diff --git a/.gitignore b/.gitignore index 459674aa..2965c515 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ instance/ dbs/ .vscode +nohup.out docs/diagrams/C4-PlantUML diff --git a/docs/operation.md b/docs/operation.md index b2cddf8c..d2d61c27 100644 --- a/docs/operation.md +++ b/docs/operation.md @@ -9,10 +9,10 @@ Harvesting is implemented as a scrapy crawler[^scrapy]. Given a sitemap, crawls ## DataONE production and testing hosts - Test server: so.test.dataone.org - - Environment: ~vieglais - - Virtual env: mnlite + - Environment: `~mnlite` + - Virtual env: `mnlite` - Production server: sonode.dataone.org - - Environment: ``~mnlite` + - Environment: `~mnlite` - Virtual env: `mnlite` ## Testing @@ -25,7 +25,7 @@ Harvesting is implemented as a scrapy crawler[^scrapy]. Given a sitemap, crawls 1. Log in to sonode.dataone.org (or so.test.dataone.org for testing) 2. `sudo su - mnlite` -3. `workon mnlite` +3. `workon mnlite` (`conda activate mnlite` on the test node) 4. `cd WORK/mnlite` 5. Initialize a new repository: `opersist -f instance/nodes/HAKAI_IYS init` 6. Create a contact subject: `opersist -f instance/nodes/HAKAI_IYS sub -o create -n "Brett Johnson" -s "http://orcid.org/0000-0001-9317-0364"` diff --git a/mnlite/mnode.py b/mnlite/mnode.py index 91db18ba..ddf2004c 100644 --- a/mnlite/mnode.py +++ b/mnlite/mnode.py @@ -45,6 +45,11 @@ ] } } +""" +Default node configuration dictionary. Defines the node document upon loading +into mnlite system service (see eg: the +`OpenTopography node document `_) +""" def getMNodeNameFromRequest(): diff --git a/mnlite/xmnlite.ini b/mnlite/xmnlite.ini new file mode 100644 index 00000000..dae672e6 --- /dev/null +++ b/mnlite/xmnlite.ini @@ -0,0 +1,44 @@ +#uWSGI configuration for mnlite +[uwsgi] +strict = true +master = true +processes = 5 +enable-threads = true +vacuum = true ; Delete sockets during shutdown +single-interpreter = true +die-on-term = true ; Shutdown when receiving SIGTERM (default is respawn) +need-app = true + +#disable-logging = true ; Disable built-in logging +#log-4xx = true ; but log 4xx's anyway +#log-5xx = true ; and 5xx's + +##harakiri = 60 ; forcefully kill workers after 60 seconds +#py-callos-afterfork = true ; allow workers to trap signals + +##max-requests = 1000 ; Restart workers after this many requests +##max-worker-lifetime = 3600 ; Restart workers after this many seconds +##reload-on-rss = 2048 ; Restart workers after this much resident memory +##worker-reload-mercy = 60 ; How long to wait before forcefully killing workers + +#cheaper-algo = busyness +#processes = 128 ; Maximum number of workers allowed +#cheaper = 8 ; Minimum number of workers allowed +#cheaper-initial = 16 ; Workers created at startup +#cheaper-overload = 1 ; Length of a cycle in seconds +#cheaper-step = 16 ; How many workers to spawn at a time +#cheaper-busyness-multiplier = 30 ; How many cycles to wait before killing workers +#cheaper-busyness-min = 20 ; Below this threshold, kill workers (if stable for multiplier cycles) +#cheaper-busyness-max = 70 ; Above this threshold, spawn new workers +##cheaper-busyness-backlog-alert = 16 ; Spawn emergency workers if more than this many requests are waiting in the queue +##cheaper-busyness-backlog-step = 2 ; How many emergency workers to create if there are too many requests in the queue + +##plugins = python +##virtualenv = /home/mnlite/miniconda3/envs/mnlite +module = mnlite:create_app() +socket = /home/mnlite/WORK/mnlite/mnlite/tmp/mnlite.sock +chmod-socket = 664 + +#stats = /tmp/stats.socket +##stats = 127.0.0.1:9191 +##stats-http = true diff --git a/mnonboard/README.md b/mnonboard/README.md new file mode 100644 index 00000000..2172963b --- /dev/null +++ b/mnonboard/README.md @@ -0,0 +1,66 @@ +# mnonboard + +This module is designed to provide a wrapper around `opersist` and `mnlite` in order to streamline the [DataONE member node onboarding process](https://github.com/DataONEorg/mnlite/blob/feature/onboarding/docs/operation.md). +It takes as input either a json document manually edited from a template, or converts direct user input to a json document. + +## Usage + +This script requires working installations of both [sonormal](https://github.com/datadavev/sonormal) and [mnlite](https://github.com/DataONEorg/mnlite) to function properly. + +### CLI options + +``` +Usage: cli [ OPTIONS ] +where OPTIONS := { + -c | --check=[ NUMBER ] + number of random metadata files to check for schema.org compliance + -d | --dump=[ FILE ] + dump default member node json file to configure manually + -h | --help + display this help message + -i | --init + initialize a new member node from scratch + -l | --load=[ FILE ] + initialize a new member node from a json file + -P | --production + run this script in production mode (uses the D1 cn API in searches) + -L | --local + run this script in local mode (will not scrape the remote site for new metadata) +} +``` + +### Onboarding process + +Let's say you are in the `mnlite` base directory. +Start by activating the `mnlite` virtual environment and changing the working directory to `./mnonboard`: + +``` +workon mnlite +cd mnonboard +``` + +**Note:** Node data is stored in `instance/nodes/` + +#### Using an existing `node.json` + +To onboard a member node with an existing `node.json` file: + +``` +python cli.py -l ../instance/nodes/BONARES/node.json +``` + +The script will guide you through the steps to set up the node and harvest its metadata. + +#### No existing `node.json` + +The script can also ask the user questions to set up the `node.json` file in an assisted manner. To do so, use the `-i` (initialize) flag: + +``` +python cli.py -i +``` + +Keep in mind that you should always check the `node.json` file to ensure correct values. + +## Other functionality + +Coming soon (see [#21](https://github.com/DataONEorg/mnlite/issues/21)) diff --git a/mnonboard/__init__.py b/mnonboard/__init__.py new file mode 100644 index 00000000..ada11b0b --- /dev/null +++ b/mnonboard/__init__.py @@ -0,0 +1,63 @@ +import os +import logging +from datetime import datetime + +from opersist.cli import LOG_DATE_FORMAT, LOG_FORMAT +from mnlite.mnode import DEFAULT_NODE_CONFIG + +DEFAULT_JSON = DEFAULT_NODE_CONFIG + +__version__ = 'v0.0.1' + +LOG_FORMAT = "%(asctime)s %(funcName)s:%(levelname)s: %(message)s" # overrides import + +FN_DATE = datetime.now().strftime('%Y-%m-%d') +HM_DATE = datetime.now().strftime('%Y-%m-%d-%H%M') +YM_DATE = datetime.now().strftime('%Y-%m') +LOG_DIR = '/var/log/mnlite/' +LOG_NAME = 'mnonboard-%s.log' % (FN_DATE) +LOG_LOC = os.path.join(LOG_DIR, LOG_NAME) + +HARVEST_LOG_NAME = '-crawl-%s.log' % YM_DATE + +def start_logging(): + """ + Initialize logger. + + :returns: The logger to use + :rtype: logging.Logger + """ + logger = logging.getLogger('mnonboard') + logger.setLevel(logging.DEBUG) + formatter = logging.Formatter(fmt=LOG_FORMAT, datefmt=LOG_DATE_FORMAT) + s = logging.StreamHandler() + s.setLevel(logging.INFO) + s.setFormatter(formatter) + # this initializes logging to file + f = logging.FileHandler(LOG_LOC) + f.setLevel(logging.DEBUG) + f.setFormatter(formatter) + # warnings also go to file + # initialize logging + logger.addHandler(s) # stream + logger.addHandler(f) # file + logger.info('----- mnonboard %s start -----' % __version__) + return logger + +L = start_logging() + +# absolute path of current file +CUR_PATH_ABS = os.path.dirname(os.path.abspath(__file__)) + +# relative path from root of mnlite dir to nodes directory +NODE_PATH_REL = 'instance/nodes/' + +def default_json(fx='Unspecified'): + """ + A function that spits out a dict to be used in onboarding. + + :returns: A dict of values to be used in member node creation + :rtype: dict + """ + L.info('%s function loading default json template.' % (fx)) + return DEFAULT_JSON diff --git a/mnonboard/cli.py b/mnonboard/cli.py new file mode 100644 index 00000000..7fcbfbc4 --- /dev/null +++ b/mnonboard/cli.py @@ -0,0 +1,155 @@ +import os, sys +import getopt +import time + +from mnonboard import utils +from mnonboard import info_chx +from mnonboard import data_chx +from mnonboard import cn +from mnonboard.defs import CFG, HELP_TEXT, SO_SRVR, CN_SRVR, CN_SRVR_BASEURL, CN_CERT_LOC, APPROVE_SCRIPT_LOC +from mnonboard import default_json, L + +def run(cfg): + """ + Wrapper around opersist that simplifies the process of onboarding a new + member node to DataONE. + + :param dict cfg: Dict containing config variables + """ + # auth + if not cfg['token']: + cfg['token'] = os.environ.get('D1_AUTH_TOKEN') + if not cfg['token']: + print('Your DataONE auth token is missing. Please enter it here and/or store it in the env variable "D1_AUTH_TOKEN".') + cfg['token'] = info_chx.req_input('Please enter your DataONE authentication token: ') + os.environ['D1_AUTH_TOKEN'] = cfg['token'] + cfg['cert_loc'] = CN_CERT_LOC[cfg['mode']] + DC = cn.init_client(cn_url=cfg['cn_url'], auth_token=cfg['token']) + if cfg['info'] == 'user': + # do the full user-driven info gathering process + ufields = info_chx.user_input() + fields = info_chx.transfer_info(ufields) + else: + # grab the info from a json + fields = utils.load_json(cfg['json_file']) + info_chx.input_test(fields) + # still need to ask the user for some names + # now we're cooking + # get the node path using the end of the path in the 'node_id' field + end_node_subj = fields['node']['node_id'].split(':')[-1] + loc = utils.node_path(nodedir=end_node_subj) + # initialize a repository there (step 5) + utils.init_repo(loc) + names = {} + for f in ('default_owner', 'default_submitter', 'contact_subject'): + # add a subject for owner and submitter (may not be necessary if they exist already) + # add subject for technical contact (step 6) + val = fields[f] if f not in 'contact_subject' else fields['node'][f] + name = utils.get_or_create_subj(loc=loc, value=val, cn_url=cfg['cn_url'], title=f) + # store this for a few steps later + names[val] = name + # set the update schedule and set the state to up + fields['node']['schedule'] = utils.set_schedule() + fields['node']['state'] = 'up' + # okay, now overwrite the default node.json with our new one (step 8) + utils.save_json(loc=os.path.join(loc, 'node.json'), jf=fields) + # add node as a subject (step 7) + utils.get_or_create_subj(loc=loc, value=fields['node']['node_id'], + cn_url=cfg['cn_url'], + name=end_node_subj) + # restart the mnlite process to pick up the new node.json (step 9) + utils.restart_mnlite() + # run scrapy to harvest metadata (step 10) + if not cfg['local']: + utils.harvest_data(loc, end_node_subj) + # now run tests + data_chx.test_mdata(loc, num_tests=cfg['check_files']) + # create xml to upload for validation (step 15) + files = utils.create_names_xml(loc, node_id=fields['node']['node_id'], names=names) + # uploading xml (proceed to step 14 and ssh to find xml in ~/d1_xml) + ssh, work_dir, node_id = utils.start_ssh(server=cfg['cn_url'], + node_id=fields['node']['node_id'], + loc=loc, + ssh=cfg['ssh']) + time.sleep(0.5) + utils.upload_xml(ssh=ssh, server=CN_SRVR[cfg['mode']], files=files, node_id=node_id, loc=loc) + # create and validate the subject in the accounts service (step 16) + utils.create_subj_in_acct_svc(ssh=ssh, cert=cfg['cert_loc'], files=files, cn=cfg['cn_url'], loc=loc) + utils.validate_subj_in_acct_svc(ssh=ssh, cert=cfg['cert_loc'], names=names, cn=cfg['cn_url'], loc=loc) + # download the node capabilities and register the node + node_filename = utils.dl_node_capabilities(ssh=ssh, baseurl=SO_SRVR[cfg['mode']], node_id=node_id, loc=loc) + utils.register_node(ssh=ssh, cert=cfg['cert_loc'], node_filename=node_filename, cn=cfg['cn_url'], loc=loc) + utils.approve_node(ssh=ssh, script_loc=APPROVE_SCRIPT_LOC, loc=loc) + # close connection + ssh.close() if ssh else None + +def main(): + """ + Uses getopt to set config values in order to call + :py:func:`mnlite.mnonboard.cli.run`. + + :returns: Config variable dict to use in :py:func:`mnlite.mnonboard.cli.run` + :rtype: dict + """ + # get arguments + try: + opts = getopt.getopt(sys.argv[1:], 'hiPvLd:l:c:', + ['help', 'init', 'production', 'verbose', 'local' 'dump=', 'load=', 'check='] + )[0] + except Exception as e: + L.error('Error: %s' % e) + print(HELP_TEXT) + exit(1) + for o, a in opts: + if o in ('-h', '--help'): + # help + print(HELP_TEXT) + exit(0) + if o in ('-i', '--init'): + # do data gathering + CFG['info'] = 'user' + if o in ('-P', '--production'): + # production case + CFG['cn_url'] = CN_SRVR_BASEURL % CN_SRVR['production'] + CFG['mode'] = 'production' + else: + # testing case + CFG['cn_url'] = CN_SRVR_BASEURL % CN_SRVR['testing'] + CFG['mode'] = 'testing' + if o in ('-d', '--dump'): + # dump default json to file + utils.save_json(a, default_json()) + exit(0) + if o in ('-l', '--load'): + # load from json file + CFG['info'] = 'json' + CFG['json_file'] = a + if o in ('-c', '--check'): + try: + CFG['check_files'] = int(a) + except ValueError: + if a == 'all': # this should probably not be used unless necessary! + CFG['check_files'] = a + else: + L.error('Option -c (--check) requires an integer number of files to check.') + print(HELP_TEXT) + exit(1) + if o in ('-L', '--local'): + CFG['local'] = True + L.info('Local mode (-L) will not scrape the remote site and will only test local files.') + L.info('running mnonboard in %s mode.\n\ +data gathering from: %s\n\ +cn_url: %s\n\ +metadata files to check: %s' % (CFG['mode'], + CFG['info'], + CFG['cn_url'], + CFG['check_files'])) + try: + run(CFG) + except KeyboardInterrupt: + print() + L.error('Caught KeyboardInterrupt, quitting...') + exit(1) + +if __name__ == '__main__': + main() diff --git a/mnonboard/cn.py b/mnonboard/cn.py new file mode 100644 index 00000000..4c5ca202 --- /dev/null +++ b/mnonboard/cn.py @@ -0,0 +1,72 @@ +from os import environ +from d1_client.cnclient import CoordinatingNodeClient +from d1_common.types.dataoneTypes import Subject, person +#import d1_admin_tools as d1np + +from . import defs + +def init_client(cn_url: str, auth_token: str): + """ + Initialize a d1_client.cnclient.CoordinatingNodeClient instance. + + :param str cn_url: The URL of the coordinating node to query (e.g. ``"https://cn-stage.test.dataone.org/cn"``) + """ + options: dict = {"headers": {"Authorization": "Bearer " + auth_token}} + return CoordinatingNodeClient(cn_url, **options) + +def get_subjects(client: CoordinatingNodeClient, orcid: str): + """ + Return a list of subjects queried from the CN client. + + :param d1_client.cnclient.CoordinatingNodeClient client: The client to query + :param str orcid: ORCiD to search for on the CN + """ + return client.getSubjectInfo(orcid) + +def get_first_subject(client: CoordinatingNodeClient, orcid: str): + """ + Return the first subject in the list queried from the CN client. + + :param d1_client.cnclient.CoordinatingNodeClient client: The client to use for the query + :param str orcid: ORCiD to search for on the CN + """ + try: + return get_subjects(client=client, orcid=orcid)[0] + except IndexError: + return None + +def get_subject_name(subject: Subject): + """ + Get the name of a subject queried from the CN. + + :param d1_common.types.dataoneTypes.Subject subject: The Subject object to get the name from + """ + first, last = subject.content()[0].content()[1], subject.content()[0].content()[2] + return "%s %s" % (first, last) + +def node_list(client: CoordinatingNodeClient): + """ + Get a list of nodes from the CN. + + :param d1_client.cnclient.CoordinatingNodeClient client: The CN client to use for the query + """ + nodes = client.listNodes() + for node in nodes.content(): + print(node.name) + return nodes + +def register_user(client: CoordinatingNodeClient, orcid: str, name: str, email: str=None): + """ + Register a user using the CN client. + + :param d1_client.cnclient.CoordinatingNodeClient client: The client to use for the query + :param str orcid: The subject's ORCiD ID + :param str name: The name of the subject + :param str email: The subject's email address + """ + +def set_nodes_properties(nodes_properties: dict, con=None): + """ + :param dict nodes_properties: + :param con: + """ diff --git a/mnonboard/data_chx.py b/mnonboard/data_chx.py new file mode 100644 index 00000000..185034a4 --- /dev/null +++ b/mnonboard/data_chx.py @@ -0,0 +1,217 @@ +import random +from pyshacl import validate +from pyshacl.errors import ShapeLoadError, ConstraintLoadError, \ + ReportableRuntimeError + +from mnonboard import L +from mnonboard.defs import SHACL_URL, SHACL_ERRORS +from mnonboard.utils import limit_tests, save_report, ask_continue +from opersist.cli import getOpersistInstance +from opersist.models.thing import Thing +from json.decoder import JSONDecodeError + +def violation_extract(viol): + """ + A function that extracts the name of the violation from + :py:func:`pyshacl.validate`. + + :param str viol: The result text, third item returned of a pyshacl.validate() run + :returns: List of violation names found in the res_text + :rtype: list[str, str, ...] + """ + lines = ['Source Shape: '] + end = '\n' + vx = [] + for line in lines: + L.info('Checking %ss' % line.split(':')[0]) + if line in viol: + for seg in viol.split(line)[1:]: + s = seg.split(end)[0] + L.debug('Found violation name: %s' % (s)) + vx.append(s) + if len(vx) > 0: + L.info('Found violations: %s' % (vx)) + return vx + else: + L.warning('Violation name was not extracted. Text block follows:\n%s' % (viol)) + return vx + +def violation_cat(hash, viol): + """ + A function that returns a CSV linestring that contains the severity of a + passed shacl violation and a comment. + + :param str hash: Path to the metadata file (based on file hash) + :param str viol: The violation name + :returns: Comma-separated list of: hash, violation category, violation name, comment + :rtype: str + """ + csvl = '%s,%s,%s,%s\n' + cat, comment = '', '' + if viol in SHACL_ERRORS['essential']: + cat = 'ESSENTIAL' + comment = SHACL_ERRORS['essential'][viol] + elif viol in SHACL_ERRORS['optional']: + cat = 'Optional' + comment = SHACL_ERRORS['optional'][viol] + elif viol in SHACL_ERRORS['internal']: + cat = 'Internal' + comment = SHACL_ERRORS['internal'][viol] + else: + cat = 'Not found' + comment = 'Violation name %s not found in SHACL_ERRORS dictionary! Consult DataONE node admin for information.' % viol + L.warning(comment) + hash = hash.split('/')[-1].split('.bin')[0] # split path and file extension from string + csvl = csvl % (hash, cat, viol, comment) + L.debug('Violation categorization for %s: %s' % (viol, cat)) + return csvl + +def violation_report(viol_dict, loc): + """ + A function that outputs a report containing information on the violations + found while shacl testing. + + :param dict viol_dict: Dictionary of violations compiled from this run of metadata checks + :param str loc: Directory of the opersist instance, where the report file will be written + """ + L.info('Creating report.') + L.debug(viol_dict) + L.info('Violation dictionary length: %s' % (len(viol_dict))) + rep_str = 'Hash,Violation level,Violation name,Comment\n' + if len(viol_dict) > 0: + for hash in viol_dict: + L.info('Working on hash %s' % (hash.split('/')[-1].split('.bin')[0])) + i = 0 + while i < len(viol_dict[hash]): + viol = violation_extract(viol_dict[hash][i][2]) + for v in viol: + rep_str = rep_str + violation_cat(hash, v) + i += 1 + L.info('Report:\n%s' % (rep_str)) + else: + rep_str = rep_str + ',,,No violations found.\n' + L.info('No violations.') + save_report(rep_str=rep_str, loc=loc) + +def test_mdata(loc, shp_graph=SHACL_URL, format='json-ld', num_tests=3): + """ + Use pyshacl to test harvested metadata. + + :param str loc: The base MN folder path in which opersist keeps its data and databases + :param str shp_graph: Shape graph to be used for testing (defaults to soso v1.2.3) + :param str format: Format of the data graphs (default: json-ld) + :param int num_tests: Number of metadata files to test (randomly selected; default=3) + """ + L.info('Starting metadata checks. Shape graph: %s' % (shp_graph)) + op = getOpersistInstance(loc) + num_things = op.countThings() + if (num_tests == 'all') and (num_things >= 500): + L.warning('User has chosen to shacl test all %s files in the set. Asking to limit...' % num_things) + # 500 will take about a minute and use a bunch of resources. let's suggest keeping it shorter than that + num_tests = limit_tests(num_things) + num_tests = num_things if num_tests == 'all' else num_tests # still might have to test all things if (num_things < 500) + L.info('Checking %s files.' % num_tests) + q = op.getSession().query(Thing) # this might be too inefficient for large sets; may need to change + i, valid_files, load_errs, tot_violations = 0, 0, 0, 0 + viol_dict = {} + while i < num_tests: + if i > 0: + L.info('Continuing to next record...') + record = '' + violati1, violati2 = 0, 0 + # get a thing and decode its path + L.info('Record check %s/%s...' % (i+1, num_tests)) + if num_tests != num_things: + thing_no = random.randint(0, num_things) + else: + thing_no = i + try: + t = q[thing_no] + except IndexError as e: + msg = 'No records in mnlite database! Aborting checks and registrations.' + L.error(f'{msg} Details: {e}') + print(msg) + exit(1) + L.info('Selected record number %s of %s in set: %s' % (thing_no, num_things, t.content)) + pth = op.contentAbsPath(t.content) + # read to object + L.info('Reading binary from %s' % (pth)) + try: + with open(pth, 'rb') as f: + record = f.read().decode('utf-8') + L.info('Success.') + L.debug('Record follows:\n%s' % (record)) + conforms, res_graph, res_text = validate(data_graph=record, + data_graph_format=format, + shacl_graph=shp_graph, + shacl_graph_format='turtle',) + viol_dict[t.content] = {0: [conforms, res_graph, res_text]} + if not conforms: + violati1 = int(res_text.split('\n')[2].split('(')[1].split(')')[0]) + constraint_viol = ' including Constraint Violations' if 'Constraint Violation' in res_text else '' + L.warning('pyshacl found %s violations.' % (violati1)) + L.debug('Details:\n%s' % (res_text)) + if (violati1 == 1) and (' not ' in res_text): + # under this condition there is one constraint violation where the record uses https + constraint_viol = ' including https vs http namespace violation' + # do a quick replace and test again for lower level violations + L.debug('Found https vs http namespace violation...replacing and testing again...') + record = record.replace('https://schema.org/', 'http://schema.org/') + conforms2, res_graph2, res_text2 = validate(data_graph=record, + data_graph_format=format, + shacl_graph=shp_graph, + shacl_graph_format='turtle',) + viol_dict[t.content][1] = [conforms2, res_graph2, res_text2] + if not conforms2: + violati2 = int(res_text2.split('\n')[2].split('(')[1].split(')')[0]) + L.warning('pyshacl found %s additional violations after correcting for https/http violation.' % (violati2)) + L.debug('Details:\n%s' % (res_text2)) + else: + L.info('Namespace https/http constraint violation is the only error found') + tot_violations = violati1 + violati2 + L.info('Total shacl violations in file: %s' % (tot_violations)) + else: + L.info('No violations found in %s' % (pth)) + viol_dict[t.content] = {0: [True, None, 'No violations.']} + valid_files += 1 + except ShapeLoadError as e: + # could be an error with either data or shacl file + L.error('pyshacl threw ShapeLoadError: %s' % e) + viol_dict[t.content] = {0: [False, None, 'ShapeLoadError: %s' % e]} + load_errs += 1 + except ConstraintLoadError as e: + # I think this is only possible when loading the shacl graph (i.e. w/ constraints) + L.error('pyshacl threw ConstraintLoadError: %s' % e) + viol_dict[t.content] = {0: [False, None, 'ConstraintLoadError']} + load_errs += 1 + except ReportableRuntimeError as e: + # not exactly sure what this is + L.error('pyshacl threw ReportableRuntimeError: %s' % e) + viol_dict[t.content] = {0: [False, None, 'ReportableRuntimeError']} + load_errs += 1 + except JSONDecodeError as e: + # malformed json in the json-ld record, this is definitely related to the data graph + L.error('JSON is malformed, this record cannot be validated. Details:\n%s' % e) + viol_dict[t.content] = {0: [False, None, 'JSONDecodeError']} + load_errs += 1 + except FileNotFoundError as e: + # somehow the file we got from the database does not exist + L.error('Could not find a file at %s' % (pth)) + viol_dict[t.content] = {0: [False, None, 'FileNotFoundError']} + load_errs += 1 + except Exception as e: + # this might have something to do with code in this function + # if it's a TypeError, it could have to do with the creation of violati1/violati2 + L.error('Error validating record %s' % (pth)) + L.error('Uncaught exception (%s): %s' % (repr(e), e)) + viol_dict[t.content] = {0: [False, None, repr(e)]} + load_errs += 1 + finally: + i += 1 + L.info('Found %s valid records out of %s checked.' % (valid_files, i)) + L.info('%s failures due to load and/or decode errors.' % (load_errs)) + violation_report(viol_dict, loc) + # close the opersist instance + op.close() + msg = f"{valid_files} fully valid records found (out of {i} checked; with {load_errs} load/decode errors). Continue?" + ask_continue(msg) diff --git a/mnonboard/defs.py b/mnonboard/defs.py new file mode 100644 index 00000000..bdcd39fa --- /dev/null +++ b/mnonboard/defs.py @@ -0,0 +1,212 @@ +import os, pwd +from mnonboard import __version__ + +ORCID_PREFIX = 'http://orcid.org/' +SHACL_URL = 'https://raw.githubusercontent.com/ESIPFed/science-on-schema.org/master/validation/shapegraphs/soso_common_v1.2.3.ttl' +NODE_ID_PREFIX = 'urn:node:' +SUBJECT_PREFIX = 'CN=' +SUBJECT_POSTFIX = ',DC=dataone,DC=org' + +CFG = { + 'info': 'user', + 'json_file': 'node.json', + 'cn_url': 'https://cn-stage.test.dataone.org/cn', + 'mode': 'testing', + 'token': None, + 'check_files': 5, + 'local': False, + 'ssh': False, +} +""" +Config dictionary. + +``'info'`` - Where the script gets data from. ``'json'`` for loaded node document or ``'user'`` for user-entered. Default: ``'user'`` +``'json_file'`` - JSON file to load, usually at ``../instance/nodes//node.json``. See :py:data:`mnlite.mnode.DEFAULT_NODE_CONFIG`. Default: ``node.json`` +``'cn_url'`` - The URL of the coordinating node. Defined by ``'mode'``. Default: ``'https://cn-stage.test.dataone.org/cn'`` +``'mode'`` - The environment to run in: ``'production'`` or default ``'testing'`` +``'token'`` - The DataONE auth token. Can be loaded from ``https://search.dataone.org/profile/http://orcid.org//s=settings/s=token`` in production +``'check_files'`` - How many schema.org records to check. Default: ``5`` +``'local'`` - If ``True``, run locally (do not run the scraper to harvest from the remote sitemap) +``'ssh'`` - If ``True``, run registration commands on the CN after checking schema.org records. Only works in ``'mode': 'testing'``. Otherwise, output a file with a list of commands to run to register the node on the CN. +""" + +SO_SRVR = { + 'production': 'sonode.dataone.org', + 'testing': 'so.test.dataone.org' +} +""" +The location of the mnlite instance serving schema.org metadata. +""" +CN_SRVR = { + 'production': 'cn.dataone.org', + 'testing': 'cn-stage.test.dataone.org' +} +""" +The location of the coordinating node. +""" + +USER_NAME = pwd.getpwuid(os.getuid())[0] + +CN_SRVR_BASEURL = 'https://%s/cn' +""" +The URL format of the CN API. +Populated with one of the servers defined in :py:data:`mnonboard.defs.CN_SRVR`. +""" + +CN_CERT_LOC = { + 'production': '/etc/dataone/client/private/urn_node_CNUCSB1.pem', + 'testing': '/etc/dataone/client/private/urn_node_cnStageUCSB1.pem' +} +""" +The location of the CN cert, used for registration. +""" + +APPROVE_SCRIPT_LOC = '/usr/local/bin/dataone-approve-node' +""" +The location of the Hazelcast node approval script. +""" + +HELP_TEXT = """DataONE member node onboard script +%s NCEAS/Ian Nesbitt + +Usage: cli [ OPTIONS ] +where OPTIONS := { + -c | --check=[ NUMBER ] + number of random metadata files to check for schema.org compliance + -d | --dump=[ FILE ] + dump default member node json file to configure manually + -h | --help + display this help message + -i | --init + initialize a new member node from scratch + -l | --load=[ FILE ] + initialize a new member node from a json file + -P | --production + run this script in production mode (uses the D1 cn API in searches) + -L | --local + run this script in local mode (will not scrape the remote site for new metadata) +} +""" % __version__ +""" +Help text for command line use. + +.. warning:: Soon to be deprecated in favor of using ``argparse``. +""" + +FIELDS = { + 'node': { + 'node_id': ['Member node_id (must be unique): ', None], + 'name': ['Repository name: ', None], + 'description': ['Repository description: ', None], + 'base_url': ['Base URL of repository: ', None], + 'subject': ['Path of repository: ', None], + 'contact_subject_name': ['Repository technical contact name: ', None], + 'contact_subject': ["Technical contact's ORCiD number: ", None], + }, + 'default_submitter_name': ['Repository submitter name: ', None], + 'default_submitter': ["Submitter's ORCiD number: ", None], + 'default_owner_name': ['Repository owner name: ', None], + 'default_owner': ["Owner's ORCiD number: ", None], + 'num_sitemap_urls': ['Number of sitemap URLs (need at least 1): ', None], +} + +FILL_FIELDS = [ + 'node_id', + 'node', + 'description', + 'base_url', + 'contact_subject', + 'default_submitter', + 'default_owner', + 'sitemap_urls' +] + +SITEMAP_URLS = [] + +SCHEDULES = { + # monthly on the 1st at 00:30 + 0: { + "hour": "0", + "day": "1", + "min": "30", + "mon": "*", + "sec": "0", + "wday": "?", + "year": "*" + }, + # daily at 00:20 + 1: { + "hour": "0", + "day": "*", + "min": "20", + "mon": "*", + "sec": "0", + "wday": "?", + "year": "*" + }, + # hourly at :01 + 2: { + "hour": "*", + "day": "*", + "min": "1", + "mon": "*", + "sec": "0", + "wday": "?", + "year": "*" + }, + # every three minutes + 3: { + "hour": "*", + "day": "*", + "min": "*/3", + "mon": "*", + "sec": "0", + "wday": "?", + "year": "*" + } +} + +SHACL_ERRORS = { + 'essential': { + # load errors + 'ShapeLoadError': 'Shape graph must load correctly', + 'JSONDecodeError': 'Metadata files must be properly formatted json-ld', + # science-on-schema.org violations + 'soso:IDShape': 'Dataset must have an ID', + # schema.org violations + 'SO:Dataset-description': 'Dataset must have a description', + 'SO:Dataset-identifier': 'Dataset identifiers must be a URL, Text or PropertyValue', + 'SO:Dataset-name': 'Name is required for a Dataset', + 'SO:Dataset-url': 'Dataset requires a URL for the location of a page describing the dataset', + }, + 'optional': { + # science-on-schema.org violations + 'soso:DatasetNS1Shape': 'Expecting SO namespace of not ', + 'soso:DatasetNS2Shape': 'Expecting SO namespace of not ', + 'soso:DatasetNS3Shape': 'Expecting SO namespace of not ', + # schema.org violations + 'SO:Dataset-isAccessibleForFree': 'It is recommended that a Dataset indicates accessibility for free or otherwise', + 'SO:Dataset-keywords': 'A Dataset should include descriptive keywords as literals or DefinedTerm', + 'SO:Dataset-sameAs': 'It is recommended that a Dataset includes a sameAs URL', + 'SO:Dataset-version': 'Dataset must have a version as Literal or Number', + # SO coordinates + 'schema:GeoCoordinates-longitude': 'It is recommended that a Dataset has a longitude coordinate in WGS-84 format', + 'schema:GeoCoordinates-latitude': 'It is recommended that a Dataset has a latitude coordinate in WGS-84 format', + }, + 'internal': { + # errors we at NCEAS had testing data + 'ConstraintLoadError': 'Constraints must load correctly', + 'ReportableRuntimeError': 'No errors can occur at runtime', + 'FileNotFoundError': 'Files must exist in the location specified', + } +} + +NAMES_DICT = { + 'ns2:person': { + '@xmlns:ns2': 'http://ns.dataone.org/service/types/v1', + 'subject': '', + 'givenName': '', + 'familyName': '', + 'verified': 'false' + } +} diff --git a/mnonboard/info_chx.py b/mnonboard/info_chx.py new file mode 100644 index 00000000..bae02569 --- /dev/null +++ b/mnonboard/info_chx.py @@ -0,0 +1,555 @@ +from d1_client.cnclient import CoordinatingNodeClient +from d1_common.types import exceptions +from os import environ + +from mnonboard.defs import FIELDS, SITEMAP_URLS, ORCID_PREFIX, SCHEDULES, NODE_ID_PREFIX, SUBJECT_PREFIX, SUBJECT_POSTFIX +from mnonboard import default_json, L +from opersist.utils import JSON_TIME_FORMAT, dtnow +from opersist.cli import getOpersistInstance + +D1_AUTH_TOKEN = environ.get('D1_AUTH_TOKEN') +""" +The authentication token for a DataONE CN. Taken from the environment if it +exists there, then from user input. +""" + + +# user info checks +def not_empty(f): + """ + Test whether a string is empty. + + :param str f: The string to test + :returns: Whether or not the string is empty + :rtype: bool + """ + return f != '' + +def req_input(desc): + """ + Require user input for a given prompt. + + :param str desc: The prompt to show the user at the input step + :returns: User input + :rtype: str + """ + while True: + i = input(desc) + L.info('User entry for %s"%s"' % (desc, i)) + if not_empty(i): + return i + else: + desc_nocolon = desc.split(':')[0] + L.warning('Empty string entered.') + print('Please enter a value for %s.' % desc_nocolon) + +def valid_orcid(orcid): + """ + Checks the validity of an ORCiD number. + + ORCiDs have 4 groupings of 4 of alphanumerics separated by dashes (-) + for a total of 19 characters, thus ``0000-0000-0000-0000`` is valid + but ``0000-0000-00000-000`` and ``0000-0000-0000-000`` are not. + Also, the last character is a checksum and can be ``X`` but we do not + validate that yet. + + This seems like overkill but is probably good to have a simple check + since it will be used to store contacts for database upkeep/maintenance. + + :param str orcid: The orcid number + :returns: Whether or not the orcid number passed checks + :rtype: bool + """ + if (len(orcid) == 19): + # it's 19 characters long. start test loop + for i in range(0,19): + # does it have a dash (-) in positions 5, 10, and 15? + if i in (4, 9, 14): + if orcid[i] in '-': + # dash exists in correct position, next test + continue + else: + # fail (not a dash) + #print('no dash at %s' % i) + L.warning('ORCiD number failed check (%s has no dash in position %s)' % (orcid, i+1)) + return False + try: + # int exists in correct position, next test + if i > 18: + # last digit can be non-integer (like X) + int(orcid[i]) + continue + except ValueError as e: + # fail (not an integer) + #print('valueerror at %s' % i) + L.warning('ORCiD number failed check (%s has no integer in position %s)' % (orcid, i+1)) + return False + # future: maybe run checksum to truly validate against spec? + # pass + L.info('ORCiD number passed checks. (%s)' % orcid) + return True + else: + # fail (not 19 characters) + #print('not 19 chars') + return False + +def base_url(descrip): + """ + Validate the base URL of the member node. Should include trailing slash. + + :param str descrip: The prompt to show the user at the base URL input step + :returns: User input + :rtype: str + """ + while True: + url = req_input(descrip) + if url[-1] in '/': + L.info('Base URL is %s' % url) + return url + else: + L.warning('Base URL must contain a trailing slash. Please try again.') + +def valid_url_prefix(url, prefix, f): + """ + Validate a URL prefix (such as for an ORCiD number). + + :param str url: The URL to test + :param str prefix: The URL prefix + :param str f: The name of the field being tested + :returns: ``True`` if the URL passed checks + :rtype: bool + """ + # orcid number will be preceded by a url prefix but no trailing slash + if prefix not in url: + L.error('URL in "%s" field does not have the correct prefix. (prefix: %s; URL: %s)' % (f, prefix, url)) + print('Please ensure the correct URL prefix (%s) preceeds URL in field "%s" (currently: %s)' % (ORCID_PREFIX, f, prefix)) + return False + if url[-1] in '/': + L.error('URL in "%s" field has a trailing slash.' % (f)) + print('Please remove the trailing slash (/) from the end of URL in field "%s"' % (f)) + return False + return True + +def sitemap_urls(num_urls): + """ + Collect the sitemap URLs. + Usually there will be just one of these but we will prepare for more. + + :param int num_urls: The number of URLs describing the sitemap + :returns: A list of sitemap URLs for the given member node + :rtype: list[str, str, ...] + """ + i = 0 + while i < num_urls: + # add URLs one at a time (should only be a few at most) + # if we start getting MNs with 10+ sitemap URLs, maybe we change to accept formatted lists from the user + SITEMAP_URLS.append(req_input("Sitemap URL #%s: " % (i+1))) + L.info('Sitemap URL #%s: %s' % (i+1, SITEMAP_URLS[i])) + i += 1 + return SITEMAP_URLS + +def enter_schedule(): + """ + Give the user a choice between three basic scheduling options. + Options are: monthly, daily, and every 3 minutes. + + :returns: User-entered integer indicating schedule choice + :rtype: int + """ + p = 'Select a starting frequency with which to scrape data from this member node.\n' \ + '0: Monthly\n' \ + '1: Daily\n' \ + '2: Hourly\n' \ + '3: Every 3 minutes\n' \ + 'Enter 0/1/2/3: ' + while True: + i = input(p) + et = 'Please enter a choice of the frequency options above.' + try: + if int(i) in SCHEDULES: + L.info('User has entered frequency option %s.' % i) + return int(i) + else: + L.warning('User entry "%s" is a number but it is not an available option.' % (i)) + print(et) + except ValueError as e: + L.warning('User entry "%s" is not an number.' % (i)) + print(et) + +def enter_int(prompt): + """ + Make sure the user enters a number of sitemap URLs of 1 or greater. + + :param str prompt: The prompt to show the user at the input step + :returns: User-entered integer indicating number of sitemap URLs + :rtype: int + """ + i = None + while True: + # make sure user enters an int + try: + # ask the user for input + i = input(prompt) + L.info('User has entered %s' % i) + i = int(i) + # must be 1 or greater + assert i >= 1 + # tests ok + return i + except ValueError as e: + L.warning('Not an integer. Error text: %s' % e) + print('Please enter an integer.') + except AssertionError as e: + L.warning("Number of database sitemap URLs can't be less than 1. (%s entered)" % i) + print('Please enter 1 or greater.') + +def cn_subj_lookup(subj, cn_url='https://cn.dataone.org/cn', debug=False): + """ + Use the DataONE API to look up whether a given ORCiD number already exists + in the system. + + :param str subj: The subject to look up + :param str cn_url: The URL for the DataONE api to send REST searches to (default: 'https://cn.dataone.org/cn') + :param bool debug: Whether to include debug info in log messages (lots of text) + :returns: Received response or False + :rtype: str or bool + """ + # this authentication method was adapted from: + # https://github.com/DataONEorg/dataone_examples/blob/master/python_examples/update_object.ipynb + options = {"headers": {"Authorization": "Bearer %s" % (D1_AUTH_TOKEN)}} + # Create the Member Node Client + client = CoordinatingNodeClient(cn_url, **options) + try: + # Get records + L.info('Starting record lookup for %s from %s' % (subj, cn_url)) + subject = client.getSubjectInfo(subj) + r = subject.content()[0].content() + name = '%s %s' % (r[1], r[2]) + L.info('Name associated with record %s found in %s: %s.' % (subj, cn_url, name)) + rt = name if not debug else r + return rt + except exceptions.NotFound as e: + estrip = str(e).split('')[1].split('')[0] + e = e if debug else estrip + L.info('Caught NotFound error from %s during lookup. Details: %s' % (cn_url, e)) + return False + except exceptions.NotAuthorized as e: + L.error('Caught NotAuthorized error from %s. Is your auth token up to date?' % (cn_url)) + exit(1) + except exceptions.DataONEException as e: + L.error('Unspecified error from %s:\n%s' % (cn_url, e)) + exit(1) + +def local_subj_lookup(subj, name, loc, retn=False): + """ + Use the local opersist instance to look up a subject. + + :param str subj: Subject id (unique) + :param str loc: Location of the opersist instance + :param str name: Name of subject + :param bool retn: Whether to return the record + :returns: Returns subject name or False if not found + :rtype: str or bool + """ + L.info('Looking up %s in sqlite database at %s' % (subj, loc)) + op = getOpersistInstance(loc) + rec = op.getSubject(subj=subj, name=name, create_if_missing=True) + op.close() + if retn: + rec = rec.asJsonDict() + L.info('Record: %s' % (rec)) + return rec['name'] + else: + return + +def set_role(loc, title, value): + """ + Set the subject's role in the opersist database accordingly. + This should be done before harvest time in order for mnlite to be able to + populate this information when requested by the web front-end or API. + + :param str loc: The location of the opersist database parent folder + :param str title: ``default_submitter`` or ``default_owner`` + :param str value: Subject ORCiD (e.g. ``"http://orcid.org/0000-0001-5828-6070"``) + """ + L.info('Setting %s as "%s" in sqlite database at %s' % (value, title, loc)) + op = getOpersistInstance(loc) + rec = op.getSubject(subj=value) + if rec: + if title in 'default_submitter': + op.setDefaultSubmitter(value) + if title in 'default_owner': + op.setDefaultOwner(value) + op.close() + L.info('OPersist record set.') + +def orcid_name(orcid, f): + """ + Ask the user for the name of an orcid number. + + :param str orcid: Subject orcid number + :param str f: json field name of inquiry + :returns: Returns user-entered subject name + :rtype: str + """ + L.info('Asking for name of %s (ORCiD number %s)' % (f, orcid)) + name = req_input('Please enter the name of %s (ORCiD number %s): ' % (f, orcid)) + L.info('User has entered "%s"' % name) + return name + +def enter_orcid(prompt): + """ + Make sure the user enters a valid orcid number. + + :param str prompt: Prompt to display at input step + :returns: Returns user-entered orcid number + :rtype: str + """ + while True: + # ask the user for an ORCiD number + o = req_input(prompt) + o = o.split('orcid.org/')[-1] # returns only number string even if this is not in string + # make sure user has entered a valid ORCiD number + if valid_orcid(o): + return ORCID_PREFIX + o + else: + L.warning("Invalid ORCiD number entered: %s" % o) + print('Please enter a valid ORCiD number (ex: 0000-0000-0000-0000).') + +def valid_format(test_value: str, prefix: str='', postfix: str=''): + """ + Make sure the node_id contains the correct format. + + :param str test_value: String to test against, for example ``node_id`` or ``subject`` + :returns: Whether or not the node_id is valid + :rtype: bool + """ + if prefix in test_value: + if postfix in test_value: + # if valid, return + return True + else: + # if invalid, ask user if they meant to do that + L.warning('Entered test value does not contain the "%s" postfix. Entry: "%s"' % (postfix, test_value)) + while True: + # prompt loop + c = input('This field usually contains the postfix "%s" but the entered one (%s) does not.\n\ + The subject should look like this: CN=urn:node:KNB,DC=dataone,DC=org\n\ + This could have *serious* downstream consequences!\n\ + Do you wish to modify the entry to fit the standard?\n\ + Please answer "yes" or "no" (yes is default): ' % (postfix, test_value)) + if c.lower() == 'no': + L.warning('User has chosen to continue with entry of %s' % (test_value)) + return True + elif (c.lower() == 'yes') or (c.lower() == ''): + L.info('User has chosen to re-enter test_value. Entry: "%s"' % (c)) + return False + else: + L.info('User has entered something other than "yes", "", or "no" and will be prompted again. Entry: "%s"' % (c)) + pass + else: + # if invalid, ask user if they meant to do that + L.warning('Entered test_value does not contain the "%s" prefix. Entry: "%s"' % (prefix, test_value)) + while True: + # prompt loop + c = input('test_value usually contains the prefix "%s" but the entered one (%s) does not.\n\ + This could have *serious* downstream consequences!\n\ + Do you wish to modify the test_value entry to fit the standard?\n\ + Please answer "yes" or "no" (yes is default): ' % (prefix, test_value)) + if c.lower() == 'no': + L.warning('User has chosen to continue with test_value entry of %s' % (test_value)) + return True + elif (c.lower() == 'yes') or (c.lower() == ''): + L.info('User has chosen to re-enter test_value. Entry: "%s"' % (c)) + return False + else: + L.info('User has entered something other than "yes", "", or "no" and will be prompted again. Entry: "%s"' % (c)) + pass + +def enter_nodeid(prompt='Unique node_id: ', id=False): + """ + Have the user enter a node_id and make sure it contains the correct id + prefix. + Loops until a valid node id is entered. + + :param str prompt: Prompt to display at input step + :param id: The node id from the user's json file or False if none + :type id: str or bool + :returns: Node identifier. Only returns if id is deemed valid + :rtype: str + """ + while True: + L.info('In loop, vars are prompt="%s", id="%s"' % (prompt, id)) + # ask the user for a node id + if not id: + print('Please ensure that the node_id is unique from that of all other member nodes!') + id = req_input(prompt) + # validate and return + if valid_format(id, prefix=NODE_ID_PREFIX): + return id + else: + # loop again + id = False + +def user_input(): + """ + We need a few pieces of information to fill the json fields. + Collects user input for necessary pieces of node.json information. + + :returns: Dictionary of fields to use for node creation. Will be written to node.json + :rtype: dict + """ + baseurl = '' + L.info('Collecting user input.') + for f in FIELDS: + # the lowest level of the dict/json structure + if f in 'node': + for nf in FIELDS[f]: + # the second level beneath 'node' + if nf in 'node_id': + FIELDS[f][nf][1] = enter_nodeid(prompt=FIELDS[f][nf][0]) + elif nf in ['contact_subject']: + FIELDS[f][nf][1] = enter_orcid(FIELDS[f][nf][0]) + elif '_name' in nf: + # put the contact subject name in a different dict + #names[nf] = req_input(FIELDS[f][nf][0]) + # postponing this step for later + pass + elif nf in 'base_url': + # get the base url + baseurl = base_url(FIELDS[f][nf][0]) + FIELDS[f][nf][1] = baseurl + elif nf in 'subject': + pass + # # set the subject field as the node id in LDAP record format (CN=urn:node:NODEID,DC=dataone,DC=org) + # # postponing this step for later as we don't know if node_id has been set yet + # FIELDS[f][nf][1] = baseurl[:-1] + else: + FIELDS[f][nf][1] = req_input(FIELDS[f][nf][0]) + elif f in ('default_submitter', 'default_owner'): + FIELDS[f][1] = enter_orcid(FIELDS[f][0]) + elif f in 'num_sitemap_urls': + FIELDS[f][1] = enter_int(FIELDS[f][0]) + elif '_name' in f: + #names[f] = req_input(FIELDS[f][0]) + # postponing this step for later + pass + else: + FIELDS[f][1] = req_input(FIELDS[f][0]) + # add the subject field now that ['node']['node_id'] is definitely populated: should be "CN=urn:node:NODEID,DC=dataone,DC=org" + FIELDS['node']['subject'] = f"{SUBJECT_PREFIX}{FIELDS['node']['node_id']}{SUBJECT_POSTFIX}" + # add the sitemap URLs field now that we're done with the loops + FIELDS['spider'] = {} + FIELDS['spider']['sitemap_urls'] = ['Sitemap URLs: ', []] + # pass the number of mn sitemap URLs to sitemap_urls() + # fx will ask the user to enter the URL(s) and return them as a dict + # we then store it as the second list item in the 'sitemap_urls' field + FIELDS['spider']['sitemap_urls'][1] = sitemap_urls(FIELDS['num_sitemap_urls'][1]) + return FIELDS + +def transfer_info(ufields): + """ + Take a user fields dict and translate it to the default json object. + + :param dict ufields: A dict of user-entered fields to be translated + :returns: A dict of user-entered fields in proper node.json format + """ + fields = default_json(fx='mnonboard.info_chx.transfer_info()') + L.info('Adding user fields to default fields.') + for f in ufields: + # take fields we want, ignore fields we don't want + if f in ['node', 'spider']: + for nf in ufields[f]: + if '_name' not in nf: + fields[f][nf] = ufields[f][nf][1] + elif ('_name' not in f) and ('num_' not in f): + fields[f] = ufields[f][1] + fields['created'] = dtnow().strftime(JSON_TIME_FORMAT) + L.info('Successfully merged. Returning json object.') + return fields + +def input_test(fields): + """ + Testing the manually filled json file. + + :param dict fields: A dict of loaded json fields to test + :returns: Returns ``True`` if all tests pass, else ``False`` + :rtype: bool + """ + L.info('Running tests on imported json.') + # first, test that there are the fields we need + test_fields = default_json(fx='mnonboard.info_chx.input_test()') + # test at nest level 1 + f = '' + try: + for f in test_fields: + if fields[f] == '': + raise ValueError('Value in field "%s" is an empty string.' % (f)) + if f in ['node_id']: + if valid_url_prefix(fields[f], NODE_ID_PREFIX, f): + L.info('%s looks like a valid nodeid') + # could test for uniqueness as well? + if f in ['default_owner', 'default_submitter']: + # test orcid records while we're here + if valid_url_prefix(fields[f], ORCID_PREFIX, f): + L.info('%s: %s has a valid ORCiD url prefix' % (f, fields[f])) + if valid_orcid(fields[f].split('/')[-1]): + L.info('%s: %s is a valid ORCiD URL' % (f, fields[f])) + else: + raise ValueError('Invalid ORCiD number "%s" in field %s' % (fields[f], f)) + else: + raise ValueError('Invalid value "%s" in field %s (must either be ORCiD number or "urn:node:NODE_NAME")' % (fields[f], f)) + except KeyError as e: + L.error('No "%s" field found in json.' % f) + print('Please add the "%s" field to the json you loaded and re-run the script.' % f) + exit(1) + except AssertionError as e: + L.error('Invalid ORCiD number %s in field "%s"' % (fields[f], f)) + print('Please correct the ORCiD number in field "%s"' % (f)) + exit(1) + except ValueError as e: + L.error(e) + print('Please add a supported value in field "%s" and re-run the script.' % (f)) + exit(1) + # nest level 2 + nf = '' + try: + for f in ['node', 'spider']: + for nf in test_fields[f]: + if fields[f][nf] == '': + raise ValueError('Value in field "%s > %s" is an empty string.' % (f, nf)) + if 'contact_subject' in nf: + # test orcid record + if not valid_url_prefix(fields[f][nf], ORCID_PREFIX, nf): + raise ValueError('Invalid ORCiD URL prefix "%s" in field %s (must be "%s")' % (fields[f][nf], nf, ORCID_PREFIX)) + if not valid_orcid(fields[f][nf].split('/')[-1]): + raise ValueError('Invalid ORCiD URL %s in field "%s > %s"' % (fields[f][nf], f, nf)) + if 'node_id' in nf: + # check that the node_id is valid and prompt user to change if it's not + fields[f][nf] = enter_nodeid(id=fields[f][nf]) + except KeyError as e: + L.error('No "%s > %s" field found in json.' % (f, nf)) + print('Please add the "%s > %s" field to the json you loaded and re-run the script.' % (f, nf)) + exit(1) + except AssertionError as e: + L.error() + print('Please correct the ORCiD number in field "%s > %s"' % (f, nf)) + exit(1) + except ValueError as e: + L.error(e) + print('Please add a value in field "%s > %s" and re-run the script.' % (f, nf)) + # nest level 3 (node > schedule fields) + nnf = '' + try: + for nnf in test_fields['node']['schedule']: + if fields['node']['schedule'][nnf] == '': + raise ValueError('Value in field "node > schedule > %s" is an empty string.' % (nnf)) + except KeyError as e: + L.error('No "node > schedule > %s" field found in json.' % (nnf)) + print('Please add the "node > schedule > %s" field to the json you loaded and re-run the script.' % (nnf)) + exit(1) + except ValueError as e: + L.error(e) + print('Please add a value in field "node > schedule > %s" and re-run the script.' % (nnf)) + L.info('Loaded json info has passed checks.') + return True diff --git a/mnonboard/utils.py b/mnonboard/utils.py new file mode 100644 index 00000000..07b6b0f1 --- /dev/null +++ b/mnonboard/utils.py @@ -0,0 +1,517 @@ +import os +import json +import subprocess +from paramiko import SSHClient +from scp import SCPClient +import urllib.parse as urlparse +import xmltodict +from pathlib import Path + +from mnonboard.defs import SCHEDULES, NAMES_DICT, SUBJECT_PREFIX, SUBJECT_POSTFIX, USER_NAME +from mnonboard import NODE_PATH_REL, CUR_PATH_ABS, LOG_DIR, HARVEST_LOG_NAME, HM_DATE, L +from mnonboard.info_chx import cn_subj_lookup, local_subj_lookup, enter_schedule, orcid_name, set_role + +def load_json(loc: str): + """ + Load json from file. + + :param str loc: File location of the json file to be loaded + :returns: Serialized json file contents + :rtype: dict + """ + L.info('Loading member node json from %s' % loc) + try: + with open(loc, 'r') as f: + j = json.load(f) + L.info('File loaded from %s' % loc) + return j + except FileNotFoundError as e: + L.error('File does not exist - %s' % e) + exit(1) + except Exception as e: + L.error('Error: %s' % e) + exit(1) + +def save_json(loc: str, jf: dict): + """ + Output json to file. + + :param str loc: File location where the json file is to be written + :param dict jf: Dictionary to be written as json + """ + L.info('Writing member node json to %s' % loc) + try: + with open(loc, 'w') as f: + json.dump(jf, f, indent=4) + L.info('File written to %s' % loc) + return + except FileExistsError as e: + L.error('File exists - %s' % e) + exit(1) + except Exception as e: + L.error('Error: %s' % e) + exit(1) + +def save_report(rep_str: str, loc: str, format: str='.csv'): + """ + Output a validation report for a set of metadata. + + :param str rep_str: Report string to be written + :param str loc: File location where the report file is to be written + :param str jf: File extension (default: .csv) + """ + fn = os.path.join(loc, 'report-%s%s' % (HM_DATE, format)) + L.info('Writing report to %s' % (fn)) + with open(fn, 'w') as f: + f.write(rep_str) + L.info('Done.') + +def dumps_json(js): + """ + Quick and dirty way to output formatted json. + + :param dict js: Dictionary to be written as json + """ + print(json.dumps(js, indent=2)) + +def node_path(nodepath: str=NODE_PATH_REL, curpath: str=CUR_PATH_ABS, nodedir: str=''): + """ + Get the absolute path of the nodes directory where new members will go. + Currently the nodes directory lives at `../instance/nodes/` (relative to + the mnonboard dir that this file is in). + + :param str nodepath: Location of the nodes directory relative to the project directory (default: 'instance/nodes/') + :param str curpath: Current absolute path of this function (default: os.path.dirname(os.path.abspath(__file__))) + :param str nodedir: Name of the node directory (example: 'HAKAI_IYS'; default: '') + :returns: Absolute path of the node directory + :rtype: str + """ + return os.path.abspath(os.path.join(curpath, '../', nodepath, nodedir)) + +def init_repo(loc: str): + ''' + Initialize a new instance using opersist. + + :param str loc: Location of the member node directory in which to initialize an opersist instance + ''' + try: + L.info('Using opersist to init new member node folder: %s' % loc) + subprocess.run(['opersist', + '--folder=%s' % (loc), + 'init'], check=True) + except Exception as e: + L.error('opersist init command failed (node folder: %s): %s' % (loc, e)) + exit(1) + +def new_subj(loc: str, name: str, value: str): + """ + Create new subject in the database using opersist. + + :param str loc: Location of the opersist instance + :param str name: Subject name (human readable) + :param str value: Subject value (unique subject id, such as orcid or member node id) + """ + try: + L.info('opersist creating new subject. Name: %s Value: %s Location: %s' % (name, value, loc)) + subprocess.run(['opersist', + '--folder=%s' % (loc), + 'sub', + '--operation=create', + '--name=%s' % name, + '--subj=%s' % value], check=True) + except Exception as e: + L.error('opersist subject creation command failed for %s (%s): %s' % (name, value, e)) + exit(1) + +def get_or_create_subj(loc: str, value: str, cn_url: str, title: str='unspecified subject', name: str=None): + """ + Get an existing subject using their ORCiD or create a new one with the + specified values. + Search is conducted first at the given coordinating node URL, then locally. + If no subject is found, a new record is created in the local opersist + instance. + + :param str loc: Location of the opersist instance + :param str value: Subject value (unique subject id, such as orcid or member node id) + :param str cn_url: The base URL of the rest API with which to search for the given subject + :param str title: The subject's role in relation to the database + :param name: Subject name (human readable) + :type name: str or None + """ + if name: + # we are probably creating a node record + L.info(f'Creating a node subject. Given node_id: {value}') + if (not SUBJECT_PREFIX in value) and (not SUBJECT_POSTFIX in value): + value = f"{SUBJECT_PREFIX}{value}{SUBJECT_POSTFIX}" + L.info(f'Node subject value: "{value}"') + else: + # name was not given. look up the orcid record in the database + name = cn_subj_lookup(subj=value, cn_url=cn_url) + if not name: + # if the name is not in either database, we will create it; else it's already there and we ignore it + L.info('%s does not exist at %s. Need a name for local record creation...' % (value, cn_url)) + # ask the user for a name with the associated position and ORCiD record + name = orcid_name(value, title) + # finally, use opersist to create the subject + local_subj_lookup(loc=loc, subj=value, name=name) + # then use opersist to set the subject's role + if title in ('default_owner', 'default_submitter'): + set_role(loc=loc, title=title, value=value) + return name + +def set_schedule(): + """ + Ask the user what schedule on which they would like to run scrapes. + Options are: monthly, daily, and every 3 minutes. + + :returns: Dictionary entry formatted based on the chosen schedule option + :rtype: dict + """ + s = enter_schedule() + return SCHEDULES[s] + +def restart_mnlite(): + """ + Subprocess call to restart the mnlite system service. Requires sudo. + """ + while True: + i = input('Do you wish to restart the mnlite service? (Y/n) ') + if i.lower() == 'n': + break + elif i.lower() in ['y', '']: + L.info('Restarting mnlite systemctl service...') + try: + subprocess.run(['sudo', 'systemctl', 'restart', 'mnlite.service'], check=True) + L.info('Done.') + break + except subprocess.CalledProcessError as e: + L.error('Error restarting mnlite system service. Is it installed on your system? Error text:\n%s' % (e)) + print('mnlite was not restarted.') + i = input('Do you wish to continue? (Y/n) ') + if i.lower() == 'n': + L.info('User has chosen to abort setup after mnlite restart failed.') + exit(1) + elif i.lower() in ['y', '']: + L.info('User has chosen to continue after mnlite restart failed.') + break + else: + L.error('Invalid input at mnlite failure continue prompt: %s' % (i)) + print('You have selected an invalid option.') + else: + L.error('Invalid input at mnlite prompt: %s' % (i)) + print('You have selected an invalid option.') + + +def harvest_data(loc: str, mn_name: str): + """ + Use scrapy to harvest data to the specified path, and output a log to the + specified location. + + :param str loc: Location of the opersist instance + :param str mn_name: Name of the member node (used to name the crawl log) + """ + log_loc = os.path.join(LOG_DIR, mn_name + HARVEST_LOG_NAME) + L.info('Starting scrapy crawl, saving to %s' % (loc)) + L.info('scrapy log location is %s' % (log_loc)) + try: + subprocess.run(['scrapy', 'crawl', 'JsonldSpider', + '--set=STORE_PATH=%s' % loc, + '--logfile=%s' % log_loc], + check=True) + L.info('scrapy crawl complete.') + except Exception as e: + L.error('Error running scrapy: %s' % e) + +def limit_tests(num_things: int): + """ + Ask the user to limit the number of tests to run on a given set of + metadata. + This will execute if the user decides to try and test more than 500 + metadata objects. + The prompt will ask them if they wish to limit the number, then return + a number based on their decision. + + :param int num_things: Initial number of things to test + :returns: Modified number of things to test + :rtype: int + """ + while True: + i = input('Testing more than 500 objects is not recommended due to performance concerns.\n\ +This may take several minutes and use critical server resources. (est: %s min)\n\ +Are you sure you want to test all %s metadata objects in this set? (y/N): ' % (round(num_things/500), num_things)) + if (i.lower() in 'n') or (i.lower() in ''): + L.info('User has chosen enter a new number of objects to test.') + while True: + n = input('Please enter a new number of metadata objects to test: ') + try: + num_things = int(n) + break + except ValueError as e: + L.error('User has not entered a number ("%s")' % n) + if num_things <= 500: + L.info('User has chosen to test %s metadata objects.' % num_things) + break + else: + L.info('User has chosen to continue testing %s objects.' % (num_things)) + break + return num_things + +def ask_continue(msg: str): + """ + A user input loop in which the user is prompted whether they want to + continue. + + :param str msg: The message to display at the prompt + """ + while True: + i = input(msg + ' (Y/n) ') + if i.lower() in 'y': + # this also implicitly matches an empty string (i.e. user presses enter) + L.info('Continuing.') + break + elif (i.lower() in 'n'): + L.info('Exiting.') + exit(1) + else: + L.info('User has not entered "y" or "n".') + print('You have entered an incorrect value. Please enter "y" to continue or "n" to quit.') + continue + +def create_names_xml(loc: str, node_id: str, names: dict): + """ + Format subject XML documents and return list of names. + + :param str loc: Location (dir) to write file to + :param str node_id: Node id of current MN + :param dict names: Dict of subject names with ORCiD as index + + :returns: List of files written + :rtype: list + """ + # make dir + loc = os.path.join(loc, 'xml') + try: + os.makedirs(loc, exist_ok=True) + except OSError as e: + L.error('OSError creating XML directory: %s' % (e)) + exit(1) + except Exception as e: + L.error('%s creating XML directory: %s' % (repr(e), e)) + exit(1) + # format NAMES_XML + node_id = node_id.split(':')[-1] + files = [] + for id in names: + namesplit = names[id].split() + first, last = namesplit[0], namesplit[-1] + xd = NAMES_DICT + xd['ns2:person']['subject'] = id + xd['ns2:person']['givenName'] = first + xd['ns2:person']['familyName'] = last + fn = os.path.join(loc, '%s_%s%s.xml' % (node_id, first[0], last)) + with open(fn, 'w') as f: + xmltodict.unparse(xd, output=f) + L.debug('XML path: %s' % fn) + files.append(fn) + return files + +def write_cmd_to(fn, cmd, desc=None, mode='a'): + """ + """ + desc = f"# {desc}\n" if desc else "" + with open(fn, mode) as f: + f.write(f"{desc}{cmd}\n") + +def start_ssh(server: str, node_id, loc: str, ssh: bool=True): + """ + Starts ssh client connection to a given server. + + :param str server: The remote CN server to connect to (e.g. ``"cn-stage-ucsb-1.test.dataone.org"``) + :param str node_id: The node identifier (e.g. ``"urn:node:OPENTOPO"``) + :param str loc: The local location of the member node directory (e.g. ``"instance/nodes/mnTestOPENTOPO"``) + :param bool ssh: ``True`` will attempt to establish a remote connection. ``False`` will return values to output command strings to file. Default: True + """ + server = server.split('https://')[1].split('/')[0] + node_id = node_id.split(':')[-1] + xml_dir = '~/d1_xml/%s' % (node_id) + local_xml_dir = f'{loc}/xml' + mkdir_cmd = 'mkdir -p %s' % (xml_dir) + cd_cmd = 'cd %s' % xml_dir + op = f'connection to {server}' + if not ssh: + return None, local_xml_dir, node_id + try: + ssh = SSHClient() + ssh.load_system_host_keys() + ssh.connect(server) + L.info('Running "%s" on %s' % (mkdir_cmd, server)) + op = f'mkdir on {server}' + ssh.exec_command(mkdir_cmd) + L.info('Running "%s" on %s' % (cd_cmd, server)) + op = f'cd on {server}' + ssh.exec_command(cd_cmd) + return ssh, xml_dir, node_id + except Exception as e: + L.error('%s running %s. Details: %s' % (repr(e), op, e)) + return None, local_xml_dir, node_id + +def upload_xml(ssh: SSHClient, files: list, node_id: str, loc: str, usern: str=USER_NAME, server: str=None): + """ + Format subject XML documents and return list of names. + + :param paramiko.SSHClient ssh: The SSH client (if one was created) or ``False`` + :type ssh: paramiko.SSHClient or bool + :param list files: List of files to upload + :param str node_id: The node identifier (e.g. ``"urn:node:OPENTOPO"``) + :param str loc: The local location of the member node directory (e.g. ``"instance/nodes/mnTestOPENTOPO"``) + :param str server: The remote CN server to connect to (e.g. ``"cn-stage-ucsb-1.test.dataone.org"``) + """ + op = '' + target_dir = f'~/d1_xml/{node_id}/' + try: + op = 'mkdir on remote server' + if ssh: + with SCPClient(ssh.get_transport()) as scp: + op = 'scp to remote server' + L.info('Copying files to remote %s : %s' % (target_dir, files)) + scp.put(files=files, remote_path=target_dir) + else: + cmd_fn = f"{loc}/commands.sh" + write_cmd_to(fn=cmd_fn, cmd=f'## Commands to be run on the CN:', mode='w') + write_cmd_to(fn=cmd_fn, cmd=f'mkdir -p {target_dir}', desc='Create and enter dir for xml files') + write_cmd_to(fn=cmd_fn, cmd=f'cd {target_dir}') + write_cmd_to(fn=cmd_fn, cmd=f'\n') + write_cmd_to(fn=cmd_fn, cmd=f'## Run on MN to transfer subject xml files to the CN (make sure username is correct):') + for f in files: + command = f"scp {f} {usern}@{server}:{target_dir}" + write_cmd_to(fn=cmd_fn, cmd=command) + write_cmd_to(fn=cmd_fn, cmd=f'\n') + except Exception as e: + L.error('%s running %s. Details: %s' % (repr(e), op, e)) + exit(1) + +def create_subj_in_acct_svc(ssh: SSHClient, cert: str, files: list, cn: str, loc: str): + """ + Create a subject in the accounts service on the CN. + + :param paramiko.SSHClient ssh: The SSH client (if one was created) or ``False`` + :type ssh: paramiko.SSHClient or bool + :param str cert: The location of the CN certificate on the remote server + :param list files: List of XML subject files to upload + :param str cn: The base https address of the CN to use for API calls (e.g. ``"https://cn-stage.test.dataone.org/cn"``) + :param str loc: The local location of the member node directory (e.g. ``"instance/nodes/mnTestOPENTOPO"``) + """ + cmd_fn = f"{loc}/commands.sh" + for f in files: + f = os.path.split(f)[1] + command = 'curl -s --cert %s -F person=@%s -X POST %s/v2/accounts' % ( + cert, f, cn + ) + if ssh: + L.info('Creating subject: %s' % (command)) + ssh.exec_command(command) + else: + L.debug(f'Command: {command}') + L.info(f'Writing cmd to {cmd_fn}: subject creation') + write_cmd_to(fn=cmd_fn, cmd="## Commands to be run by an admin on the CN:") + write_cmd_to(fn=cmd_fn, cmd=command, desc=f"Create subject: {f}") + +def validate_subj_in_acct_svc(ssh: SSHClient, cert: str, names: dict, cn: str, loc: str): + """ + Validate the subjects created using + :py:func:`mnlite.mnonboard.utils.create_subj_in_acct_svc`. + + :param paramiko.SSHClient ssh: The SSH client (if one was created) or ``False`` + :type ssh: paramiko.SSHClient or bool + :param str cert: The location of the CN certificate on the remote server + :param dict names: Dictionary of names indexed by ORCiD (e.g. ``{"http://orcid.org/0000-0001-5828-6070": "Ian Nesbitt"}``) + :param str cn: The base https address of the CN to use for API calls (e.g. ``"https://cn-stage.test.dataone.org/cn"``) + :param str loc: The local location of the member node directory (e.g. ``"instance/nodes/mnTestOPENTOPO"``) + """ + cmd_fn = f"{loc}/commands.sh" + for n in names: + orcid_urlenc = urlparse.quote(n, safe='-') + command = 'curl -s --cert %s -X PUT %s/v2/accounts/verification/%s' % ( + cert, cn, orcid_urlenc + ) + if ssh: + L.info('Validating subject: %s' % (command)) + ssh.exec_command(command) + else: + L.debug(f'Command: {command}') + L.info(f'Writing cmd to {cmd_fn}: subject validation') + write_cmd_to(fn=cmd_fn, cmd=command, desc=f"Validate subject: {n}") + +def dl_node_capabilities(ssh: SSHClient, baseurl: str, node_id: str, loc: str): + """ + Download the node capabilities xml document from the SO server and save it + to file. + + :param paramiko.SSHClient ssh: The SSH client (if one was created) or ``False`` + :type ssh: paramiko.SSHClient or bool + :param str baseurl: The base URL of the schema.org server to download node config from (e.g. ``"so.test.dataone.org"``) + :param str node_id: The end triplet of the node identifier (e.g. ``"OPENTOPO"``) + :param str loc: The local location of the member node directory (e.g. ``"instance/nodes/mnTestOPENTOPO"``) + :returns: Location of the xml filepath where the node doc is saved + :rtype: str + """ + cmd_fn = f"{loc}/commands.sh" + target_dir = f'~/d1_xml/{node_id}' + node_filename = '%s/%s-node.xml' % (target_dir, node_id) + command = 'curl "https://%s/%s/v2/node" > %s' % (baseurl, node_id, node_filename) + if ssh: + L.info('Downloading node capabilities: %s' % (command)) + ssh.exec_command(command) + else: + L.info(f'Writing cmd to {cmd_fn}: node capabilities') + L.debug(f'Command: {command}') + write_cmd_to(fn=cmd_fn, cmd=command, desc=f"Download {node_id} node capabilities") + return node_filename + +def register_node(ssh: SSHClient, cert: str, node_filename: str, cn: str, loc: str): + """ + Registers the node in the CN. + + :param paramiko.SSHClient ssh: The SSH client (if one was created) or ``False`` + :type ssh: paramiko.SSHClient or bool + :param str node_filename: The xml filepath returned by :py:func:`mnlite.mnonboard.utils.dl_node_capabilities` + :param str loc: The local location of the member node directory (e.g. ``"instance/nodes/mnTestOPENTOPO"``) + """ + cmd_fn = f"{loc}/commands.sh" + node_filename = os.path.split(node_filename)[1] + mn = node_filename.split('-')[0] + command = """curl --cert %s -X POST -F 'node=@%s' "%s/v2/node" """ % ( + cert, node_filename, cn + ) + if ssh: + L.info('Registering node: %s' % (command)) + ssh.exec_command(command) + else: + L.info(f'Writing cmd to {cmd_fn}: node registration') + L.debug(f'Command: {command}') + write_cmd_to(fn=cmd_fn, cmd=command, desc=f"Register {node_filename} with CN") + +def approve_node(ssh: SSHClient, script_loc: str, loc: str): + """ + Starting the node approval script. + + .. warning:: This does not work over SSH! + + .. note:: + + In the future, this will be deprecated in favor of a method that does + not use Hazelcast. + + :param paramiko.SSHClient ssh: The SSH client (if one was created) or ``False`` + :type ssh: paramiko.SSHClient or bool + :param str script_loc: The location of the node 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"https://github.com/datadavev/json-canonicalization.git", branch = "develop"} scrapyd = "^1.2.1" diskcache = "^5.2.1" Flask-Cors = "^3.0.10" flask_accept = "^0.0.6" -pyld = {git = "https://github.com/datadavev/pyld.git", tag = "2.0.4-dev_ddv-0.1"} -sonormal = {path = "../../sonormal", develop=true } +pyld = {git = "https://github.com/datadavev/pyld.git", tag = "ddv-2.1.0"} +sonormal = {path = "../sonormal", develop=true } #pyjnius = "^1.3.0" +jinja2 = "<3.0" +markupsafe = "^2.0.1,<2.1" +itsdangerous = "^2.0.1,<2.1" +werkzeug = "^2.0.3,<2.1" +dataone-libclient = "^3.5.0" +pyshacl = "^0.22.2" +attrs = ">=21.3.0" +paramiko = "^3.2.0" +scp = "^0.14.5" +xmltodict = "^0.13.0" +dataone-common = "^3.5.2" +uwsgi = "^2.0.22" [tool.poetry.dev-dependencies] pytest = "^6.1.2" black = {version = "^20.8b1", allow-prereleases = true} -jupyter-book = "^0.11.1" +#jupyter-book = "^0.11.1" # need to find a new option watchdog = "^2.1.3" argh = "^0.26.2" sphinxcontrib-plantuml = "^0.21" sphinxcontrib-drawio = "^0.0.13" [tool.poetry.scripts] +mnonboard="mnonboard.cli:main" opersist= "opersist.cli:main" curly="scripts.curly:main" diff --git a/soscan/middlewares.py b/soscan/middlewares.py index 4cebb98b..468d5a6e 100644 --- a/soscan/middlewares.py +++ b/soscan/middlewares.py @@ -111,7 +111,7 @@ def process_exception(self, request, exception, spider): # - return None: continue processing this exception # - return a Response object: stops process_exception() chain # - return a Request object: stops process_exception() chain - pass + spider.logger.error(f'{repr(exception)}: {exception}\n{request}') def spider_opened(self, spider): spider.logger.info("Spider opened: %s" % spider.name) diff --git a/soscan/opersistpipeline.py b/soscan/opersistpipeline.py index abfc5fca..77fb7931 100644 --- a/soscan/opersistpipeline.py +++ b/soscan/opersistpipeline.py @@ -101,5 +101,5 @@ def process_item(self, item, spider): ) except Exception as e: - self.logger.error(e) + self.logger.error(f"{repr(e)}: {e}") return item diff --git a/soscan/settings.py b/soscan/settings.py index 6d0d09b1..9122cf5b 100644 --- a/soscan/settings.py +++ b/soscan/settings.py @@ -16,11 +16,15 @@ # Crawl responsibly by identifying yourself (and your website) on the user-agent -# USER_AGENT = 'soscan (+http://www.yourdomain.com)' +USER_AGENT = 'soscan (+https://dataone.org/)' # Obey robots.txt rules ROBOTSTXT_OBEY = True +# Setting fingerprinter implementation to avoid deprecation warning +# https://docs.scrapy.org/en/latest/topics/request-response.html#request-fingerprinter-implementation +REQUEST_FINGERPRINTER_IMPLEMENTATION = '2.7' + # Configure maximum concurrent requests performed by Scrapy (default: 16) # CONCURRENT_REQUESTS = 32 @@ -43,13 +47,12 @@ # COOKIES_ENABLED = False # Disable Telnet Console (enabled by default) -# TELNETCONSOLE_ENABLED = False +TELNETCONSOLE_ENABLED = False # Override the default request headers: -# DEFAULT_REQUEST_HEADERS = { -# 'Accept': 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8', -# 'Accept-Language': 'en', -# } +DEFAULT_REQUEST_HEADERS = { + 'Accept': 'application/ld+json,text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8', +} # Enable or disable spider middlewares # See https://docs.scrapy.org/en/latest/topics/spider-middleware.html @@ -61,8 +64,13 @@ # See https://docs.scrapy.org/en/latest/topics/downloader-middleware.html DOWNLOADER_MIDDLEWARES = { "soscan.middlewares.SoscanDownloaderMiddleware": 543, + "scrapy.downloadermiddlewares.redirect.RedirectMiddleware": 543, + "scrapy.downloadermiddlewares.robotstxt.RobotsTxtMiddleware": 543, } +# Whether the Redirect middleware will be enabled +REDIRECT_ENABLED = True + # Enable or disable extensions # See https://docs.scrapy.org/en/latest/topics/extensions.html # EXTENSIONS = { @@ -79,21 +87,21 @@ # Enable and configure the AutoThrottle extension (disabled by default) # See https://docs.scrapy.org/en/latest/topics/autothrottle.html -# AUTOTHROTTLE_ENABLED = True +AUTOTHROTTLE_ENABLED = True # The initial download delay -# AUTOTHROTTLE_START_DELAY = 5 +AUTOTHROTTLE_START_DELAY = 2 # The maximum download delay to be set in case of high latencies -# AUTOTHROTTLE_MAX_DELAY = 60 +AUTOTHROTTLE_MAX_DELAY = 60 # The average number of requests Scrapy should be sending in parallel to # each remote server -# AUTOTHROTTLE_TARGET_CONCURRENCY = 1.0 +AUTOTHROTTLE_TARGET_CONCURRENCY = 2.0 # Enable showing throttling stats for every response received: -# AUTOTHROTTLE_DEBUG = False +AUTOTHROTTLE_DEBUG = True # Enable and configure HTTP caching (disabled by default) # See https://docs.scrapy.org/en/latest/topics/downloader-middleware.html#httpcache-middleware-settings # HTTPCACHE_ENABLED = True -# HTTPCACHE_EXPIRATION_SECS = 0 +# HTTPCACHE_EXPIRATION_SECS = 60 # HTTPCACHE_DIR = 'httpcache' -# HTTPCACHE_IGNORE_HTTP_CODES = [] +# HTTPCACHE_IGNORE_HTTP_CODES = [500, 501, 502, 503, 510] # HTTPCACHE_STORAGE = 'scrapy.extensions.httpcache.FilesystemCacheStorage' diff --git a/soscan/settings_sitemap.py b/soscan/settings_sitemap.py index 6f4c0bcd..4dcb0a80 100644 --- a/soscan/settings_sitemap.py +++ b/soscan/settings_sitemap.py @@ -7,7 +7,7 @@ NEWSPIDER_MODULE = "soscan.spiders" # Crawl responsibly by identifying yourself (and your website) on the user-agent -# USER_AGENT = 'soscan (+http://www.yourdomain.com)' +USER_AGENT = 'soscan_sitemap (+http://dataone.org/)' # Obey robots.txt rules ROBOTSTXT_OBEY = True @@ -65,21 +65,21 @@ # Enable and configure the AutoThrottle extension (disabled by default) # See https://docs.scrapy.org/en/latest/topics/autothrottle.html -# AUTOTHROTTLE_ENABLED = True +AUTOTHROTTLE_ENABLED = True # The initial download delay -# AUTOTHROTTLE_START_DELAY = 5 +AUTOTHROTTLE_START_DELAY = 2 # The maximum download delay to be set in case of high latencies -# AUTOTHROTTLE_MAX_DELAY = 60 +AUTOTHROTTLE_MAX_DELAY = 60 # The average number of requests Scrapy should be sending in parallel to # each remote server -# AUTOTHROTTLE_TARGET_CONCURRENCY = 1.0 +AUTOTHROTTLE_TARGET_CONCURRENCY = 1.0 # Enable showing throttling stats for every response received: -# AUTOTHROTTLE_DEBUG = False +AUTOTHROTTLE_DEBUG = True # Enable and configure HTTP caching (disabled by default) # See https://docs.scrapy.org/en/latest/topics/downloader-middleware.html#httpcache-middleware-settings -# HTTPCACHE_ENABLED = True -# HTTPCACHE_EXPIRATION_SECS = 0 -# HTTPCACHE_DIR = 'httpcache' -# HTTPCACHE_IGNORE_HTTP_CODES = [] +HTTPCACHE_ENABLED = True +HTTPCACHE_EXPIRATION_SECS = 60 +HTTPCACHE_DIR = 'httpcache' +HTTPCACHE_IGNORE_HTTP_CODES = [500, 501, 502, 503, 510] # HTTPCACHE_STORAGE = 'scrapy.extensions.httpcache.FilesystemCacheStorage' diff --git a/soscan/sonormalizepipeline.py b/soscan/sonormalizepipeline.py index b94c274e..59a263c5 100644 --- a/soscan/sonormalizepipeline.py +++ b/soscan/sonormalizepipeline.py @@ -4,6 +4,19 @@ import json import opersist.rdfutils +def consolidate_list(l: list, sep: str=', '): + """ + Takes a list of strings and returns a list with one consolidated string, + separated by ``sep``. This can help when a repository has mistakenly + split their description/title strings. + """ + consolidated = '' + for li in l: + if consolidated != '': + consolidated += sep + consolidated += li + return [consolidated] + class SoscanNormalizePipeline: """ @@ -35,21 +48,73 @@ def process_item(self, item, spider): require_identifier = True jsonld = item["jsonld"] - options = {"base": item["url"]} + version = jsonld.get('version', None) + version = jsonld.get('@version', '1.1') if not version else version + version = '1.0' if version == '1' else version + jldversion = f'json-ld-{version}' + self.logger.debug(f"process_item: version {jldversion}") + options = {"base": item["url"], "processingMode": jldversion} + + # consolidate any lists that might cause the indexer to misfire + name = jsonld.get('name', None) + desc = jsonld.get('description', None) + nstr, dstr = '[none]', '[none]' + if name == None: + graph = jsonld.get('@graph', None) + if graph and isinstance(graph, list): + name = graph[0].get('name', None) + desc = graph[0].get('description', None) + nstr = 'jsonld["@graph"][0]["name"]' + dstr = 'jsonld["@graph"][0]["description"]' + elif graph: + # this probably doesn't exist..? try to get vars anyway + self.logger.warn(f'Something weird has happened: the dataset graph at jsonld["@graph"] is not a list but instead {type(graph)}\nURL: {item["url"]}') + self.logger.debug(f'Content of jsonld["@graph"]: {graph}') + try: + name = graph.get('name', None) + desc = graph.get('description', None) + except Exception as e: + raise scrapy.exceptions.DropItem(f"JSON-LD error ({repr(e)}): {e} - URL: {item['url']}") + nstr = 'jsonld["@graph"]["name"]' + dstr = 'jsonld["@graph"]["description"]' + else: + nstr = 'jsonld["name"]' + dstr = 'jsonld["description"]' + + if name: + if (isinstance(name, list)) and (len(name) > 1): + self.logger.debug(f'Consolidating list of {len(name)} items at {nstr}: {name}') + # can't think of a better way to do this + exec(f'{nstr} = consolidate_list(name)') + self.logger.debug(f'New list at {nstr}: {name}') + else: + raise scrapy.exceptions.DropItem(f"JSON-LD no dataset name found: {item['url']}") + + if desc: + if (isinstance(desc, list)) and (len(desc) > 1): + self.logger.debug(f'Consolidating list of {len(desc)} items at {dstr}: {desc}') + exec(f'{dstr} = consolidate_list(desc)') + self.logger.debug(f'New list at {dstr}: {desc}') + else: + self.logger.warning(f'JSON-LD no dataset description found: {item["url"]}') + + try: normalized = sonormal.sosoNormalize(jsonld, options=options) except Exception as e: raise scrapy.exceptions.DropItem(f"JSON-LD normalization failed: {e}") + ids = [] try: - _framed = sonormal.normalize.frameSODataset(normalized) + _framed = sonormal.normalize.frameSODataset(normalized, options=options) ids = sonormal.normalize.getDatasetsIdentifiers(_framed) except Exception as e: raise scrapy.exceptions.DropItem(f"JSON-LD identifier extract failed: {e}") if len(ids) < 1: raise scrapy.exceptions.DropItem( - f"JSON-LD no ids, not a Dataset: {item['url']}" + f"JSON-LD no ids: {item['url']}\n" + f"Framed dataset:\n{_framed}" ) # TODO: identifiers @@ -57,16 +122,42 @@ def process_item(self, item, spider): # Use the first identifier value provided for series_id # PID will be computed from the object checksum - item["alt_identifiers"] = None + item["series_id"] = None + item["alt_identifiers"] = [] if len(ids) > 0: + self.logger.debug(f"ids found: {ids}") if len(ids[0]["identifier"]) > 0: item["series_id"] = ids[0]["identifier"][0] + self.logger.debug(f'Using first identifier for series_id: {item["series_id"]}') if len(ids[0]["identifier"]) > 1: item["alt_identifiers"] = ids[0]["identifier"][1:] - elif require_identifier: - raise scrapy.exceptions.DropItem( - f"JSON-LD no identifier: {item['url']}" - ) + self.logger.debug(f'alt_identifiers: {item["alt_identifiers"]}') + else: + # if the first identifier is an empty list, we need to look for others + self.logger.warning(f'Empty identifier in first Dataset grouping') + g = 0 + for group in ids: + g += 1 + self.logger.info(f'Dataset grouping {g}: {group}') + if len(group["identifier"]) > 0: + if item["series_id"] is None: + item["series_id"] = group["identifier"][0] + self.logger.info(f'Using identifier {g} for series_id: {item["series_id"]}') + if len(group["identifier"]) > 1: + item["alt_identifiers"].append(group["identifier"][1:]) + else: + item["alt_identifiers"].append(group["identifier"][0:]) + self.logger.debug(f'alt_identifiers: {item["alt_identifiers"]}') + if require_identifier and item["series_id"] is None: + raise scrapy.exceptions.DropItem( + f"JSON-LD no identifier: {item['url']}\n" + f"Framed dataset:\n{json.dumps(_framed, indent=2)}\n" + f"Framing context:\n{json.dumps(sonormal.SO_DATASET_FRAME, indent=2)}\n" + ) + if item["series_id"] == "doi:": + raise scrapy.exceptions.DropItem( + f"JSON-LD DOI URI empty: {item['url']}" + ) item["identifier"] = None item["normalized"] = normalized item["format_id"] = opersist.rdfutils.DATASET_FORMATID diff --git a/soscan/spiders/jsonldspider.py b/soscan/spiders/jsonldspider.py index 77d8ee7b..19215c3b 100644 --- a/soscan/spiders/jsonldspider.py +++ b/soscan/spiders/jsonldspider.py @@ -1,7 +1,9 @@ import os +from scrapy.settings import BaseSettings import sonormal import pyld import email.utils +from pathlib import Path try: import orjson as json @@ -52,6 +54,10 @@ def __init__(self, *args, **kwargs): if not urls is None: self.sitemap_urls = urls.split(" ") self.lastmod_filter = kwargs.get("lastmod", None) + self.start_point = None + self.url_match = None + self.reversed = None + self.which_jsonld = 0 if len(self.sitemap_urls) < 1: raise ValueError("At least one sitemap URL is required.") if self.lastmod_filter is not None: @@ -81,6 +87,27 @@ def from_crawler(cls, crawler, *args, **kwargs): **kwargs ) spider._set_crawler(crawler) + # incorporate MN-specific settings + mn_settings = Path(f'{node_path}/settings.json') + if mn_settings.exists(): + with open(mn_settings) as cs: + _cs = json.loads(cs.read()) + for s in _cs: + spider.settings.set(s, _cs[s], priority='spider') + spider.logger.info(f'Setting override from {mn_settings}: set {s} to {_cs[s]}') + if s in "lastmod_filter": + spider.lastmod_filter = dateparser.parse( + _cs[s], + settings={"RETURN_AS_TIMEZONE_AWARE": True}, + ) + if s in "start_point": + spider.start_point = _cs.get(s, None) + if s in "url_match": + spider.url_match = _cs.get(s, None) + if s in "reversed": + spider.reversed = _cs.get(s, None) + if s in "which_jsonld": + spider.which_jsonld = _cs.get(s, None) return spider def sitemap_filter(self, entries): @@ -99,22 +126,60 @@ def sitemap_filter(self, entries): Returns: None """ + y = 0 + i = 0 + if self.reversed: + self.logger.info(f'Reading the sitemap in reverse order') + entries = reversed(list(entries.__iter__())) + self.logger.info(f'Entries in reversed sitemap list: {len(entries)}') for entry in entries: - ts = entry.get("lastmod", None) - if not ts is None: - # convert TS to a datetime for comparison - ts = dateparser.parse( - ts, - settings={"RETURN_AS_TIMEZONE_AWARE": True}, - ) - # preserve the converted timestamp in the entry - entry["lastmod"] = ts - - if self.lastmod_filter is not None and ts is not None: - if ts > self.lastmod_filter: - yield entry - else: - yield entry + i += 1 + if ((self.start_point is not None) and (self.start_point <= i)) or (self.start_point is None): + if self.start_point == i: + self.logger.info(f'Starting scrape at record {i}') + ts = entry.get("lastmod", None) + if not ts is None: + # convert TS to a datetime for comparison + ts = dateparser.parse( + ts, + settings={"RETURN_AS_TIMEZONE_AWARE": True}, + ) + # preserve the converted timestamp in the entry + entry["lastmod"] = ts + + if self.lastmod_filter is not None and ts is not None: + if ts > self.lastmod_filter: + if self.url_match: + if self.url_match in entry['loc']: + self.logger.debug(f'Yielding record {i}: {entry}') + y += 1 + yield entry + else: + self.logger.debug(f'url_match skipping record {i}: {self.url_match} not in {entry}') + else: + self.logger.debug(f'Yielding record {i}: {entry}') + y += 1 + yield entry + else: + self.logger.debug(f'lastmod_filter skipping record {i}: (ts {ts}) {entry}') + else: + if self.url_match: + if self.url_match in entry['loc']: + self.logger.debug(f'Yielding record {i}: {entry}') + y += 1 + yield entry + else: + self.logger.debug(f'url_match skipping record {i}: {self.url_match} not in {entry}') + else: + self.logger.debug(f'Yielding record {i}: {entry["loc"]}') + y += 1 + yield entry + if (self.start_point is not None) and (self.start_point > i): + if i == 1: + self.logger.info(f'Skipping to start_point at record {self.start_point}') + self.logger.debug(f'start_point skipping record {i}: {entry}') + self.logger.info(f'Total number of sitemap entries: {i}') + self.logger.info(f'Yielded entries from sitemap: {y}') def parse(self, response, **kwargs): """ @@ -138,7 +203,13 @@ def parse(self, response, **kwargs): "extractAllScripts": True, "json_parse_strict": json_parse_strict, } - jsonld = pyld.jsonld.load_html(response.body, response.url, None, options) + contenttype = response.headers.get("Content-Type").decode() + #self.logger.debug(f'Response Content-Type: {contenttype} from {response.url}') + if contenttype in ["application/ld+json", "application/octet-stream"]: + self.logger.debug(f'Content-Type is "{contenttype}"; assuming json object and loading directly') + jsonld = json.loads(response.text, strict=options.get("json_parse_strict", False)) + else: + jsonld = pyld.jsonld.load_html(response.body, response.url, None, options) # for j_item in jsonld: # item = soscan.items.SoscanItem() # item["source"] = response.url @@ -155,6 +226,8 @@ def parse(self, response, **kwargs): # format_id if len(jsonld) == 1: jsonld=jsonld[0] + else: + jsonld=jsonld[self.which_jsonld] item = soscan.items.SoscanItem() item["url"] = response.url @@ -176,5 +249,5 @@ def parse(self, response, **kwargs): item["jsonld"] = jsonld yield item except Exception as e: - self.logger.error("parse: url: %s, error: %s", response.url, e) + self.logger.error("parse: url: %s, %s: %s", response.url, repr(e), e) yield None diff --git a/tests/testHDsitemap.xml b/tests/testHDsitemap.xml new file mode 100644 index 00000000..a512fbad --- /dev/null +++ b/tests/testHDsitemap.xml @@ -0,0 +1,15 @@ + + + + https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/K3OIJQ + 2015-04-11 + + + https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/XFUVJJ + 2023-09-26 + + + https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/4NLGYN + 2021-05-10 + + \ No newline at end of file diff --git a/tests/testUSAPjsonld01.html b/tests/testUSAPjsonld01.html new file mode 100644 index 00000000..08d6a3c0 --- /dev/null +++ b/tests/testUSAPjsonld01.html @@ -0,0 +1,209 @@ + + + + United States Antarctic Program Data Center (USAP-DC) + + + + + + + + + + \ No newline at end of file diff --git a/tests/testUSAPjsonld02.html b/tests/testUSAPjsonld02.html new file mode 100644 index 00000000..f116794d --- /dev/null +++ b/tests/testUSAPjsonld02.html @@ -0,0 +1,211 @@ + + + + United States Antarctic Program Data Center (USAP-DC) + + + + + + + + + + \ No newline at end of file diff --git a/tests/testUSAPsitemap.xml b/tests/testUSAPsitemap.xml new file mode 100644 index 00000000..5d67a8b6 --- /dev/null +++ b/tests/testUSAPsitemap.xml @@ -0,0 +1,11 @@ + + + + https://raw.githubusercontent.com/DataONEorg/mnlite/develop/tests/testUSAPjsonld01.html + 2024-03-06 + + + https://raw.githubusercontent.com/DataONEorg/mnlite/develop/tests/testUSAPjsonld02.html + 2024-03-06 + + \ No newline at end of file