def update_olog_uid(uid, text, attachments):
'''Update olog book logid entry cotaining uid string with text and attachments files
uid: string, the uid of a scan or a specficial string (only gives one log entry)
text: the text to update, will add this text to the old text
attachments: add new attachment files
An example:
filename1 = '/XF11ID/analysis/2016_2/yuzhang/Results/August/af8f66/Report_uid=af8f66.pdf'
atch=[ Attachment(open(filename1, 'rb')) ]
update_olog_uid( uid='af8f66', text='Add xpcs pdf report', attachments= atch )
'''
olog_client = SimpleOlogClient(
url='https://logbook.nsls2.bnl.gov/Olog-11-ID/Olog',
username='******',
password='******')
client = OlogClient(url='https://logbook.nsls2.bnl.gov/Olog-11-ID/Olog',
username='******',
password='******')
logid = olog_client.find(search=uid)[0]['id']
#print(attachments)
update_olog_id(logid, text, attachments)
def update_olog_id(logid, text, attachments):
'''Update olog book logid entry with text and attachments files
logid: integer, the log entry id
text: the text to update, will add this text to the old text
attachments: add new attachment files
An example:
filename1 = '/XF11ID/analysis/2016_2/yuzhang/Results/August/af8f66/Report_uid=af8f66.pdf'
atch=[ Attachment(open(filename1, 'rb')) ]
update_olog_id( logid=29327, text='add_test_atch', attachmenents= atch )
'''
url = 'https://logbook.nsls2.bnl.gov/Olog-11-ID/Olog'
olog_client = SimpleOlogClient(url=url,
username='******',
password='******')
client = OlogClient(url='https://logbook.nsls2.bnl.gov/Olog-11-ID/Olog',
username='******',
password='******')
old_text = olog_client.find(id=logid)[0]['text']
upd = LogEntry(
text=old_text + '\n' + text,
attachments=attachments,
logbooks=[Logbook(name='Operations', owner=None, active=True)])
upL = client.updateLog(logid, upd)
print(
'The url=%s was successfully updated with %s and with the attachments'
% (url, text))
def __init__(self, logbook):
self.logbook = logbook
from pyOlog import SimpleOlogClient
self.client = SimpleOlogClient()
# Check at init time we are in an IPython session.
from IPython import get_ipython # noqa: F401
Call:
{{ start.signature }}
{% endif %}
Metadata
--------
{% for k, v in start.items() -%}
{%- if k not in ['plan_name', 'plan_args'] -%}{{ k }} : {{ v }}
{% endif -%}
{%- endfor -%}"""
bluesky.callbacks.olog.TEMPLATES['desc'] = """
{{- start.plan_name }} ['{{ start.uid[:6] }}'] (scan num: {{ start.scan_id }})"""
bluesky.callbacks.olog.TEMPLATES['call'] = """RE({{ start.plan_name }}(
{%- for k, v in start.plan_args.items() %}{%- if not loop.first %} {% endif %}{{ k }}={{ v }}
{%- if not loop.last %},
{% endif %}{% endfor %}))
"""
LOGBOOKS = ['Comissioning'] # list of logbook names to publish to
simple_olog_client = SimpleOlogClient()
generic_logbook_func = simple_olog_client.log
configured_logbook_func = partial(generic_logbook_func, logbooks=LOGBOOKS)
cb = logbook_cb_factory(configured_logbook_func)
RE.subscribe('start', cb)
loogbook = simple_olog_client
import esm # general ESM routines: e2g(), g2e(), angles()
def configure_olog(user_ns, *, callback=None, subscribe=True):
"""
Setup a callback that publishes some metadata from the RunEngine to Olog.
Also, add the public contents of pyOlog.ophyd_tools to the namespace.
This is expected to be run after :func:`configure_base`. It expects to find
an instance of RunEngine named ``RE`` in the user namespace. Additionally,
if the user namespace contains the name ``logbook``, that is expected to be
an instance ``pyOlog.SimpleOlogClient``.
Parameters
----------
user_ns: dict
a namespace --- for example, ``get_ipython().user_ns``
callback : callable, optional
a hook for customizing the logbook_cb_factory; if None a default is
used
subscribe : boolean, optional
True by default. Set to False to skip the subscription. (You still get
pyOlog.ophyd_tools.)
Returns
-------
names : list
list of names added to the namespace
Examples
--------
Configure the Olog.
>>>> configure_olog(get_ipython().user_ns);
"""
# Conceptually our task is simple: add a subscription to the RunEngine that
# publishes to the Olog using the Python wrapper of its REST API, pyOlog.
# In practice this is messy because we have deal with the many-layered API
# of pyOlog and, more importantly, ensure that slowness or errors from the
# Olog do not affect the run. Historically the Olog deployment has not been
# reliable, so it is important to be robust against these issues. Of
# course, by ignoring Olog errors, we leave gaps in the log, which is not
# great, but since all data is saved to a databroker anyway, we can always
# re-generate them later.
ns = {} # We will update user_ns with this at the end.
from bluesky.callbacks.olog import logbook_cb_factory
from functools import partial
from pyOlog import SimpleOlogClient
import queue
import threading
from warnings import warn
# This is for pyOlog.ophyd_tools.get_logbook, which simply looks for
# a variable called 'logbook' in the global IPython namespace.
if "logbook" in user_ns:
simple_olog_client = user_ns["logbook"]
else:
simple_olog_client = SimpleOlogClient()
ns["logbook"] = simple_olog_client
if subscribe:
if callback is None:
# list of logbook names to publish to
LOGBOOKS = ("Data Acquisition", )
generic_logbook_func = simple_olog_client.log
configured_logbook_func = partial(generic_logbook_func,
logbooks=LOGBOOKS)
callback = logbook_cb_factory(configured_logbook_func)
def submit_to_olog(queue, cb):
while True:
name, doc = queue.get() # waits until document is available
try:
cb(name, doc)
except Exception as exc:
warn("This olog is giving errors. This will not be logged."
"Error:" + str(exc))
olog_queue = queue.Queue(maxsize=100)
olog_thread = threading.Thread(target=submit_to_olog,
args=(olog_queue, callback),
daemon=True)
olog_thread.start()
def send_to_olog_queue(name, doc):
try:
olog_queue.put((name, doc), block=False)
except queue.Full:
warn("The olog queue is full. This will not be logged.")
RE = user_ns["RE"]
RE.subscribe(send_to_olog_queue, "start")
import pyOlog.ophyd_tools
import_star(pyOlog.ophyd_tools, ns)
user_ns.update(ns)
return list(ns)
