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nested_ummzgbif_functionv3.py
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nested_ummzgbif_functionv3.py
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# Z:\UMMZ>python ummzgbif_functionv3.py UMMZ-TEST > log.txt
# nohup python3 ./scripts/nested_ummzgbif_functionv3.py /deepbluedata-globus/upload/UMMZ/Transfer-12-11-2020/ > ./scripts/nested_log.txt &
'''
Emails for ummz
All of UMMZ:
Divisions:
'''
"""
Example:
Folder name: ummz-mammals-164676
"institutioncode": "ummz","collectioncode": "mammals","catalognumber": "164676"
"""
import os
from sys import argv
#import idigbio
import datetime
import glob
import fnmatch
import re
#from pygbif import occurrences as occ
import shutil
from pandas import read_excel
import json
import requests
import csv
now = datetime.datetime.now()
def parsefolder(fn):
if fn.startswith(('ummz-', 'UMMZ-')):
initSplit = fn.split("_")
tripleSplit = initSplit[0]
fsplit = tripleSplit.split("-")
if len(fsplit) <= 2:
print("Missing catalog number, contact UMMZ")
return
else:
ic = fsplit[0] #institutioncode
cc = fsplit[1] #collectioncode --> use this to get contact email
cn = fsplit[2] #catalognumber
return ic, cc, cn
else:
print("Incorrect folder name! %s" %fn)
return
def getgbif(ic, cc, cn):
"""
Using the GBIF library, fetch UMMZ records
"""
#https://www.gbif.org/occurrence/search?catalog_number=246790&collection_code=herps&institution_code=ummz
#https://www.gbif.org/occurrence/1987105097
gbif_baseurl = 'https://api.gbif.org/v1/'
#url = gbif_baseurl + 'occurrence/search?' + 'catalog_number=' + cn + '&collection_code=' + cc + '&institution_code=' + ic
#print(url)
results = requests.get(gbif_baseurl + 'occurrence/search?' + 'catalog_number=' + cn + '&collection_code=' + cc + '&institution_code=' + ic)
#https://api.gbif.org/v1/occurrence/search?catalog_number=124092&collection_code=mammals&institution_code=ummz
key_list = json.loads(results.content.decode())
#print(data)
#print("line 80: %s " % key_list['results'])
#for item in key_list['results']:
#key = print(item['key'])
#htmltext = key_list.json
#print(htmltext)
#key_list = occ.search(institutionCode=ic,collectionCode=cc,catalogNumber=cn)
if key_list['results'] == []:
print("No GBIF record for %s contact UMMZ" % fname)
ummzdict['ic'] = "error"
ummzdict['cc'] = "error"
ummzdict['cn'] = "error"
return ummzdict
else:
gbif_baseurl = 'https://api.gbif.org/v1/'
# need to get the GBIF Key from above to use in the Fragment URL below:
for item in key_list['results']:
#print(item['key'])
#key = print(item['key'])
url = gbif_baseurl + 'occurrence/' + str(item['key']) + '/fragment'
#print(url)
record_results = requests.get(gbif_baseurl + 'occurrence/' + str(item['key']) + '/fragment')
record_list = json.loads(record_results.content.decode())
#print(record_list)
#print(record_list['scientificName'])
ummzdict['yuuid'] = item["key"]
ummzdict['sciName'] = record_list["scientificName"]
ummzdict['keyWords'] = (record_list["kingdom"], record_list["phylum"], record_list["class"], record_list["order"], record_list["family"], record_list["scientificName"], ummzdict['yuuid'])
#print(ummzdict)
return ummzdict
def getmediagroup(up, fn, ic, cc, cn, uid):
uf = ""
filepath = ""
#ummzfiles = os.listdir(fn) # really need to zip these folders
mgpath = '%s/%s/' % (up, fn)
mgName = [dI for dI in os.listdir(mgpath) if os.path.isdir(os.path.join(mgpath, dI))]
for folders in mgName:
#print(type(folders))
if folders.startswith(("Raw", "Recon")):
mgfolder = os.path.join(mgpath, folders)
#print("mgfolder= %s" % mgfolder)
zfolders = "%s" % folders
try:
# Modify zip name to include Darwin core triple and GBIF occurrence ID
# shutil.make_archive(name_of_zip, 'zip', folder_to_be_zipped) mgfolder + ic + "-" + cc + "-" + cn + "-" + uid
zfiles = shutil.make_archive(mgfolder + "-" + str(uid), 'tar', mgfolder)
except OSError:
pass
zfilesplit = zfiles.split('/') # for Mac/Linux
#zfilesplit = zfiles.split('\\') # for Windows
zsplit = zfilesplit[len(zfilesplit)-1]
uf = uf + (" - %s\n" % (zsplit))
if "Raw" in zsplit:
rawZsplit = zsplit
if "Recon" in zsplit:
reconZsplit = zsplit
#filepath = filepath + (" - /deepbluedata-globus/upload/UMMZ/%s/%s/%s\n" % (up, fn, zsplit))
filepath = filepath + (" - %s/%s/%s\n" % (up, fn, zsplit))
#Get tifs and ply files for previews
plyfile = [f for f in os.listdir(mgfolder) if f.endswith('.ply')]
if len(plyfile) != 0:
uf = uf + (" - %s\n" % (plyfile[0]))
#filepath = filepath + (" - /deepbluedata-prep/UMMZ/%s/%s\n" % (mgfolder, plyfile[0]))
filepath = filepath + (" - %s/%s\n" % (mgfolder, plyfile[0]))
if "Skull" in folders:
img_files = [f for f in os.listdir(mgfolder) if f.endswith('.tif')]
uf = uf + (" - %s\n" % (img_files[0]))
#filepath = filepath + (" - /deepbluedata-prep/UMMZ/%s/%s\n" % (mgfolder, img_files[0]))
filepath = filepath + (" - %s/%s\n" % (mgfolder, img_files[0]))
if "WholeBody" in folders:
img_files = [f for f in os.listdir(mgfolder) if f.endswith('.tif')]
fbimg = int(len(img_files)/2)
uf = uf + (" - %s\n" % (img_files[fbimg]))
#filepath = filepath + (" - /deepbluedata-prep/UMMZ/%s/%s\n" % (mgfolder, img_files[fbimg]))
filepath = filepath + (" - %s/%s\n" % (mgfolder, img_files[fbimg]))
return mgName, uf, filepath, rawZsplit, reconZsplit
def xtekdata(mgName, rawZsplit, reconZsplit):
mgdesc = list()
msMetadata = list()
for mgroup in mgName:
#print(mgroup)
mdDict = dict()
#msMetadata['mdDict']['name'] = mgroup
#mdDict['part'] = mgroup
if mgroup == 'surface_model':
continue
else:
xpath = '%s/%s/%s/' % (ummzpath,fname, mgroup)
xtekpath = os.listdir(xpath)
#print('mgfolder= %s' % (mgroup))
if "WholeBody" in mgroup:
mdDict['part'] = "WholeBody"
else:
mdDict['part'] = "Skull"
#mdDict['part'] = roiName
#xteckVol = 1
#if line.startswith("InputFolderName"):
match = re.search(r'\b\d{4}-\d\d?-\d\d?\b', fname)
ummzdict['scandate'] = datetime.datetime.strptime(match.group(), '%Y-%m-%d').date()
#print(filedate)
mdDict['scandate'] = ummzdict['scandate']
#shortMGroup = re.sub(r'-\b\d{4}-\d\d?-\d\d?\b', '', mgroup)
for xtek in xtekpath:
#xteckVol = 1
if xtek.endswith(("_01.xtekct", ".xtekVolume")):
xtekfolder = os.path.join(xpath, xtek)
xtekfile = open(xtekfolder, "r")
#print(xtekfile)
for line in xtekfile:
if re.match("VoxelSizeX=", line):
voxRes = re.split('=', line)[-1]
#print(voxres)
if re.match("VoxelsX=", line):
voxX = re.split('=', line)[-1]
mdDict['x_spacing'] = voxX.rstrip('\r\n')
#print(voxX)
if re.match("VoxelsY=", line):
voxY = re.split('=', line)[-1]
mdDict['y_spacing'] = voxY.rstrip('\r\n')
#print(voxY)
if re.match("VoxelsZ=", line):
voxZ = re.split('=', line)[-1]
mdDict['z_spacing'] = voxZ.rstrip('\r\n')
#print(voxZ)
if re.match("Projections=", line):
proj = re.split('=', line)[-1]
#print(proj)
'''
if "Recon" in mgroup:
numtif = voxZ.rstrip('\r\n')
dataType = "Reconstructed -"
if "Raw" in mgroup:
numtif = proj.rstrip('\r\n')
dataType = "Raw -"
'''
mdDict['media_type'] = "CT Image Series"
mdDict['occurrence_id'] = "urn:catalog:" + ummzdict['ic'] + ":" + ummzdict['cc'] + ":" + ummzdict['cn']
mdDict["institution_code"] = ummzdict['ic']
mdDict["collection_code"] = ummzdict['cc']
mdDict["catalog_number"] = ummzdict['cn']
mdDict["device_model"] = "XT H225ST"
mdDict["device_manufacturer"] = "Nikon"
mdDict["device_modality"] = "Micro/Nano X-Ray Computed Tomography"
mdDict["device_description"] = ""
mdDict["device_organization_name"] = "University of Michigan Museum of Zoology"
#mdDict["x_spacing"] = voxX
#mdDict["y_spacing"] = voxY
#mdDict["z_spacing"] = voxZ
mdDict["unit"] = "mm"
if "Raw" in mgroup:
#print("RAW Group")
numtif = proj.rstrip('\r\n')
mdDict["number_of_images_in_set"] = proj.rstrip('\r\n')
mdDict["processing_activity_type"] = "Raw"
mdDict["media_ct_series_type"] = "Projections"
mdDict["file_name"] = rawZsplit
# mdDict["parent_file_name"] = RAW filename is parent of Recon file
if "Recon" in mgroup:
#print("RECON Group")
numtif = mdDict['z_spacing'].rstrip('\r\n')
mdDict["media_ct_number_of_images_in_set"] = mdDict['z_spacing'].rstrip('\r\n')
mdDict["processing_activity_type"] = "Reconstructed"
mdDict["media_ct_series_type"] = "Reconstructed Image Stack"
mdDict["file_name"] = reconZsplit
mdDict["parent_file_name"] = rawZsplit
if "WholeBody" in mgroup:
roiName = "WholeBody"
else:
roiName = "Skull"
mdDict["license"] = "https://creativecommons.org/licenses/by-nc-sa/4.0/"
#ydesc = (" :description:\n - 'Scan of specimen %s:%s:%s (%s) - %s . Dataset includes %s TIF images (each %s x %s x 1 voxel at %s mm resolution, derived from %s scan projections), xtek and vgi files for volume reconstruction.'\n" % (ummzdict['ic'], ummzdict['cc'], ummzdict['cn'], ummzdict['sciName'], shortMGroup, numtif, voxX.rstrip('\r\n'), voxY.rstrip('\r\n'), voxres.rstrip('\r\n'), proj.rstrip('\r\n'))) #from xtek
ydesc = ("Scan of specimen %s:%s:%s (%s) - %s. %s Dataset includes %s TIF images (each %s x %s x 1 voxel at %s mm resolution, derived from %s scan projections), xtek and vgi files for volume reconstruction." % (ummzdict['ic'], ummzdict['cc'], ummzdict['cn'], ummzdict['sciName'], mdDict['part'], mdDict["processing_activity_type"], numtif, mdDict['x_spacing'], mdDict['y_spacing'], voxRes.rstrip('\r\n'), proj.rstrip('\r\n'))) #from xtek
#print(ydesc)
mgdesc.append(ydesc)
break
#else:
#xteckVol = 0
#continue
#if xteckVol == 0:
#print("No *.xtekVolume file found in %s!" % xpath)
#print(mdDict)
msMetadata.append(mdDict)
ummzdict['desc'] = mgdesc
return ummzdict['desc'], msMetadata, roiName
def createyml(fname, uf, filepath, gbifl1, roiName):
emailDict = {"birds" : "[email protected]", "fish" : "[email protected]" , "herps" : "[email protected]", "insects": "[email protected]" , "mammals" : "[email protected]", "mollusks" : "[email protected]"}
ownauth = emailDict.get(gbifl1, "")
collDict = {"birds" : "Division of Birds", "fish" : "sj139222d" , "herps" : "05741r77z", "insects": "Division of Insects" , "mammals" : "nv935298c", "mollusks" : "Division of Mollusks"}
collID = collDict.get(gbifl1, "")
#ytop = "---\n:user:\n :visibility: open\n :email: [email protected]\n :ingester: '[email protected]'\n :source: DBDv2\n :works:\n :depositor: [email protected]\n"
ytop = ("---\n:user:\n :visibility: restricted\n :email: '%s'\n :ingester: '[email protected]'\n :source: DBDv2\n :mode: build\n :works:\n :depositor: [email protected]\n" % (ownauth))
yownauth = (" :owner: '%s'\n :authoremail: '%s'\n" % (ownauth, ownauth))
ytitle = (" :title: \n - 'Computed tomography voxel dataset for %s:%s:%s-%s-%s' \n" % (ummzdict['ic'], ummzdict['cc'], ummzdict['cn'],ummzdict['sciName'], roiName))
ydate = (" :date_uploaded:\n - '%s'\n" % (now.year))
yrefby = (" :referenced_by:\n - 'For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/%s'\n" % (ummzdict['yuuid'])) #build URL from iDigBio uuid\n - ''\n"
#ymethod = " :methodology: 'This dataset was created at the University of Michigan Museum of Zoology using a procedure involving computed tomography (CT) hardware. After retrieving the specimen from the museum''s archives, staff secured the specimen in the Nikon XT H 225 ST and initiated the scanning process, which included capturing projections by rotating the specimen. The device''s associated software CT-Pro-3D and the projections were then used to reconstruct a set of TIFF images, with each corresponding to a slice of the three-dimensional object (one voxel in height). In addition, the software created a .xtek volume file (included here), which contains details about the scanning environment, projections, and reconstructions.'\n"
ymethod = " :methodology:\n - 'This dataset was created at the University of Michigan Museum of Zoology using a procedure involving computed tomography (CT) hardware. After retrieving the specimen from the museum''s archives, staff secured the specimen in the Nikon XT H 225 ST and initiated the scanning process, which included capturing projections by rotating the specimen. The device''s associated software CT-Pro-3D and the projections were then used to reconstruct a set of TIFF images, with each corresponding to a slice of the three-dimensional object (one voxel in height). In addition, the software created a .xtek volume file (included here), which contains details about the scanning environment, projections, and reconstructions.'\n"
ypartof = " :part_of:\n - 'part of'\n"
ycreator = " :creator:\n - 'University of Michigan Museum of Zoology'\n"
ykw = (" :keyword:\n - %s\n - 'computed tomography'\n - 'X-ray'\n - '3D' \n" % ('\n - '.join("'{0}'".format(w) for w in ummzdict['keyWords'])))
yrights = (" :rights_license:\n - https://creativecommons.org/licenses/by-nc-sa/4.0/ \n")
ydatecov = (" :date_coverage:\n - '%s'\n" % (ummzdict['scandate'])) #from xtek
ysubject = (" :subject_discipline:\n - 'Science'\n")
#ybib = (" :bibliographic_citation:\n - 'For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/%s'\n" % (ummzdict['yuuid'])) #build URL from iDigBio uuid
ydesclist = (" :description:\n - %s\n" % ('\n - '.join("'{0}'".format(w) for w in ummzdict['desc'])))
ylang = (" :language:\n - 'English'\n")
ycurnote = (" :curation_notes_admin:\n - 'UMMZ Batch Ingest'\n")
ydoi = (" :doi: 'mint_now'\n")
ycoll = (" :in_collections:\n - %s \n" % (collID))
yfilename = (" :filenames:\n%s" % (uf)) #pull from directory
yfiles = (" :files:\n%s" % (filepath)) #pull from directory
file_name = '%s/%s.yml' % (ummzpath, fname)
f = open(file_name, 'w') # open file in write mode
f.write(ytop)
f.write(ycoll)
f.write(yownauth)
f.write(ycreator)
f.write(ytitle)
#f.write(ydate)
f.write(yrefby)
f.write(ymethod)
f.write(ykw)
#for desc in ummzdict['desc']:
f.write(ydesclist)
f.write(yrights)
f.write(ydatecov)
f.write(ysubject)
#f.write(ybib)
f.write(ylang)
f.write(ycurnote)
f.write(ydoi)
f.write(yfilename)
f.write(yfiles)
f.close()
return
### Start here!!
#get folder name from the system to parse into query fields
#python3 ./scripts/nested_ummzgbif_functionv3.py /deepbluedata-globus/upload/UMMZ/Transfer-12-11-2020/ > ./scripts/nested_log.txt
topDir = [d for d in os.listdir(argv[1]) if os.path.isdir(os.path.join(argv[1], d))]
#print(type(topDir))
#os.chdir('./' + argv[1] + '/')
os.chdir(argv[1])
#print(os.getcwd())
for nestDir in topDir:
#print(nestDir)
#ummzpath = './' + nestDir +'/'
ummzpath = argv[1] + nestDir
print(ummzpath)
folderName = [dI for dI in os.listdir(ummzpath) if os.path.isdir(os.path.join(ummzpath,dI))]
print(folderName)
#error handling for folder names (ex: not including catalognumber)
msMetadata = dict()
msFilePath = ummzpath + '/' + "DBD_file_manifest.csv"
with open(msFilePath, mode='w', encoding='utf8', newline='') as csv_file:
fieldnames = ["file_name", "ms_id", "media_type", "ingestable", "parent_file_name", "parent_ms_id", "parent_identifier", "occurrence_id", "institution_code", "collection_code", "catalog_number", "scandate", "device_model", "device_manufacturer", "device_modality", "device_description", "device_organization_name", "x_spacing", "y_spacing", "z_spacing", "unit", "number_of_images_in_set", "processing_activity_type", "creator", "part", "license", "media_ct_series_type", "media_ct_number_of_images_in_set"]
writer = csv.DictWriter(csv_file, fieldnames=fieldnames)
writer.writeheader()
for fname in folderName:
#print(fname)
ummzdict = dict()
gbiflist = parsefolder(fname)
if gbiflist == None:
continue
else:
# Get data from GBIF
#morphosourcemd(ummzpath, fname)
ummzdict['ic'] = gbiflist[0]
ummzdict['cc'] = gbiflist[1]
ummzdict['cn'] = gbiflist[2]
#print(ummzdict['ic'], ummzdict['cc'], ummzdict['cn'])
getgbif(ummzdict['ic'], ummzdict['cc'], ummzdict['cn'])
#print(ummzdict)
if ummzdict['ic'] == "error":
continue
mgName, uf, filepath, rawZsplit, reconZsplit = getmediagroup(ummzpath, fname, ummzdict['ic'], ummzdict['cc'], ummzdict['cn'], ummzdict['yuuid']) # Get media groups zip media group folders
desc, msMetadata, roiName = xtekdata(mgName, rawZsplit, reconZsplit) # Get values from xtekVolume
#create file with MorphoSource metadata for each work
writer.writerows(msMetadata)
createyml(fname, uf, filepath, gbiflist[1], roiName)
csv_file.close()
#create a file manifest for MorphoSource of all datasets in batch