RE2022-209: workspace uploader (working script)

src/loaders/common/loader_common_names.py

@@ -5,6 +5,11 @@
 
 # Arguments Descriptions
 
+# Name for root directory argument
+ROOT_DIR_ARG_NAME = "root_dir"
+# Description of the --root_dir argument in various loaders programs.
+ROOT_DIR_DESCR = "Root directory for the collections project."
+
 # Name for load version argument
 LOAD_VER_ARG_NAME = "load_ver"
 # Description of the --load_ver argument in various loaders programs.
@@ -33,6 +38,7 @@
 """
 File structure at NERSC for loader programs
 """
+WS = "WS"  # workspace
 
 ROOT_DIR = (
     "/global/cfs/cdirs/kbase/collections"  # root directory for the collections project
@@ -71,7 +77,7 @@
 # JSON keys in the download metadata file in a download directory
 SOURCE_METADATA_FILE_KEYS = ["upa", "name", "type", "timestamp"]
 # callback server docker image name
-CALLBACK_IMAGE_NAME = "scanon/callback"
+CALLBACK_IMAGE_NAME = "kbase/callback:test"  #TODO switch to kbase/callback:latest
 
 # a list of IDs provided to the computation script
 DATA_ID_COLUMN_HEADER = "genome_id"  # TODO DATA_ID change to data ID for generality
@@ -120,3 +126,8 @@
 # TODO DOWNLOAD if we settle on a standard file name scheme for downloaders we can get
 #               rid of this
 STANDARD_FILE_EXCLUDE_SUBSTRINGS = ['cds_from', 'rna_from', 'ERR']
+
+KB_BASE_URL_MAP = {'CI': 'https://ci.kbase.us/services/',
+                   'NEXT': 'https://next.kbase.us/services/',
+                   'APPDEV': 'https://appdev.kbase.us/services/',
+                   'PROD': 'https://kbase.us/services/'}

src/loaders/common/loader_helper.py

@@ -1,9 +1,12 @@
 import argparse
+import itertools
 import json
 import os
 import socket
+import stat
 import subprocess
 import time
+import uuid
 from collections import defaultdict
 from contextlib import closing
 from pathlib import Path
@@ -13,15 +16,18 @@
 
 import src.common.storage.collection_and_field_names as names
 from src.common.storage.db_doc_conversions import collection_data_id_key
-from src.loaders.common import loader_common_names
 from src.loaders.common.loader_common_names import (
+    COLLECTION_SOURCE_DIR,
     DOCKER_HOST,
     FATAL_ERROR,
     FATAL_STACKTRACE,
     FATAL_TOOL,
     IMPORT_DIR,
     KB_AUTH_TOKEN,
+    SDK_JOB_DIR,
+    SOURCE_DATA_DIR,
     SOURCE_METADATA_FILE_KEYS,
+    WS,
 )
 
 """
@@ -144,7 +150,7 @@ def get_token(token_filepath):
 
 def start_podman_service(uid: int):
     """
-    Start podman service. Used by workspace_downloader.py script.
+    Start podman service. Used by workspace_downloader.py and workspace_uploader.py scripts.
 
     uid - the integer unix user ID of the user running the service.
     """
@@ -154,7 +160,8 @@ def start_podman_service(uid: int):
     time.sleep(1)
     return_code = proc.poll()
     if return_code:
-        raise ValueError(f"The command {command} failed with return code {return_code}")
+        raise ValueError(f"The command {command} failed with return code {return_code}. "
+                         f"Podman service failed to start")
     os.environ["DOCKER_HOST"] = DOCKER_HOST.format(uid)
     return proc
 
@@ -179,69 +186,138 @@ def is_upa_info_complete(upa_dir: str):
     return True
 
 
-def make_collection_source_dir(
-        root_dir: str,
-        env: str,
-        collection: str,
-        source_ver: str
-) -> str:
+def make_job_dir(root_dir, username):
+    """Helper function that creates a job_dir for a user under root directory."""
+    job_dir = os.path.join(root_dir, SDK_JOB_DIR, username, uuid.uuid4().hex)
+    os.makedirs(job_dir, exist_ok=True)
+    # only user can read, write, or execute
+    os.chmod(job_dir, stat.S_IRWXU)
+    return job_dir
+
+
+def make_job_data_dir(job_dir):
+    """Helper function that creates a temporary directory for sharing files beteween the host and container."""
+    data_dir = os.path.join(job_dir, "workdir/tmp")
+    os.makedirs(data_dir)
+    return data_dir
+
+
+def make_sourcedata_ws_dir(root_dir, env, workspace_id):
+    """Helper function that creates a output directory for a specific workspace id under root directory."""
+    output_dir = os.path.join(root_dir, SOURCE_DATA_DIR, WS, env, str(workspace_id))
+    os.makedirs(output_dir, exist_ok=True)
+    return output_dir
+
+
+def make_collection_source_dir(root_dir: str, env: str, collection: str, source_ver: str) -> str:
     """
     Helper function that creates a collection & source_version and link in data
     to that collection from the overall source data dir.
     """
-    csd = os.path.join(root_dir, loader_common_names.COLLECTION_SOURCE_DIR, env, collection, source_ver)
-    os.makedirs(csd, exist_ok=True)
-    return csd
+    collection_source_dir = os.path.join(root_dir, COLLECTION_SOURCE_DIR, env, collection, source_ver)
+    os.makedirs(collection_source_dir, exist_ok=True)
+    return collection_source_dir
 
 
-def create_softlinks_in_csd(csd: str, work_dir: str, genome_ids: list[str], taxonomy_files: list[str] = None) -> None:
+def create_softlinks_in_collection_source_dir(
+        collection_source_dir: str,
+        work_dir: str,
+        genome_ids: list[str],
+        taxonomy_files:list[str] = None
+) -> None:
     """
     Create softlinks in the collection source dir to the genome files in the work dir.
     """
     if not taxonomy_files:
         taxonomy_files = []
 
     for genome_id in genome_ids:
-        genome_dir = os.path.join(work_dir, genome_id)
-        csd_genome_dir = os.path.join(csd, genome_id)
-        create_softlink_between_dirs(csd_genome_dir, genome_dir)
+        target_dir = os.path.join(work_dir, genome_id)
+        new_dir = os.path.join(collection_source_dir, genome_id)
+        create_softlink_between_dirs(new_dir, target_dir)
 
     for taxonomy_file in taxonomy_files:
-        csd_file = os.path.join(csd, taxonomy_file)
-        sd_file = os.path.join(work_dir, taxonomy_file)
-        create_softlink_between_files(csd_file, sd_file)
+        new_file = os.path.join(collection_source_dir, taxonomy_file)
+        target_file = os.path.join(work_dir, taxonomy_file)
+        create_softlink_between_files(new_file, target_file)
 
-    print(f"Genome files in {csd} \nnow link to {work_dir}")
+    print(f"Genome files in {collection_source_dir} \nnow link to {work_dir}")
 
 
-def create_softlink_between_dirs(csd_dir, sd_dir):
+def create_softlink_between_dirs(new_dir, target_dir):
     """
-    Creates a softlink between two directories.
+    Creates a softlink from new_dir to the contents of target_dir.
     """
-    if os.path.exists(csd_dir):
+    if os.path.exists(new_dir):
         if (
-                os.path.isdir(csd_dir)
-                and os.path.islink(csd_dir)
-                and os.readlink(csd_dir) == sd_dir
+                os.path.isdir(new_dir)
+                and os.path.islink(new_dir)
+                and os.readlink(new_dir) == target_dir
         ):
             return
         raise ValueError(
-            f"{csd_dir} already exists and does not link to {sd_dir} as expected"
+            f"{new_dir} already exists and does not link to {target_dir} as expected"
+        )
+    os.symlink(target_dir, new_dir, target_is_directory=True)
+
+
+def create_softlink_between_files(new_file, target_file):
+    """
+    Creates a softlink from new_file to the contents of target_file.
+    """
+    if os.path.exists(new_file):
+        if (os.path.islink(new_file) and os.readlink(new_file) == target_file):
+            return
+        raise ValueError(
+            f"{new_file} already exists and does not link to {target_file} as expected"
         )
-    os.symlink(sd_dir, csd_dir, target_is_directory=True)
+    os.symlink(target_file, new_file)
 
 
-def create_softlink_between_files(csd_file, sd_file):
+def create_hardlink_between_files(new_file, target_file):
     """
-    Creates a softlink between two files.
+    Creates a hardlink from new_file to the contents of target_file.
     """
-    if os.path.exists(csd_file):
-        if (os.path.islink(csd_file) and os.readlink(csd_file) == sd_file):
+    if os.path.exists(new_file):
+        if os.path.samefile(target_file, new_file):
             return
         raise ValueError(
-            f"{csd_file} already exists and does not link to {sd_file} as expected"
+            f"{new_file} already exists and does not link to {target_file} as expected"
+        )
+    os.link(target_file, new_file)
+
+
+def list_objects(wsid, conf, object_type, include_metadata=False, batch_size=10000):
+    """
+    List all objects information given a workspace ID.
+    """
+    if batch_size > 10000:
+        raise ValueError("Maximum value for listing workspace objects is 10000")
+
+    maxObjectID = conf.ws.get_workspace_info({"id": wsid})[4]
+    batch_input = [
+        [idx + 1, idx + batch_size] for idx in range(0, maxObjectID, batch_size)
+    ]
+    objs = [
+        conf.ws.list_objects(
+            _list_objects_params(wsid, min_id, max_id, object_type, include_metadata)
         )
-    os.symlink(sd_file, csd_file)
+        for min_id, max_id in batch_input
+    ]
+    res_objs = list(itertools.chain.from_iterable(objs))
+    return res_objs
+
+
+def _list_objects_params(wsid, min_id, max_id, type_str, include_metadata):
+    """Helper function that creates params needed for list_objects function."""
+    params = {
+        "ids": [wsid],
+        "minObjectID": min_id,
+        "maxObjectID": max_id,
+        "type": type_str,
+        "includeMetadata": int(include_metadata),
+    }
+    return params
 
 
 def get_ip():

src/loaders/compute_tools/tool_common.py

@@ -91,7 +91,8 @@ def __init__(
                                 (default: PROD)
           --load_ver LOAD_VER   KBase load version (e.g. r207.kbase.1). (defaults to
                                 the source version)
-          --root_dir ROOT_DIR   Root directory.
+          --root_dir ROOT_DIR   Root directory for the collections project.
+                                (default: /global/cfs/cdirs/kbase/collections)
           --threads THREADS     Total number of threads used by the script. (default:
                                 half of system cpu count)
           --program_threads PROGRAM_THREADS
@@ -127,11 +128,12 @@ def __init__(
         kbase_collection = getattr(args, loader_common_names.KBASE_COLLECTION_ARG_NAME)
         source_ver = getattr(args, loader_common_names.SOURCE_VER_ARG_NAME)
         load_ver = getattr(args, loader_common_names.LOAD_VER_ARG_NAME)
+        root_dir = getattr(args, loader_common_names.ROOT_DIR_ARG_NAME)
         if not load_ver:
             load_ver = source_ver
 
         self._allow_missing_files = kbase_collection in _IGNORE_MISSING_FILES_COLLECTIONS
-        self._source_data_dir = Path(args.root_dir,
+        self._source_data_dir = Path(root_dir,
                                      loader_common_names.COLLECTION_SOURCE_DIR,
                                      env,
                                      kbase_collection,
@@ -149,7 +151,7 @@ def __init__(
         self._threads = max(1, self._threads)
 
         self._work_dir = Path(
-            Path(args.root_dir),
+            Path(root_dir),
             loader_common_names.COLLECTION_DATA_DIR,
             env,
             kbase_collection,
@@ -186,9 +188,11 @@ def _parse_args(self):
             f'--{loader_common_names.LOAD_VER_ARG_NAME}', type=str,
             help=loader_common_names.LOAD_VER_DESCR + ' (defaults to the source version)'
         )
-
         optional.add_argument(
-            '--root_dir', type=str, default=loader_common_names.ROOT_DIR, help='Root directory.'
+            f'--{loader_common_names.ROOT_DIR_ARG_NAME}',
+            type=str,
+            default=loader_common_names.ROOT_DIR,
+            help=f'{loader_common_names.ROOT_DIR_DESCR} (default: {loader_common_names.ROOT_DIR})'
         )
         optional.add_argument(
             '--threads', type=int,

src/loaders/genome_collection/compute_genome_taxa_count.py

@@ -31,7 +31,7 @@
 optional arguments:
   --env {CI,NEXT,APPDEV,PROD,NONE}
                         Environment containing the data to be processed. (default: PROD)
-  --root_dir ROOT_DIR   Root directory for the collections project (default: /global/cfs/cdirs/kbase/collections)
+  --root_dir ROOT_DIR   Root directory for the collections project. (default: /global/cfs/cdirs/kbase/collections)
   --input_source {GTDB,genome_attributes}
                         Input file source
  
@@ -122,15 +122,19 @@ def main():
         default='PROD',
         help="Environment containing the data to be processed. (default: PROD)",
     )
-    optional.add_argument('--root_dir', type=str, default=loader_common_names.ROOT_DIR,
-                          help=f'Root directory for the collections project (default: {loader_common_names.ROOT_DIR})')
+    optional.add_argument(
+        f'--{loader_common_names.ROOT_DIR_ARG_NAME}',
+        type=str,
+        default=loader_common_names.ROOT_DIR,
+        help=f'{loader_common_names.ROOT_DIR_DESCR} (default: {loader_common_names.ROOT_DIR})'
+    )
 
     optional.add_argument('--input_source', type=str, choices=VALID_SOURCE, default='GTDB',
                           help='Input file source')
 
     args = parser.parse_args()
     load_files = args.load_files
-    root_dir = args.root_dir
+    root_dir = getattr(args, loader_common_names.ROOT_DIR_ARG_NAME)
     load_version = getattr(args, loader_common_names.LOAD_VER_ARG_NAME)
     kbase_collection = getattr(args, loader_common_names.KBASE_COLLECTION_ARG_NAME)
     env = getattr(args, loader_common_names.ENV_ARG_NAME)

src/loaders/genome_collection/parse_tool_results.py

@@ -843,8 +843,12 @@ def main():
                           help=f'Extract results from tools. '
                                f'(default: retrieve all available sub-directories in the '
                                f'[{loader_common_names.LOAD_VER_ARG_NAME}] directory)')
-    optional.add_argument('--root_dir', type=str, default=loader_common_names.ROOT_DIR,
-                          help=f'Root directory for the collections project. (default: {loader_common_names.ROOT_DIR})')
+    optional.add_argument(
+        f'--{loader_common_names.ROOT_DIR_ARG_NAME}',
+        type=str,
+        default=loader_common_names.ROOT_DIR,
+        help=f'{loader_common_names.ROOT_DIR_DESCR} (default: {loader_common_names.ROOT_DIR})'
+    )
     optional.add_argument('--check_genome', action="store_true",
                           help='Ensure a corresponding genome exists for every assembly')
     optional.add_argument(
@@ -859,9 +863,9 @@ def main():
     kbase_collection = getattr(args, loader_common_names.KBASE_COLLECTION_ARG_NAME)
     source_ver = getattr(args, loader_common_names.SOURCE_VER_ARG_NAME)
     load_ver = getattr(args, loader_common_names.LOAD_VER_ARG_NAME)
+    root_dir = getattr(args, loader_common_names.ROOT_DIR_ARG_NAME)
     if not load_ver:
         load_ver = source_ver
-    root_dir = args.root_dir
     check_genome = args.check_genome
 
     if not args.skip_retrieve_sample:

src/loaders/jobs/taskfarmer/task_generator.py

@@ -331,8 +331,12 @@ def main():
 
     optional.add_argument(f'--{loader_common_names.LOAD_VER_ARG_NAME}', type=str,
                           help=loader_common_names.LOAD_VER_DESCR + ' (defaults to the source version)')
-    optional.add_argument('--root_dir', type=str, default=loader_common_names.ROOT_DIR,
-                          help=f'Root directory for the collections project. (default: {loader_common_names.ROOT_DIR})')
+    optional.add_argument(
+        f'--{loader_common_names.ROOT_DIR_ARG_NAME}',
+        type=str,
+        default=loader_common_names.ROOT_DIR,
+        help=f'{loader_common_names.ROOT_DIR_DESCR} (default: {loader_common_names.ROOT_DIR})'
+    )
     optional.add_argument('--submit_job', action='store_true', help='Submit job to slurm')
     optional.add_argument('--force', action='store_true', help='Force overwrite of existing job directory')
     optional.add_argument('--source_file_ext', type=str, default='.fa',
@@ -345,10 +349,10 @@ def main():
     kbase_collection = getattr(args, loader_common_names.KBASE_COLLECTION_ARG_NAME)
     source_ver = getattr(args, loader_common_names.SOURCE_VER_ARG_NAME)
     load_ver = getattr(args, loader_common_names.LOAD_VER_ARG_NAME)
+    root_dir = getattr(args, loader_common_names.ROOT_DIR_ARG_NAME)
     if not load_ver:
         load_ver = source_ver
 
-    root_dir = args.root_dir
     source_data_dir = make_collection_source_dir(root_dir, env, kbase_collection, source_ver)
     source_file_ext = args.source_file_ext