def specimen_id_from_name(spec_name):
"""Return the LIMS ID of a specimen give its name.
"""
recs = lims.query("select id from specimens where name='%s'" % spec_name)
if len(recs) == 0:
raise ValueError('No LIMS specimen named "%s"' % spec_name)
return recs[0]['id']
def parent_specimen(specimen):
if isinstance(specimen, int):
q = """select parent_id from specimens where specimens.id=%d""" % specimen
else:
q = """select parent_id from specimens where specimens.name='%s'""" % specimen
recs = lims.query(q)
return recs[0]['parent_id']
def parent_specimen(spec_id):
q = """
select parent_id from specimens
where specimens.id=%d
""" % spec_id
recs = lims.query(q)
return recs[0]['parent_id']
def child_specimens(spec_id):
q = """
select id from specimens
where specimens.parent_id=%d
""" % spec_id
recs = lims.query(q)
return [rec['id'] for rec in recs]
def cell_cluster_data_paths(cluster_id):
recs = lims.query("""
select ephys_roi_results.storage_directory
from specimens
join ephys_roi_results on ephys_roi_results.id=specimens.ephys_roi_result_id
where specimens.id=%d
""" % cluster_id)
return [r['storage_directory'] for r in recs]
def specimen_tags(specimen):
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
q = """
select name from specimen_tags
join specimen_tags_specimens on specimen_tags_specimens.specimen_tag_id=specimen_tags.id
where specimen_tags_specimens.specimen_id=%d""" % specimen
recs = lims.query(q)
return [rec['name'] for rec in recs]
def child_specimens(specimen):
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
q = """
select id from specimens
where specimens.parent_id=%d
""" % specimen
recs = lims.query(q)
return [rec['id'] for rec in recs]
def specimen_metadata(spec_id):
recs = lims.query(
"select data from specimen_metadata where specimen_id=%d" % spec_id)
meta = recs[0]['data']
if meta == '':
return None
return json.loads(
meta
) # unserialization corrects for a LIMS bug; we can remove this later.
def specimen_type(spec_id):
q = """
select specimen_types.name from specimens
left join specimen_types_specimens on specimen_types_specimens.specimen_id=specimens.id
left join specimen_types on specimen_types.id=specimen_types_specimens.specimen_type_id
where specimens.id=%d
""" % spec_id
recs = lims.query(q)
return recs[0]['name']
def parent_specimen(specimen):
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
q = """
select parent_id from specimens
where specimens.id=%d
""" % spec_id
recs = lims.query(q)
return recs[0]['parent_id']
def cell_cluster_data_paths(specimen):
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
recs = lims.query("""
select ephys_roi_results.storage_directory
from specimens
join ephys_roi_results on ephys_roi_results.id=specimens.ephys_roi_result_id
where specimens.id=%d
""" % specimen)
return [r['storage_directory'] for r in recs]
def cell_cluster_ids(spec_id):
q = """
select id from specimens
join specimen_types_specimens on specimen_types_specimens.specimen_id=specimens.id
join specimen_types on specimen_types.id=specimen_types_specimens.specimen_type_id
where specimens.parent_id=%d
and specimen_types.name='CellCluster'
""" % spec_id
recs = lims.query(q)
return [rec['id'] for rec in recs]
def get_trigger_dir(specimen_name):
"""Returns the path for trigger files for each project
"""
q = """
select projects.trigger_dir from projects
left join specimens on projects.id = specimens.project_id
where specimens.name = '%s'
""" % specimen_name
recs = lims.query(q)
return recs[0]['trigger_dir']
def specimen_type(specimen):
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
q = """
select specimen_types.name from specimens
left join specimen_types_specimens on specimen_types_specimens.specimen_id=specimens.id
left join specimen_types on specimen_types.id=specimen_types_specimens.specimen_type_id
where specimens.id=%d
""" % specimen
recs = lims.query(q)
return recs[0]['name']
def specimen_metadata(spec_id):
recs = lims.query(
"select data from specimen_metadata where specimen_id=%d" % spec_id)
if len(recs) == 0:
return None
meta = recs[0]['data']
if meta == '':
return None
if isinstance(meta, str):
meta = json.loads(
meta
) # unserialization corrects for a LIMS bug; we can remove this later.
return meta
def specimen_species(specimen_name):
"""returns species information
"""
q = """
select organisms.name as species
from specimens left join donors on specimens.donor_id = donors.id
left join organisms on donors.organism_id = organisms.id
where specimens.name = '%s';
""" % specimen_name
r = lims.query(q)
if len(r) == 0:
raise ValueError("Could not find donor information")
return r[0]['species']
def specimen_images(specimen_name):
"""Return a list of (image ID, treatment) pairs for a specimen.
"""
q = """
select sub_images.id, treatments.name from specimens
join image_series on image_series.specimen_id=specimens.id
join sub_images on sub_images.image_series_id=image_series.id
join images on images.id = sub_images.image_id
left join treatments on treatments.id = images.treatment_id
where specimens.name='%s';
""" % specimen_name
r = lims.query(q)
return [(rec['id'], rec['name']) for rec in r]
def cluster_cells(cluster):
"""Return information about a CellCluster's child cells.
"""
if not isinstance(cluster, int):
cluster = specimen_id_from_name(cluster)
q = """select child.id, child.name, child.x_coord, child.y_coord, child.external_specimen_name, child.ephys_qc_result
from specimens parent
left join specimens child on child.parent_id=parent.id
where parent.id=%d
""" % cluster
recs = lims.query(q)
return recs
def get_incoming_dir(specimen_name):
"""Returns the path for incoming files for each project
"""
q = """
select projects.incoming_directory from projects
left join specimens on projects.id = specimens.project_id
where specimens.name='%s'
""" % specimen_name
recs = lims.query(q)
if recs[0]['incoming_directory'] == None:
trigger_dir = get_trigger_dir(specimen_name)
return os.path.dirname(os.path.dirname(trigger_dir))
else:
return recs[0]['incoming_directory']
def specimen_ephys_roi_plans(spec_name):
"""Return a list of all ephys roi plans for this specimen.
"""
sid = specimen_id_from_name(spec_name)
recs = lims.query("""
select
ephys_roi_plans.id as ephys_roi_plan_id,
ephys_specimen_roi_plans.id as ephys_specimen_roi_plan_id,
ephys_roi_plans.name as name
from
ephys_specimen_roi_plans
join ephys_roi_plans on ephys_specimen_roi_plans.ephys_roi_plan_id=ephys_roi_plans.id
where
ephys_specimen_roi_plans.specimen_id=%d
""" % sid)
return recs
def specimen_metadata(specimen):
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
recs = lims.query(
"select data from specimen_metadata where specimen_id=%d" % specimen)
if len(recs) == 0:
return None
meta = recs[0]['data']
if meta == '':
return None
if isinstance(meta, basestring):
meta = json.loads(
meta
) # unserialization corrects for a LIMS bug; we can remove this later.
return meta
def cell_cluster_ids(specimen):
"""Return the IDs of all cell-cluster children of *specimen*.
Parameters
----------
specimen : int | str
Either the ID (int) or name (str) of the specimen.
"""
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
q = """
select specimens.id from specimens
join specimen_types_specimens on specimen_types_specimens.specimen_id=specimens.id
join specimen_types on specimen_types.id=specimen_types_specimens.specimen_type_id
where specimens.parent_id=%d
and specimen_types.name='CellCluster'
""" % specimen
recs = lims.query(q)
return [rec['id'] for rec in recs]
def specimen_ephys_roi_plans(specimen):
"""Return a list of all ephys roi plans for this specimen.
Parameters
----------
specimen : int | str
Either the ID (int) or name (str) of the specimen.
"""
if not isinstance(specimen, int):
specimen = specimen_id_from_name(specimen)
recs = lims.query("""
select
ephys_roi_plans.id as ephys_roi_plan_id,
ephys_specimen_roi_plans.id as ephys_specimen_roi_plan_id,
ephys_roi_plans.name as name
from
ephys_specimen_roi_plans
join ephys_roi_plans on ephys_specimen_roi_plans.ephys_roi_plan_id=ephys_roi_plans.id
where
ephys_specimen_roi_plans.specimen_id=%d
""" % specimen)
return recs
def specimen_info(specimen_name=None, specimen_id=None):
"""Return a dictionary of information about a slice specimen queried from LIMS.
Also generates information about the hemisphere and which side of the slice
was patched.
Returns
-------
organism : "mouse" or "human"
age : age of specimen in days at time of sectioning
date_of_birth : donor's date of birth
genotype : the full genotype of the donor as recorded in labtracks
weight : weight in grams
sex : 'M', 'F', or
plane_of_section : 'coronal' or 'sagittal'
hemisphere : 'left' or 'right'
thickness : speimen slice thickness (unscaled meters)
section_instructions : description of the slice angle and target region
used for sectioning
flipped : boolean; if True, then the slice was flipped relative to its
blockface image during recording
sectioning_mount_side : the side of the tissue that was mounted during
sectioning
exposed_surface : The surface that was exposed during the experiment (right,
left, anterior, or posterior)
section_number : indicates the order this slice was sectioned (1=first)
"""
# Query all interesting information about this specimen from LIMS
query = """
select
organisms.name as organism,
ages.days as age,
donors.date_of_birth as date_of_birth,
donors.full_genotype as genotype,
donors.weight as weight,
genders.name as sex,
tissue_processings.section_thickness_um as thickness,
tissue_processings.instructions as section_instructions,
plane_of_sections.name as plane_of_section,
flipped_specimens.name as flipped,
specimens.histology_well_name as histology_well_name,
specimens.carousel_well_name as carousel_well_name,
specimens.parent_id as parent_id,
specimens.name as specimen_name,
specimens.id as specimen_id
from specimens
left join donors on specimens.donor_id=donors.id
left join organisms on donors.organism_id=organisms.id
left join ages on donors.age_id=ages.id
left join genders on donors.gender_id=genders.id
left join tissue_processings on specimens.tissue_processing_id=tissue_processings.id
left join plane_of_sections on tissue_processings.plane_of_section_id=plane_of_sections.id
left join flipped_specimens on flipped_specimens.id = specimens.flipped_specimen_id
"""
if specimen_name is not None:
sid = specimen_name.strip()
query += "where specimens.name='%s';" % sid
elif specimen_id is not None:
sid = specimen_id
query += "where specimens.id='%d';" % sid
else:
raise ValueError("Must specify specimen name or ID")
r = lims.query(query)
if len(r) != 1:
raise Exception(
"LIMS lookup for specimen '%s' returned %d results (expected 1)" %
(sid, len(r)))
rec = r[0]
# convert thickness to unscaled
rec['thickness'] = rec['thickness'] * 1e-6
# convert organism to more easily searchable form
rec['organism'] = {
'Mus musculus': 'mouse',
'H**o Sapiens': 'human'
}[rec['organism']]
# convert flipped to bool
rec['flipped'] = {
'flipped': True,
'not flipped': False,
'not checked': None
}[rec['flipped']]
# Parse the specimen name to extract more information about the plane of section.
# Mouse format is:
# driver1;reporter1;driver2;reporter2-AAAAAA.BB.CC
# AAAAAA = donor ID
# BB = slice number
# CC = orientation and hemisphere
spec_name = rec['specimen_name']
if rec['organism'] == 'mouse':
m = re.match(r'(.*)(-(\d{6,7}))?(\.(\d{2}))(\.(\d{2}))$', spec_name)
if m is None:
raise Exception('Could not parse mouse specimen name: "%s"' %
spec_name)
rec['section_number'] = int(m.groups()[4])
# The last number contains information about the orientation and hemisphere
orientation_num = m.groups()[6]
plane, hem, mount = {
'01': ('coronal', 'left', 'anterior'),
'02': ('coronal', 'right', 'anterior'),
'03': ('coronal', 'left', 'posterior'),
'04': ('coronal', 'right', 'posterior'),
'05': ('sagittal', 'left', 'right'),
'06': ('sagittal', 'right', 'left'),
}[orientation_num]
if plane != rec['plane_of_section']:
raise ValueError(
"Slice orientation from specimen name (.%s=%s) does not match plane_of_section recorded in LIMS (%s)"
% (orientation_num, plane, rec['plane_of_section']))
rec['hemisphere'] = hem
rec['sectioning_mount_side'] = mount
# decide which surface was patched
if rec['flipped'] is True:
rec['exposed_surface'] = mount
elif rec['flipped'] is False:
rec['exposed_surface'] = {
'anterior': 'posterior',
'posterior': 'anterior',
'right': 'left',
'left': 'right'
}[mount]
else:
rec['exposed_surface'] = None
# Human format is:
# Haa.bb.ccc.dd.ee.ff
elif rec['organism'] == 'human':
m = re.match(r'H(\d+)\.(\d+)\.(\d+)\.(\d+)\.(\d+)(\.(\d+))?$',
spec_name)
if m is None:
raise Exception('Could not parse human specimen name: "%s"' %
spec_name)
rec['hemisphere'] = None
rec['sectioning_mount_side'] = None
rec['exposed_surface'] = None
rec['human_donor_site'] = int(m.groups()[1])
rec['human_donor_number'] = int(m.groups()[2])
rec['block_number'] = int(m.groups()[3])
rec['section_number'] = int(m.groups()[4])
rec['subsection_number'] = None if m.groups()[6] is None else int(
m.groups()[6])
else:
raise Exception('Unsupported organism: "%s"' % rec['organism'])
return rec
def specimen_images(specimen):
"""Return a list of dicts describing images for a specimen.
Each dict looks like::
{'id': sub_image_id, 'file': image_file_path, 'treatment': treatment_name, 'resolution': um_per_px, 'url': lims_url}
If an image is a stack, then the values for 'id' and 'file' will be lists.
Parameters
----------
specimen : int | str
Either the ID (int) or name (str) of the specimen.
"""
field = 'id' if isinstance(specimen, int) else 'name'
images = []
# First get a list of all image series for the specimen
q = """
select image_series.id, image_series.is_stack from specimens
join image_series on image_series.specimen_id=specimens.id
where specimens.%s='%s' and
image_series.type='FocalPlaneImageSeries';
""" % (field, specimen)
# for each image series, get all sub images and decide whether to treat them as
# a stack or a set of images with different treatments
for image_series in lims.query(q):
q = """
select distinct sub_images.id, images.jp2, scans.resolution, treatments.name, slides.storage_directory from image_series
join sub_images on sub_images.image_series_id=image_series.id
join images on images.id = sub_images.image_id
left join treatments on treatments.id = images.treatment_id
left join slides on slides.id=images.slide_id
left join scans on scans.slide_id=slides.id
where image_series.id=%d;
""" % image_series['id']
results = lims.query(q)
if image_series['is_stack'] is True:
image_ids = {}
image_files = {}
# sift through stack and group images by treatment and resolution
for image in results:
key = (image['name'], image['resolution'])
image_ids.setdefault(key, []).append(image['id'])
image_files.setdefault(
key, []).append(image['storage_directory'].rstrip('/') +
'/' + image['jp2'])
for k in image_ids:
# not sure how to generate an image stack url
images.append({
'id': image_ids[k],
'file': image_files[k],
'treatment': k[0],
'resolution': k[1],
'url': None,
'image_series': image_series['id']
})
else:
for image in results:
if image['storage_directory'] is None:
path = None
else:
path = image['storage_directory'].rstrip(
'/') + '/' + image['jp2']
url = "http://lims2/siv?sub_image=%d" % image['id']
images.append({
'id': image['id'],
'file': path,
'treatment': image['name'],
'resolution': image['resolution'],
'url': url,
'image_series': image_series['id']
})
return images
def specimen_name(spec_id):
recs = lims.query("select name from specimens where id=%s" % spec_id)
if len(recs) == 0:
raise ValueError('No LIMS specimen with ID %d' % spec_id)
return recs[0]['name']
def cell_cluster_ids(spec_id):
recs = lims.query("select id from specimens where specimens.parent_id=%d" %
spec_id)
return [rec['id'] for rec in recs]
