295 local configuration

abm/VERSION

@@ -1 +1 @@
-2.9.0-dev.8
+2.9.0-dev.9

abm/lib/common.py

@@ -2,6 +2,8 @@
 import os
 import subprocess
 import sys
+from pathlib import Path
+
 from math import ceil
 
 import bioblend.galaxy
@@ -405,6 +407,40 @@ def find_history(gi, name_or_id):
     return history[0]['id']
 
 
+def find_dataset(gi, history_id, name_or_id):
+    try:
+        dataset = gi.datasets.show_dataset(name=name_or_id)
+        return dataset['id']
+    except:
+        pass
+
+    try:
+        dataset = gi.datasets.show_dataset(name_or_id)
+        return dataset['id']
+    except:
+        pass
+    return None
+    # print("Calling get_datasets")
+    # datasets = gi.datasets.get_datasets(history_id=history_id, name=name_or_id)
+    # if datasets is None:
+    #     print("Not found")
+    #     return None
+    # if len(datasets) == 0:
+    #     print("No datasets found (len == 0)")
+    #     return None
+    # return datasets[0]['id']
+
+
+def find_config(name: str) -> str:
+    if os.path.exists(".abm"):
+        if os.path.exists(f".abm/{name}"):
+            return f".abm/{name}"
+    config = os.path.join(Path.home(), ".abm", name)
+    if os.path.exists(config):
+        return config
+    return None
+
+
 def _get_dataset_data(gi, name_or_id):
     print(f"Getting dataset data for {name_or_id}")
     def make_result(data):

abm/lib/dataset.py

@@ -7,7 +7,7 @@
 import yaml
 from bioblend.galaxy import dataset_collections
 from common import (Context, _get_dataset_data, _make_dataset_element, connect,
-                    find_history, print_json)
+                    find_history, print_json, find_config, find_dataset)
 
 
 def do_list(context: Context, argv: list):
@@ -162,45 +162,55 @@ def collection(context: Context, args: list):
 
 
 def import_from_config(context: Context, args: list):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-c', '--create', help='create a new history for the dataset', required=False, default=None)
+    parser.add_argument('-f', '--file', help='use instead of the datasets.yml', required=False, default=None)
+    parser.add_argument('--history', help='add datasets to the given history', required=False, default=None)
+    parser.add_argument('-n', '--name', help='set the name of the dataset', required=False, default=None)
+    parser.add_argument('keys', help='the key of the dataset to import', nargs='+')
     gi = None
-    key = None
     history = None
     kwargs = {}
-    while len(args) > 0:
-        arg = args.pop(0)
-        if arg in ['--hs', '--hist', '--history']:
-            history = args.pop(0)
-        elif arg in ['-c', '--create']:
-            gi = connect(context)
-            history = gi.histories.create_history(args.pop(0)).get('id')
-        elif arg in ['-n', '--name']:
-            kwargs['file_name'] = args.pop(0)
-        elif key is not None:
-            print(f"ERROR: key already set: {key}")
+    argv = parser.parse_args(args)
+    if argv.name is not None:
+        if len(argv.keys) > 1:
+            print("ERROR: cannot specify --name with multiple keys")
             return
-        else:
-            key = arg
+        kwargs['file_name'] = argv.name
 
-    configfile = os.path.join(Path.home(), '.abm', 'datasets.yml')
-    if not os.path.exists(configfile):
-        print("ERROR: ABM has not been configured to import datasets.")
-        print(f"Please create {configfile}")
+    if argv.create is not None and argv.history is not None:
+        print("ERROR: cannot specify both --create and --history")
         return
 
+    if argv.create is not None:
+        gi = connect(context)
+        history = gi.histories.create_history(argv.create).get('id')
+    if argv.history is not None:
+        gi = connect(context)
+        history = find_history(gi, argv.history)
+    if argv.file is not None:
+        configfile = argv.file
+        if not os.path.exists(configfile):
+            print(f"ERROR: the specified file {configfile} was not found")
+            return
+    else:
+        configfile = find_config("datasets.yml")
+        if configfile is None:
+            print("ERROR: ABM has not been configured to import datasets.")
+            print(f"Please create {configfile}")
+            return
     with open(configfile, 'r') as f:
         datasets = yaml.safe_load(f)
-    if not key in datasets:
-        print(f"ERROR: dataset {key} has not been defined.")
-        return
-    url = datasets[key]
-
     if gi is None:
         gi = connect(context)
-    if history is not None:
-        history = find_history(gi, history)
-
-    response = gi.tools.put_url(url, history, **kwargs)
-    print(json.dumps(response, indent=4))
+    for key in argv.keys:
+        if not key in datasets:
+            print(f"ERROR: dataset {key} has not been defined.")
+        else:
+            url = datasets[key]
+            print(f"Importing {key} from {url}")
+            response = gi.tools.put_url(url, history, **kwargs)
+            print(json.dumps(response, indent=4))
 
 
 def _import_from_url(gi, history, url, **kwargs):
@@ -240,9 +250,17 @@ def rename(context: Context, args: list):
         print("ERROR: please provide the history ID, dataset ID, and new name.")
         return
     gi = connect(context)
-    response = gi.histories.update_dataset(args[0], args[1], name=args[2])
-    result = {'state': response['state'], 'name': response['name']}
-    print(json.dumps(result, indent=4))
+    hid = find_history(gi, args[0])
+    if hid is None:
+        print("ERROR: no such history")
+        return
+    dsid = find_dataset(gi, hid, args[1])
+    if dsid is None:
+        print("ERROR: no such dataset")
+        return
+    response = gi.histories.update_dataset(hid, dsid, name=args[2])
+    # result = {'state': response['state'], 'name': response['name']}
+    print(json.dumps(response, indent=4))
 
 
 def test(context: Context, args: list):

abm/lib/history.py

@@ -10,7 +10,7 @@
 from bioblend.galaxy.objects import GalaxyInstance
 from lib.common import (Context, connect, find_history, parse_profile,
                         print_json, summarize_metrics, print_markdown_table,
-                        get_float_key, get_str_key, print_table_header, try_for)
+                        get_float_key, get_str_key, print_table_header, try_for, find_config)
 
 #
 # History related functions
@@ -194,55 +194,29 @@ def _import(context: Context, args: list):
 
 
 def himport(context: Context, args: list):
-    def error_message(msg='Invalid command'):
-        print(f"ERROR: {msg}")
-        print(f"USAGE: {sys.argv[0]} history import SERVER HISTORY_ID JEHA_ID")
-        print(f"       {sys.argv[0]} history import http://GALAXY_SERVER_URL")
-        print(f"       {sys.argv[0]} history import [dna|rna]")
-
-    wait = True
-    if '-n' in args:
-        args.remove('-n')
-        wait = False
-    if '--no-wait' in args:
-        args.remove('--no-wait')
-        wait = False
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-n', '--no-wait', action='store_true', help='Do not wait for the import to complete', default=False)
+    parser.add_argument('-f', '--file', help='Use the specified histories.yml file', required=False, default=None)
+    parser.add_argument('identifier', help='The history alias or URL to import')
+    argv = parser.parse_args(args)
 
-    if len(args) == 1:
-        if 'http' in args[0]:
-            url = args[0]
+    wait = not argv.no_wait
+    if argv.identifier.startswith('http'):
+        url = argv.identifier
+    else:
+        if argv.file is not None:
+            config = argv.file
         else:
-            datasets = None
-            config = f'{os.path.dirname(os.path.abspath(__file__))}/histories.yml'
-            # First load the histories.yml file that is packaged with abm
-            if os.path.exists(config):
-                with open(config, 'r') as f:
-                    datasets = yaml.safe_load(f)
-            # Then load the user histories.yml, if any
-            userfile = os.path.join(Path.home(), ".abm", "histories.yml")
-            if os.path.exists(userfile):
-                if datasets is None:
-                    datasets = {}
-                with open(userfile, 'r') as f:
-                    userdata = yaml.safe_load(f)
-                    for key, item in userdata.items():
-                        datasets[key] = item
-            if datasets is None:
-                error_message("No history URLs have been configured.")
-                return
-            if not args[0] in datasets:
-                error_message('Please specify a URL or name of the history to import')
-                return
-            url = datasets[args[0]]
-    elif len(args) == 3:
-        server, key, kube, master = parse_profile(args[0])
-        if server is None:
-            error_message(f"Invalid server profile name: {args[0]}")
+            config = find_config("histories.yml")
+        if config is None:
+            print("ERROR: No histories.yml file found.")
             return
-        url = f"{server}history/export_archive?id={args[1]}&jeha_id={args[2]}"
-    else:
-        error_message()
-        return
+        with open(config, 'r') as f:
+            histories = yaml.safe_load(f)
+        if argv.identifier not in histories:
+            print(f"ERROR: No such history {argv.identifier}")
+            return
+        url = histories[argv.identifier]
 
     gi = connect(context)
     print(f"Importing history from {url}")

abm/lib/menu.yml

@@ -89,8 +89,8 @@
       help: download a dataset from the server
     - name: ['import', 'imp']
       handler: dataset.import_from_config
-      params: KEY [--hs|--hist|--history HISTORY_ID | -c|--create "History name"]
-      help: imports a dataset to the server from a URL specified in the datasets.yml config file.
+      params: '[--hs|--hist|--history HISTORY_ID | -c|--create "History name"] KEY [KEY...]'
+      help: imports one or more datasets to the server from a URL specified in the datasets.yml config file.
     - name: ['list', 'ls']
       handler: dataset.do_list
       help: lists all the datasets on the server

abm/lib/workflow.py

@@ -8,7 +8,7 @@
 import requests
 import yaml
 from common import Context, connect, summarize_metrics, print_markdown_table, get_float_key, get_str_key, \
-    print_table_header
+    print_table_header, find_config
 from planemo.galaxy.workflows import install_shed_repos
 from planemo.runnable import for_path, for_uri
 
@@ -118,26 +118,28 @@ def import_from_url(context: Context, args: list):
 
 
 def import_from_config(context: Context, args: list):
-    print("Importing workflow from configuration")
     key = None
     install = True
+    config = None
     for arg in args:
         if arg in ['-n', '--no-tools']:
             print("Skipping tools")
             install = False
+        elif arg in ['-f', '--file']:
+            config = arg
         else:
             key = arg
     if key is None:
         print("ERROR: no workflow ID given")
         return
 
-
-    userfile = os.path.join(Path.home(), ".abm", "workflows.yml")
-    if not os.path.exists(userfile):
+    if config is None:
+        config = find_config("workflows.yml")
+    if config is None:
         print("ERROR: this instance has not been configured to import workflows.")
-        print(f"Please configure {userfile} to enable workflow imports")
+        print(f"Please configure a workflows.yml file to enable imports")
         return
-    with open(userfile, 'r') as f:
+    with open(config, 'r') as f:
         workflows = yaml.safe_load(f)
     if not key in workflows:
         print(f"ERROR: no such workflow: {key}")