def updateTagGroup(self, tagGroupKey, name=None, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
if not tagGroup.writePermissions(self.user):
raise Errors.AUTHENTICATION
# update the name
if name:
tagGroup.name = name
metadata.limitFields(self.fields)
try:
tagGroup.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# add new tag to response for success
metadata.put('id', tagGroup.pk)
metadata.put('name', tagGroup.name)
metadata.put('user', tagGroup.user.username)
metadata.put('dateCreated', tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('lastModified', tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('imageId', tagGroup.picture.pk)
metadata.put('isPrivate', tagGroup.isPrivate)
return metadata
def getTagGroup(self, tagGroupKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tagGroup.readPermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
metadata.put('id', tagGroup.pk)
metadata.put('name', tagGroup.name)
metadata.put('user', tagGroup.user.username)
metadata.put('dateCreated',
tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('lastModified',
tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('imageId', tagGroup.picture.pk)
metadata.put('isPrivate', tagGroup.isPrivate)
return metadata
def deleteGeneLink(self, geneLinkKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
geneLink = GeneLink.objects.get(pk__exact=geneLinkKey)
else:
geneLink = geneLinkKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_GENE_LINK_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not geneLink.writePermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
metadata.put('id', geneLink.pk)
metadata.put('tagId', geneLink.tag.pk)
metadata.put(
'feature',
LimitDict(
self.fields, {
'uniqueName': geneLink.feature.uniquename,
'name': geneLink.feature.name,
'organismId': geneLink.feature.organism.organism_id
}))
try:
geneLink.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
return metadata
def deleteTagGroup(self, tagGroupKey, isKey=True):
metadata = WebServiceObject()
try:
if isKey:
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tagGroup.writePermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put("id", tagGroup.pk)
metadata.put("name", tagGroup.name)
metadata.put("dateCreated", tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put("lastModified", tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put("imageId", tagGroup.picture.pk)
try:
tagGroup.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
return metadata
def getTag(self, tagKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tag.readPermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
if metadata.allowsField('points'):
tagPoints = TagPoint.objects.filter(tag__exact=tag)
points = []
for tagPoint in tagPoints:
points.append({'x': tagPoint.pointX, 'y': tagPoint.pointY})
metadata.put('points', points)
metadata.put('id', tag.pk)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
return metadata
def deleteGeneLink(self, geneLinkKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
geneLink = GeneLink.objects.get(pk__exact=geneLinkKey)
else:
geneLink = geneLinkKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_GENE_LINK_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not geneLink.writePermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
metadata.put('id', geneLink.pk)
metadata.put('tagId', geneLink.tag.pk)
metadata.put('feature',
LimitDict(self.fields, {
'uniqueName' : geneLink.feature.uniquename,
'name' : geneLink.feature.name,
'organismId' : geneLink.feature.organism.organism_id
})
)
try:
geneLink.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
return metadata
def getTagGroup(self, tagGroupKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tagGroup.readPermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
metadata.put('id', tagGroup.pk)
metadata.put('name', tagGroup.name)
metadata.put('user', tagGroup.user.username)
metadata.put('dateCreated', tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('lastModified', tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('imageId', tagGroup.picture.pk)
metadata.put('isPrivate', tagGroup.isPrivate)
return metadata
def getGeneLink(self, geneLinkKey, isKey=True):
metadata = WebServiceObject()
try:
if isKey:
geneLink = GeneLink.objects.get(pk__exact=geneLinkKey)
else:
geneLink = geneLinkKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_GENE_LINK_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not geneLink.readPermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
metadata.put('id', geneLink.pk)
metadata.put('user', geneLink.user.username)
metadata.put('tagId', geneLink.tag.pk)
metadata.put('feature',
LimitDict(self.fields, {
'uniqueName' : geneLink.feature.uniquename,
'name': geneLink.feature.name,
'organismId' : geneLink.feature.organism.organism_id
})
)
return metadata
def createGeneLink(self, tagKey, name=None, uniqueName=None, organismId=None, isKey=True):
metadata = WebServiceObject()
try:
if isKey:
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
if not tag.writePermissions(self.user):
raise Errors.AUTHENTICATION
try:
feature = None
if name and organismId:
feature = Feature.objects.filter(name=name, organism=organismId)
if uniqueName:
if feature:
feature = feature & Feature.objects.filter(uniquename=uniqueName)
else:
feature = Feature.objects.filter(uniquename=uniqueName)
if not feature:
error = ""
if name and organismId:
error += "name: " + name + ", organismId: " + organismId
if uniqueName:
comma = ", " if error else ""
error += comma + "uniqueName: " + uniqueName
raise Errors.NO_MATCHING_FEATURE.setCustom(error)
geneLink = GeneLink(tag=tag, feature=feature)
geneLink.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
metadata.put('id', geneLink.pk)
metadata.put('user', geneLink.user.username)
metadata.put('tagId', geneLink.tag.pk)
metadata.put('feature',
LimitDict(self.fields, {
'uniqueName' : geneLink.feature.uniquename,
'name' : geneLink.feature.name,
'organismId' : geneLink.feature.organism.organism_id
})
)
return metadata
def createTag(self, tagGroupKey, points, name, color, isKey=True):
metadata = WebServiceObject()
tagPoints = []
try:
if isKey:
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
if not tagGroup.writePermissions(self.user):
raise Errors.AUTHENTICATION
# create the new tag points to put in the tag
try:
for counter, point in enumerate(points):
tagPoints.append(TagPoint(pointX=float(point['x']), pointY=float(point['y']) , rank=counter+1))
except (TypeError, KeyError, ValueError):
raise Errors.INVALID_SYNTAX.setCustom('points')
try:
# create new tag color
try:
if len(color) == 3:
tagColor = TagColor.objects.get_or_create(red=int(color[0]), green=int(color[1]), blue=int(color[2]))[0]
except (ValueError, TypeError):
raise Errors.INVALID_SYNTAX.setCustom('color')
# start saving the new tag now that it has passed all tests
tag = Tag(name=name, color=tagColor, group=tagGroup, user=self.user)
tag.save()
for tagPoint in tagPoints:
tagPoint.tag = tag
tagPoint.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put('id', tag.pk)
metadata.put('user', tag.user.username)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
metadata.put('points', points)
return metadata
def addQtl(self, qtl, pq_id, imageKey):
metadata = WebServiceObject()
print 'test 1'
# get picture instance with imageKey
try:
image = Picture.objects.get(pk__exact=imageKey)
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not self.user:
raise Errors.NO_USER_KEY
else:
userID = self.user
try:
# save the new note
if pq_id:
# update
pictureQtl = PictureQtl.objects.get(pk__exact=pq_id)
if pictureQtl:
pictureQtl.qtl = qtl
pictureQtl.picture = image
pictureQtl.user = userID
pictureQtl.save()
else:
# error
print 'Error: no PictureQtl.pk found!'
else:
# add new
pictureQtl = PictureQtl(qtl=qtl, picture=image, user=userID)
print 'test: trying store qtl.'
pictureQtl.save()
print 'test: qtl saved.'
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put('pq_id', pictureQtl.pk)
metadata.put('picture', pictureQtl.picture.pk)
metadata.put('qtl', pictureQtl.qtl)
metadata.put('user', pictureQtl.user.username)
metadata.put('dateCreated',
pictureQtl.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
return metadata
def deleteImage(self, imageKey, isKey=True):
organisms = []
metadata = WebServiceObject()
try:
if isKey:
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.writePermissions(self.user):
raise Errors.AUTHENTICATION
if not self.fields or 'organisms' in self.fields:
defTags = PictureDefinitionTag.objects.filter(picture__exact=image)
for tag in defTags:
try:
organisms.append({
'commonName': tag.organism.common_name,
'abbreviation': tag.organism.abbreviation,
'genus': tag.organism.genus,
'species': tag.organism.species,
'id': tag.organism.pk
})
except ObjectDoesNotExist:
None
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organisms)
metadata.put('description', image.description)
metadata.put('altText', image.altText)
metadata.put('uploadedBy', image.user.username)
metadata.put('uploadDate',
image.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', image.imageName.url)
metadata.put('thumbnail', image.thumbnail.url)
metadata.put('id', image.pk)
try:
image.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
return metadata
def deleteImage(self, imageKey, isKey=True):
organisms = []
metadata = WebServiceObject()
try:
if isKey:
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.writePermissions(self.user):
raise Errors.AUTHENTICATION
if not self.fields or 'organisms' in self.fields:
defTags = PictureDefinitionTag.objects.filter(picture__exact=image)
for tag in defTags:
try:
organisms.append({
'commonName' : tag.organism.common_name,
'abbreviation' : tag.organism.abbreviation,
'genus' : tag.organism.genus,
'species' : tag.organism.species,
'id' : tag.organism.pk
})
except ObjectDoesNotExist:
None
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organisms)
metadata.put('description', image.description)
metadata.put('altText', image.altText)
metadata.put('uploadedBy', image.user.username)
metadata.put('uploadDate', image.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', image.imageName.url)
metadata.put('thumbnail', image.thumbnail.url)
metadata.put('id', image.pk)
try:
image.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
return metadata
def addNote(self, notes, pn_id, imageKey):
metadata = WebServiceObject()
# get picture instance with imageKey
try:
image = Picture.objects.get(pk__exact=imageKey)
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not self.user:
raise Errors.NO_USER_KEY
else:
userID = self.user
try:
# save the new note
if pn_id:
# update
pictureNotes = PictureNotes.objects.get(pk__exact=pn_id)
if pictureNotes:
pictureNotes.notes = notes
pictureNotes.picture = image
pictureNotes.user = userID
pictureNotes.save()
else:
# error
print 'Error: no picture_notes.pk found!'
else:
# add new
pictureNotes = PictureNotes(notes=notes, picture=image, user=userID)
pictureNotes.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put('pn_id', pictureNotes.pk)
metadata.put('picture', pictureNotes.picture.pk)
metadata.put('notes', pictureNotes.notes)
metadata.put('user', pictureNotes.user.username)
metadata.put('dateCreated', pictureNotes.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
return metadata
def getImageMetadata(self, imageKey, isKey=True):
organisms = []
metadata = WebServiceObject()
try:
if (isKey):
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.readPermissions(self.user):
raise Errors.AUTHENTICATION
if not self.fields or 'organisms' in self.fields:
defTags = PictureDefinitionTag.objects.filter(picture__exact=image)
for tag in defTags:
organisms.append({
'commonName': tag.organism.common_name,
'abbreviation': tag.organism.abbreviation,
'genus': tag.organism.genus,
'species': tag.organism.species,
'id': tag.organism.pk
})
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organisms)
metadata.put('description', image.description)
metadata.put('altText', image.altText)
metadata.put('uploadedBy', image.user.username)
metadata.put('uploadDate',
image.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', image.imageName.url)
metadata.put('thumbnail', image.thumbnail.url)
metadata.put('id', image.pk)
# add to recently viewed images if there is a user
if self.user and self.user.is_authenticated():
RecentlyViewedPicture.objects.get_or_create(
user=self.user, picture=image)[0].save()
return metadata
def getImageMetadata(self, imageKey, isKey=True):
organisms = []
metadata = WebServiceObject()
try:
if (isKey):
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.readPermissions(self.user):
raise Errors.AUTHENTICATION
if not self.fields or 'organisms' in self.fields:
defTags = PictureDefinitionTag.objects.filter(picture__exact=image)
for tag in defTags:
organisms.append({
'commonName' : tag.organism.common_name,
'abbreviation' : tag.organism.abbreviation,
'genus' : tag.organism.genus,
'species' : tag.organism.species,
'id' : tag.organism.pk
})
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organisms)
metadata.put('description', image.description)
metadata.put('altText', image.altText)
metadata.put('uploadedBy', image.user.username)
metadata.put('uploadDate', image.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', image.imageName.url)
metadata.put('thumbnail', image.thumbnail.url)
metadata.put('id', image.pk)
# add to recently viewed images if there is a user
if self.user and self.user.is_authenticated():
RecentlyViewedPicture.objects.get_or_create(user=self.user, picture=image)[0].save()
return metadata
def getQtl(self, imageKey):
metadata = WebServiceObject()
try:
pictureQtl = PictureQtl.objects.filter(
picture__exact=imageKey).order_by('-dateCreated')[:1].get()
except (ObjectDoesNotExist, ValueError):
return metadata
metadata.limitFields(self.fields)
metadata.put('pq_id', pictureQtl.pk)
metadata.put('picture', pictureQtl.picture.pk)
metadata.put('qtl', pictureQtl.qtl)
metadata.put('user', pictureQtl.user.username)
metadata.put('dateCreated',
pictureQtl.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
return metadata
def getNote(self, imageKey):
metadata = WebServiceObject()
try:
pictureNotes = PictureNotes.objects.filter(
picture__exact=imageKey).order_by('-dateCreated')[:1].get()
except (ObjectDoesNotExist, ValueError):
return metadata
#except Exception:
# raise Errors.INTERNAL_ERROR
metadata.limitFields(self.fields)
metadata.put('pn_id', pictureNotes.pk)
metadata.put('picture', pictureNotes.picture.pk)
metadata.put('notes', pictureNotes.notes)
metadata.put('user', pictureNotes.user.username)
metadata.put('dateCreated',
pictureNotes.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
return metadata
def deleteTag(self, tagKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_GENE_LINK_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tag.writePermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
if metadata.allowsField('points'):
tagPoints = TagPoint.objects.filter(tag__exact=tag)
points = []
for tagPoint in tagPoints:
points.append({
'x' : tagPoint.pointX,
'y' : tagPoint.pointY
})
metadata.put('points', points)
metadata.put('id', tag.pk)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
try:
tag.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
def deleteTag(self, tagKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_GENE_LINK_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tag.writePermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
if metadata.allowsField('points'):
tagPoints = TagPoint.objects.filter(tag__exact=tag)
points = []
for tagPoint in tagPoints:
points.append({
'x' : tagPoint.pointX,
'y' : tagPoint.pointY
})
metadata.put('points', points)
metadata.put('id', tag.pk)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
try:
tag.delete()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
def getTag(self, tagKey, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_KEY
except Exception:
raise Errors.INTERNAL_ERROR
if not tag.readPermissions(self.user):
raise Errors.AUTHENTICATION
metadata.limitFields(self.fields)
if metadata.allowsField('points'):
tagPoints = TagPoint.objects.filter(tag__exact=tag)
points = []
for tagPoint in tagPoints:
points.append({
'x' : tagPoint.pointX,
'y' : tagPoint.pointY
})
metadata.put('points', points)
metadata.put('id', tag.pk)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
return metadata
def createTagGroup(self, imageKey, name, isKey=True):
metadata = WebServiceObject()
try:
if isKey:
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.writePermissions(self.user):
raise Errors.AUTHENTICATION
# start saving the new tag now that it has passed all tests
tagGroup = TagGroup(name=name, picture=image, user=self.user)
try:
tagGroup.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put('id', tagGroup.pk)
metadata.put('name', tagGroup.name)
metadata.put('user', tagGroup.user.username)
metadata.put('dateCreated',
tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('lastModified',
tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('imageId', tagGroup.picture.pk)
metadata.put('isPrivate', tagGroup.isPrivate)
return metadata
def createTagGroup(self, imageKey, name, isKey=True):
metadata = WebServiceObject()
try:
if isKey:
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.writePermissions(self.user):
raise Errors.AUTHENTICATION
# start saving the new tag now that it has passed all tests
tagGroup = TagGroup(name=name, picture=image, user=self.user)
try:
tagGroup.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put('id', tagGroup.pk)
metadata.put('name', tagGroup.name)
metadata.put('user', tagGroup.user.username)
metadata.put('dateCreated', tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('lastModified', tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('imageId', tagGroup.picture.pk)
metadata.put('isPrivate', tagGroup.isPrivate)
return metadata
def updateTagGroup(self, tagGroupKey, name=None, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
if not tagGroup.writePermissions(self.user):
raise Errors.AUTHENTICATION
# update the name
if name:
tagGroup.name = name
metadata.limitFields(self.fields)
try:
tagGroup.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# add new tag to response for success
metadata.put('id', tagGroup.pk)
metadata.put('name', tagGroup.name)
metadata.put('user', tagGroup.user.username)
metadata.put('dateCreated',
tagGroup.dateCreated.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('lastModified',
tagGroup.lastModified.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('imageId', tagGroup.picture.pk)
metadata.put('isPrivate', tagGroup.isPrivate)
return metadata
def createImageMetadata(self,
image,
description,
altText,
organisms,
isKey=True):
organismsArr = []
metadata = WebServiceObject()
if not (self.user and self.user.is_authenticated()):
raise Errors.AUTHENTICATION
filetype = imghdr.what(image.file)
if not filetype or filetype not in set(
['gif', 'tiff', 'jpeg', 'bmp', 'png']):
raise Errors.INVALID_IMAGE_TYPE
wrappedFile, thumbnailFile, filename, thumbnailName = handleUpload(
image)
if self.user.is_staff:
upload = Picture(user=self.user,
isPrivate=False,
imageName=wrappedFile.file,
thumbnail=thumbnailFile.file)
else:
upload = Picture(user=self.user,
isPrivate=True,
imageName=wrappedFile.file,
thumbnail=thumbnailFile.file)
try:
upload.save()
except DatabaseError as e:
transaction.rollback()
os.remove(filename)
os.remove(thumbnailName)
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
os.remove(filename)
os.remove(thumbnailName)
# now that image has been properly uploaded add the metadata to it
organismField = not self.fields or 'organisms' in self.fields
if organisms:
newOrganisms = Organism.objects.filter(organism_id__in=organisms)
newDefTags = []
for newOrg in newOrganisms:
newDefTags.append(
PictureDefinitionTag(picture=upload, organism=newOrg))
try:
for newTag in newDefTags:
newTag.save()
if organismField:
organismsArr.append({
'commonName': newTag.organism.common_name,
'abbreviation': newTag.organism.abbreviation,
'genus': newTag.organism.genus,
'species': newTag.organism.species,
'id': newTag.organism.pk
})
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
if description:
upload.description = description
try:
upload.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
if altText:
upload.altText = altText
try:
upload.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organismsArr)
metadata.put('description', upload.description)
metadata.put('altText', upload.altText)
metadata.put('uploadedBy', upload.user.username)
metadata.put('uploadDate',
upload.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', upload.imageName.url)
metadata.put('thumbnail', upload.thumbnail.url)
metadata.put('id', upload.pk)
return metadata
def createTag(self, tagGroupKey, points, name, color, isKey=True):
metadata = WebServiceObject()
tagPoints = []
try:
if isKey:
tagGroup = TagGroup.objects.get(pk__exact=tagGroupKey)
else:
tagGroup = tagGroupKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
if not tagGroup.writePermissions(self.user):
raise Errors.AUTHENTICATION
# create the new tag points to put in the tag
try:
for counter, point in enumerate(points):
tagPoints.append(
TagPoint(pointX=float(point['x']),
pointY=float(point['y']),
rank=counter + 1))
except (TypeError, KeyError, ValueError):
raise Errors.INVALID_SYNTAX.setCustom('points')
try:
# create new tag color
try:
if len(color) == 3:
tagColor = TagColor.objects.get_or_create(
red=int(color[0]),
green=int(color[1]),
blue=int(color[2]))[0]
except (ValueError, TypeError):
raise Errors.INVALID_SYNTAX.setCustom('color')
# start saving the new tag now that it has passed all tests
tag = Tag(name=name,
color=tagColor,
group=tagGroup,
user=self.user)
tag.save()
for tagPoint in tagPoints:
tagPoint.tag = tag
tagPoint.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
# add new tag to response for success
metadata.put('id', tag.pk)
metadata.put('user', tag.user.username)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
metadata.put('points', points)
return metadata
def updateTag(self,
tagKey,
points=None,
name=None,
color=None,
isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_KEY
if not tag.writePermissions(self.user):
raise Errors.AUTHENTICATION
# update the description
if name:
tag.name = name
# update the color (ignores bad syntax)
try:
if color and len(color) == 3:
tagColor = TagColor.objects.get_or_create(red=color[0],
green=color[1],
blue=color[2])[0]
tag.color = tagColor
except (ValueError, TypeError):
raise Errors.INVALID_SYNTAX.setCustom('color')
oldTagPoints = list(TagPoint.objects.filter(tag__exact=tag))
# updates the tag points for this tag
if points:
# first we delete the old tag points (they aren't helpful anymore)
# TODO: add Trash database for restoring accidental changes
try:
newTagPointModels = []
# Save the new tag points
# create the new tag points to put in the tag
for counter, point in enumerate(points):
newTagPointModels.append(
TagPoint(pointX=float(point['x']),
pointY=float(point['y']),
rank=counter + 1))
except (TypeError, KeyError, ValueError):
raise Errors.INVALID_SYNTAX.setCustom('points')
metadata.limitFields(self.fields)
try:
tag.save()
if points:
for newTagPoint in newTagPointModels:
newTagPoint.tag = tag
newTagPoint.save()
for tagPoint in oldTagPoints:
tagPoint.delete()
metadata.put('points', points)
else:
tagPoints = []
for tagPoint in oldTagPoints:
tagPoints.append({
'x': tagPoint.pointX,
'y': tagPoint.pointY
})
metadata.put('points', tagPoints)
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# add new tag to response for success
metadata.put('id', tag.pk)
metadata.put('user', tag.user)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
return metadata
def editImageMetadata(self, imageKey, description, altText, organisms, isKey=True):
organismsArr = []
metadata = WebServiceObject()
try:
if isKey:
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
if not image.writePermissions(self.user):
raise Errors.AUTHENTICATION
defTags = PictureDefinitionTag.objects.filter(picture__exact=image)
organismField = not self.fields or 'organisms' in self.fields
if organisms:
newOrganisms = Organism.objects.filter(organism_id__in=organisms)
newDefTags = []
for newOrg in newOrganisms:
newDefTags.append(PictureDefinitionTag(picture=image, organism=newOrg))
try:
defTags.delete()
for newTag in newDefTags:
newTag.save()
if organismField:
organismsArr.append({
'commonName' : newTag.organism.common_name,
'abbreviation' : newTag.organism.abbreviation,
'genus' : newTag.organism.genus,
'species' : newTag.organism.species,
'id' : newTag.organism.pk
})
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
if description:
image.description = description
try:
image.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
if altText:
image.altText = altText
try:
image.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
metadata.limitFields(self.fields)
if not organisms and organismField:
for defTag in defTags:
organisms.append({
'commonName' : defTag.organism.common_name,
'abbreviation' : defTag.organism.abbreviation,
'genus' : defTag.organism.genus,
'species' : defTag.organism.species,
'id' : defTag.organism.pk
})
# put in the information we care about
metadata.put('organisms', organismsArr)
metadata.put('description', image.description)
metadata.put('altText', image.altText)
metadata.put('uploadedBy', image.user.username)
metadata.put('uploadDate', image.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', image.imageName.url)
metadata.put('thumbnail', image.thumbnail.url)
metadata.put('id', image.pk)
return metadata
def createImageMetadata(self, image, description, altText, organisms, isKey=True):
organismsArr = []
metadata = WebServiceObject()
if not (self.user and self.user.is_authenticated()):
raise Errors.AUTHENTICATION
filetype = imghdr.what(image.file)
if not filetype or filetype not in set(['gif', 'tiff', 'jpeg', 'bmp', 'png']):
raise Errors.INVALID_IMAGE_TYPE
wrappedFile, thumbnailFile, filename, thumbnailName = handleUpload(image)
if self.user.is_staff:
upload = Picture(user=self.user, isPrivate=False, imageName=wrappedFile.file, thumbnail=thumbnailFile.file)
else:
upload = Picture(user=self.user, isPrivate=True, imageName=wrappedFile.file, thumbnail=thumbnailFile.file)
try:
upload.save()
except DatabaseError as e:
transaction.rollback()
os.remove(filename)
os.remove(thumbnailName)
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
os.remove(filename)
os.remove(thumbnailName)
# now that image has been properly uploaded add the metadata to it
organismField = not self.fields or 'organisms' in self.fields
if organisms:
newOrganisms = Organism.objects.filter(organism_id__in=organisms)
newDefTags = []
for newOrg in newOrganisms:
newDefTags.append(PictureDefinitionTag(picture=upload, organism=newOrg))
try:
for newTag in newDefTags:
newTag.save()
if organismField:
organismsArr.append({
'commonName' : newTag.organism.common_name,
'abbreviation' : newTag.organism.abbreviation,
'genus' : newTag.organism.genus,
'species' : newTag.organism.species,
'id' : newTag.organism.pk
})
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
if description:
upload.description = description
try:
upload.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
if altText:
upload.altText = altText
try:
upload.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organismsArr)
metadata.put('description', upload.description)
metadata.put('altText', upload.altText)
metadata.put('uploadedBy', upload.user.username)
metadata.put('uploadDate', upload.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', upload.imageName.url)
metadata.put('thumbnail', upload.thumbnail.url)
metadata.put('id', upload.pk)
return metadata
def createGeneLink(self, tagKey, name=None, allele=None, organismId=None, isKey=True):
metadata = WebServiceObject()
try:
if isKey:
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_GROUP_KEY
if not tag.writePermissions(self.user):
raise Errors.AUTHENTICATION
try:
feature = None
if name and organismId:
feature = Feature.objects.filter(name=name, organism=organismId)
if not feature:
error = "Could not find a feature with the parameters: "
if name and organismId:
error += "name: " + name + ", organismId: " + organismId
raise Errors.NO_MATCHING_FEATURE.setCustom(error)
elif len(feature) > 1:
error = "Multiple matches for parameters: "
if name and organismId:
error += "name: " + name + ", organismId: " + organismId
error += "\n\n Responses: \n\n"
for f in feature:
error += "uniquename: " + f.uniquename + ", name: " + f.name + ", organism: " + f.organism.common_name + "\n\n"
raise Errors.NO_MATCHING_FEATURE.setCustom(error)
if allele:
vID = None
vID = Variation.objects.using('mgdb').filter(name__exact=allele)
if not vID:
errorAllele = Errors.NO_MATCHING_ALLELE.setCustom(allele)
raise errorAllele
geneLink = GeneLink(tag=tag, feature=feature[0], user=self.user, allele=allele)
geneLink.save()
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# limit metadata return
metadata.limitFields(self.fields)
metadata.put('id', geneLink.pk)
metadata.put('user', geneLink.user.username)
metadata.put('tagId', geneLink.tag.pk)
metadata.put('feature',
LimitDict(self.fields, {
'uniqueName' : geneLink.feature.uniquename,
'name' : geneLink.feature.name,
'allele': geneLink.allele,
'organismId' : geneLink.feature.organism.organism_id
})
)
return metadata
def getImageMetadata(self, imageKey, isKey=True):
# TODO: getImageMetadata() should be refactorized because it is used for all image loading parts
# including image list even thumbnail image. It potentially has unnecessary database queries.
organisms = []
geneIDs = []
metadata = WebServiceObject()
try:
if (isKey):
image = Picture.objects.get(pk__exact=imageKey)
else:
image = imageKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_IMAGE_KEY
# Get gene information
geneSymbol = None
geneName = None
if image is not None:
# Gene ID
pictureGIDs = PictureGeneID.objects.filter(picture__exact=image)
for picGID in pictureGIDs:
geneIDs.append({
'geneID': picGID.gene_id,
'version': picGID.version
})
pictureMbs = PictureMgdb.objects.filter(picture__exact=image)
for pMb in pictureMbs:
geneSymbol = pMb.locus_name
geneName = pMb.locus_full_name
break
if not image.readPermissions(self.user):
raise Errors.AUTHENTICATION
if not self.fields or 'organisms' in self.fields:
defTags = PictureDefinitionTag.objects.filter(picture__exact=image)
for tag in defTags:
organisms.append({
'commonName': tag.organism.common_name,
'abbreviation': tag.organism.abbreviation,
'genus': tag.organism.genus,
'species': tag.organism.species,
'id': tag.organism.pk
})
# Get all imageID for imageName
images = Picture.objects.filter(imageName__exact=image.imageName)
# Get Image Notes Information
notes_id = ''
notes = ''
notesBy = ''
pictureNotesAPI = NotesAPI(self.user)
for imageID in images:
pictureNotes = pictureNotesAPI.getNote(imageID).getObject()
if pictureNotes:
notes_id = pictureNotes['pn_id']
notes = pictureNotes['notes']
notesBy = pictureNotes['user']
break
# Get QTL information
qtls_id = ''
qtl = ''
pictureQtlAPI = QtlAPI(self.user)
for imageID in images:
pictureQtl = pictureQtlAPI.getQtl(imageID).getObject()
if pictureQtl:
qtls_id = pictureQtl['pq_id']
qtl = pictureQtl['qtl']
break
metadata.limitFields(self.fields)
# put in the information we care about
metadata.put('organisms', organisms)
metadata.put('description', image.description)
metadata.put('altText', image.altText)
metadata.put('uploadedBy', image.user.username)
metadata.put('uploadDate',
image.uploadDate.strftime("%Y-%m-%d %H:%M:%S"))
metadata.put('url', image.imageName.url)
metadata.put('thumbnail', image.thumbnail.url)
metadata.put('id', image.pk)
metadata.put('geneIDs', geneIDs)
metadata.put('geneSymbol', geneSymbol)
metadata.put('geneName', geneName)
metadata.put('notes_id', notes_id)
metadata.put('notes', notes)
metadata.put('notesBy', notesBy)
metadata.put('qtls_id', qtls_id)
metadata.put('qtl', qtl)
return metadata
def updateTag(self, tagKey, points=None, name=None, color=None, isKey=True):
metadata = WebServiceObject()
try:
if (isKey):
tag = Tag.objects.get(pk__exact=tagKey)
else:
tag = tagKey
except (ObjectDoesNotExist, ValueError):
raise Errors.INVALID_TAG_KEY
if not tag.writePermissions(self.user):
raise Errors.AUTHENTICATION
# update the description
if name:
tag.name = name
# update the color (ignores bad syntax)
try:
if color and len(color) == 3:
tagColor = TagColor.objects.get_or_create(red=color[0], green=color[1], blue=color[2])[0]
tag.color = tagColor
except (ValueError, TypeError):
raise Errors.INVALID_SYNTAX.setCustom('color')
oldTagPoints = list(TagPoint.objects.filter(tag__exact=tag))
# updates the tag points for this tag
if points:
# first we delete the old tag points (they aren't helpful anymore)
# TODO: add Trash database for restoring accidental changes
try:
newTagPointModels = []
# Save the new tag points
# create the new tag points to put in the tag
for counter, point in enumerate(points):
newTagPointModels.append(TagPoint(pointX=float(point['x']), pointY=float(point['y']) , rank=counter+1))
except (TypeError, KeyError, ValueError):
raise Errors.INVALID_SYNTAX.setCustom('points')
metadata.limitFields(self.fields)
try:
tag.save()
if points:
for newTagPoint in newTagPointModels:
newTagPoint.tag = tag
newTagPoint.save()
for tagPoint in oldTagPoints:
tagPoint.delete()
metadata.put('points', points)
else:
tagPoints = []
for tagPoint in oldTagPoints:
tagPoints.append({
'x' : tagPoint.pointX,
'y' : tagPoint.pointY
})
metadata.put('points', tagPoints)
except DatabaseError as e:
transaction.rollback()
raise Errors.INTEGRITY_ERROR.setCustom(str(e))
# add new tag to response for success
metadata.put('id', tag.pk)
metadata.put('user', tag.user)
metadata.put('color', [tag.color.red, tag.color.green, tag.color.blue])
metadata.put('name', tag.name)
return metadata
