Merge branch 'master' into pixi

Author: jennydaman

pfcon/base_storage.py

@@ -3,8 +3,9 @@
 """
 
 import logging
+import os
 import abc
-import shutil
+import shutil, errno
 
 
 logger = logging.getLogger(__name__)
@@ -38,3 +39,76 @@ def delete_data(self, job_dir):
         Delete job data from the local storage.
         """
         shutil.rmtree(job_dir)
+
+    def process_chrislink_files(self, job_incoming_dir):
+        """
+        Rearrange the local job incoming directory tree by creating folders that trace
+        the source dirs pointed by ChRIS link files.
+        """
+        self.job_incoming_dir = job_incoming_dir
+        self._linked_paths = set()
+        self._nlinks = 0
+        self._already_copied_src_set = set()
+
+        self._process_chrislink_files(job_incoming_dir)
+
+        linked_path_top_folders = set()
+        for path in self._linked_paths:
+            linked_path_top_folders.add(path.split('/', 1)[0])
+
+        for folder in linked_path_top_folders:
+            if folder not in self._linked_paths:
+                self.deletesrc(os.path.join(job_incoming_dir, folder))
+
+        return self._nlinks
+
+    def _process_chrislink_files(self, dir):
+        """
+        Recursively expand (substitute by actual folders) and remove ChRIS link files.
+        """
+        for root, dirs, files in os.walk(dir):
+            for filename in files:
+                if filename.endswith('.chrislink'):
+                    link_file_path = os.path.join(root, filename)
+
+                    if not link_file_path.startswith(tuple(self._already_copied_src_set)):  # only expand a link once
+                        with open(link_file_path, 'rb') as f:
+                            rel_path = f.read().decode().strip()
+                            abs_path = os.path.join(self.job_incoming_dir, rel_path)
+
+                            if os.path.isfile(abs_path):
+                                rel_path = os.path.dirname(rel_path)
+                                abs_path = os.path.dirname(abs_path)
+
+                            source_trace_dir = rel_path.replace('/', '_')
+                            dst_path = os.path.join(root, source_trace_dir)
+
+                            if not os.path.isdir(dst_path):  # only copy once to a dest path
+                                self.copysrc(abs_path, dst_path)
+                                self._already_copied_src_set.add(abs_path)
+                                self._process_chrislink_files(dst_path)  # recursive call
+
+                            self._linked_paths.add(rel_path)
+
+                        os.remove(link_file_path)
+                        self._nlinks += 1
+
+    @staticmethod
+    def copysrc(src, dst):
+        try:
+            shutil.copytree(src, dst)
+        except OSError as e:
+            if e.errno in (errno.ENOTDIR, errno.EINVAL):
+                shutil.copy(src, dst)
+            else:
+                raise
+
+    @staticmethod
+    def deletesrc(src):
+        try:
+            shutil.rmtree(src)
+        except OSError as e:
+            if e.errno in (errno.ENOTDIR, errno.EINVAL):
+                os.remove(src)
+            else:
+                raise

pfcon/config.py

@@ -28,7 +28,7 @@ def __init__(self):
 
         if self.PFCON_INNETWORK:
             self.STORAGE_ENV = env('STORAGE_ENV', 'swift')
-            if self.STORAGE_ENV not in ('swift', 'filesystem'):
+            if self.STORAGE_ENV not in ('swift', 'filesystem', 'fslink'):
                 raise ValueError(f"Unsupported value '{self.STORAGE_ENV}' for STORAGE_ENV")
         else:
             self.STORAGE_ENV = env('STORAGE_ENV', 'zipfile')

pfcon/filesystem_storage.py

@@ -1,6 +1,8 @@
 """
-Handle filesystem-based (eg. mounted directory) storage. This is used when pfcon is
-in-network and configured to directly access the data from a filesystem.
+Handle filesystem-based storage. This is used when pfcon is in-network and configured
+to directly access the data from a ChRIS shared filesystem. It assumes that both the
+input (read-only)and the output (read-write) directories in the shared storage are
+directly mounted into the plugin container.
 """
 
 import logging
@@ -24,7 +26,7 @@ def __init__(self, config):
 
         self.fs_mount_base_dir = config.get('STOREBASE_MOUNT')
 
-    def store_data(self, job_id, job_incoming_dir, data=None, **kwargs):
+    def store_data(self, job_id, job_incoming_dir, data, **kwargs):
         """
         Count the number of files in the specified job incoming directory.
         """

pfcon/fslink_storage.py

@@ -0,0 +1,114 @@
+"""
+Handle filesystem-based storage. This is used when pfcon is in-network and configured
+to directly access the data from a ChRIS shared filesystem. It only assumes that the
+output (read-write) directory in the shared storage is directly mounted into the plugin
+container. Unlike the 'filesystem' storage this supports ChRIS links.
+"""
+
+import logging
+import datetime
+import os
+import shutil
+
+
+from .filesystem_storage import FileSystemStorage
+
+
+logger = logging.getLogger(__name__)
+
+
+class FSLinkStorage(FileSystemStorage):
+
+    def store_data(self, job_id, job_incoming_dir, data, **kwargs):
+        """
+        Copy all the files from the filesystem tree under each input folder (storage
+        prefix) in the specified data list into the specified job incoming directory.
+        """
+        self.job_id = job_id
+        self.job_output_path = kwargs['job_output_path']
+
+        all_file_paths = set()
+
+        for storage_path in data:
+            storage_path = storage_path.strip('/')
+            file_paths = set()
+            visited_paths = set()
+
+            self._find_all_file_paths(storage_path, file_paths, visited_paths)
+
+            for f_path in file_paths:
+                if f_path not in all_file_paths:  # copy a given file only once
+                    fs_file_path = os.path.join(self.fs_mount_base_dir, f_path)
+
+                    rel_file_path = f_path.replace(storage_path, '', 1).lstrip('/')
+                    local_file_path = os.path.join(job_incoming_dir, rel_file_path)
+
+                    try:
+                        shutil.copy(fs_file_path, local_file_path)
+                    except FileNotFoundError:
+                        os.makedirs(os.path.dirname(local_file_path))
+                        shutil.copy(fs_file_path, local_file_path)
+
+                    all_file_paths.add(f_path)
+
+        nfiles = len(all_file_paths)
+        logger.info(f'{nfiles} files fetched from the filesystem for job {job_id}')
+
+        nlinks = self.process_chrislink_files(job_incoming_dir)
+        nfiles -= nlinks
+
+        return {
+            'jid': job_id,
+            'nfiles': nfiles,
+            'timestamp': f'{datetime.datetime.now()}',
+            'path': job_incoming_dir
+        }
+
+    def delete_data(self, job_dir):
+        """
+        Delete job data from the local storage.
+        """
+        shutil.rmtree(job_dir)
+
+    def _find_all_file_paths(self, storage_path, file_paths, visited_paths):
+        """
+        Find all file paths under the passed storage path (prefix) by
+        recursively following ChRIS links. The resulting set of file paths is given
+        by the file_paths set argument.
+        """
+        if not storage_path.startswith(tuple(visited_paths)):  # avoid infinite loops
+            visited_paths.add(storage_path)
+            job_id = self.job_id
+            job_output_path = self.job_output_path
+            fs_abs_path = os.path.join(self.fs_mount_base_dir, storage_path)
+
+            l_ls = []
+            if os.path.isfile(fs_abs_path):
+                l_ls.append(fs_abs_path)
+            else:
+                for root, dirs, files in os.walk(fs_abs_path):
+                    for filename in files:
+                        l_ls.append(os.path.join(root, filename))
+
+            for abs_file_path in l_ls:
+                if abs_file_path.endswith('.chrislink'):
+                    try:
+                        with open(abs_file_path, 'rb') as f:
+                            linked_path =  f.read().decode().strip()
+                    except Exception as e:
+                        logger.error(f'Failed to read file {abs_file_path} for '
+                                     f'job {job_id}, detail: {str(e)}')
+                        raise
+
+                    if f'{job_output_path}/'.startswith(linked_path.rstrip('/') + '/'):
+                        # link files are not allowed to point to the job output dir or
+                        # any of its ancestors
+                        logger.error(f'Found invalid input path {linked_path} for job '
+                                     f'{job_id} pointing to an ancestor of the job '
+                                     f'output dir: {job_output_path}')
+                        raise ValueError(f'Invalid input path: {linked_path}')
+
+                    self._find_all_file_paths(linked_path, file_paths,
+                                              visited_paths)  # recursive call
+                file_paths.add(abs_file_path.replace(self.fs_mount_base_dir, '',
+                                                  1).lstrip('/'))

pfcon/resources.py

@@ -13,6 +13,7 @@
 from .zip_file_storage import ZipFileStorage
 from .swift_storage import SwiftStorage
 from .filesystem_storage import FileSystemStorage
+from .fslink_storage import FSLinkStorage
 
 
 logger = logging.getLogger(__name__)
@@ -80,7 +81,7 @@ def post(self):
         if self.pfcon_innetwork:
             if args.input_dirs is None:
                 abort(400, message='input_dirs: field is required')
-            if self.storage_env == 'filesystem' and args.output_dir is None:
+            if args.output_dir is None:
                 abort(400, message='output_dir: field is required')
         else:
             if request.files['data_file'] is None:
@@ -99,31 +100,50 @@ def post(self):
             input_dir = args.input_dirs[0].strip('/')
             output_dir = args.output_dir.strip('/')
             incoming_dir = os.path.join(self.storebase_mount, input_dir)
+
             storage = FileSystemStorage(app.config)
             try:
-                d_info = storage.store_data(job_id, incoming_dir)
+                d_info = storage.store_data(job_id, incoming_dir, None)
             except Exception as e:
                 logger.error(f'Error while accessing files from shared filesystem '
                              f'for job {job_id}, detail: {str(e)}')
-                abort(400, message='input_dirs: Error accessing files from shared '
-                                   'filesystem')
+                abort(400,
+                      message='input_dirs: Error accessing files from shared filesystem')
         else:
             incoming_dir = os.path.join(self.storebase_mount, input_dir)
-            outgoing_dir = os.path.join(self.storebase_mount, output_dir)
             os.makedirs(incoming_dir, exist_ok=True)
-            os.makedirs(outgoing_dir, exist_ok=True)
 
             if self.pfcon_innetwork:
                 if self.storage_env == 'swift':
+                    outgoing_dir = os.path.join(self.storebase_mount, output_dir)
+                    os.makedirs(outgoing_dir, exist_ok=True)
+
                     storage = SwiftStorage(app.config)
                     try:
-                        d_info = storage.store_data(job_id, incoming_dir, args.input_dirs)
+                        d_info = storage.store_data(job_id, incoming_dir, args.input_dirs,
+                                                    job_output_path=args.output_dir.strip('/'))
                     except ClientException as e:
                         logger.error(f'Error while fetching files from swift and '
                                      f'storing job {job_id} data, detail: {str(e)}')
-                        abort(400, message='input_dirs: Error fetching files from swift')
+                        abort(400,
+                              message='input_dirs: Error fetching files from swift')
+
+                elif self.storage_env == 'fslink':
+                    output_dir = args.output_dir.strip('/')
+                    storage = FSLinkStorage(app.config)
+                    try:
+                        d_info = storage.store_data(job_id, incoming_dir, args.input_dirs,
+                                                    job_output_path=output_dir)
+                    except Exception as e:
+                        logger.error(f'Error while accessing files from shared filesystem '
+                                     f'and storing job {job_id} data, detail: {str(e)}')
+                        abort(400,
+                              message='input_dirs: Error copying files from shared filesystem')
             else:
                 if self.storage_env == 'zipfile':
+                    outgoing_dir = os.path.join(self.storebase_mount, output_dir)
+                    os.makedirs(outgoing_dir, exist_ok=True)
+
                     storage = ZipFileStorage(app.config)
                     data_file = request.files['data_file']
                     try:
@@ -187,11 +207,14 @@ def delete(self, job_id):
         storage = None
 
         if self.pfcon_innetwork:
-            if self.storage_env == 'swift':
+            if self.storage_env == 'filesystem':
+                storage = FileSystemStorage(app.config)
+
+            elif self.storage_env == 'swift':
                 storage = SwiftStorage(app.config)
 
-            elif self.storage_env == 'filesystem':
-                storage = FileSystemStorage(app.config)
+            elif self.storage_env == 'fslink':
+                storage = FSLinkStorage(app.config)
         else:
             if self.storage_env == 'zipfile':
                 storage = ZipFileStorage(app.config)
@@ -229,7 +252,7 @@ def get(self, job_id):
         download_name = f'{job_id}.zip'
         mimetype = 'application/zip'
 
-        if self.pfcon_innetwork and self.storage_env == 'filesystem':
+        if self.pfcon_innetwork and self.storage_env in ('filesystem', 'fslink'):
             job_output_path = request.args.get('job_output_path')
             if not job_output_path:
                 abort(400, message='job_output_path: query parameter is required')
@@ -239,7 +262,11 @@ def get(self, job_id):
             if not os.path.isdir(outgoing_dir):
                 abort(404)
 
-            storage = FileSystemStorage(app.config)
+            if self.storage_env == 'filesystem':
+                storage = FileSystemStorage(app.config)
+            else:
+                storage = FSLinkStorage(app.config)
+
             content = storage.get_data(job_id, outgoing_dir,
                                        job_output_path=job_output_path)
             download_name = f'{job_id}.json'