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Merge remote-tracking branch 'bikalabs/master' into feature/LIMS-2252…
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…-schedule-sampling
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@xispa
xispa committed Jul 1, 2016
2 parents bab528e + 1428bab commit a582e2b
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Showing 18 changed files with 827 additions and 436 deletions.
7 changes: 6 additions & 1 deletion bika/lims/__init__.py
View file
Expand Up @@ -31,11 +31,16 @@
allow_module('bika.lims.permissions')
allow_module('bika.lims.utils')
allow_module('json')
allow_module('pdb')
allow_module('zope.i18n.locales')
allow_module('zope.component')
allow_module('plone.registry.interfaces')

import App
debug_mode = App.config.getConfiguration().debug_mode
if debug_mode:
allow_module('pdb')
allow_module('pudb')

def initialize(context):

from content.analysis import Analysis
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176 changes: 7 additions & 169 deletions bika/lims/browser/analysisrequest/add.py
View file
@@ -1,6 +1,5 @@
import json
from bika.lims.utils.sample import create_sample
from bika.lims.utils.samplepartition import create_samplepartition
from bika.lims.workflow import doActionFor
import plone

Expand All @@ -16,7 +15,7 @@
from bika.lims.utils import getHiddenAttributesForClass, dicts_to_dict
from bika.lims.utils import t
from bika.lims.utils import tmpID
from bika.lims.utils.analysisrequest import create_analysisrequest
from bika.lims.utils.analysisrequest import create_analysisrequest as crar
from magnitude import mg
from plone.app.layout.globals.interfaces import IViewView
from Products.Archetypes import PloneMessageFactory as PMF
Expand Down Expand Up @@ -443,7 +442,7 @@ def __call__(self):
ARs = []
for arnum, state in valid_states.items():
# Create the Analysis Request
ar = create_analysisrequest(
ar = crar(
portal_catalog(UID=state['Client'])[0].getObject(),
self.request,
state
Expand Down Expand Up @@ -471,170 +470,9 @@ def __call__(self):
return json.dumps({'success': message})



from bika.lims import deprecated
@deprecated(comment="bika.lims.browser.analysisrequest.add."
"create_analysisrequest is deprecated and will be removed "
"in Bika LIMS 3.3", replacement=crar)
def create_analysisrequest(context, request, values):
"""Create an AR.
:param context the container in which the AR will be created (Client)
:param request the request object
:param values a dictionary containing fieldname/value pairs, which
will be applied. Some fields will have specific code to handle them,
and others will be directly written to the schema.
:return the new AR instance
Special keys present (or required) in the values dict, which are not present
in the schema:
- Partitions: data about partitions to be created, and the
analyses that are to be assigned to each.
- Prices: custom prices set in the HTML form.
- ResultsRange: Specification values entered in the HTML form.
"""
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')

# Create new sample or locate the existing for secondary AR
sample = False
if values['Sample']:
if ISample.providedBy(values['Sample']):
secondary = True
sample = values['Sample']
samplingworkflow_enabled = sample.getSamplingWorkflowEnabled()
else:
brains = bc(UID=values['Sample'])
if brains:
secondary = True
sample = brains[0].getObject()
samplingworkflow_enabled = sample.getSamplingWorkflowEnabled()
if not sample:
secondary = False
sample = create_sample(context, request, values)
samplingworkflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()

# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
ar.setSample(sample)

# processform renames the sample, this requires values to contain the Sample.
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)

# Object has been renamed
ar.edit(RequestID=ar.getId())

# Set initial AR state
workflow_action = 'sampling_workflow' if samplingworkflow_enabled \
else 'no_sampling_workflow'
workflow.doActionFor(ar, workflow_action)


# We need to send a list of service UIDS to setAnalyses function.
# But we may have received a list of titles, list of UIDS,
# list of keywords or list of service objects!
service_uids = []
for obj in values['Analyses']:
uid = False
# service objects
if hasattr(obj, 'portal_type') and obj.portal_type == 'AnalysisService':
uid = obj.UID()
# Analysis objects (shortcut for eg copying analyses from other AR)
elif hasattr(obj, 'portal_type') and obj.portal_type == 'Analysis':
uid = obj.getService()
# Maybe already UIDs.
if not uid:
bsc = getToolByName(context, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', UID=obj)
if brains:
uid = brains[0].UID
# Maybe already UIDs.
if not uid:
bsc = getToolByName(context, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=obj)
if brains:
uid = brains[0].UID
if uid:
service_uids.append(uid)
else:
logger.info("In analysisrequest.add.create_analysisrequest: cannot "
"find uid of this service: %s" % obj)

# Set analysis request analyses
ar.setAnalyses(service_uids,
prices=values.get("Prices", []),
specs=values.get('ResultsRange', []))
analyses = ar.getAnalyses(full_objects=True)

skip_receive = ['to_be_sampled', 'sample_due', 'sampled', 'to_be_preserved']
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
sample_state = workflow.getInfoFor(sample, 'review_state')
if sample_state not in skip_receive:
doActionFor(ar, 'receive')

for analysis in analyses:
doActionFor(analysis, 'sample_due')
analysis_state = workflow.getInfoFor(analysis, 'review_state')
if analysis_state not in skip_receive:
doActionFor(analysis, 'receive')

if not secondary:
# Create sample partitions
partitions = []
for n, partition in enumerate(values['Partitions']):
# Calculate partition id
partition_prefix = sample.getId() + "-P"
partition_id = '%s%s' % (partition_prefix, n + 1)
partition['part_id'] = partition_id
# Point to or create sample partition
if partition_id in sample.objectIds():
partition['object'] = sample[partition_id]
else:
partition['object'] = create_samplepartition(
sample,
partition
)
# now assign analyses to this partition.
obj = partition['object']
for analysis in analyses:
if analysis.getService().UID() in partition['services']:
analysis.setSamplePartition(obj)

partitions.append(partition)

# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not samplingworkflow_enabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
doActionFor(ar, lowest_state)

# Transition pre-preserved partitions
for p in partitions:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
workflow.doActionFor(part, 'preserve')

# Return the newly created Analysis Request
return ar
return crar(context, request, values)
16 changes: 0 additions & 16 deletions bika/lims/browser/analysisrequest/templates/ar_add_by_col.pt
View file
Expand Up @@ -140,22 +140,6 @@
</tal:columns>
</tr>

<!--
<tr>
<th colspan="3" style="background-color: #FFF">
</th>
<tal:block repeat="arnum python:range(view.ar_count)">
<td>
<input type="button" value="Create Profile"
tal:attributes="
class string:ar_${arnum}_save_profile;
name string:save_profile;
id string:ar_${arnum}_save_profile;
" />
</td>
</tal:block>
</tr>
-->
</tfoot>
</table>

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21 changes: 7 additions & 14 deletions bika/lims/browser/js/bika.lims.loader.js
View file
Expand Up @@ -79,8 +79,8 @@ window.bika.lims.controllers = {
['ClientSamplingRoundAddEditView'],

// Sampling Rounds PrintView
".samplinground-print-form":
['SamplingRoundtPrintView'],
"#sr_publish_container":
['SamplingRoundPrintView'],

// Reference Samples
".portaltype-referencesample.template-analyses":
Expand Down Expand Up @@ -211,18 +211,11 @@ window.bika.lims.loadControllers = function(all, controllerKeys) {
controllers[key].forEach(function(js) {
if (all == true || $.inArray(key, controllerKeys) >= 0 || $.inArray(js, _bika_lims_loaded_js) < 0) {
console.debug('[bika.lims.loader] Loading '+js);
try {
obj = new window[js]();
obj.load();
// Register the object for further access
window.bika.lims[js]=obj;
_bika_lims_loaded_js.push(js);
} catch (e) {
// statements to handle any exceptions
var msg = '[bika.lims.loader] Unable to load '+js+": "+ e.message +"\n"+e.stack;
console.warn(msg);
window.bika.lims.error(msg);
}
obj = new window[js]();
obj.load();
// Register the object for further access
window.bika.lims[js]=obj;
_bika_lims_loaded_js.push(js);
}
});
}
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