Hello everyone. I work with Mekom Solutions a contributing organization to OpenMRS and we are currently working on the OpenMRS 3.
For OpenMRS 3 we are using SENAITE as the LIMS component. Due to the way we will package our OpenMRS 3 distributions it will not be practical to manually configure the various components and we have already built tools for most of the components that we are using (OpenMRS itself, Odoo, … etc) that allow us to initialize them at start up without requiring user interventions
We are able to initialize SENAITE by uploading an xlsx file on the web UI which works great. But we need to be able do it at startup as well.
For our use case I have made an attempt to create a python script to initialize SENAITE given a configuration file. The code below may look familiar because it is adapted from here
from plone import api as ploneapi
from Products.CMFCore.utils import getToolByName
from bika.lims import PMF
from bika.lims import logger
from bika.lims.interfaces import ISetupDataImporter
from openpyxl import load_workbook
from pkg_resources import resource_filename
from zope.component import getAdapters
import traceback
import tempfile
import transaction
try:
from zope.component.hooks import getSite
except:
# Plone < 4.3
from zope.app.component.hooks import getSite
class LoadSetupData():
def __init__(self, context):
self.context = context
# dependencies to resolve
self.deferred = []
def solve_deferred(self, deferred=None):
unsolved = []
deferred = deferred if deferred else self.deferred
for d in self.deferred:
src_obj = d['src_obj']
src_field = src_obj.getField(d['src_field'])
multiValued = src_field.multiValued
src_mutator = src_field.getMutator(src_obj)
src_accessor = src_field.getAccessor(src_obj)
tool = getToolByName(self.context, d['dest_catalog'])
try:
proxies = tool(d['dest_query'])
except:
continue
if len(proxies) > 0:
obj = proxies[0].getObject()
if multiValued:
value = src_accessor()
value.append(obj.UID())
else:
value = obj.UID()
src_mutator(value)
else:
unsolved.append(d)
self.deferred = unsolved
return len(unsolved)
def load_data(self):
self.dataset_project = 'bika.lims'
self.dataset_name = 'test'
workbook = None
try:
workbook = load_workbook(filename='/home/enyachoke/Code/Mekom/senaite/senaitelims/src/collective.initializer/src/collective/initializer/configuration.xlsx') # , use_iterators=True)
except AttributeError:
print ""
print traceback.format_exc()
print "Error while loading "
adapters = [[name, adapter]
for name, adapter
in list(getAdapters((self.context, ), ISetupDataImporter))]
for sheetname in workbook.get_sheet_names():
transaction.savepoint()
ad_name = sheetname.replace(" ", "_")
if ad_name in [a[0] for a in adapters]:
adapter = [a[1] for a in adapters if a[0] == ad_name][0]
adapter(self, workbook, self.dataset_project, self.dataset_name)
adapters = [a for a in adapters if a[0] != ad_name]
transaction.commit()
for name, adapter in adapters:
transaction.savepoint()
adapter(self, workbook, self.dataset_project, self.dataset_name)
transaction.commit()
check = len(self.deferred)
while len(self.deferred) > 0:
new = self.solve_deferred()
logger.info("solved %s of %s deferred references" % (
check - new, check))
if new == check:
raise Exception("%s unsolved deferred references: %s" % (
len(self.deferred), self.deferred))
check = new
logger.info("Rebuilding bika_setup_catalog")
bsc = getToolByName(self.context, 'bika_setup_catalog')
bsc.clearFindAndRebuild()
logger.info("Rebuilding bika_catalog")
bc = getToolByName(self.context, 'bika_catalog')
bc.clearFindAndRebuild()
logger.info("Rebuilding bika_analysis_catalog")
bac = getToolByName(self.context, 'bika_analysis_catalog')
bac.clearFindAndRebuild()
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message)
def main(app):
loader = LoadSetupData(app.senaite)
loader.load_data()
if "app" in locals():
main(app)
I have tested the script with the after-installhook of collective.recipe.plonesite and it seems to work okay. My concern is that my combined experience working with Plone and SENAITE is less that 2 weeks and am not sure if my approach is any good. @Espurna @xispa any thoughts on this.