copy report file instead of symlink

delivery/models/runfolder.py

@@ -41,7 +41,8 @@ def __init__(
             self,
             file_path,
             base_path=None,
-            file_checksum=None
+            file_checksum=None,
+            file_operation="symlink"
     ):
         """
         A `RunfolderFile` object representing a file in the runfolder
@@ -54,11 +55,15 @@ def __init__(
         :param file_path: the path to the file
         :param base_path: a path relative to which the file will be considered
         :param file_checksum: a computed checksum for the file
+        :param file_operation: the file operation to perform, symlink (default) or copy
         """
         self.file_path = os.path.abspath(file_path)
         self.file_name = os.path.basename(file_path)
         self.base_path = base_path or os.path.dirname(self.file_path)
         self.checksum = file_checksum
+        self.file_operation = file_operation \
+            if file_operation and file_operation in ["symlink", "copy"] \
+            else "symlink"
 
     @classmethod
     def create_object_from_path(
@@ -68,7 +73,8 @@ def create_object_from_path(
             filesystem_service,
             metadata_service,
             base_path=None,
-            checksums=None
+            checksums=None,
+            file_operation="symlink"
     ):
         checksums = checksums or {}
         relative_file_path = filesystem_service.relpath(
@@ -83,5 +89,6 @@ def create_object_from_path(
         return cls(
             file_path,
             base_path=base_path,
-            file_checksum=checksum
+            file_checksum=checksum,
+            file_operation=file_operation
         )

delivery/models/sample.py

@@ -47,7 +47,9 @@ def __init__(
             read_no=None,
             is_index=None,
             base_path=None,
-            checksum=None):
+            checksum=None,
+            file_operation="symlink"
+    ):
         """
         A `SampleFile` object
 
@@ -64,11 +66,13 @@ def __init__(
         :param is_index: if True, the sequence file contains index sequences
         :param base_path: a path relative to which the file will be considered
         :param checksum: the MD5 checksum for this SampleFile
+        :param file_operation: the file operation to perform, symlink (default) or copy
         """
         super(SampleFile, self).__init__(
             sample_path,
             base_path=base_path,
-            file_checksum=checksum
+            file_checksum=checksum,
+            file_operation=file_operation
         )
         self.sample_name = sample_name
         self.sample_index = sample_index
@@ -88,4 +92,6 @@ def __hash__(self):
             self.lane_no,
             self.read_no,
             self.is_index,
-            self.checksum))
+            self.checksum,
+            self.file_operation
+        ))

delivery/repositories/project_repository.py

@@ -324,7 +324,8 @@ def get_project_readme(
                     filesystem_service=self.filesystem_service,
                     metadata_service=self.metadata_service,
                     base_path=self.filesystem_service.dirname(readme_file),
-                    checksums=checksums
+                    checksums=checksums,
+                    file_operation="copy"
                 )
             ]
         except FileNotFoundError:

delivery/services/file_system_service.py

@@ -1,6 +1,7 @@
 
 import os
 import logging
+import shutil
 
 log = logging.getLogger(__name__)
 
@@ -91,6 +92,19 @@ def symlink(self, source, link_name):
         self.makedirs(self.dirname(link_name), exist_ok=True)
         return os.symlink(source, link_name)
 
+    @staticmethod
+    def copy(source, dest):
+        """
+        Shadows shutil.copyfile
+        :param source:
+        :param dest:
+        :return: None
+        """
+        try:
+            return shutil.copyfile(source, dest)
+        except IsADirectoryError:
+            return shutil.copytree(source, dest, symlinks=True)
+
     @staticmethod
     def mkdir(path):
         """

delivery/services/organise_service.py

@@ -128,10 +128,11 @@ def organise_project(self, runfolder, project, organised_projects_path, lanes):
 
     def organise_project_file(self, project_file, organised_project_path):
         """
-        Find and symlink the project report to the organised project directory.
+        Find and symlink or copy the project-associated files to the organised project directory.
 
-        :param project: a Project instance representing the project before organisation
-        :param organised_project: a Project instance representing the project after organisation
+        :param project_file: a RunfolderFile instance representing the project-associated file
+        before organisation
+        :param organised_project_path: path where the project will be organised
         """
 
         # the relative path from the project file base to the project file (e.g. plots/filename.png)
@@ -145,11 +146,16 @@ def organise_project_file(self, project_file, organised_project_path):
             organised_project_path,
             relpath
         )
-        # the relative path from the symlink to the original file
-        link_path = self.file_system_service.relpath(
-            project_file.file_path,
-            self.file_system_service.dirname(link_name))
-        self.file_system_service.symlink(link_path, link_name)
+        if project_file.file_operation == "copy":
+            self.file_system_service.copy(project_file.file_path, link_name)
+        else:
+            # the relative path from the symlink to the original file
+            link_path = self.file_system_service.relpath(
+                project_file.file_path,
+                self.file_system_service.dirname(link_name)
+            )
+            self.file_system_service.symlink(link_path, link_name)
+
         return RunfolderFile(
             link_name,
             base_path=organised_project_path,
@@ -203,8 +209,15 @@ def organise_sample_file(self, sample_file, organised_sample_path, lanes):
 
         # create the symlink in the supplied directory and relative to the file's original location
         link_name = os.path.join(organised_sample_path, sample_file.file_name)
-        relative_path = self.file_system_service.relpath(sample_file.file_path, organised_sample_path)
-        self.file_system_service.symlink(relative_path, link_name)
+        if sample_file.file_operation == "copy":
+            self.file_system_service.copy(sample_file.file_path, link_name)
+        else:
+            relative_path = self.file_system_service.relpath(
+                sample_file.file_path,
+                organised_sample_path
+            )
+            self.file_system_service.symlink(relative_path, link_name)
+
         return SampleFile(
             sample_path=link_name,
             sample_name=sample_file.sample_name,