adding cli

matscholar/__init__.py

@@ -1 +1,21 @@
+import os
+import yaml
 from matscholar.rest import Rester
+
+SETTINGS_FILE = os.path.join(os.path.expanduser("~"), ".msclirc.yaml")
+
+def _load_settings():
+    try:
+        with open(SETTINGS_FILE, "rt") as f:
+            d = yaml.safe_load(f)
+    except IOError:
+        # If there are any errors, default to using environment variables
+        # if present.
+        d = {}
+        for k, v in os.environ.items():
+            if k.startswith("MATSCHOLAR_"):
+                d[k] = v
+    return d
+
+
+SETTINGS = _load_settings()

matscholar/cli/__init__.py

@@ -0,0 +1,8 @@
+# coding: utf-8
+# Copyright (c) Matscholar Development Team.
+# Distributed under the terms of the MIT License.
+
+"""
+This package contains the matscholar command line interface. Its entry point is defined in setup.py.
+"""
+

matscholar/cli/mscli.py

@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+# Copyright (c) Matscholar Development Team.
+# Distributed under the terms of the MIT License.
+
+from __future__ import print_function, unicode_literals
+
+import click
+from PyInquirer import prompt
+from matscholar.cli.mscli_config import set_config
+from matscholar.collect import ScopusCollector
+
+@click.group()
+def cli():
+    pass
+
+@click.command("configure")
+def configure():
+    """Used to configure Matscholar configuration settings."""
+
+    questions = [
+        {
+            'type': 'input',
+            'name': 'MATSCHOLAR_NAME',
+            'message': 'Whate is your full name?',
+        },
+        {
+            'type': 'input',
+            'name': 'MATSCHOLAR_TEXT_MINING_KEY',
+            'message': 'Enter your Scopus API text mining key '
+                       '(obtained at https://dev.elsevier.com/apikey/manage) ',
+        },
+        {
+            'type': 'input',
+            'name': 'MATSCHOLAR_USER',
+            'message': 'Enter your Matscholar username',
+        },
+        {
+            'type': 'password',
+            'name': 'MATSCHOLAR_PASSWORD',
+            'message': 'Enter your Matscholar password',
+        },
+    ]
+
+    answers = prompt(questions)
+    set_config(answers)
+
+@click.command("contribute")
+@click.option('--count', default=1, help='number of blocks')
+def contribute(count):
+    """Used to contribute data to Matscholar database."""
+    collector = ScopusCollector()
+    collector.contribute(num_blocks=count)
+
+cli.add_command(configure)
+cli.add_command(contribute)
+
+def main():
+    cli()
+
+# from matscholar.cli.mscli_config import configure_mscli
+# from matscholar.cli.mscli_query import do_query
+#
+# def main():
+#     parser = argparse.ArgumentParser(description="""
+#     Welcome to mscli (The materials scholar command line interface)
+#     This script works based on several sub-commands with their own options.
+#     To see the options for the sub-commands, type "mscli sub-command -h".""")
+#
+#     subparsers = parser.add_subparsers()
+#
+#     parser_config = subparsers.add_parser(
+#         "set", help="Tool for modifying config variables in .msclirc.yaml configuration file.")
+#     groups = parser_config.add_mutually_exclusive_group(required=True)
+#     groups.add_argument("-a", "--add", dest="var_spec", nargs="+",
+#                         help="Variables to add in the form of space "
+#                              "separated key value pairs. E.g., "
+#                              "MATSCHOLAR_TEXT_MINING_KEY <api key>")
+#     parser_config.set_defaults(func=configure_mscli)
+#
+#     #TODO: add query on Rester to CLI
+#
+#
+#     parser_collect = subparsers.add_parser(
+#         "collect",
+#         help="Collect data from the Scopus API and add to the Materials Scholar Database. "
+#              "(For internal use by Matscholar collaborators.)")
+#
+#     group = parser_collect.add_mutually_exclusive_group(required=False)
+#     group.add_argument(
+#         "-k", "--key", dest="api_key", metavar="format",
+#         choices=["poscar", "cif", "cssr"], type=str.lower,
+#         help="Get structures from Materials Project and write them to a "
+#              "specified format.")
+#     group.add_argument(
+#         "-e", "--entries", dest="entries", metavar="filename",
+#         help="Get entries from Materials Project and write them to "
+#              "serialization file. JSON and YAML supported.")
+#     group.add_argument(
+#         "-d", "--data", dest="data", metavar="fields", nargs="*",
+#         help="Print a summary of entries in the Materials Project satisfying "
+#              "the criteria. Supply field names to include additional data. "
+#              "By default, the Materials Project id, formula, spacegroup, "
+#              "energy per atom, energy above hull are shown.")
+#     parser_query.set_defaults(func=do_query)
+#
+#     try:
+#         import argcomplete
+#         argcomplete.autocomplete(parser)
+#     except ImportError:
+#         # argcomplete not present.
+#         pass
+#
+#     args = parser.parse_args()
+#
+#     try:
+#         getattr(args, "func")
+#     except AttributeError:
+#         parser.print_help()
+#         sys.exit(0)
+#     args.func(args)
+
+
+if __name__ == "__main__":
+    main()

matscholar/cli/mscli_config.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+# coding: utf-8
+# Copyright (c) Matscholar Development Team.
+# Distributed under the terms of the MIT License.
+
+import os
+import sys
+import shutil
+from monty.serialization import loadfn, dumpfn
+
+from matscholar import SETTINGS_FILE
+
+
+def add_config_var(args):
+    d = {}
+    if os.path.exists(SETTINGS_FILE):
+        shutil.copy(SETTINGS_FILE, SETTINGS_FILE + ".bak")
+        print("Existing %s backed up to %s"
+              % (SETTINGS_FILE, SETTINGS_FILE + ".bak"))
+        d = loadfn(SETTINGS_FILE)
+    toks = args.var_spec
+    if len(toks) % 2 != 0:
+        print("Bad variable specification!")
+        sys.exit(-1)
+    for i in range(int(len(toks) / 2)):
+        d[toks[2 * i]] = toks[2 * i + 1]
+    dumpfn(d, SETTINGS_FILE, default_flow_style=False)
+    print("New %s written!" % (SETTINGS_FILE))
+
+
+def set_config(config):
+    if os.path.exists(SETTINGS_FILE):
+        shutil.copy(SETTINGS_FILE, SETTINGS_FILE + ".bak")
+        print("Existing %s backed up to %s"
+              % (SETTINGS_FILE, SETTINGS_FILE + ".bak"))
+    dumpfn(config, SETTINGS_FILE, default_flow_style=False)
+    print("New %s written!" % (SETTINGS_FILE))
+
+
+def configure_mscli(args):
+    if args.var_spec:
+        add_config_var(args)

matscholar/cli/mscli_query.py

@@ -0,0 +1,19 @@
+# coding: utf-8
+# Copyright (c) Materials Intelligence.
+# Distributed under the terms of the BSD License.
+
+
+"""
+Run a query on the Materials Scholar Rest API
+"""
+
+from matscholar import Rester
+import json
+from monty.serialization import dumpfn
+import re
+from tabulate import tabulate
+
+
+def do_query(args):
+    #TODO: Implement this.
+    pass