Merged lazyimport.

auto_complete_install.sh

+#!/usr/bin/env bash
+if [[ $(basename $SHELL) = 'bash' ]];
+then
+    if [ -f ~/.bashrc ];
+    then
+        echo "Installing bash autocompletion..."
+        grep -q '_NOMAD_COMPLETE' ~/.bashrc
+        if [[ $? -ne 0 ]]; then
+            echo "" >> ~/.bashrc
+            echo 'eval "$(_NOMAD_COMPLETE=source nomad)"' >> ~/.bashrc
+        fi
+    fi
+elif [[ $(basename $SHELL) = 'zsh' ]];
+then
+    if [ -f ~/.zshrc ];
+    then
+        echo "Installing zsh autocompletion..."
+        grep -q 'nomad-autocompletion' ~/.zshrc
+        if [[ $? -ne 0 ]]; then
+            echo "" >> ~/.zshrc
+            echo "autoload bashcompinit" >> ~/.zshrc
+            echo "bashcompinit" >> ~/.zshrc
+            echo 'eval "$(_NOMAD_COMPLETE=source nomad)"' >> ~/.nomad-autocompletion.sh
+            echo "source ~/.nomad-autocompletion.sh" >> ~/.zshrc
+        fi
+    fi
+fi
\ No newline at end of file

lazy_import.py

+from types import ModuleType
+import sys
+from importlib._bootstrap import _ImportLockContext
+from six import raise_from
+from importlib import reload as reload_module
+
+
+__all__ = ['lazy_module', 'LazyModule', '_MSG']
+
+
+_CLS_ATTRS = (
+    '_lazy_import_error_strings', '_lazy_import_error_msgs', '_lazy_import_callables',
+    '_lazy_import_submodules', '__repr__'
+)
+
+_DICT_DELETION = ('_lazy_import_submodules',)
+
+_MSG = ("{caller} attempted to use a functionality that requires module "
+        "{module}, but it couldn't be loaded. Please install {install_name} "
+        "and retry.")
+
+
+class LazyModule(ModuleType):
+    def __getattribute__(self, attr):
+        if attr not in ('__name__', '__class__', '__spec__'):
+            try:
+                name = '%s.%s' % (self.__name__, attr)
+                return sys.modules[name]
+            except KeyError:
+                pass
+
+            try:
+                return type(self)._lazy_import_callables[attr]
+            except (AttributeError, KeyError):
+                _load_module(self)
+        return super(LazyModule, self).__getattribute__(attr)
+
+    def __setattr__(self, attr, value):
+        _load_module(self)
+        return super(LazyModule, self).__setattr__(attr, value)
+
+
+def _clean_lazy_submodule_refs(module):
+    module_class = type(module)
+    for entry in _DICT_DELETION:
+        try:
+            names = getattr(module_class, entry)
+        except AttributeError:
+            continue
+        for name in names:
+            try:
+                super(LazyModule, module).__delattr__(name)
+            except AttributeError:
+                pass
+
+
+def _clean_lazymodule(module):
+    module_class = type(module)
+    _clean_lazy_submodule_refs(module)
+
+    module_class.__getattribute__ = ModuleType.__getattribute__
+    module_class.__setattr__ = ModuleType.__setattr__
+    class_attrs = {}
+    for attr in _CLS_ATTRS:
+        try:
+            class_attrs[attr] = getattr(module_class, attr)
+            delattr(module_class, attr)
+        except AttributeError:
+            pass
+    return class_attrs
+
+
+def _reset_lazy_submodule_refs(module):
+    module_class = type(module)
+    for entry in _DICT_DELETION:
+        try:
+            names = getattr(module_class, entry)
+        except AttributeError:
+            continue
+        for name, submodule in names.items():
+            super(LazyModule, module).__setattr__(name, submodule)
+
+
+def _reset_lazymodule(module, class_attrs):
+    module_class = type(module)
+    del module_class.__getattribute__
+    del module_class.__setattr__
+    try:
+        del module_class._LOADING
+    except AttributeError:
+        pass
+
+    for attr in _CLS_ATTRS:
+        try:
+            setattr(module_class, attr, class_attrs[attr])
+        except KeyError:
+            pass
+
+    _reset_lazy_submodule_refs(module)
+
+
+def _load_module(module):
+    module_class = type(module)
+    if not issubclass(module_class, LazyModule):
+        raise TypeError('Not an instance of LazyModule')
+    with _ImportLockContext():
+        parent, _, module_name = module.__name__.rpartition('.')
+        if not hasattr(module_class, '_lazy_import_error_msgs'):
+            return
+        module_class._LOADING = True
+        try:
+            if parent:
+                setattr(sys.modules[parent], module_name, module)
+            if not hasattr(module_class, '_LOADING'):
+                return
+            cached_data = _clean_lazymodule(module)
+            try:
+                reload_module(module)
+            except Exception:
+                _reset_lazymodule(module, cached_data)
+                raise
+            else:
+                delattr(module_class, '_LOADING')
+                _reset_lazy_submodule_refs(module)
+        except (AttributeError, ImportError):
+            msg = module_class._lazy_import_error_msgs['msg']
+            raise_from(ImportError(msg.format(**module_class._lazy_import_error_strings)), None)
+
+
+def _lazy_module(module_name, error_strings):
+    with _ImportLockContext():
+        full_module_name = module_name
+        full_submodule_name = None
+        submodule_name = ''
+        while module_name:
+            try:
+                module = sys.modules[module_name]
+                module_name = ''
+            except KeyError:
+                err_strs = error_strings.copy()
+                err_strs.setdefault('module', module_name)
+
+                class _LazyModule(LazyModule):
+                    _lazy_import_error_msgs = {'msg': err_strs.pop('msg')}
+                    msg_callable = err_strs.pop('msg_callable', None)
+                    if msg_callable:
+                        _lazy_import_error_msgs['msg_callable'] = msg_callable
+                    _lazy_import_error_strings = err_strs
+                    _lazy_import_callables = {}
+                    _lazy_import_submodules = {}
+
+                    def __repr__(self):
+                        return 'Lazily-loaded module %s' % self.__name__
+
+                _LazyModule.__name__ = 'module'
+                module = sys.modules[module_name] = _LazyModule(module_name)
+
+            if full_submodule_name:
+                submodule = sys.modules[full_submodule_name]
+                ModuleType.__setattr__(module, submodule_name, submodule)
+                _LazyModule._lazy_import_submodules[submodule_name] = submodule
+
+            full_submodule_name = module_name
+            module_name, _, submodule_name = module_name.rpartition('.')
+
+        return sys.modules[full_module_name]
+
+
+def lazy_module(module_name, level='leaf'):
+    module_base_name = module_name.partition('.')[0]
+    error_strings = {}
+    try:
+        caller = sys._getframe(3).f_globals['__name__']
+    except AttributeError:
+        caller = 'Python'
+    error_strings.setdefault('caller', caller)
+    error_strings.setdefault('install_name', module_base_name)
+    error_strings.setdefault('msg', _MSG)
+
+    module = _lazy_module(module_name, error_strings)
+
+    if level == 'base':
+        return sys.modules[module_base_name]
+    elif level == 'leaf':
+        return module
+    else:
+        raise ValueError('Must be base or leaf')

nomad/cli/__init__.py

@@ -19,11 +19,26 @@ that offers various functionality to the command line user.
 Use it from the command line with ``nomad --help`` or ``python -m nomad.cli --help`` to learn
 more.
 '''
+import lazy_import
 
-from nomad.utils import POPO
+lazy_import.lazy_module('click')
+lazy_import.lazy_module('logging')
+lazy_import.lazy_module('os')
+lazy_import.lazy_module('typing')
+lazy_import.lazy_module('json')
+lazy_import.lazy_module('sys')
+lazy_import.lazy_module('nomad.config')
+lazy_import.lazy_module('nomad.infrastructure')
+lazy_import.lazy_module('nomad.utils')
+lazy_import.lazy_module('nomad.parsing')
+lazy_import.lazy_module('nomad.normalizing')
+lazy_import.lazy_module('nomad.datamodel')
+lazy_import.lazy_module('nomadcore')
 
-from . import dev, admin, client, parse
-from .cli import cli
+from nomad.utils import POPO  # noqa
+
+from . import dev, admin, client, parse  # noqa
+from .cli import cli  # noqa
 
 
 def run_cli():

nomad/cli/admin/__init__.py

@@ -12,5 +12,42 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import lazy_import
 
-from . import admin, uploads, entries, run, clean, users
+lazy_import.lazy_module('typing')
+lazy_import.lazy_module('click')
+lazy_import.lazy_module('asyncio')
+lazy_import.lazy_module('concurrent.futures')
+lazy_import.lazy_module('datetime')
+lazy_import.lazy_module('time')
+lazy_import.lazy_module('elasticsearch_dsl')
+lazy_import.lazy_module('elasticsearch')
+lazy_import.lazy_module('os')
+lazy_import.lazy_module('shutil')
+lazy_import.lazy_module('tabulate')
+lazy_import.lazy_module('sys')
+lazy_import.lazy_module('io')
+lazy_import.lazy_module('re')
+lazy_import.lazy_module('uuid')
+lazy_import.lazy_module('json')
+lazy_import.lazy_module('threading')
+lazy_import.lazy_module('numpy')
+lazy_import.lazy_module('requests')
+lazy_import.lazy_module('pymongo')
+lazy_import.lazy_module('mongoengine')
+lazy_import.lazy_module('ase')
+lazy_import.lazy_module('bs4')
+lazy_import.lazy_module('matid')
+lazy_import.lazy_module('matid.symmetry.symmetryanalyzer')
+lazy_import.lazy_module('matid.utils.segfault_protect')
+lazy_import.lazy_module('nomad.normalizing')
+lazy_import.lazy_module('nomad.processing')
+lazy_import.lazy_module('nomad.search')
+lazy_import.lazy_module('nomad.datamodel')
+lazy_import.lazy_module('nomad.infrastructure')
+lazy_import.lazy_module('nomad.utils')
+lazy_import.lazy_module('nomad.config')
+lazy_import.lazy_module('nomad.files')
+lazy_import.lazy_module('nomad.archive')
+
+from . import admin, uploads, entries, run, clean, users  # noqa

nomad/cli/admin/admin.py

@@ -11,37 +11,31 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-from typing import Callable, List
+import typing
 import click
 import datetime
-from elasticsearch_dsl import Q
-import elasticsearch.helpers
+import elasticsearch_dsl
+import elasticsearch
 import sys
 import io
 import re
 import uuid
 import json
-from io import StringIO
 import threading
 
 import numpy as np
 import requests
-from ase import Atoms
-import ase.io
-from bs4 import BeautifulSoup
-from matid import SymmetryAnalyzer
+import ase
+import bs4
+import matid
 
 from nomad import processing as proc, search, datamodel, infrastructure, utils, config
-from nomad.normalizing.aflow_prototypes import get_normalized_wyckoff
+from nomad import normalizing
 from nomad.cli.cli import cli
-from nomad import config
-from nomad.normalizing.springer import update_springer_data
 
 
 def __run_processing(
-        uploads, parallel: int, process: Callable[[proc.Upload], None], label: str,
-        reprocess_running: bool = False):
+        uploads, parallel: int, process, label: str, reprocess_running: bool = False):
     if isinstance(uploads, (tuple, list)):
         uploads_count = len(uploads)
 
@@ -50,7 +44,7 @@ def __run_processing(
         uploads = list(uploads)  # copy the whole mongo query set to avoid cursor timeouts
 
     cv = threading.Condition()
-    threads: List[threading.Thread] = []
+    threads: typing.List[threading.Thread] = []
 
     state = dict(
         completed_count=0,
@@ -137,7 +131,7 @@ def lift_embargo(dry, parallel):
     infrastructure.setup_elastic()
 
     request = search.SearchRequest()
-    request.q = Q('term', with_embargo=True) & Q('term', published=True)
+    request.q = elasticsearch_dsl.Q('term', with_embargo=True) & elasticsearch_dsl.Q('term', published=True)
     request.quantity('upload_id', 1000)
     result = request.execute()
 
@@ -413,7 +407,7 @@ def prototypes_update(ctx, filepath, matches_only):
             newdict = {}
 
             # Make prototype plaintext
-            prototype = BeautifulSoup(protodict["Prototype"], "html5lib").getText()
+            prototype = bs4.BeautifulSoup(protodict["Prototype"], "html5lib").getText()
 
             # Add to new dictionary
             newdict['Notes'] = protodict['Notes']
@@ -425,12 +419,12 @@ def prototypes_update(ctx, filepath, matches_only):
             newdict['aflow_prototype_id'] = protodict['AFLOW Prototype']
             newdict['aflow_prototype_url'] = 'http://www.aflowlib.org/CrystalDatabase/' + protodict['href'][2:]
 
-            # Download cif or poscar if possible make ASE Atoms object if possible
+            # Download cif or poscar if possible make ASE ase.Atoms object if possible
             # to obtain labels, positions, cell
             cifurl = 'http://www.aflowlib.org/CrystalDatabase/CIF/' + protodict['href'][2:-5] + '.cif'
             r = requests.get(cifurl, allow_redirects=True)
             cif_str = r.content.decode("utf-8")
-            cif_file = StringIO()
+            cif_file = io.StringIO()
             cif_file.write(cif_str)
             cif_file.seek(0)
             try:
@@ -442,7 +436,7 @@ def prototypes_update(ctx, filepath, matches_only):
                     poscarurl = 'http://www.aflowlib.org/CrystalDatabase/POSCAR/' + protodict['href'][2:-5] + '.poscar'
                     r = requests.get(poscarurl, allow_redirects=True)
                     poscar_str = r.content.decode("utf-8")
-                    poscar_file = StringIO()
+                    poscar_file = io.StringIO()
                     poscar_file.write(poscar_str)
                     poscar_file.seek(0)
                     atoms = ase.io.read(poscar_file, format='vasp')
@@ -496,7 +490,7 @@ def prototypes_update(ctx, filepath, matches_only):
             pos = np.array(prototype["atom_positions"])
             labels = prototype["atom_labels"]
             cell = np.array(prototype["lattice_vectors"])
-            atoms = Atoms(
+            atoms = ase.Atoms(
                 symbols=labels,
                 positions=pos,
                 cell=cell,
@@ -506,7 +500,7 @@ def prototypes_update(ctx, filepath, matches_only):
             # Try to first see if the space group can be matched with the one in AFLOW
             tolerance = config.normalize.symmetry_tolerance
             try:
-                symm = SymmetryAnalyzer(atoms, tolerance)
+                symm = matid.SymmetryAnalyzer(atoms, tolerance)
                 spg_number = symm.get_space_group_number()
                 wyckoff_matid = symm.get_wyckoff_letters_conventional()
                 norm_system = symm.get_conventional_system()
@@ -517,7 +511,7 @@ def prototypes_update(ctx, filepath, matches_only):
                 # letters to the data.
                 if spg_number == aflow_spg_number:
                     atomic_numbers = norm_system.get_atomic_numbers()
-                    normalized_wyckoff_matid = get_normalized_wyckoff(atomic_numbers, wyckoff_matid)
+                    normalized_wyckoff_matid = normalizing.aflow_prototypes.get_normalized_wyckoff(atomic_numbers, wyckoff_matid)
                     prototype["normalized_wyckoff_matid"] = normalized_wyckoff_matid
                 else:
                     n_unmatched += 1
@@ -537,4 +531,4 @@ def prototypes_update(ctx, filepath, matches_only):
 @click.option('--max-n-query', default=10, type=int, help='Number of unsuccessful springer request before returning an error. Default is 10.')
 @click.option('--retry-time', default=120, type=int, help='Time in seconds to retry after unsuccessful request. Default is 120.')
 def springer_update(max_n_query, retry_time):
-    update_springer_data(max_n_query, retry_time)
+    normalizing.springer.update_springer_data(max_n_query, retry_time)

nomad/cli/admin/clean.py

@@ -15,11 +15,11 @@
 import click
 import os
 import shutil
-from tabulate import tabulate
-from elasticsearch_dsl import A
+import tabulate
+import elasticsearch_dsl
 
 from nomad import config as nomad_config, infrastructure, processing
-from nomad.search import Search
+from nomad import search as nomad_search
 
 from .admin import admin
 
@@ -53,7 +53,7 @@ def clean(dry, skip_calcs, skip_fs, skip_es, staging_too, force):
 
             for upload in missing_uploads:
                 mongo_client[nomad_config.mongo.db_name]['calc'].remove(dict(upload_id=upload))
-                Search(index=nomad_config.elastic.index_name).query('term', upload_id=upload).delete()
+                elasticsearch_dsl.Search(index=nomad_config.elastic.index_name).query('term', upload_id=upload).delete()
         else:
             print('Found %s uploads that have calcs in mongo, but there is no upload entry.' % len(missing_uploads))
             print('List first 10:')
@@ -103,8 +103,8 @@ def clean(dry, skip_calcs, skip_fs, skip_es, staging_too, force):
                 print(path)
 
     if not skip_es:
-        search = Search(index=nomad_config.elastic.index_name)
-        search.aggs.bucket('uploads', A('terms', field='upload_id', size=12000))
+        search = nomad_search.Search(index=nomad_config.elastic.index_name)
+        search.aggs.bucket('uploads', elasticsearch_dsl.A('terms', field='upload_id', size=12000))
         response = search.execute()
 
         to_delete = list(
@@ -122,8 +122,8 @@ def clean(dry, skip_calcs, skip_fs, skip_es, staging_too, force):
                     'Will delete %d calcs in %d uploads from ES. Press any key to continue ...' %
                     (calcs, len(to_delete)))
             for upload, _ in to_delete:
-                Search(index=nomad_config.elastic.index_name).query('term', upload_id=upload).delete()
+                nomad_search.Search(index=nomad_config.elastic.index_name).query('term', upload_id=upload).delete()
         else:
             print('Found %d calcs in %d uploads from ES with no upload in mongo.' % (calcs, len(to_delete)))
             print('List first 10:')
-            tabulate(to_delete, headers=['id', '#calcs'])
+            tabulate.tabulate(to_delete, headers=['id', '#calcs'])

nomad/cli/admin/migration.py

@@ -12,22 +12,23 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from typing import Dict, Any
-from mongoengine import Document, IntField, StringField, DictField
-from pymongo import UpdateOne
+
+import typing
+import mongoengine
+import pymongo
 import time
 import datetime
 import json
 
 from nomad import utils, processing as proc, search
-from nomad.datamodel import EntryMetadata
-from nomad.cli.client.mirror import transform_reference, tarnsform_user_id, transform_dataset
+from nomad import datamodel
+from nomad.cli.client import mirror
 
 
 __logger = utils.get_logger(__name__)
 
 
-class SourceCalc(Document):
+class SourceCalc(mongoengine.Document):
     '''
     Mongo document used as a calculation, upload, and metadata db and index
     build from a given source db. Each :class:`SourceCacl` entry relates
@@ -36,12 +37,12 @@ class SourceCalc(Document):
     specific path segment that identifies an upload on the CoE repo FS(s) without
     any prefixes (e.g. $EXTRACTED, /data/upload, etc.)
     '''
-    pid = IntField(primary_key=True)
-    mainfile = StringField()
-    upload = StringField()
-    metadata = DictField()
+    pid = mongoengine.IntField(primary_key=True)
+    mainfile = mongoengine.StringField()
+    upload = mongoengine.StringField()
+    metadata = mongoengine.DictField()
 
-    migration_version = IntField(default=-1)
+    migration_version = mongoengine.IntField(default=-1)
 
     extracted_prefix = '$EXTRACTED/'
     sites = ['/data/nomad/extracted/', '/nomad/repository/extracted/']
@@ -67,7 +68,7 @@ def update_user_metadata(bulk_size: int = 1000, update_index: bool = False, **kw
     # iterate the source index in bulk
     size = SourceCalc.objects(**kwargs).count()
     count = 0
-    important_changes: Dict[str, Any] = dict(missing_calcs=dict(), replaced=dict(), lifted_embargo=list())
+    important_changes: typing.Dict[str, typing.Any] = dict(missing_calcs=dict(), replaced=dict(), lifted_embargo=list())
 
     try:
         for start in range(0, size, bulk_size):
@@ -96,16 +97,16 @@ def update_user_metadata(bulk_size: int = 1000, update_index: bool = False, **kw
                         important_changes['missing_calcs'].setdefault(source.upload, []).append(source.pid)
                         continue
 
-                target_metadata = EntryMetadata(**target.metadata)
-                source_metadata_normalized: Dict[str, Any] = dict(
+                target_metadata = datamodel.EntryMetadata(**target.metadata)
+                source_metadata_normalized: typing.Dict[str, typing.Any] = dict(
                     comment=source.metadata.get('comment'),
-                    references={transform_reference(ref) for ref in source.metadata['references']},
-                    coauthors={tarnsform_user_id(user['id']) for user in source.metadata['coauthors']},
-                    shared_with={tarnsform_user_id(user['id']) for user in source.metadata['shared_with']},
-                    datasets={transform_dataset(ds) for ds in source.metadata['datasets']},
+                    references={mirror.transform_reference(ref) for ref in source.metadata['references']},
+                    coauthors={mirror.tarnsform_user_id(user['id']) for user in source.metadata['coauthors']},
+                    shared_with={mirror.tarnsform_user_id(user['id']) for user in source.metadata['shared_with']},
+                    datasets={mirror.transform_dataset(ds) for ds in source.metadata['datasets']},
                     with_embargo=source.metadata['with_embargo'])
 
-                target_metadata_normalized: Dict[str, Any] = dict(
+                target_metadata_normalized: typing.Dict[str, typing.Any] = dict(
                     comment=target_metadata.comment,
                     references=set(target_metadata.references),
                     coauthors=set(target_metadata.coauthors),
@@ -115,7 +116,7 @@ def update_user_metadata(bulk_size: int = 1000, update_index: bool = False, **kw
 
                 if source_metadata_normalized != target_metadata_normalized:
                     # do a full update of all metadata!
-                    update = UpdateOne(
+                    update = pymongo.UpdateOne(
                         dict(_id=target.calc_id),
                         {
                             "$set": {

nomad/cli/admin/run.py

@@ -14,7 +14,7 @@
 
 import click
 import asyncio
-from concurrent.futures import ProcessPoolExecutor
+from concurrent import futures as concurrent_futures
 
 from nomad import config
 from .admin import admin
@@ -54,7 +54,7 @@ def run_worker():
 
 @run.command(help='Run both app and worker.')
 def appworker():
-    executor = ProcessPoolExecutor(2)
+    executor = concurrent_futures.ProcessPoolExecutor(2)
     loop = asyncio.get_event_loop()
     loop.run_in_executor(executor, run_app)
     loop.run_in_executor(executor, run_worker)

nomad/cli/admin/uploads.py

@@ -11,13 +11,11 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-from typing import List
+import typing
 import click
-from tabulate import tabulate
-from mongoengine import Q
-from elasticsearch_dsl import Q as ESQ
-from pymongo import UpdateOne
+import tabulate
+import mongoengine
+import pymongo
 import elasticsearch_dsl as es
 import json
 
@@ -34,23 +32,25 @@ from .admin import admin, __run_processing
 @click.option('--code', multiple=True, type=str, help='Select only uploads with calcs of given codes')
 @click.option('--query-mongo', is_flag=True, help='Select query mongo instead of elastic search.')
 @click.pass_context
-def uploads(ctx, user: str, staging: bool, processing: bool, outdated: bool, code: List[str], query_mongo):
+def uploads(
+        ctx, user: str, staging: bool, processing: bool, outdated: bool,
+        code: typing.List[str], query_mongo: bool):
     infrastructure.setup_mongo()
     infrastructure.setup_elastic()
 
-    query = Q()
+    query = mongoengine.Q()
     if user is not None:
-        query &= Q(user_id=user)
+        query &= mongoengine.Q(user_id=user)
     if staging:
-        query &= Q(published=False)