diff webapollo.py @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/webapollo.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,745 @@
+import requests
+import json
+import collections
+from BCBio import GFF
+import StringIO
+import logging
+logging.getLogger("requests").setLevel(logging.CRITICAL)
+log = logging.getLogger()
+
+
+
+class WebApolloInstance(object):
+
+    def __init__(self, url, username, password):
+        self.apollo_url = url
+        self.username = username
+        self.password = password
+
+        self.annotations = AnnotationsClient(self)
+        self.groups = GroupsClient(self)
+        self.io = IOClient(self)
+        self.organisms = OrganismsClient(self)
+        self.users = UsersClient(self)
+        self.metrics = MetricsClient(self)
+        self.bio = RemoteRecord(self)
+
+    def __str__(self):
+        return '<WebApolloInstance at %s>' % self.apollo_url
+
+
+class GroupObj(object):
+    def __init__(self, **kwargs):
+        self.name = kwargs['name']
+
+        if 'id' in kwargs:
+            self.groupId = kwargs['id']
+
+
+class UserObj(object):
+    ROLE_USER = 'USER'
+    ROLE_ADMIN = 'ADMIN'
+
+    def __init__(self, **kwargs):
+        # Generally expect 'userId', 'firstName', 'lastName', 'username' (email)
+        for attr in kwargs.keys():
+            setattr(self, attr, kwargs[attr])
+
+        if 'groups' in kwargs:
+            groups = []
+            for groupData in kwargs['groups']:
+                groups.append(GroupObj(**groupData))
+            self.groups = groups
+
+        self.__props = kwargs.keys()
+
+
+    def isAdmin(self):
+        if hasattr(self, 'role'):
+            return self.role == self.ROLE_ADMIN
+        return False
+
+    def refresh(self, wa):
+        # This method requires some sleeping usually.
+        newU = wa.users.loadUser(self).toDict()
+        for prop in newU:
+            setattr(self, prop, newU[prop])
+
+    def toDict(self):
+        data = {}
+        for prop in self.__props:
+            data[prop] = getattr(self, prop)
+        return data
+
+    def __str__(self):
+        return '<User %s: %s %s <%s>>' % (self.userId, self.firstName,
+                                          self.lastName, self.username)
+
+
+class Client(object):
+
+    def __init__(self, webapolloinstance, **requestArgs):
+        self._wa = webapolloinstance
+
+        self.__verify = requestArgs.get('verify', True)
+        self._requestArgs = requestArgs
+
+        if 'verify' in self._requestArgs:
+            del self._requestArgs['verify']
+
+    def request(self, clientMethod, data, post_params={}, isJson=True):
+        url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod
+
+        headers = {
+            'Content-Type': 'application/json'
+        }
+
+        data.update({
+            'username': self._wa.username,
+            'password': self._wa.password,
+        })
+
+        r = requests.post(url, data=json.dumps(data), headers=headers,
+                          verify=self.__verify, params=post_params, **self._requestArgs)
+
+        if r.status_code == 200:
+            if isJson:
+                d = r.json()
+                if 'username' in d:
+                    del d['username']
+                if 'password' in d:
+                    del d['password']
+                return d
+            else:
+                return r.text
+
+        # @see self.body for HTTP response body
+        raise Exception("Unexpected response from apollo %s: %s" %
+                        (r.status_code, r.text))
+
+    def get(self, clientMethod, get_params):
+        url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod
+        headers = {}
+
+        r = requests.get(url, headers=headers, verify=self.__verify,
+                         params=get_params, **self._requestArgs)
+        if r.status_code == 200:
+            d = r.json()
+            if 'username' in d:
+                del d['username']
+            if 'password' in d:
+                del d['password']
+            return d
+        # @see self.body for HTTP response body
+        raise Exception("Unexpected response from apollo %s: %s" %
+                        (r.status_code, r.text))
+
+
+class MetricsClient(Client):
+    CLIENT_BASE = '/metrics/'
+
+    def getServerMetrics(self):
+        return self.get('metrics', {})
+
+
+class AnnotationsClient(Client):
+    CLIENT_BASE = '/annotationEditor/'
+
+    def _update_data(self, data):
+        if not hasattr(self, '_extra_data'): raise Exception("Please call setSequence first")
+        data.update(self._extra_data)
+        return data
+
+    def setSequence(self, sequence, organism):
+        self._extra_data = {
+            'sequence': sequence,
+            'organism': organism,
+        }
+
+    def setDescription(self, featureDescriptions):
+        data = {
+            'features': featureDescriptions,
+        }
+        data = self._update_data(data)
+        return self.request('setDescription', data)
+
+    def setName(self, uniquename, name):
+        # TODO
+        data = {
+            'features': [
+                {
+                    'uniquename': uniquename,
+                    'name': name,
+                }
+            ],
+        }
+        data = self._update_data(data)
+        return self.request('setName', data)
+
+    def setNames(self, features):
+        # TODO
+        data = {
+            'features': features,
+        }
+        data = self._update_data(data)
+        return self.request('setName', data)
+
+    def setStatus(self, statuses):
+        # TODO
+        data = {
+            'features': statuses,
+        }
+        data = self._update_data(data)
+        return self.request('setStatus', data)
+
+    def setSymbol(self, symbols):
+        data = {
+            'features': symbols,
+        }
+        data.update(self._extra_data)
+        return self.request('setSymbol', data)
+
+    def getComments(self, features):
+        data = {
+            'features': features,
+        }
+        data = self._update_data(data)
+        return self.request('getComments', data)
+
+    def addAttribute(self, features):
+        data = {
+            'features': features,
+        }
+        data = self._update_data(data)
+        return self.request('addAttribute', data)
+
+    def getFeatures(self):
+        data = self._update_data({})
+        return self.request('getFeatures', data)
+
+    def getSequence(self, uniquename):
+        data = {
+            'features': [
+                {'uniquename': uniquename}
+            ]
+        }
+        data = self._update_data(data)
+        return self.request('getSequence', data)
+
+    def addFeature(self, feature, trustme=False):
+        if not trustme:
+            raise NotImplementedError("Waiting on better docs from project. If you know what you are doing, pass trustme=True to this function.")
+
+        data = {}
+        data.update(feature)
+        data = self._update_data(data)
+        return self.request('addFeature', data)
+
+    def addTranscript(self, transcript, trustme=False):
+        if not trustme:
+            raise NotImplementedError("Waiting on better docs from project. If you know what you are doing, pass trustme=True to this function.")
+
+        data = {}
+        data.update(transcript)
+        data = self._update_data(data)
+        return self.request('addTranscript', data)
+
+    # addExon, add/delete/updateComments, addTranscript skipped due to docs
+
+    def duplicateTranscript(self, transcriptId):
+        data = {
+            'features': [{'uniquename': transcriptId}]
+        }
+
+        data = self._update_data(data)
+        return self.request('duplicateTranscript', data)
+
+    def setTranslationStart(self, uniquename, start):
+        data = {
+            'features': [{
+                'uniquename': uniquename,
+                'location': {
+                    'fmin': start
+                }
+            }]
+        }
+        data = self._update_data(data)
+        return self.request('setTranslationStart', data)
+
+    def setTranslationEnd(self, uniquename, end):
+        data = {
+            'features': [{
+                'uniquename': uniquename,
+                'location': {
+                    'fmax': end
+                }
+            }]
+        }
+        data = self._update_data(data)
+        return self.request('setTranslationEnd', data)
+
+    def setLongestOrf(self, uniquename):
+        data = {
+            'features': [{
+                'uniquename': uniquename,
+            }]
+        }
+        data = self._update_data(data)
+        return self.request('setLongestOrf', data)
+
+    def setBoundaries(self, uniquename, start, end):
+        data = {
+            'features': [{
+                'uniquename': uniquename,
+                'location': {
+                    'fmin': start,
+                    'fmax': end,
+                }
+            }]
+        }
+        data = self._update_data(data)
+        return self.request('setBoundaries', data)
+
+    def getSequenceAlterations(self):
+        data = {
+        }
+        data = self._update_data(data)
+        return self.request('getSequenceAlterations', data)
+
+    def setReadthroughStopCodon(self, uniquename):
+        data = {
+            'features': [{
+                'uniquename': uniquename,
+            }]
+        }
+        data = self._update_data(data)
+        return self.request('setReadthroughStopCodon', data)
+
+    def deleteSequenceAlteration(self, uniquename):
+        data = {
+            'features': [{
+                'uniquename': uniquename,
+            }]
+        }
+        data = self._update_data(data)
+        return self.request('deleteSequenceAlteration', data)
+
+    def flipStrand(self, uniquenames):
+        data = {
+            'features': [
+                {'uniquename': x} for x in uniquenames
+            ]
+        }
+        data = self._update_data(data)
+        return self.request('flipStrand', data)
+
+    def mergeExons(self, exonA, exonB):
+        data = {
+            'features': [
+                {'uniquename': exonA},
+                {'uniquename': exonB},
+            ]
+        }
+        data = self._update_data(data)
+        return self.request('mergeExons', data)
+
+    # def splitExon(): pass
+
+    def deleteFeatures(self, uniquenames):
+        assert isinstance(uniquenames, collections.Iterable)
+        data = {
+            'features': [
+                {'uniquename': x} for x in uniquenames
+            ]
+        }
+        data = self._update_data(data)
+        return self.request('deleteFeature', data)
+
+    # def deleteExon(): pass
+
+    # def makeIntron(self, uniquename, ): pass
+
+    def getSequenceSearchTools(self):
+        return self.get('getSequenceSearchTools', {})
+
+    def getCannedComments(self):
+        return self.get('getCannedComments', {})
+
+    def searchSequence(self, searchTool, sequence, database):
+        data = {
+            'key': searchTool,
+            'residues': sequence,
+            'database_id': database,
+        }
+        return self.request('searchSequences', data)
+
+    def getGff3(self, uniquenames):
+        assert isinstance(uniquenames, collections.Iterable)
+        data = {
+            'features': [
+                {'uniquename': x} for x in uniquenames
+            ]
+        }
+        data = self._update_data(data)
+        return self.request('getGff3', data, isJson=False)
+
+
+class GroupsClient(Client):
+    CLIENT_BASE = '/group/'
+
+    def createGroup(self, name):
+        data = {'name': name}
+        return self.request('createGroup', data)
+
+    def getOrganismPermissionsForGroup(self, group):
+        data = {
+            'id': group.groupId,
+            'name': group.name,
+        }
+        return self.request('getOrganismPermissionsForGroup', data)
+
+    def loadGroups(self, group=None):
+        data ={}
+        if group is not None:
+            data['groupId'] = group.groupId
+
+        return self.request('loadGroups', data)
+
+    def deleteGroup(self, group):
+        data = {
+            'id': group.groupId,
+            'name': group.name,
+        }
+        return self.request('deleteGroup', data)
+
+    def updateGroup(self, group, newName):
+        # TODO: Sure would be nice if modifying ``group.name`` would invoke
+        # this?
+        data = {
+            'id': group.groupId,
+            'name': newName,
+        }
+        return self.request('updateGroup', data)
+
+    def updateOrganismPermission(self, group, organismName,
+                                 administrate=False, write=False, read=False,
+                                 export=False):
+        data = {
+            'groupId': group.groupId,
+            'name': organismName,
+            'administrate': administrate,
+            'write': write,
+            'export': export,
+            'read': read,
+        }
+        return self.request('updateOrganismPermission', data)
+
+    def updateMembership(self, group, users):
+        data = {
+            'groupId': group.groupId,
+            'user': [user.email for user in users]
+        }
+        return self.request('updateMembership', data)
+
+
+class IOClient(Client):
+    CLIENT_BASE = '/IOService/'
+
+    def write(self, exportType='FASTA', seqType='peptide',
+              exportFormat='text', sequences=None, organism=None,
+              output='text', exportAllSequences=False,
+              exportGff3Fasta=False):
+        if exportType not in ('FASTA', 'GFF3'):
+            raise Exception("exportType must be one of FASTA, GFF3")
+
+        if seqType not in ('peptide', 'cds', 'cdna', 'genomic'):
+            raise Exception("seqType must be one of peptide, cds, dna, genomic")
+
+        if exportFormat not in ('gzip', 'text'):
+            raise Exception("exportFormat must be one of gzip, text")
+
+        if output not in ('file', 'text'):
+            raise Exception("output must be one of file, text")
+
+        data = {
+            'type': exportType,
+            'seqType': seqType,
+            'format': exportFormat,
+            'sequences': sequences,
+            'organism': organism,
+            'output': output,
+            'exportAllSequences': exportAllSequences,
+            'exportGff3Fasta': exportGff3Fasta,
+        }
+
+        return self.request('write', data, isJson=output == 'file')
+
+    def download(self, uuid, outputFormat='gzip'):
+
+        if outputFormat.lower() not in ('gzip', 'text'):
+            raise Exception("outputFormat must be one of file, text")
+
+        data = {
+            'format': outputFormat,
+            'uuid': uuid,
+        }
+        return self.request('write', data)
+
+
+class OrganismsClient(Client):
+    CLIENT_BASE = '/organism/'
+
+    def addOrganism(self, commonName, directory, blatdb=None, species=None,
+                    genus=None, public=False):
+        data = {
+            'commonName': commonName,
+            'directory': directory,
+            'publicMode': public,
+        }
+
+        if blatdb is not None:
+            data['blatdb'] = blatdb
+        if genus is not None:
+            data['genus'] = genus
+        if species is not None:
+            data['species'] = species
+
+        return self.request('addOrganism', data)
+
+    def findAllOrganisms(self):
+        return self.request('findAllOrganisms', {})
+
+    def findOrganismByCn(self, cn):
+        orgs = self.findAllOrganisms()
+        orgs = [x for x in orgs if x['commonName'] == cn]
+        if len(orgs) == 0:
+            raise Exception("Unknown common name")
+        else:
+            return orgs[0]
+
+    def deleteOrganism(self, organismId):
+        return self.request('deleteOrganism', {'id': organismId})
+
+    def deleteOrganismFeatures(self, organismId):
+        return self.request('deleteOrganismFeatures', {'id': organismId})
+
+    def getSequencesForOrganism(self, commonName):
+        return self.request('getSequencesForOrganism', {'organism': commonName})
+
+    def updateOrganismInfo(self, organismId, commonName, directory, blatdb=None, species=None, genus=None, public=False):
+        data = {
+            'id': organismId,
+            'name': commonName,
+            'directory': directory,
+            'publicMode': public,
+        }
+
+        if blatdb is not None:
+            data['blatdb'] = blatdb
+        if genus is not None:
+            data['genus'] = genus
+        if species is not None:
+            data['species'] = species
+
+        return self.request('updateOrganismInfo', data)
+
+
+class UsersClient(Client):
+    CLIENT_BASE = '/user/'
+
+    def getOrganismPermissionsForUser(self, user):
+        data = {
+            'userId': user.userId,
+        }
+        return self.request('getOrganismPermissionsForUser', data)
+
+    def updateOrganismPermission(self, user, organism, administrate=False,
+                                 write=False, export=False, read=False):
+        data = {
+            'userId': user.userId,
+            'organism': organism,
+            'ADMINISTRATE': administrate,
+            'WRITE': write,
+            'EXPORT': export,
+            'READ': read,
+        }
+        return self.request('updateOrganismPermission', data)
+
+    def loadUser(self, user):
+        return self.loadUserById(user.userId)
+
+    def loadUserById(self, userId):
+        res = self.request('loadUsers', {'userId': userId})
+        if isinstance(res, list):
+            # We can only match one, right?
+            return UserObj(**res[0])
+        else:
+            return res
+
+    def loadUsers(self, email=None):
+        res = self.request('loadUsers', {})
+        data = [UserObj(**x) for x in res]
+        if email is not None:
+            data = [x for x in data if x.username == email]
+
+        return data
+
+    def addUserToGroup(self, group, user):
+        data = {'group': group.name, 'userId': user.userId}
+        return self.request('addUserToGroup', data)
+
+    def removeUserFromGroup(self, group, user):
+        data = {'group': group.name, 'userId': user.userId}
+        return self.request('removeUserFromGroup', data)
+
+    def createUser(self, email, firstName, lastName, newPassword, role="user", groups=None):
+        data = {
+            'firstName': firstName,
+            'lastName': lastName,
+            'email': email,
+            'role': role,
+            'groups': [] if groups is None else groups,
+            # 'availableGroups': [],
+            'newPassword': newPassword,
+            # 'organismPermissions': [],
+        }
+        return self.request('createUser', data)
+
+    def deleteUser(self, user):
+        return self.request('deleteUser', {'userId': user.userId})
+
+    def updateUser(self, user, email, firstName, lastName, newPassword):
+        data = {
+            'userId': user.userId,
+            'email': email,
+            'firstName': firstName,
+            'lastName': lastName,
+            'newPassword': newPassword,
+        }
+        return self.request('updateUser', data)
+
+
+class RemoteRecord(Client):
+    CLIENT_BASE = None
+
+    def ParseRecord(self, cn):
+        org = self._wa.organisms.findOrganismByCn(cn)
+        self._wa.annotations.setSequence(org['commonName'], org['id'])
+
+        data = StringIO.StringIO(self._wa.io.write(
+            exportType='GFF3',
+            seqType='genomic',
+            exportAllSequences=False,
+            exportGff3Fasta=True,
+            output="text",
+            exportFormat="text",
+            sequences=cn,
+        ))
+        data.seek(0)
+
+        for record in GFF.parse(data):
+            yield WebApolloSeqRecord(record, self._wa)
+
+
+class WebApolloSeqRecord(object):
+    def __init__(self, sr, wa):
+        self._sr = sr
+        self._wa = wa
+
+    def __dir__(self):
+        return dir(self._sr)
+
+    def __getattr__(self, key):
+        if key in ('_sr', '_wa'):
+            print self.__dict__
+            return self.__dict__[key]
+        else:
+            if key == 'features':
+                return (WebApolloSeqFeature(x, self._wa)
+                        for x in self._sr.__dict__[key])
+            else:
+                return self._sr.__dict__[key]
+
+    def __setattr__(self, key, value):
+        if key in ('_sd', '_wa'):
+            self.__dict__[key] = value
+        else:
+            self._sr.__dict__[key] = value
+            # Methods acting on the SeqRecord object
+            print key, value
+
+
+class WebApolloSeqFeature(object):
+    def __init__(self, sf, wa):
+        self._sf = sf
+        self._wa = wa
+
+    def __dir__(self):
+        return dir(self._sf)
+
+    def __getattr__(self, key):
+        if key in ('_sf', '_wa'):
+            return self.__dict__[key]
+        else:
+            return self._sf.__dict__[key]
+
+    def __setattr__(self, key, value):
+        if key in ('_sf', '_wa'):
+            self.__dict__[key] = value
+        else:
+            # Methods acting on the SeqFeature object
+            if key == 'location':
+                if value.strand != self._sf.location.strand:
+                    self.wa.annotations.flipStrand(
+                        self._sf.qualifiers['ID'][0]
+                    )
+
+                self.wa.annotations.setBoundaries(
+                    self._sf.qualifiers['ID'][0],
+                    value.start,
+                    value.end,
+                )
+
+                self._sf.__dict__[key] = value
+            else:
+                self._sf.__dict__[key] = value
+                print key, value
+
+def _tnType(feature):
+    if feature.type in ('gene', 'mRNA', 'exon', 'CDS'):
+        return feature.type
+    else:
+        return 'exon'
+
+def _yieldFeatData(features):
+    for f in features:
+        current = {
+            'location': {
+                'strand': f.strand,
+                'fmin': int(f.location.start),
+                'fmax': int(f.location.end),
+            },
+            'type': {
+                'name': _tnType(f),
+                'cv': {
+                    'name': 'sequence',
+                }
+            },
+        }
+        if f.type in ('gene', 'mRNA'):
+            current['name'] = f.qualifiers.get('Name', [f.id])[0]
+        if hasattr(f, 'sub_features') and len(f.sub_features) > 0:
+            current['children'] = [x for x in _yieldFeatData(f.sub_features)]
+
+        yield current
+
+def featuresToFeatureSchema(features):
+    compiled = []
+    for feature in features:
+        if feature.type != 'gene':
+            log.warn("Not able to handle %s features just yet...", feature.type)
+            continue
+
+        for x in _yieldFeatData([feature]):
+            compiled.append(x)
+    return compiled