
+        )
+
+        # Add filters based on the provided arguments
+        if super_type:
+            query = query.filter(self.Base.classes.generic_instance.super_type == super_type)
+        if btype:
+            query = query.filter(self.Base.classes.generic_instance.btype == btype)
+        if b_sub_type:
+            query = query.filter(self.Base.classes.generic_instance.b_sub_type == b_sub_type)
+        if version:
+            query = query.filter(self.Base.classes.generic_instance.version == version)
+
+        # Add the JSON path extraction and distinct filtering after the base filters
+        query = query.with_entities(
             func.distinct(
                 func.jsonb_extract_path_text(
                     self.Base.classes.generic_instance.json_addl['properties'], *json_path
@@ -713,11 +731,17 @@ def get_unique_property_values(self, property_key):
             func.jsonb_extract_path_text(
                 self.Base.classes.generic_instance.json_addl['properties'], *json_path
             ).isnot(None)
-        ).all()
+        )
+
+        # Execute the query and get the results
+        results = query.all()
+
+        # Extract unique values from the query results
+        unique_values = [value[0] for value in results if value[0] is not None]
 
-        unique_values = [value[0] for value in query if value[0] is not None]
         return unique_values
 
+
     def query_template_by_component_v2(
         self, super_type=None, btype=None, b_sub_type=None, version=None
     ):
@@ -2862,7 +2886,7 @@ def create_file(
         else:
             logging.warning(f"No data provided for file creation: {file_data, url}")
             new_file.bstatus = "no file data provided"
-            self.session.commit()
+            self.session.commit() 
 
         if create_locked:
             self.lock_file(new_file.euid)

bloom_lims/config/file/file_set.json

@@ -3,12 +3,27 @@
     "1.0": {
       "description": "Generic File Set",
       "properties": {
-        "name": "A Generic File Set",
+        "name": "",
         "comments": "",
         "lab_code":"",
         "tag":"",
-        "description":""
+        "tags":[],
+        "duration":"",
+        "ref_type":"",
+        "description":"",
+        "creating_user": "",
+        "rclone_config": {}
       },
+      "ui_form_properties" : [ 
+        {"property_key":"name","form_label":"Set Name", "required": false, "value_type": "string"}, 
+        {"property_key":"description","form_label":"Set Description", "required": false, "value_type":"string"},
+        {"property_key":"tag","form_label":"Tag", "required": false, "value_type":"uid-interactive"},
+        {"property_key":"tags","form_label":"Tags", "required": false, "value_type":"list"},
+        {"property_key": "creating_user", "form_label":"Creating User", "required":false, "value_type":"uid-static"},
+        {"property_key": "ref_type", "form_label":"Ref Type", "required":false, "value_type":"query-only-uid-statuc"},
+        {"property_key": "comments", "form_label": "Comments", "required": false, "value_type": "string"}       
+      ],
+      "controlled_properties": { },
       "expected_inputs": [],
       "expected_outputs": [],
       "singleton": "0",

bloom_shell.py

@@ -5,8 +5,8 @@
 import sys
 import os
 
-bobdb = BloomObj(BLOOMdb3())
+bob = BloomObj(BLOOMdb3())
 
 
 from IPython import embed
-embed()
+embed()