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caosdb
Software
caosdb-advanced-user-tools
Commits
f0e7434e
Commit
f0e7434e
authored
3 years ago
by
Henrik tom Wörden
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FIX: example script
parent
9c1411d5
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2 merge requests
!39
Release 0.4.0
,
!20
created draft for generic analysis method
Changes
1
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src/caosadvancedtools/serverside/examples/example_script.py
+28
-11
28 additions, 11 deletions
src/caosadvancedtools/serverside/examples/example_script.py
with
28 additions
and
11 deletions
src/caosadvancedtools/serverside/examples/example_script.py
+
28
−
11
View file @
f0e7434e
...
@@ -26,6 +26,17 @@
...
@@ -26,6 +26,17 @@
"""
"""
An exemplary script that illustrates how scripts can be used in conjunction
An exemplary script that illustrates how scripts can be used in conjunction
with the generic_analysis module.
with the generic_analysis module.
Data model:
Analysis:
sources: REFEERENCE
scripts: FILE
results: REFEERENCE
mean_value: DOUBLE
Person:
Email: TEXT
"""
"""
import
argparse
import
argparse
...
@@ -37,7 +48,7 @@ from datetime import datetime
...
@@ -37,7 +48,7 @@ from datetime import datetime
import
caosdb
as
db
import
caosdb
as
db
import
matplotlib.pyplot
as
plt
import
matplotlib.pyplot
as
plt
import
numpy
as
np
import
numpy
as
np
from
caosadvancedtools.cfood
import
assure_property_is
from
caosadvancedtools.cfood
import
assure_property_is
,
get_property
from
caosadvancedtools.guard
import
INSERT
,
UPDATE
from
caosadvancedtools.guard
import
INSERT
,
UPDATE
from
caosadvancedtools.guard
import
global_guard
as
guard
from
caosadvancedtools.guard
import
global_guard
as
guard
from
caosadvancedtools.serverside.helper
import
send_mail
as
main_send_mail
from
caosadvancedtools.serverside.helper
import
send_mail
as
main_send_mail
...
@@ -47,7 +58,7 @@ logger = logging.getLogger(__name__)
...
@@ -47,7 +58,7 @@ logger = logging.getLogger(__name__)
guard
.
set_level
(
level
=
UPDATE
)
guard
.
set_level
(
level
=
UPDATE
)
def
send_mail
(
self
,
changes
,
receipient
):
def
send_mail
(
changes
,
receipient
):
"""
calls sendmail in order to send a mail to the curator about pending
"""
calls sendmail in order to send a mail to the curator about pending
changes
changes
...
@@ -78,11 +89,15 @@ The following changes where done automatically.
...
@@ -78,11 +89,15 @@ The following changes where done automatically.
def
main
(
args
):
def
main
(
args
):
if
hasattr
(
args
,
"
auth_token
"
)
and
args
.
auth_token
:
db
.
configure_connection
(
auth_token
=
args
.
auth_token
)
# TODO (maybe) can these checks be replaced by a more declaritive appoach?
# TODO (maybe) can these checks be replaced by a more declaritive appoach?
try
:
try
:
dataAnalysisRecord
=
db
.
Record
(
id
=
args
.
entityid
).
retrieve
()
dataAnalysisRecord
=
db
.
Record
(
id
=
args
.
entityid
).
retrieve
()
except
db
.
TransactionError
:
except
db
.
TransactionError
:
logger
.
error
(
"
Cannot retrieve
dataAnalysis
Record with id ={}
"
.
format
(
logger
.
error
(
"
Cannot retrieve Record with id ={}
"
.
format
(
args
.
entityid
args
.
entityid
))
))
...
@@ -123,40 +138,42 @@ def main(args):
...
@@ -123,40 +138,42 @@ def main(args):
# An update should only be done if necessary: assure_property_is should be
# An update should only be done if necessary: assure_property_is should be
# used instead of direct calls to 'update'.
# used instead of direct calls to 'update'.
to_be_updated
=
[]
to_be_updated
=
db
.
Container
()
assure_property_is
(
assure_property_is
(
dataAnalysisRecord
,
dataAnalysisRecord
,
"
mean_value
"
,
"
mean_value
"
,
mean
,
mean
,
to_be_updated
=
to_be_updated
to_be_updated
=
to_be_updated
)
)
# TODO (maybe) this is not really meaningful since an uploaded file will
always
# TODO (maybe) this is not really meaningful since an uploaded file will
# be different.... Compare checksums of files?
#
always
be different.... Compare checksums of files?
assure_property_is
(
assure_property_is
(
dataAnalysisRecord
,
dataAnalysisRecord
,
"
results
"
,
"
results
"
,
fig
.
id
,
[
fig
.
id
]
,
to_be_updated
=
to_be_updated
to_be_updated
=
to_be_updated
)
)
if
len
(
to_be_updated
)
>
0
:
if
len
(
to_be_updated
)
>
0
:
people
=
db
.
execute_query
(
"
FIND RECORD Person WHICH IS REFERENCEED BY
"
print
(
to_be_updated
)
to_be_updated
.
update
()
people
=
db
.
execute_query
(
"
FIND RECORD Person WHICH IS REFERENCED BY
"
"
{}
"
.
format
(
dataAnalysisRecord
.
id
))
"
{}
"
.
format
(
dataAnalysisRecord
.
id
))
for
person
in
people
:
for
person
in
people
:
if
person
.
get_property
(
"
Email
"
)
is
not
None
:
if
person
.
get_property
(
"
Email
"
)
is
not
None
:
send_mail
(
to_be_updated
,
receipient
=
person
.
get_property
(
send_mail
(
[
str
(
el
)
for
el
in
to_be_updated
],
"
Email
"
))
receipient
=
person
.
get_property
(
"
Email
"
)
.
value
)
# TODO (must) what should be done with the old file? Removed if not referenced?
# TODO (must) what should be done with the old file? Removed if not referenced?
# TODO (maybe) inform about updates (reuse stuff from crawler.py?)
# TODO (maybe) inform about updates (reuse stuff from crawler.py?)
# TODO (must) sketch meaningful logging
# TODO (must) sketch meaningful logging
# TODO (must) how to send an email?
def
parse_args
():
def
parse_args
():
parser
=
argparse
.
ArgumentParser
(
description
=
__doc__
,
parser
=
argparse
.
ArgumentParser
(
description
=
__doc__
,
formatter_class
=
RawTextHelpFormatter
)
formatter_class
=
RawTextHelpFormatter
)
parser
.
add_argument
(
"
--auth-token
"
)
parser
.
add_argument
(
"
entityid
"
,
parser
.
add_argument
(
"
entityid
"
,
help
=
"
The ID of the DataAnalysis Record.
"
,
type
=
int
)
help
=
"
The ID of the DataAnalysis Record.
"
,
type
=
int
)
...
...
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