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Merge pull request #46 from Galithil/master
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Handles NoIndex samples
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@vezzi
vezzi authored Nov 18, 2016
2 parents 0fa291d + 033fef7 commit eb0841c
Showing 1 changed file with 26 additions and 32 deletions.
58 changes: 26 additions & 32 deletions LIMS2DB/classes.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
from genologics_sql.tables import *
from genologics_sql.queries import *
from genologics_sql.tables import Artifact, Container, EscalationEvent, GlsFile, Process, Project, Researcher, ReagentType
from genologics_sql.queries import get_children_processes, get_processes_in_history
from LIMS2DB.diff import diff_objects
from sqlalchemy import text
from sqlalchemy.orm.exc import NoResultFound
Expand Down Expand Up @@ -69,7 +69,7 @@ def __init__(self, lims, crawler, log):
for i in crawler.starting_proc.all_inputs():
if sample in i.samples:
pjs[p.id]['samples'][sample.name]['rec_ctrl']['status'] = i.qc_flag

for output in crawler.starting_proc.all_outputs():
if output.type == "Analyte" and sample in output.samples:
pjs[p.id]['samples'][sample.name]['location'] = output.location[1]
Expand All @@ -86,7 +86,7 @@ def __init__(self, lims, crawler, log):
if 'Concentration' in inp.udf and 'Conc. Units' in inp.udf:
onelib['concentration'] = "{0} {1}".format(round(inp.udf['Concentration'], 2), inp.udf['Conc. Units'])
if 'Molar Conc. (nM)' in inp.udf:
onelib['concentration'] = "{0} nM".format(round(inp.udf['Molar Conc. (nM)'], 2))
onelib['concentration'] = "{0} nM".format(round(inp.udf['Molar Conc. (nM)'], 2))
if 'Size (bp)' in inp.udf:
onelib['size'] = round(inp.udf['Size (bp)'], 2)
if 'NeoPrep Machine QC' in inp.udf and onelib['status'] == 'UNKNOWN':
Expand All @@ -106,10 +106,10 @@ def __init__(self, lims, crawler, log):
pjs[p.id]['samples'][sample.name]['sequencing_status'] = inp.qc_flag

self.obj['projects'] = pjs


class LimsCrawler:

def __init__(self, lims, starting_proc=None, starting_inputs=None):
self.lims = lims
self.starting_proc = starting_proc
Expand Down Expand Up @@ -205,7 +205,7 @@ def __init__(self, session, log, step):

def build(self):
self.obj['id'] = self.start.luid
self.obj['last_aggregate'] = None
self.obj['last_aggregate'] = None
if self.start.daterun:
self.obj["date_run"] = self.start.daterun.strftime("%Y-%m-%d")
else:
Expand All @@ -231,23 +231,23 @@ def build(self):
where piot.processid = {0}".format(self.start.processid)

input_arts = self.session.query(Artifact).from_statement(text(query)).all()

for inp in input_arts:
sample = inp.samples[0]
project = sample.project
if not project:
continue # control samples do not have projects
if project.luid not in self.obj['projects']:
self.obj['projects'][project.luid] = {'application': project.udf_dict.get('Application'),
'name': project.name,
'library': project.udf_dict.get('Library construction method'),
'samples': {}}
self.obj['projects'][project.luid] = {'application': project.udf_dict.get('Application'),
'name': project.name,
'library': project.udf_dict.get('Library construction method'),
'samples': {}}
if project.closedate:
self.obj['projects'][project.luid]['close_date'] = project.closedate.strftime("%Y-%m-%d")
if sample.name not in self.obj['projects'][project.luid]['samples']:
self.obj['projects'][project.luid]['samples'][sample.name] = {'customer_name': sample.udf_dict.get('Customer Name'),
'sequencing_status': 'UNKNOWN', 'library_status': 'UNKNOWN',
'rec_ctrl': {}, 'library': {}, 'sequencing': {}}
self.obj['projects'][project.luid]['samples'][sample.name] = {'customer_name': sample.udf_dict.get('Customer Name'),
'sequencing_status': 'UNKNOWN', 'library_status': 'UNKNOWN',
'rec_ctrl': {}, 'library': {}, 'sequencing': {}}

self.obj['projects'][project.luid]['samples'][sample.name]['rec_ctrl']['status'] = inp.qc_flag

Expand All @@ -258,7 +258,7 @@ def build(self):

out = self.session.query(Artifact).from_statement(text(query)).one()
self.obj['projects'][project.luid]['samples'][sample.name]['location'] = out.containerplacement.api_string

query = "select pc.* from process pc \
inner join processiotracker piot on piot.processid=pc.processid \
inner join artifact_ancestor_map aam on aam.artifactid=piot.inputartifactid \
Expand Down Expand Up @@ -296,7 +296,7 @@ def build(self):
self.obj['projects'][project.luid]['samples'][sample.name]['library'][agr.luid]['concentration'] = "{0:.2f} {1}".format(agr_inp.udf_dict['Concentration'], agr_inp.udf_dict['Conc. Units'])
if 'Size (bp)' in agr_inp.udf_dict:
self.obj['projects'][project.luid]['samples'][sample.name]['library'][agr.luid]['size'] = round(agr_inp.udf_dict['Size (bp)'], 2)

query = "select pc.* from process pc \
inner join processiotracker piot on piot.processid=pc.processid \
inner join artifact_ancestor_map aam on aam.artifactid=piot.inputartifactid \
Expand Down Expand Up @@ -355,7 +355,7 @@ def save(self):
my_mod = doc.pop('modification_time', None)
my_crea = doc.pop('creation_time', None)
diffs = diff_objects(doc, self.obj)
if diffs:
if diffs:
self.obj['_id'] = my_id
self.obj['_rev'] = my_rev
self.obj['creation_time'] = my_crea
Expand Down Expand Up @@ -578,7 +578,7 @@ def get_library_preps(self, sample):
agrlibvals = get_children_processes(self.session, one_libprep.processid, pc_cg.AGRLIBVAL.keys(), sample.processid, 'daterun desc')
agrlibval = None
for agrlv in agrlibvals:
# for small rna (and maybe others), there is more than one agrlibval, and I should not get the latest one,
# for small rna (and maybe others), there is more than one agrlibval, and I should not get the latest one,
# but the latest one that ran at sample level, not a pool level.
# get input artifact of a given process that belongs to sample
query = "select art.* from artifact art \
Expand Down Expand Up @@ -634,7 +634,7 @@ def get_library_preps(self, sample):
self.obj['samples'][sample.name]['library_prep'][prepname]['prep_status'] = inp_artifact.qc_flag
self.obj['samples'][sample.name]['library_prep'][prepname]['library_validation'][agrlibval.luid]['well_location'] = inp_artifact.containerplacement.api_string
self.obj['samples'][sample.name]['library_prep'][prepname]['library_validation'][agrlibval.luid]['reagent_labels'] = [rg.name for rg in inp_artifact.reagentlabels]
if not 'By user' in self.obj['details']['library_construction_method']:
if 'By user' not in self.obj['details']['library_construction_method']:
# if finlib, these are already computed
self.obj['samples'][sample.name]['library_prep'][prepname]['reagent_label'] = inp_artifact.reagentlabels[0].name
self.obj['samples'][sample.name]['library_prep'][prepname]['barcode'] = self.extract_barcode(inp_artifact.reagentlabels[0].name)
Expand Down Expand Up @@ -669,12 +669,12 @@ def get_library_preps(self, sample):
caliper_file = self.session.query(GlsFile).from_statement(text(query)).one()
self.obj['samples'][sample.name]['library_prep'][prepname]['library_validation'][agrlibval.luid]['caliper_image'] = "sftp://{host}/home/glsftp/{uri}".format(host=self.host, uri=caliper_file.contenturi)
except NoResultFound:
self.log.info("Did not find a libprep caliper image for sample {}".format(sample.name))
self.log.info("Did not find a libprep caliper image for sample {}".format(sample.name))
# handling neoprep
if "NeoPrep" in agrlibval.type.displayname:
self.obj['samples'][sample.name]['library_prep'][prepname]['library_validation'][agrlibval.luid]['conc_units'] = "nM"
self.obj['samples'][sample.name]['library_prep'][prepname]['library_validation'][agrlibval.luid]['conc_units'] = "nM"
self.obj['samples'][sample.name]['library_prep'][prepname]['library_validation'][agrlibval.luid]['concentration'] = inp_artifact.udf_dict['Normalized conc. (nM)']
# get output resultfile named like the sample of a Neoprep QC
# get output resultfile named like the sample of a Neoprep QC
query = "select art.* from artifact art \
inner join artifact_sample_map asm on art.artifactid=asm.artifactid \
inner join outputmapping om on art.artifactid=om.outputartifactid \
Expand Down Expand Up @@ -743,7 +743,7 @@ def get_library_preps(self, sample):
preprep = self.session.query(Process).from_statement(text(query)).first()
self.obj['samples'][sample.name]['library_prep'][prepname]['pre_prep_start_date'] = preprep.daterun.strftime("%Y-%m-%d")
except AttributeError:
self.log.info("Did not find a preprep for sample {}".format(sample.name))
self.log.info("Did not find a preprep for sample {}".format(sample.name))

# get seqruns
seqs = get_children_processes(self.session, one_libprep.processid, pc_cg.SEQUENCING.keys(), sample=sample.processid)
Expand Down Expand Up @@ -832,6 +832,8 @@ def get_library_preps(self, sample):

def extract_barcode(self, chain):
bcp = re.compile("[ATCG\-]{4,}")
if "NoIndex" in chain:
return chain
if '(' not in chain:
barcode = chain
else:
Expand All @@ -852,11 +854,3 @@ def find_couch_sampleid(self, sample_run):
view = db.view('names/name_to_id')
for row in view[sample_run]:
return row.id








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