Source code for biothings.hub.dataload.dumper

import time
import os
import pprint
import cgi
from datetime import datetime
import asyncio
from functools import partial
import inspect
import subprocess

from biothings.utils.hub_db import get_src_dump
from biothings.utils.common import timesofar, rmdashfr
from biothings.utils.loggers import get_logger
from biothings.hub import DUMPER_CATEGORY, UPLOADER_CATEGORY
from biothings import config as btconfig
from biothings.utils.manager import BaseSourceManager, ResourceError
from biothings.hub.dataload.uploader import set_pending_to_upload

logging = btconfig.logger

from typing import Optional

[docs]class DumperException(Exception): pass
class BaseDumper(object): # override in subclass accordingly SRC_NAME = None SRC_ROOT_FOLDER = None # source folder (without version/dates) # Should an upload be triggered after dump ? AUTO_UPLOAD = True # attribute used to generate data folder path suffix SUFFIX_ATTR = "release" # Max parallel downloads (None = no limit). MAX_PARALLEL_DUMP = None # waiting time between download (0.0 = no waiting) SLEEP_BETWEEN_DOWNLOAD = 0.0 # keep all release (True) or keep only the latest ? ARCHIVE = True SCHEDULE = None # crontab format schedule, if None, won't be scheduled def __init__(self, src_name=None, src_root_folder=None, log_folder=None, archive=None): # unpickable attrs, grouped self.init_state() self.src_name = src_name or self.SRC_NAME self.src_root_folder = src_root_folder or self.SRC_ROOT_FOLDER self.log_folder = log_folder or btconfig.LOG_FOLDER self.archive = archive or self.ARCHIVE self.to_dump = [] self.release = None self.t0 = time.time() self.logfile = None self.prev_data_folder = None self.timestamp = time.strftime('%Y%m%d') self.prepared = False self.steps = ["dump", "post"] def init_state(self): self._state = { "client": None, "src_dump": None, "logger": None, "src_doc": None, } # specific setters for attrs that can't be pickled # note: we can't use a generic __setattr__ as it collides # (infinite recursion) with __getattr__, and we can't use # __getattr__ as well as @x.setter required @property(x) to # be defined. We'll be explicit there... @property def client(self): if not self._state["client"]: try: self.prepare_client() except Exception as e: # if accessed but not ready, then just ignore and return invalid value for a client logging.exception("Can't prepare client: %s" % e) return None return self._state["client"] @property def src_dump(self): if not self._state["src_dump"]: self.prepare() return self._state["src_dump"] @property def logger(self): if not self._state["logger"]: self.prepare() return self._state["logger"] @property def src_doc(self): # this one is pickable but it's a lazy load # (based on non-pickable src_dump) if not self._state["src_doc"]: self.prepare() return self._state["src_doc"] @client.setter def client(self, value): self._state["client"] = value @src_dump.setter def src_dump(self, value): self._state["src_dump"] = value @logger.setter def logger(self, value): self._state["logger"] = value @src_doc.setter def src_doc(self, value): self._state["src_doc"] = value def create_todump_list(self, force=False, **kwargs): """Fill self.to_dump list with dict("remote":remote_path,"local":local_path) elements. This is the todo list for the dumper. It's a good place to check whether needs to be downloaded. If 'force' is True though, all files will be considered for download""" raise NotImplementedError("Define in subclass") def prepare_client(self): """do initialization to make the client ready to dump files""" raise NotImplementedError("Define in subclass") def need_prepare(self): """check whether some prepare step should executed before running dump""" def release_client(self): """Do whatever necessary (like closing network connection) to "release" the client""" raise NotImplementedError("Define in subclass") def remote_is_better(self, remotefile, localfile): '''Compared to local file, check if remote file is worth downloading. (like either bigger or newer for instance)''' raise NotImplementedError("Define in subclass") def download(self, remotefile, localfile): """ Download "remotefile' to local location defined by 'localfile' Return relevant information about remotefile (depends on the actual client) """ raise NotImplementedError("Define in subclass") def post_download(self, remotefile, localfile): """Placeholder to add a custom process once a file is downloaded. This is a good place to check file's integrity. Optional""" pass def post_dump(self, *args, **kwargs): """ Placeholder to add a custom process once the whole resource has been dumped. Optional. """ pass def setup_log(self): self.logger, self.logfile = get_logger("dump_%s" % self.src_name) def prepare(self, state={}): if self.prepared: return if state: # let's be explicit, _state takes what it wants for k in self._state: self._state[k] = state[k] return self.prepare_src_dump() self.setup_log() def unprepare(self): """ reset anything that's not pickable (so self can be pickled) return what's been reset as a dict, so self can be restored once pickled """ state = { "client": self._state["client"], "src_dump": self._state["src_dump"], "logger": self._state["logger"], "src_doc": self._state["src_doc"], } for k in state: self._state[k] = None self.prepared = False return state def prepare_src_dump(self): # Mongo side self.src_dump = get_src_dump() self.src_doc = self.src_dump.find_one({'_id': self.src_name}) or {} def register_status(self, status, transient=False, **extra): try: # if status is "failed" and depending on where it failed, # we may not be able to get the new_data_folder (if dumper didn't reach # the release information for instance). Default to current if failing data_folder = self.new_data_folder except DumperException: data_folder = self.current_data_folder release = getattr(self, self.__class__.SUFFIX_ATTR) if release is None: # it has not been set by the dumper before while exploring # remote site. maybe we're just running post step ? # back-compatibility; use "release" at root level if not found under "download" release = self.src_doc.get( "download", {}).get("release") or self.src_doc.get("release") self.logger.error( "No release set, assuming: data_folder: %s, release: %s" % (data_folder, release)) # make sure to remove old "release" field to get back on track for field in ["release", "data_folder"]: if self.src_doc.get(field): self.logger.warning("Found '%s'='%s' at root level, convert to new format" % (field, self.src_doc[field])) self.src_doc.pop(field) self.src_doc.update({ '_id': self.src_name, 'download': { 'release': release, 'data_folder': data_folder, 'logfile': self.logfile, 'started_at':, 'status': status } }) # only register time when it's a final state if transient: self.src_doc["download"]["pid"] = os.getpid() else: self.src_doc["download"]["time"] = timesofar(self.t0) if "download" in extra: self.src_doc["download"].update(extra["download"]) else: self.src_doc.update(extra) @asyncio.coroutine def dump(self, steps=None, force=False, job_manager=None, check_only=False, **kwargs): ''' Dump (ie. download) resource as needed this should be called after instance creation 'force' argument will force dump, passing this to create_todump_list() method. ''' # signature says it's optional but for now it's not... assert job_manager # check what to do self.steps = steps or self.steps if type(self.steps) == str: self.steps = [self.steps] strargs = "[steps=%s]" % ",".join(self.steps) try: if "dump" in self.steps: pinfo = self.get_pinfo() pinfo["step"] = "check" # if last download failed (or was interrupted), we want to force the dump again try: if self.src_doc["download"]["status"] in [ "failed", "downloading" ]: "Forcing dump because previous failed (so let's try again)" ) force = True except (AttributeError, KeyError): # no src_doc or no download info pass # TODO: blocking call for now, FTP client can't be properly set in thread after self.create_todump_list(force=force, **kwargs) # make sure we release (disconnect) client so we don't keep an open # connection for nothing self.release_client() if self.to_dump: if check_only:"New release available, '%s', %s file(s) to download" % (self.release, len(self.to_dump)), extra={"notify": True}) return self.release # mark the download starts self.register_status("downloading", transient=True) # unsync to make it pickable state = self.unprepare() yield from self.do_dump(job_manager=job_manager) # then restore state self.prepare(state) else: # if nothing to dump, don't do post process self.logger.debug("Nothing to dump", extra={"notify": True}) return "Nothing to dump" if "post" in self.steps: got_error = False pinfo = self.get_pinfo() pinfo["step"] = "post_dump" # for some reason (like maintaining object's state between pickling). # we can't use process there. Need to use thread to maintain that state without # building an unmaintainable monster job = yield from job_manager.defer_to_thread( pinfo, partial(self.post_dump, job_manager=job_manager)) def postdumped(f): nonlocal got_error if f.exception(): got_error = f.exception() job.add_done_callback(postdumped) yield from job if got_error: raise got_error # set it to success at the very end self.register_status("success") if self.__class__.AUTO_UPLOAD: set_pending_to_upload(self.src_name)"success %s" % strargs, extra={"notify": True}) except (KeyboardInterrupt, Exception) as e: self.logger.error("Error while dumping source: %s" % e) import traceback self.logger.error(traceback.format_exc()) self.register_status("failed", download={"err": str(e), "tb": traceback.format_exc()}) self.logger.error("failed %s: %s" % (strargs, e), extra={"notify": True}) raise finally: if self.client: self.release_client() def get_predicates(self): """ Return a list of predicates (functions returning true/false, as in math logic) which instructs/dictates if job manager should start a job (process/thread) """ def no_corresponding_uploader_running(job_manager): """ Don't download data if the associated uploader is running """ return len([j for j in if j["source"].split(".")[0] == self.src_name and j["category"] == UPLOADER_CATEGORY]) == 0 return [no_corresponding_uploader_running] def get_pinfo(self): """ Return dict containing information about the current process (used to report in the hub) """ pinfo = { "category": DUMPER_CATEGORY, "source": self.src_name, "step": None, "description": None } preds = self.get_predicates() if preds: pinfo["__predicates__"] = preds return pinfo @property def new_data_folder(self): """Generate a new data folder path using src_root_folder and specified suffix attribute. Also sync current (aka previous) data folder previously registeted in database. This method typically has to be called in create_todump_list() when the dumper actually knows some information about the resource, like the actual release. """ if self.archive: if getattr( self, self.__class__.SUFFIX_ATTR) is None: # defined but not set # if step is "post" only, it means we didn't even check a new version and we # want to run "post" step on current version again if self.steps == ["post"]: return self.current_data_folder else: raise DumperException( "Can't generate new data folder, attribute used for suffix (%s) isn't set" % self.__class__.SUFFIX_ATTR) suffix = getattr(self, self.__class__.SUFFIX_ATTR) return os.path.join(self.src_root_folder, suffix) else: return os.path.join(self.src_root_folder, 'latest') @property def current_data_folder(self): try: return self.src_doc.get( "download", {}).get("data_folder") or self.new_data_folder except DumperException: # exception raied from new_data_folder generation, we give up return None @property def current_release(self): return self.src_doc.get("download", {}).get("release") @asyncio.coroutine def do_dump(self, job_manager=None):"%d file(s) to download" % len(self.to_dump)) # should downloads be throttled ? max_dump = self.__class__.MAX_PARALLEL_DUMP and asyncio.Semaphore( self.__class__.MAX_PARALLEL_DUMP) courtesy_wait = self.__class__.SLEEP_BETWEEN_DOWNLOAD got_error = None jobs = [] self.unprepare() for todo in self.to_dump: remote = todo["remote"] local = todo["local"] def done(f): try: _ = f.result() nonlocal max_dump nonlocal got_error if max_dump: #self.logger.debug("Releasing download semaphore: %s" % max_dump) max_dump.release() self.post_download(remote, local) except Exception as e: self.logger.exception("Error downloading '%s': %s" % (remote, e)) got_error = e pinfo = self.get_pinfo() pinfo["step"] = "dump" pinfo["description"] = remote if max_dump: yield from max_dump.acquire() if courtesy_wait: yield from asyncio.sleep(courtesy_wait) job = yield from job_manager.defer_to_process( pinfo, partial(, remote, local)) job.add_done_callback(done) jobs.append(job) # raise error as soon as we get it: # 1. it prevents from launching things for nothing # 2. if we gather the error at the end of the loop *and* if we # have more errors than the queue size, we get stuck if got_error: raise got_error yield from asyncio.gather(*jobs) if got_error: raise got_error"%s successfully downloaded" % self.SRC_NAME) self.to_dump = [] def prepare_local_folders(self, localfile): localdir = os.path.dirname(localfile) if not os.path.exists(localdir): try: os.makedirs(localdir) except FileExistsError: # ignore, might exist now (parallelization occuring...) pass from ftplib import FTP class FTPDumper(BaseDumper): FTP_HOST = '' CWD_DIR = '' FTP_USER = '' FTP_PASSWD = '' FTP_TIMEOUT = 10 * 60.0 # we want dumper to timout if necessary BLOCK_SIZE: Optional[int] = None # default is still kept at 8KB # TODO: should we add a __del__ to make sure to close ftp connection ? # ftplib has a context __enter__, but we don't use it that way ("with ...") def _get_optimal_buffer_size(self) -> int: if self.BLOCK_SIZE is not None: return self.BLOCK_SIZE # else: known_optimal_sizes = { '': 33554432, # see for reason # add new ones above 'DEFAULT': 8192, } normalized_host = self.FTP_HOST.lower() if normalized_host in known_optimal_sizes: return known_optimal_sizes[normalized_host] else: return known_optimal_sizes['DEFAULT'] def prepare_client(self): # FTP side self.client = FTP(self.FTP_HOST, timeout=self.FTP_TIMEOUT) self.client.login(self.FTP_USER, self.FTP_PASSWD) if self.CWD_DIR: self.client.cwd(self.CWD_DIR) def need_prepare(self): return not self.client or (self.client and not self.client.file) def release_client(self): assert self.client self.client.close() self.client = None def download(self, remotefile, localfile): self.prepare_local_folders(localfile) self.logger.debug("Downloading '%s' as '%s'" % (remotefile, localfile)) block_size = self._get_optimal_buffer_size() if self.need_prepare(): self.prepare_client() try: with open(localfile, "wb") as out_f: self.client.retrbinary(cmd='RETR %s' % remotefile, callback=out_f.write, blocksize=block_size) # set the mtime to match remote ftp server response = self.client.sendcmd('MDTM ' + remotefile) code, lastmodified = response.split() # an example: 'last-modified': '20121128150000' lastmodified = time.mktime( datetime.strptime(lastmodified, '%Y%m%d%H%M%S').timetuple()) os.utime(localfile, (lastmodified, lastmodified)) return code except Exception as e: self.logger.error("Error while downloading %s: %s" % (remotefile, e)) self.release_client() raise finally: self.release_client() def remote_is_better(self, remotefile, localfile): """'remotefile' is relative path from current working dir (CWD_DIR), 'localfile' is absolute path""" try: res = os.stat(localfile) except FileNotFoundError: # no local file, remote is always better return True local_lastmodified = int(res.st_mtime)"Getting modification time for '%s'" % remotefile) response = self.client.sendcmd('MDTM ' + remotefile) code, remote_lastmodified = response.split() remote_lastmodified = int( time.mktime( datetime.strptime(remote_lastmodified, '%Y%m%d%H%M%S').timetuple())) if remote_lastmodified > local_lastmodified: self.logger.debug( "Remote file '%s' is newer (remote: %s, local: %s)" % (remotefile, remote_lastmodified, local_lastmodified)) return True local_size = res.st_size self.client.sendcmd("TYPE I") response = self.client.sendcmd('SIZE ' + remotefile) code, remote_size = map(int, response.split()) if remote_size > local_size: self.logger.debug( "Remote file '%s' is bigger (remote: %s, local: %s)" % (remotefile, remote_size, local_size)) return True self.logger.debug("'%s' is up-to-date, no need to download" % remotefile) return False
[docs]class LastModifiedBaseDumper(BaseDumper): ''' Use SRC_URLS as a list of URLs to download and implement create_todump_list() according to that list. Shoud be used in parallel with a dumper talking the actual underlying protocol ''' SRC_URLS = [] # must be overridden in subclass
[docs] def set_release(self): """ Set self.release attribute as the last-modified datetime found in the last SRC_URLs element (so releae is the datetime of the last file to download) """ raise NotImplementedError("Implement me in sub-class")
[docs] def create_todump_list(self, force=False): assert type( self.__class__.SRC_URLS) is list, "SRC_URLS should be a list" assert self.__class__.SRC_URLS, "SRC_URLS list is empty" self.set_release() # so we can generate new_data_folder for src_url in self.__class__.SRC_URLS: filename = os.path.basename(src_url) new_localfile = os.path.join(self.new_data_folder, filename) try: current_localfile = os.path.join(self.current_data_folder, filename) except TypeError: # current data folder doesn't even exist current_localfile = new_localfile remote_better = self.remote_is_better(src_url, current_localfile) if force or current_localfile is None or remote_better: new_localfile = os.path.join(self.new_data_folder, filename) self.to_dump.append({ "remote": src_url, "local": new_localfile })
[docs]class LastModifiedFTPDumper(LastModifiedBaseDumper): """ SRC_URLS containing a list of URLs pointing to files to download, use FTP's MDTM command to check whether files should be downloaded The release is generated from the last file's MDTM in SRC_URLS, and formatted according to RELEASE_FORMAT. See also LastModifiedHTTPDumper, working the same way but for HTTP protocol. Note: this dumper is a wrapper over FTPDumper, one URL will give one FTPDumper instance. """ RELEASE_FORMAT = "%Y-%m-%d"
[docs] def prepare_client(self): pass
[docs] def release_client(self): pass
def get_client_for_url(self, url): split = urlparse.urlsplit(url) klass = type( "dynftpdumper", (FTPDumper, ), { "FTP_HOST": split.hostname, "CWD_DIR": "/".join(split.path.split("/")[:-1]), "FTP_USER": split.username or '', "FTP_PASSWD": split.password or '', "SRC_NAME": self.__class__.SRC_NAME, "SRC_ROOT_FOLDER": self.__class__.SRC_ROOT_FOLDER, }) ftpdumper = klass() ftpdumper.prepare_client() return ftpdumper def get_remote_file(self, url): split = urlparse.urlsplit(url) remotef = split.path.split("/")[-1] return remotef
[docs] def set_release(self): url = self.__class__.SRC_URLS[-1] ftpdumper = self.get_client_for_url(url) remotefile = self.get_remote_file(url) response = ftpdumper.client.sendcmd('MDTM ' + remotefile) code, lastmodified = response.split() lastmodified = time.mktime( datetime.strptime(lastmodified, '%Y%m%d%H%M%S').timetuple()) dt = datetime.fromtimestamp(lastmodified) self.release = dt.strftime(self.__class__.RELEASE_FORMAT) ftpdumper.release_client()
[docs] def remote_is_better(self, urlremotefile, localfile): ftpdumper = self.get_client_for_url(urlremotefile) remotefile = self.get_remote_file(urlremotefile) isitbetter = ftpdumper.remote_is_better(remotefile, localfile) ftpdumper.release_client() return isitbetter
[docs] def download(self, urlremotefile, localfile, headers={}): ftpdumper = self.get_client_for_url(urlremotefile) remotefile = self.get_remote_file(urlremotefile) return, localfile)
import requests
[docs]class HTTPDumper(BaseDumper): """Dumper using HTTP protocol and "requests" library""" VERIFY_CERT = True IGNORE_HTTP_CODE = [ ] # list of HTTP code to ignore in case on non-200 response RESOLVE_FILENAME = False # global trigger to get filenames from headers # when available
[docs] def prepare_client(self): self.client = requests.Session() self.client.verify = self.__class__.VERIFY_CERT
[docs] def need_prepare(self): return not self.client
[docs] def release_client(self): self.client.close() self.client = None
[docs] def remote_is_better(self, remotefile, localfile): return True
[docs] def download(self, remoteurl, localfile, headers={}): self.prepare_local_folders(localfile) res = self.client.get(remoteurl, stream=True, headers=headers) if not res.status_code == 200: if res.status_code in self.__class__.IGNORE_HTTP_CODE:"Remote URL gave http code %s, ignored" % (remoteurl, res.status_code)) return else: raise DumperException("Error while downloading '%s' (status: %s, reason: %s)" % (remoteurl, res.status_code, res.reason)) # issue biothings.api #3: take filename from header if specified # note: this has to explicit, either on a globa (class) level or per file to dump if self.__class__.RESOLVE_FILENAME and res.headers.get( "content-disposition"): parsed = cgi.parse_header(res.headers["content-disposition"]) # looks like: ('attachment', {'filename': 'the_filename.txt'}) if parsed and parsed[0] == "attachment" and parsed[1].get( "filename"): # localfile is an absolute path, replace last part localfile = os.path.join(os.path.dirname(localfile), parsed[1]["filename"]) self.logger.debug("Downloading '%s' as '%s'" % (remoteurl, localfile)) fout = open(localfile, 'wb') for chunk in res.iter_content(chunk_size=512 * 1024): if chunk: fout.write(chunk) fout.close() return res
[docs]class LastModifiedHTTPDumper(HTTPDumper, LastModifiedBaseDumper): """Given a list of URLs, check Last-Modified header to see whether the file should be downloaded. Sub-class should only have to declare SRC_URLS. Optionally, another field name can be used instead of Last-Modified, but date format must follow RFC 2616. If that header doesn't exist, it will always download the data (bypass) The release is generated from the last file's Last-Modified in SRC_URLS, and formatted according to RELEASE_FORMAT. """ LAST_MODIFIED = "Last-Modified" ETAG = "ETag" RELEASE_FORMAT = "%Y-%m-%d" RESOLVE_FILENAME = True # resolve by default as this dumper is called # with a list of URLs only, without any information # about the local filename to store data in
[docs] def remote_is_better(self, remotefile, localfile): res = self.client.head(remotefile, allow_redirects=True) if self.__class__.LAST_MODIFIED not in res.headers: self.logger.warning("Header '%s' doesn't exist, can determine if remote is better, assuming it is..." % self.__class__.LAST_MODIFIED) return True remote_dt = datetime.strptime( res.headers[self.__class__.LAST_MODIFIED], '%a, %d %b %Y %H:%M:%S GMT') remote_lastmodified = time.mktime(remote_dt.timetuple()) try: res = os.stat(localfile) local_lastmodified = int(res.st_mtime) except (FileNotFoundError, TypeError): return True # doesn't even exist, need to dump if remote_lastmodified > local_lastmodified: self.logger.debug( "Remote file '%s' is newer (remote: %s, local: %s)" % (remotefile, remote_lastmodified, local_lastmodified)) return True else: return False
[docs] def set_release(self): url = self.__class__.SRC_URLS[-1] res = self.client.head(url, allow_redirects=True) for h in self.__class__.LAST_MODIFIED: try: remote_dt = datetime.strptime( res.headers[self.__class__.LAST_MODIFIED], '%a, %d %b %Y %H:%M:%S GMT') # also set release attr self.release = remote_dt.strftime( self.__class__.RELEASE_FORMAT) except KeyError: self.release = res.headers[self.__class__.ETAG]
class WgetDumper(BaseDumper): def create_todump_list(self, force=False, **kwargs): """Fill self.to_dump list with dict("remote":remote_path,"local":local_path) elements. This is the todo list for the dumper. It's a good place to check whether needs to be downloaded. If 'force' is True though, all files will be considered for download""" raise NotImplementedError("Define in subclass") def prepare_client(self): """Check if 'wget' executable exists""" ret = os.system("type wget 2>&1 > /dev/null") if not ret == 0: raise DumperException("Can't find wget executable") def need_prepare(self): return False def release_client(self): pass def remote_is_better(self, remotefile, localfile): return True def download(self, remoteurl, localfile): self.prepare_local_folders(localfile) cmdline = "wget %s -O %s" % (remoteurl, localfile) return_code = os.system(cmdline) if return_code == 0:"Success.") else: self.logger.error("Failed with return code (%s)." % return_code)
[docs]class FilesystemDumper(BaseDumper): """ This dumpers works locally and copy (or move) files to datasource folder """ FS_OP = "cp" # or 'mv' if file needs to be delete from original folder, # or 'ln' is a symlink should be created
[docs] def prepare_client(self): """Check if 'cp' and 'mv' executable exists...""" for cmd in ["cp", "mv", "ln"]: ret = os.system("type %s 2>&1 > /dev/null" % cmd) if not ret == 0: raise DumperException("Can't find '%s' executable" % cmd)
[docs] def need_prepare(self): return False
[docs] def release_client(self): pass
[docs] def remote_is_better(self, remotefile, localfile): res = os.stat(remotefile) remote_lastmodified = int(res.st_mtime) res = os.stat(localfile) local_lastmodified = int(res.st_mtime) if remote_lastmodified > local_lastmodified: return True else: return False
[docs] def download(self, remotefile, localfile): self.prepare_local_folders(localfile) if self.__class__.FS_OP == "ln": cmdline = "rm -f %s && ln -s %s %s" % (localfile, remotefile, localfile) else: cmdline = "%s -f %s %s" % (self.__class__.FS_OP, remotefile, localfile) return_code = os.system(cmdline) if return_code == 0:"Success.") else: self.logger.error("Failed with return code (%s)." % return_code)
[docs]class DummyDumper(BaseDumper): """DummyDumper will do nothing... (useful for datasources that can't be downloaded anymore but still need to be integrated, ie. fill src_dump, etc...) """ def __init__(self, *args, **kwargs): # make sure we don't create empty directory each time it's launched # so create a non-archiving dumper super(DummyDumper, self).__init__(archive=False, *args, **kwargs) self.release = ""
[docs] def prepare_client(self):"Dummy dumper, will do nothing") pass
[docs] @asyncio.coroutine def dump(self, force=False, job_manager=None, *args, **kwargs): self.logger.debug("Dummy dumper, nothing to download...") self.prepare_local_folders( os.path.join(self.new_data_folder, "dummy_file")) # this is the only interesting thing happening here pinfo = self.get_pinfo() pinfo["step"] = "post_dump" job = yield from job_manager.defer_to_thread( pinfo, partial(self.post_dump, job_manager=job_manager)) yield from asyncio.gather(job) # consume future"Registering success") self.register_status("success") if self.__class__.AUTO_UPLOAD: set_pending_to_upload(self.src_name)"success", extra={"notify": True})
[docs]class ManualDumper(BaseDumper): ''' This dumper will assist user to dump a resource. It will usually expect the files to be downloaded first (sometimes there's no easy way to automate this process). Once downloaded, a call to dump() will make sure everything is fine in terms of files and metadata ''' def __init__(self, *args, **kwargs): super(ManualDumper, self).__init__(*args, **kwargs) # overide @property, it'll be set manually in this case (ie. not dynamically generated) # because it's a manual dumper and user specifies data folder path explicitely # (and see below) self._new_data_folder = None @property def new_data_folder(self): return self._new_data_folder @new_data_folder.setter def new_data_folder(self, value): self._new_data_folder = value def prepare(self, state={}): self.setup_log() if self.prepared: return if state: # let's be explicit, _state takes what it wants for k in self._state: self._state[k] = state[k] return self.prepare_src_dump()
[docs] def prepare_client(self): "Manual dumper, assuming data will be downloaded manually")
[docs] @asyncio.coroutine def dump(self, path, release=None, force=False, job_manager=None, **kwargs): if os.path.isabs(path): self.new_data_folder = path elif path: self.new_data_folder = os.path.join(self.src_root_folder, path) else: self.new_data_folder = self.src_root_folder if release is None: # take latest path part, usually it's the release self.release = os.path.basename(self.new_data_folder) else: self.release = release # sanity check if not os.path.exists(self.new_data_folder): raise DumperException( "Can't find folder '%s' (did you download data first ?)" % self.new_data_folder) if not os.listdir(self.new_data_folder): raise DumperException( "Directory '%s' is empty (did you download data first ?)" % self.new_data_folder) pinfo = self.get_pinfo() pinfo["step"] = "post_dump" strargs = "[path=%s,release=%s]" % (self.new_data_folder, self.release) job = yield from job_manager.defer_to_thread( pinfo, partial(self.post_dump, job_manager=job_manager)) yield from asyncio.gather(job) # consume future # ok, good to go self.register_status("success") if self.__class__.AUTO_UPLOAD: set_pending_to_upload(self.src_name)"success %s" % strargs, extra={"notify": True})"Manually dumped resource (data_folder: '%s')" % self.new_data_folder)
from urllib import parse as urlparse from bs4 import BeautifulSoup
[docs]class GoogleDriveDumper(HTTPDumper):
[docs] def prepare_client(self): # FIXME: this is not very useful... super(GoogleDriveDumper, self).prepare_client()
[docs] def remote_is_better(self, remotefile, localfile): return True
def get_document_id(self, url): pr = urlparse.urlparse(url) if "" in url or "" in url: q = urlparse.parse_qs(pr.query) doc_id = q.get("id") if not doc_id: raise DumperException( "Can't extract document ID from URL '%s'" % url) return doc_id.pop() elif "" in url: frags = pr.path.split("/") ends = ["view", "edit"] if frags[-1] in ends: doc_id = frags[-2] return doc_id else: raise DumperException( "URL '%s' doesn't end with %s, can't extract document ID" % (url, ends)) raise DumperException( "Don't know how to extract document ID from URL '%s'" % url)
[docs] def download(self, remoteurl, localfile): ''' remoteurl is a google drive link containing a document ID, such as: -<1234567890ABCDEF> -<1234567890ABCDEF>/view It can also be just a document ID ''' self.prepare_local_folders(localfile) if remoteurl.startswith("http"): doc_id = self.get_document_id(remoteurl) else: doc_id = remoteurl"Found document ID: %s" % doc_id) # first pass: get download URL with "confirm" code dl_url = "" % doc_id res = requests.get(dl_url) html = BeautifulSoup(res.text, "html.parser") link = html.find("a", {"id": "uc-download-link"}) if not link: raise DumperException("Can't find a download link from '%s': %s" % (dl_url, html)) href = link.get("href") # now build the final GET request, using cookies to simulate browser return super(GoogleDriveDumper, self).download( "" + href, localfile, headers={"cookie": res.headers["set-cookie"]})
[docs]class GitDumper(BaseDumper): """ Git dumper gets data from a git repo. Repo is stored in SRC_ROOT_FOLDER (without versioning) and then versions/releases are fetched in SRC_ROOT_FOLDER/<release> """ GIT_REPO_URL = None DEFAULT_BRANCH = "master" def _clone(self, repourl, localdir):"git clone '%s' into '%s'" % (repourl, localdir)) subprocess.check_call(["git", "clone", repourl, localdir]) def _pull(self, localdir, commit): # fetch+merge"git pull data (commit %s) into '%s'" % (commit,localdir)) old = os.path.abspath(os.curdir) try: os.chdir(localdir) # discard changes, we don't want to activate a conflit resolution session... cmd = ["git", "reset", "--hard", "HEAD"] subprocess.check_call(cmd) # then fetch latest code (local repo, not applied to code base yet) cmd = ["git", "fetch", "--all"] subprocess.check_call(cmd) if commit != "HEAD": # first get the latest code from repo # (if a newly created branch is avail in remote, we can't check it out)"git checkout to commit %s" % commit) cmd = ["git", "checkout", commit] subprocess.check_call(cmd) else: # if we were on a detached branch (due to specific commit checkout) # we need to make sure to go back to master (re-attach) cmd = ["git", "checkout", self.__class__.DEFAULT_BRANCH] subprocess.check_call(cmd) # then merge cmd = ["git", "merge"] subprocess.check_call(cmd) # and then get the commit hash out = subprocess.check_output(["git", "rev-parse", "HEAD"]) self.release = "HEAD (%s)" % out.decode().strip() finally: os.chdir(old) pass @property def new_data_folder(self): # we don't keep release in data folder path # as it's a git repo return self.src_root_folder
[docs] @asyncio.coroutine def dump(self, release="HEAD", force=False, job_manager=None, **kwargs): assert self.__class__.GIT_REPO_URL, "GIT_REPO_URL is not defined" #assert self.__class__.ARCHIVE == False, "Git dumper can't keep multiple versions (but can move to a specific commit hash)" got_error = None self.release = release def do(): do_clone = False if force: # force is also a way to clean and start from scratch rmdashfr(self.src_root_folder) if not os.path.exists(self.src_root_folder): # data folder doesn't even exist, no git files yet, we need to clone os.makedirs(self.src_root_folder) do_clone = True self.register_status("downloading", transient=True) if do_clone: self._clone(self.__class__.GIT_REPO_URL, self.src_root_folder) self._pull(self.src_root_folder, release) pinfo = self.get_pinfo() job = yield from job_manager.defer_to_thread(pinfo, partial(do)) def done(f): nonlocal got_error try: _ = f.result() self.register_status("success") except Exception as e: got_error = e self.logger.exception("failed: %s" % e, extra={"notify": True}) self.register_status("failed", download={"err": str(e)}) raise job.add_done_callback(done) yield from job
[docs] def prepare_client(self): """Check if 'git' executable exists""" ret = os.system("type git 2>&1 > /dev/null") if not ret == 0: raise DumperException("Can't find 'git' executable")
[docs] def need_prepare(self): return True
[docs] def release_client(self): pass
[docs] def remote_is_better(self, remotefile, localfile): return True
[docs] def download(self, remotefile, localfile): self.prepare_local_folders(localfile) cmdline = "wget %s -O %s" % (remoteurl, localfile) return_code = os.system(cmdline) if return_code == 0:"Success.") else: self.logger.error("Failed with return code (%s)." % return_code)
[docs]class DumperManager(BaseSourceManager): SOURCE_CLASS = BaseDumper
[docs] def get_source_ids(self): """Return displayable list of registered source names (not private)""" # skip private ones starting with __ # skip those deriving from bt.h.autoupdate.dumper.BiothingsDumper, they're used for autohub # and considered internal (note: only one dumper per source, so [0]) from biothings.hub.autoupdate.dumper import BiothingsDumper registered = sorted([src for src,klasses in self.register.items() if not src.startswith("__") and not issubclass(klasses[0],BiothingsDumper)]) return registered
def __repr__(self): return "<%s [%d registered]: %s>" % (self.__class__.__name__, len(self.register), self.get_source_ids())
[docs] def clean_stale_status(self): # not uysing mongo query capabilities as hub backend could be ES, SQLlite, etc... # so manually iterate src_dump = get_src_dump() srcs = src_dump.find() for src in srcs: if src.get("download", {}).get("status", None) == "downloading": logging.warning( "Found stale datasource '%s', marking download status as 'canceled'" % src["_id"]) src["download"]["status"] = "canceled" src_dump.replace_one({"_id": src["_id"]}, src)
def create_instance(self, klass): logging.debug("Creating new %s instance" % klass.__name__) inst = klass() return inst
[docs] def register_classes(self, klasses): for klass in klasses: # supersede/monkey-patch klass with potiential existing conf values from DB btconfig.supersede(klass) if klass.SRC_NAME: if len(self.register.get(klass.SRC_NAME, [])) >= 1: raise ResourceError("Can't register %s for source '%s', dumper already registered: %s" % (klass, klass.SRC_NAME, self.register[klass.SRC_NAME])) self.register.setdefault(klass.SRC_NAME, []).append(klass) else: try: self.register[] = klass except AttributeError as e: logging.error("Can't register class %s: %s" % (klass, e)) continue
[docs] def dump_all(self, force=False, **kwargs): """ Run all dumpers, except manual ones """ jobs = [] for src in self.register: job = self.dump_src(src, force=force, skip_manual=True, **kwargs) jobs.extend(job) return asyncio.gather(*jobs)
def dump_src(self, src, force=False, skip_manual=False, schedule=False, check_only=False, **kwargs): if src in self.register: klasses = self.register[src] else: raise DumperException( "Can't find '%s' in registered sources (whether as main or sub-source)" % src) jobs = [] try: for i, klass in enumerate(klasses): if issubclass(klass, ManualDumper) and skip_manual: logging.warning("Skip %s, it's a manual dumper" % klass) continue crontab = None if schedule: if klass.SCHEDULE: crontab = klass.SCHEDULE else: raise DumperException("Missing scheduling information") job = self.job_manager.submit( partial(self.create_and_dump, klass, force=force, job_manager=self.job_manager, check_only=check_only, **kwargs), schedule=crontab) jobs.append(job) return jobs except Exception as e: logging.error("Error while dumping '%s': %s" % (src, e)) raise
[docs] def call(self, src, method_name, *args, **kwargs): """ Create a dumper for datasource "src" and call method "method_name" on it, with given arguments. Used to create arbitrary calls on a dumper. "method_name" within dumper definition must a coroutine. """ if src in self.register: klasses = self.register[src] else: raise DumperException( "Can't find '%s' in registered sources (whether as main or sub-source)" % src) jobs = [] try: for i, klass in enumerate(klasses): pfunc = partial(self.create_and_call, klass, method_name, *args, **kwargs) job = asyncio.ensure_future(pfunc()) jobs.append(job) return jobs except Exception as e: logging.error("Error while dumping '%s': %s" % (src, e)) raise
@asyncio.coroutine def create_and_dump(self, klass, *args, **kwargs): inst = self.create_instance(klass) res = yield from inst.dump(*args, **kwargs) return res @asyncio.coroutine def create_and_call(self, klass, method_name, *args, **kwargs): inst = self.create_instance(klass) res = yield from getattr(inst, method_name)(*args, **kwargs) return res
[docs] def schedule_all(self, raise_on_error=False, **kwargs): """ Run all dumpers, except manual ones """ errors = {} for src in self.register: try: self.dump_src(src, skip_manual=True, schedule=True, **kwargs) except Exception as e: errors[src] = e if raise_on_error: raise if errors: logging.warning("Found errors while scheduling:\n%s" % pprint.pformat(errors)) return errors
def source_info(self, source=None): src_dump = get_src_dump() src_ids = self.get_source_ids() if source: if source in src_ids: src_ids = [source] else: return None res = [] for _id in src_ids: src = src_dump.find_one({"_id": _id}) or {} assert len( self.register[_id] ) == 1, "Found more than one dumper for source '%s': %s" % ( _id, self.register[_id]) dumper = self.register[_id][0] src.setdefault("download", {}) src["download"]["dumper"] = {"name": "%s.%s" % (inspect.getmodule(dumper).__name__, dumper.__name__), "bases": ["%s.%s" % (inspect.getmodule(k).__name__, k.__name__) for k in dumper.__bases__ if inspect.getmodule(k)], "manual": issubclass(dumper, ManualDumper)} src["name"] = _id src["_id"] = _id res.append(src) if source: return res.pop() else: return res def dump_info(self): res = {} for name, klasses in self.register.items(): res[name] = [klass.__name__ for klass in klasses] return res