Use labxchem filepaths for synchweb attachments

Author: rowanwalker96

src/dlstbx/wrapper/pandda_xchem.py

@@ -106,7 +106,7 @@ def run(self):
 
             self.log.info(e.stdout)
             self.log.error(e.stderr)
-            self.send_attachments_to_ispyb(attachments, final_directory, batch)
+            self.send_attachments_to_ispyb(attachments, batch)
             return False
 
         restraints = compound_dir / f"{CompoundCode}.restraints.cif"
@@ -147,7 +147,7 @@ def run(self):
             self.log.info(e.stdout)
             with open(pandda2_log, "w") as log_file:
                 log_file.write(e.stdout)
-            self.send_attachments_to_ispyb(attachments, final_directory, batch)
+            self.send_attachments_to_ispyb(attachments, batch)
             return False
 
         with open(pandda2_log, "w") as log_file:
@@ -177,7 +177,7 @@ def run(self):
             self.log.info(
                 (f"No events in {events_yaml}, can't continue with PanDDA2 Rhofit")
             )
-            self.send_attachments_to_ispyb(attachments, final_directory, batch)
+            self.send_attachments_to_ispyb(attachments, batch)
             return False
 
         with open(events_yaml, "r") as file:
@@ -243,7 +243,7 @@ def run(self):
             self.log.error(f"Rhofit command: '{rhofit_command}' failed")
             self.log.info(e.stdout)
             self.log.error(e.stderr)
-            self.send_attachments_to_ispyb(attachments, final_directory, batch)
+            self.send_attachments_to_ispyb(attachments, batch)
             return True
 
         # -------------------------------------------------------
@@ -339,7 +339,7 @@ def run(self):
         # attachments.extend([json_results])
 
         self.log.info(f"Attachments list: {attachments}")
-        self.send_attachments_to_ispyb(attachments, final_directory, batch)
+        self.send_attachments_to_ispyb(attachments, batch)
 
         self.log.info(f"Auto PanDDA2 pipeline finished successfully for dtag {dtag}")
         return True
@@ -501,7 +501,7 @@ def get_contact_chain(self, protein_st, ligand_st):
 
         return min(chain_counts, key=lambda _x: chain_counts[_x])
 
-    def send_attachments_to_ispyb(self, attachments, final_directory, batch):
+    def send_attachments_to_ispyb(self, attachments, batch):
         if batch:  # synchweb attachments not supported for array job processing
             return
         for f in attachments:
@@ -524,9 +524,8 @@ def send_attachments_to_ispyb(self, attachments, final_directory, batch):
                 else:
                     continue
                 try:
-                    shutil.copy(f, final_directory)
                     result_dict = {
-                        "file_path": str(final_directory),
+                        "file_path": str(f.parents[0]),
                         "file_name": f.name,
                         "file_type": file_type,
                         "importance_rank": importance_rank,

src/dlstbx/wrapper/pipedream_xchem.py

@@ -2,7 +2,6 @@
 
 import json
 import os
-import shutil
 import sqlite3
 import subprocess
 from pathlib import Path
@@ -95,7 +94,7 @@ def run(self):
             )
             self.log.info(e.stdout)
             self.log.error(e.stderr)
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return False
 
         restraints = compound_dir / f"{CompoundCode}.restraints.cif"
@@ -152,7 +151,7 @@ def run(self):
                 stderr.write(e.stderr)
 
             attachments.extend([out_dir / "stderr.out"])
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return False
 
         self.log.info(f"Pipedream finished successfully for dtag {dtag}")
@@ -194,7 +193,7 @@ def run(self):
                 )
         except Exception as e:
             self.log.info(f"Can't continue with pipedream postprocessing: {e}")
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return True
 
         # Post-processing: Generate maps and run edstats
@@ -206,7 +205,7 @@ def run(self):
             os.system(f"gemmi sf2map --sample 5 {str(refine_mtz)} {map_fofc} 2>&1")
         except Exception as e:
             self.log.debug(f"Cannot continue with pipedream postprocessing: {e}")
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return True
 
         try:
@@ -229,15 +228,15 @@ def run(self):
             self.log.debug(
                 "Can't continue with pipedream postprocessing: resolution range None"
             )
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return True
 
         # Run edstats if both maps exist and resolution range is found
         if not map_2fofc.exists() or not map_fofc.exists():
             self.log.debug(
                 "Can't continue with pipedream postprocessing: maps not found"
             )
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return True
 
         edstats_out = postrefine_dir / "edstats.out"
@@ -258,13 +257,13 @@ def run(self):
             self.log.error(f"Edstats command: '{edstats_command}' failed")
             self.log.info(e.stdout)
             self.log.error(e.stderr)
-            self.send_attachments_to_ispyb(attachments, final_directory)
+            self.send_attachments_to_ispyb(attachments)
             return True
 
         self.log.info(f"Pipedream postprocessing finished successfully for dtag {dtag}")
 
         attachments.extend([edstats_out])
-        self.send_attachments_to_ispyb(attachments, final_directory)
+        self.send_attachments_to_ispyb(attachments)
         return True
 
     def process_pdb_file(self, dimple_pdb: Path):
@@ -355,7 +354,7 @@ def save_dataset_metadata(
             with open(json_file, "w", encoding="utf-8") as f:
                 json.dump(data, f, indent=2)
 
-    def send_attachments_to_ispyb(self, attachments, final_directory):
+    def send_attachments_to_ispyb(self, attachments):
         for f in attachments:
             if f.exists():
                 if f.suffix == ".html":
@@ -382,9 +381,8 @@ def send_attachments_to_ispyb(self, attachments, final_directory):
                 else:
                     continue
                 try:
-                    shutil.copy(f, final_directory)
                     result_dict = {
-                        "file_path": str(final_directory),
+                        "file_path": str(f.parents[0]),
                         "file_name": f.name,
                         "file_type": file_type,
                         "importance_rank": importance_rank,