dryad2dataverse 0.7.5__tar.gz → 0.7.9__tar.gz

{dryad2dataverse-0.7.5/src/dryad2dataverse.egg-info → dryad2dataverse-0.7.9}/PKG-INFO

@@ -1,30 +1,40 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: dryad2dataverse
-Version: 0.7.5
+Version: 0.7.9
 Summary: Utility for copying and syncing data from a Dryad data repository to a Dataverse repository
-Author-email: Paul Lesack <paul.lesack@ubc.ca>
-Project-URL: Homepage, https://ubc-library-rc.github.io/dryad2dataverse
-Project-URL: Documentation, https://ubc-library-rc.github.io/dryad2dataverse
-Project-URL: Repository, https://github.com/ubc-library-rc/dryad2dataverse.git
-Project-URL: Tracker, https://github.com/ubc-library-rc/dryad2dataverse/issues
+License: MIT
 Keywords: Harvard Dataverse,Dataverse,research data management,data repository,Dryad,datadryad.org,dataverse.org
+Author: Paul Lesack
+Author-email: paul.lesack@ubc.ca
+Requires-Python: >=3.9, <4
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Education
 Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Education
 Classifier: Topic :: Internet :: WWW/HTTP :: Site Management
 Classifier: Topic :: Utilities
-Requires-Python: >=3.6
+Requires-Dist: certifi (>=2022.12.7)
+Requires-Dist: chardet (>=3.0.4)
+Requires-Dist: charset-normalizer (>=2.0.4)
+Requires-Dist: idna (>=2.10.0)
+Requires-Dist: pycryptodome (>=3.20.0)
+Requires-Dist: pydoc-markdown (>=4.8.2,<5.0.0)
+Requires-Dist: requests (>=2.26.0)
+Requires-Dist: requests-toolbelt (>=0.9.1)
+Requires-Dist: setuptools (>=80.8.0,<81.0.0)
+Requires-Dist: urllib3 (>=1.26.6)
+Project-URL: Bug Tracker, https://github.com/ubc-library-rc/dryad2dataverse/issues
+Project-URL: Documentation, https://ubc-library-rc.github.io/dryad2dataverse
+Project-URL: Homepage, https://ubc-library-rc.github.io/dryad2dataverse
+Project-URL: Repository, https://github.com/ubc-library-rc/dryad2dataverse.git
 Description-Content-Type: text/markdown
-Requires-Dist: certifi>=2022.12.7
-Requires-Dist: charset-normalizer>=2.0.4
-Requires-Dist: chardet>=3.0.4
-Requires-Dist: idna>=2.10.0
-Requires-Dist: pycryptodome>=3.20.0
-Requires-Dist: requests>=2.26.0
-Requires-Dist: requests-toolbelt>=0.9.1
-Requires-Dist: urllib3>=1.26.6
 
 # dryad2dataverse
 
@@ -77,3 +87,4 @@ This very terse description is by no means the entirety of the documentation. Co
 A (much) more user-friendly version of the documentation is available at <https://ubc-library-rc.github.io/dryad2dataverse>, including full `dryadd` documentation and API information.
 
 Or if you've cloned the git repostory above, you can use [mkdocs](https://www.mkdocs.org/) and `mkdocs serve` to have a local server version of the documentation. 
+

dryad2dataverse-0.7.9/pyproject.toml

@@ -0,0 +1,60 @@
+[project]
+name = "dryad2dataverse"
+version = "0.7.9"
+description = "Utility for copying and syncing data from a Dryad data repository to a Dataverse repository"
+authors = [
+    {name = "Paul Lesack",email = "paul.lesack@ubc.ca"}
+]
+license = {text = "MIT"}
+readme = "README.md"
+requires-python = ">=3.9, <4"
+dependencies = [
+    "certifi (>=2022.12.7)",
+    "charset-normalizer (>=2.0.4)",
+    "chardet (>=3.0.4)",
+    "idna (>=2.10.0)",
+    "pycryptodome (>=3.20.0)",
+    "requests (>=2.26.0)",
+    "requests-toolbelt (>=0.9.1)",
+    "urllib3 (>=1.26.6)",
+    "pydoc-markdown (>=4.8.2,<5.0.0)",
+    "setuptools (>=80.8.0,<81.0.0)"
+]
+
+keywords =['Harvard Dataverse',
+	'Dataverse',
+	'research data management',
+	'data repository',
+	'Dryad',
+	'datadryad.org',
+	'dataverse.org']
+
+
+[project.scripts]
+#This should be restructured one day
+dryadd = 'dryad2dataverse.scripts.dryadd:main'
+
+[project.urls]
+Homepage = 'https://ubc-library-rc.github.io/dryad2dataverse'
+Documentation = 'https://ubc-library-rc.github.io/dryad2dataverse'
+Repository = 'https://github.com/ubc-library-rc/dryad2dataverse.git'
+"Bug Tracker" = 'https://github.com/ubc-library-rc/dryad2dataverse/issues'
+
+
+[tool.poetry]
+classifiers = ['Development Status :: 4 - Beta',
+			   'Environment :: Console',
+			   'Intended Audience :: Education',
+			   'License :: OSI Approved :: MIT License',
+			   'Topic :: Education',
+			   'Topic :: Internet :: WWW/HTTP :: Site Management',
+			   'Topic :: Utilities']
+
+[tool.poetry.group.dev.dependencies]
+pylint = ">=3.3.6"
+mkdocs = ">=1.6.1"
+pydoc-markdown = ">=4.8.2"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"

{dryad2dataverse-0.7.5 → dryad2dataverse-0.7.9}/src/dryad2dataverse/__init__.py

@@ -24,7 +24,7 @@ Modules included:
 '''
 import sys
 
-VERSION = (0, 7, 5)
+VERSION = (0, 7, 9)
 __version__ = '.'.join([str(x) for x in VERSION])
 USERAGENT = (f'dryad2dataverse/v{__version__} ({sys.platform.capitalize()}); '
              f'Python {sys.version[:sys.version.find("(")-1]}')

{dryad2dataverse-0.7.5 → dryad2dataverse-0.7.9}/src/dryad2dataverse/scripts/dryadd.py

@@ -15,6 +15,7 @@ import logging
 import logging.handlers
 import os
 import pathlib
+import pprint
 import shutil
 import smtplib
 import sys
@@ -28,9 +29,12 @@ import dryad2dataverse.serializer
 import dryad2dataverse.transfer
 from dryad2dataverse.handlers import SSLSMTPHandler
 
-VERSION = (0, 6, 2)
+VERSION = (0, 7, 1)
 __version__ = '.'.join([str(x) for x in VERSION])
 
+USER_AGENT = {'User-agent': dryad2dataverse.USERAGENT}
+
+
 DRY = 'https://datadryad.org/api/v2'
 
 def new_content(serial):
@@ -215,6 +219,7 @@ def get_records(ror: 'str', mod_date=None, verbosity=True, timeout=100):
     '''
     headers = {'accept':'application/json',
                'Content-Type':'application/json'}
+    headers.update(USER_AGENT)
     per_page = 1
     params = {'affiliation' : ror,
               'per_page' : per_page}
@@ -344,6 +349,24 @@ def argp():
                         required=False,
                         dest='log',
                         default='/var/log/dryadd.log')
+    parser.add_argument('--loglevel',
+                        help='Log level of server rotating log. Choose one of '
+                        'debug, info, warning, error or critical. '
+                        'Note: case sensitive. '
+                        'Default: logging.warning.',
+                        required=False,
+                        dest='loglevel',
+                        default='warning',
+                        choices=['debug', 'info', 'warning','error','critical'])
+    parser.add_argument('--email-loglevel',
+                        help='Log level of email log. Choose one of '
+                        'debug, info, warning, error or critical. '
+                        'Note: case sensitive. '
+                        'Default: warning',
+                        required=False,
+                        dest='email_loglevel',
+                        default='warning',
+                        choices=['debug', 'info', 'warning','error','critical'])
     parser.add_argument('-l', '--no_force_unlock',
                         help='No forcible file unlock. Required '
                         'if /lock endpint is restricted',
@@ -389,16 +412,14 @@ def argp():
                         default=5,
                         dest='testlimit')
     parser.add_argument('--version', action='version',
-                        version='%(prog)s '+__version__
-                        +'; dryad2dataverse '+
-                        dryad2dataverse.__version__,
+                        version='dryad2dataverse ' + dryad2dataverse.__version__,
                         help='Show version number and exit')
 
     return parser
 
 def set_constants(args):
     '''
-    Set the appropriate dryad2dataverse constants
+    Set the appropriate dryad2dataverse "constants"
     '''
     dryad2dataverse.constants.DV_CONTACT_EMAIL = args.contact
     dryad2dataverse.constants.DV_CONTACT_ = args.contact
@@ -407,6 +428,8 @@ def set_constants(args):
         dryad2dataverse.constants.DVURL = args.url
     if args.dbase:
         dryad2dataverse.constants.DBASE = args.dbase
+    if args.tmp:
+        dryad2dataverse.constants.TMP = args.tmp
 
 def email_log(mailhost, fromaddr, toaddrs, credentials, port=465, secure=(),
               level=logging.WARNING, timeout=100):
@@ -526,7 +549,31 @@ def verbo(verbosity:bool, **kwargs)->None:
         for key, value in kwargs.items():
             print(f'{key}: {value}')
 
-def main(log='/var/log/dryadd.log', level=logging.WARNING):
+def anonymizer(args: argparse.Namespace) -> dict:
+    '''
+    Redacts sensitive info for the log when parsing arguments and returns a dictionary
+    with cleaner values.
+    '''
+    clean_me = args.__dict__.copy()#Don't work on the real thing!
+    cleanser = {x : 'REDACTED' for x in ['email', 'mailserve',
+                                         'key', 'mailserve',
+                                         'pwd', 'recipients', 
+                                         'user']}
+    clean_me.update(cleanser)
+    return clean_me
+
+def bulklog(message, *logfuncs):
+    '''
+    Convenience logging function
+
+    message : str
+        log message
+    logfuncs: logging.Logger[.debug, .info, etc. method]
+    '''
+    for log in logfuncs:
+        log('%s', message)
+
+def main():
     '''
     Main Dryad transfer daemon
 
@@ -540,16 +587,26 @@ def main(log='/var/log/dryadd.log', level=logging.WARNING):
     #pylint: disable=too-many-locals
     parser = argp()
     args = parser.parse_args()
-    if args.log:
-        log = args.log
-    logger = rotating_log(log, level)
+
+    #Ensure log can be written
+    logpath = pathlib.Path(args.log)
+    if not logpath.parent.exists():
+        os.makedirs(logpath.parent)
 
     set_constants(args)
+
+    logger = rotating_log(args.log,
+                          level=logging.getLevelName(args.loglevel.upper()))
+
     elog = email_log(args.mailserv, args.email, args.recipients,
-                     (args.user, args.pwd), port=args.port)
+                     (args.user, args.pwd), port=args.port,
+                     level = logging.getLevelName(args.email_loglevel.upper()))
 
 
     logger.info('Beginning update process')
+    for logme in [elog, logger]:
+        logme.debug('Command line arguments: %s' , pprint.pprint(anonymizer(args)))
+
     monitor = dryad2dataverse.monitor.Monitor(args.dbase)
     #copy the database to make a backup, because paranoia is your friend
     if os.path.exists(dryad2dataverse.constants.DBASE):
@@ -688,7 +745,7 @@ def main(log='/var/log/dryadd.log', level=logging.WARNING):
         elog.info('Completed update process')
         finished = ('Dryad to Dataverse transfers completed',
                     ('Dryad to Dataverse transfer daemon has completed.\n'
-                     f'Log available at: {log}'))
+                     f'Log available at: {args.log}'))
         notify(finished, **vars(args))
 
     except dryad2dataverse.exceptions.DataverseBadApiKeyError as api_err:

dryad2dataverse-0.7.5/.gitignore

@@ -1,42 +0,0 @@
-**/__pycache__/**
-**pyc
-**~
-*cfg
-*log
-analysis/crosswalk/.~*
-bin
-bin/**
-dryad2dataverse.egg-info
-filediff.py
-flake8.txt
-gitnotes.md
-include
-include/**
-lib
-lib/**
-tests/junk*.db
-tests/*bak.json
-tmp
-tmp/**
-x.py
-minisample.py
-man
-man/**
-daemon*
-daemon.cmd.soroban_test.txt
-daemon*.cmd.txt
-.readthedocs**
-docs/.readthe*
-scripts/dryadd_testing.py
-site/
-tests/basic_file_JSON.json
-binary_files
-binary_files/**
-scripts/testpickle
-scripts/dryadd_t.py
-dist/
-dist/**
-build/
-build/**
-bin/
-bin/**

dryad2dataverse-0.7.5/PKG-INFO

@@ -1,79 +0,0 @@
-Metadata-Version: 2.1
-Name: dryad2dataverse
-Version: 0.7.5
-Summary: Utility for copying and syncing data from a Dryad data repository to a Dataverse repository
-Author-email: Paul Lesack <paul.lesack@ubc.ca>
-Project-URL: Homepage, https://ubc-library-rc.github.io/dryad2dataverse
-Project-URL: Documentation, https://ubc-library-rc.github.io/dryad2dataverse
-Project-URL: Repository, https://github.com/ubc-library-rc/dryad2dataverse.git
-Project-URL: Tracker, https://github.com/ubc-library-rc/dryad2dataverse/issues
-Keywords: Harvard Dataverse,Dataverse,research data management,data repository,Dryad,datadryad.org,dataverse.org
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Education
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Topic :: Education
-Classifier: Topic :: Internet :: WWW/HTTP :: Site Management
-Classifier: Topic :: Utilities
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-Requires-Dist: certifi>=2022.12.7
-Requires-Dist: charset-normalizer>=2.0.4
-Requires-Dist: chardet>=3.0.4
-Requires-Dist: idna>=2.10.0
-Requires-Dist: pycryptodome>=3.20.0
-Requires-Dist: requests>=2.26.0
-Requires-Dist: requests-toolbelt>=0.9.1
-Requires-Dist: urllib3>=1.26.6
-
-# dryad2dataverse
-
-**dryad2dataverse** is a [Python](https://python.org) package and an associated console line application which allows easier transfer of metadata and data from a Dryad data repository (ie, <https://datadryad.org>) to a [Dataverse](https://dataverse.org/ "Dataverse software main site") repository. Dryad2dataverse is pure Python and should run on any platform which supports Python 3.6 or greater.
-
-Data transfers between repositories require local storage, so not all platforms will be equally suitable.
-
-## Installing
-
-`pip install dryad2dataverse`
-
-## Usage
-
-Most users will likely just want to use the command line transfer and monitor tool (`dryadd`) but the tools are available in any Python environment
-
-### Command line application
-
-`dryadd [all the various options]`
-
-see all the options available with
-
-`dryadd -h`
-
-Initiate a transfer from a [Dryad](https://datadryad.org) repository to a [Dataverse](https://dataverse.org) repository.
-
-### Using the package
-
-```
-#Serializer
-import dryad2dataverse.serializer
-#Transfer
-import dryad2dataverse.transfer
-#Monitor
-#import dryad2dataverse.monitor
-
-i_heart_dryad = dryad2dataverse.serializer.Serializer('doi:10.5061/dryad.2rbnzs7jp')
-dv = dryad2dataverse.transfer.Transfer(i_heart_dryad)
-dv.download_files()
-dv.upload_study(targetDv='dryad')
-dv.upload_files()
-
-#For an explanation look at the more detailed docs
-#You know, like where your API key goes.
-```
-
-## Documentation
-
-This very terse description is by no means the entirety of the documentation. Complete plain text documentation is available in the `docs` directory of (https://github.com/ubc-library-rc/dryad2dataverse), beginning with `index.md`.
-
-A (much) more user-friendly version of the documentation is available at <https://ubc-library-rc.github.io/dryad2dataverse>, including full `dryadd` documentation and API information.
-
-Or if you've cloned the git repostory above, you can use [mkdocs](https://www.mkdocs.org/) and `mkdocs serve` to have a local server version of the documentation. 

dryad2dataverse-0.7.5/docs/_config.yml

@@ -1,15 +0,0 @@
-title: dryad2dataverse 
-remote_theme: ubc-library-rc/rc-theme
-color_scheme: rc
-github_repo_url: "https://github.com/ubc-library-rc/dryad2dataverse/" 
-
-# license information for workshop content
-license_name: "MIT License"
-license_url: "https://opensource.org/licenses/MIT"
-#license_image_url: "https://i.creativecommons.org/l/by/4.0/88x31.png"
-
-# required for building jekyll site locally
-plugins:
-  - jekyll-remote-theme
-  - jekyll-seo-tag
-