Exemplo n.º 1
0
    def from_json(self, is_create, json_obj, sess_obj):
        # do base attrs
        self.base_from_json(is_create, json_obj)
        self.set_attrs_from_json(json_obj, self.LIB_TYPE)
        self.set_attrs_from_json(json_obj, self.LIB_INSERT_LEN)

        self.set_attrs_from_json(json_obj, self.SAMPLE)
#        stage_name == 'upload'
        stage_name_list = json_obj[self.SEQUENCESET_ID_ARRAY]
        #print "stage_name_list "+str(stage_name_list)
        sequence_file_names = []
        sequence_file_names = [x['file_name'] for x in stage_name_list if x['stage_name'] == 'upload']
        sequence_file_ids = []
        sequence_file_ids = [x['id'] for x in stage_name_list if x['stage_name'] == 'upload']
        
#        sequence_file_names = [x['file_name'] for x in stage_name_list if x['stage_name'] == 'upload']
#        for dict in stage_name_list:
#            if dict['stage_name'] == 'upload':
#                stage_name = dict['file_name']
#                sequence_file_names.append(stage_name)

#        stage_name = json_obj[self.SEQUENCESET_ID_ARRAY]['stage_name']
#        self.sequence_set_ids = ",".join(json_obj[self.SEQUENCESET_ID_ARRAY])  # just keep this as a string everywhere until being used
        self.sequence_set_ids = ",".join([str(i) for i in sequence_file_ids])
        self.sequence_set_names = ",".join([str(i) for i in sequence_file_names])
        mobedac_logger.info("library has sequence set ids: " + self.sequence_set_ids)
#        print self.sequence_set_ids
        # now put the objects into the real child collection
        # have to do deletes on all existing child sample associations that are not in the new sample set
#        BaseMoBEDAC.update_child_collection(SequenceSetORM, self.sequencesets, json_obj[LibraryORM.SEQUENCESET_IDS], sess_obj)
        return self
Exemplo n.º 2
0
 def handle_POST(self, current_session, *vpath, **params):
     """ Create an object
     """
     try:
         if self.orm_class is SubmissionORM:
             submission_obj = self.orm_class({})
             mobedac_logger.info("In handle_POST1:")
             # AV here when get first send
             json_obj = self.json_from_body()
             submission_obj.from_json(True, json_obj, current_session)
             submission_obj.initialize_for_processing(current_session)                
             return str(submission_obj.id)
         else:
             # create the object
             new_obj = self.orm_class({})
             mobedac_logger.info("In handle_POST2:")
             json_obj = self.json_from_body()
             new_obj.from_json(True, json_obj, current_session)
             current_session.add(new_obj)
             current_session.commit()
             return new_obj.id
     except Exception as e:
         self.log_exception("There was an error attempting to service the POST request")
         current_session.rollback()
         cherrypy.response.status = 500
         return "There was an error attempting to service the request"
Exemplo n.º 3
0
 def json_from_body(self):
     cl = cherrypy.request.headers['Content-Length']
     rawbody = cherrypy.request.body.read(int(cl))
     decoded_rawbody = unidecode(rawbody)
     mobedac_logger.info("restresource got JSON string: " + decoded_rawbody)
     json_obj = json.loads(decoded_rawbody)
     return json_obj
    def getFromMOBEDAC(cls, id, source, sess_obj):
        conn = None
        complete_url = ""
        try:
            # dev mode?
            my_remote_objects_are_local = get_parm("remote_objects_are_local")
            if get_parm("remote_objects_are_local").lower() == 'true':
                new_obj = cls.get_instance(id, sess_obj)
                if new_obj == None:
                    raise ObjectRetrievalException(
                        "Unable to retrieve object: " + id + " from db")
            else:
                headers = {'content-type': 'application/json'}
                conn = httplib.HTTPConnection(get_parm("mobedac_host"))
                object_path = cls.get_REST_sub_path()
                #                complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_key")
                #                complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_     38 key")
                complete_url = get_parm(
                    "mobedac_base_path") + "r/" + object_path + "/" + id
                if (conn.host == "localhost"
                        or conn.host == "api.metagenomics.anl.gov"):
                    complete_url = get_parm(
                        "mobedac_base_path"
                    ) + object_path + "/" + id + "?auth=" + get_parm(
                        "mobedac_auth_key")
                complete_url += "&template=1"
                conn.request("GET", complete_url)
                response = conn.getresponse()
                data = response.read()
                # if all went ok then build an object
                if response.status != httplib.OK:
                    raise ObjectRetrievalException(
                        "Unable to retrieve object: " + id + " from host: " +
                        get_parm('mobedac_host') + " url: " + complete_url)
                new_obj = cls({})
                decoded_data = unidecode(data).strip()
                mobedac_logger.info("complete_url: " + complete_url)
                mobedac_logger.info("json string for object id_1: " + id +
                                    " json: " + decoded_data)
                json_obj = json.loads(decoded_data)
                #mobedac_logger.info("json obj: " + str(json_obj))
                new_obj.from_json(True, json_obj, sess_obj)
            return new_obj
        except ObjectRetrievalException as ore:
            exc_type, exc_value, exc_traceback = sys.exc_info()
            traceback.print_exception(exc_type, exc_value, exc_traceback)
            raise ore
        except Exception as e:
            raise ObjectRetrievalException("Unable to retrieve object: " + id +
                                           " from host: " +
                                           get_parm('mobedac_host') +
                                           " url: " + complete_url +
                                           " error: " + str(e))

        finally:
            if conn != None:
                conn.close()
    def getFromMOBEDAC(cls, id, source, sess_obj):
        conn = None
        complete_url = ""
        try:
            # dev mode?
            my_remote_objects_are_local = get_parm("remote_objects_are_local")
            if get_parm("remote_objects_are_local").lower() == 'true':
                new_obj = cls.get_instance(id, sess_obj)
                if new_obj == None:
                    raise ObjectRetrievalException("Unable to retrieve object: " + id + " from db");
            else:
                headers = {'content-type': 'application/json'}
                conn = httplib.HTTPConnection(get_parm("mobedac_host"))
                object_path = cls.get_REST_sub_path()
#                complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_key")
#                complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_     38 key")
                complete_url = get_parm("mobedac_base_path") + "r/" + object_path + "/" + id
                if (conn.host == "localhost" or conn.host == "api.metagenomics.anl.gov"):
                    complete_url = get_parm("mobedac_base_path") + object_path + "/" + id + "?auth=" + get_parm("mobedac_auth_key")
                complete_url +=  "&template=1" 
                conn.request("GET", complete_url)
                response = conn.getresponse()
                data = response.read()
                # if all went ok then build an object
                if response.status != httplib.OK:
                    raise ObjectRetrievalException("Unable to retrieve object: " + id + " from host: " + get_parm('mobedac_host') + " url: " + complete_url)
                new_obj = cls({})
                decoded_data = unidecode(data).strip()
                mobedac_logger.info("complete_url: "+complete_url)
                mobedac_logger.info("json string for object id_1: " + id + " json: " + decoded_data)
                json_obj = json.loads(decoded_data)
                #mobedac_logger.info("json obj: " + str(json_obj))
                new_obj.from_json(True, json_obj, sess_obj)
            return new_obj
        except ObjectRetrievalException as ore:
            exc_type, exc_value, exc_traceback = sys.exc_info()
            traceback.print_exception(exc_type, exc_value, exc_traceback)   
            raise ore
        except Exception as e:
            raise ObjectRetrievalException("Unable to retrieve object: " + id + " from host: " + get_parm('mobedac_host') + " url: " + complete_url + " error: " + str(e))

        
        finally:
            if conn != None:
                conn.close() 
Exemplo n.º 6
0
    def from_json(self, is_create, json_obj, sess_obj):
        # do base attrs
        self.base_from_json(is_create, json_obj)
        self.set_attrs_from_json(json_obj, self.LIB_TYPE)
        self.set_attrs_from_json(json_obj, self.LIB_INSERT_LEN)

        self.set_attrs_from_json(json_obj, self.SAMPLE)
        #        stage_name == 'upload'
        stage_name_list = json_obj[self.SEQUENCESET_ID_ARRAY]
        #print "stage_name_list "+str(stage_name_list)
        sequence_file_names = []
        sequence_file_names = [
            x['file_name'] for x in stage_name_list
            if x['stage_name'] == 'upload'
        ]
        sequence_file_ids = []
        sequence_file_ids = [
            x['id'] for x in stage_name_list if x['stage_name'] == 'upload'
        ]

        #        sequence_file_names = [x['file_name'] for x in stage_name_list if x['stage_name'] == 'upload']
        #        for dict in stage_name_list:
        #            if dict['stage_name'] == 'upload':
        #                stage_name = dict['file_name']
        #                sequence_file_names.append(stage_name)

        #        stage_name = json_obj[self.SEQUENCESET_ID_ARRAY]['stage_name']
        #        self.sequence_set_ids = ",".join(json_obj[self.SEQUENCESET_ID_ARRAY])  # just keep this as a string everywhere until being used
        self.sequence_set_ids = ",".join([str(i) for i in sequence_file_ids])
        self.sequence_set_names = ",".join(
            [str(i) for i in sequence_file_names])
        mobedac_logger.info("library has sequence set ids: " +
                            self.sequence_set_ids)
        #        print self.sequence_set_ids
        # now put the objects into the real child collection
        # have to do deletes on all existing child sample associations that are not in the new sample set
        #        BaseMoBEDAC.update_child_collection(SequenceSetORM, self.sequencesets, json_obj[LibraryORM.SEQUENCESET_IDS], sess_obj)
        return self
    def initialize_for_processing(self, sess_obj):

        # need to call back to mobedac and figure out all the other objects etc
        libraries = self.library_ids
        # now loop and gather all info
        project_hash = {}
        sample_hash = {}
        library_hash = {}
        detail_objs = []
        for lib_id in libraries:
            try:
                mobedac_logger.info("\nRetrieving remote library: " + str(lib_id))
                library_hash[lib_id] = curr_library = LibraryORM.getFromMOBEDAC(lib_id, None, sess_obj)
            except Exception as e:
                # some kind of error
                raise SubmissionException("There was an error retrieving library: " + str(lib_id) + " error: " + str(e))

            mobedac_logger.info("sample: " + str(curr_library.sample))

            sample_id = str(curr_library.sample)
            mobedac_logger.info("file_name(s) " + str(curr_library.sequence_set_names))

            #
            #             # THIS DOESN'T WORK 2013-3-27
            #             try:
            #                 mobedac_logger.info("Retrieving remote sample: " + str(sample_id));
            #                 # getFromMOBEDAC is in basmobedac.py
            #                 sample_hash[sample_id] = curr_sample = SampleORM.getFromMOBEDAC(sample_id, None, sess_obj)
            #             except Exception as e:
            #                 # some kind of error
            #                 raise SubmissionException("There was an error retrieving sample: " + str(sample_id) + " error: " + str(e))
            #
            #             project_id = curr_sample.project
            #             try:
            #                 mobedac_logger.info("Retrieving remote project: " + str(project_id));
            #                 project_hash[project_id] = curr_project = ProjectORM.getFromMOBEDAC(project_id, None, sess_obj)
            #                 mobedac_logger.info("done Retrieving remote project: " + str(project_id));
            #             except Exception as e:
            #                 # some kind of error
            #                 raise SubmissionException("There was an error retrieving project: " + str(project_id) + " error: " + str(e))

            # do some sanity check/validation on the library and project information
            # mobedac_logger.info("library domain: " + curr_library.get_domain())
            # mobedac_logger.info("library run_key: " + curr_library.get_run_key())
            # mobedac_logger.info("library region: " + curr_library.get_region())
            # mobedac_logger.info("project metadatastr: " + curr_project.mbd_metadata)
            #             if not(curr_library.get_run_key()):
            #                 raise SubmissionException("The library: " + str(lib_id) + " is missing a run key")
            #             if not(curr_library.get_domain()):
            #                 raise SubmissionException("The library: " + str(lib_id) + " is missing a domain")
            #             if not(curr_library.get_region()):
            #                 raise SubmissionException("The library: " + str(lib_id) + " is missing a region")
            #             #if not(curr_project.get_metadata_json()['vamps_id']):
            #                 raise SubmissionException("The project: " + str(lib_id) + " is missing a vamps_id")
            # check the primers
            #            primers = curr_library.get_primers()
            # if only 1 primer and it isn't a BOTH direction then complain
            #            forward_found = False
            #            reverse_found = False
            mobedac_logger.info("done Retrieving remote objects")
            #             for primer in primers:
            #                 dir = primer['direction'].lower()
            #                 if dir == 'f':
            #                     forward_found = True
            #                 elif dir == 'r':
            #                     reverse_found = True
            #             if not(forward_found) or not(reverse_found):
            #                 raise SubmissionException("You must supply at least 1 forward primer and 1 reverse primer.")
            #             mobedac_logger.info("done with primers");

            # now what will the official project name be in vamps for this library?
            #            curr_library_domain = curr_library.get_domain()
            #            curr_library_region = curr_library.get_region()
            #            domain_region_suffix = '_' + curr_library_domain[0].upper() + curr_library_region.lower()
            #            vamps_project_name = curr_project.get_metadata_json()['vamps_id']['value'] + domain_region_suffix

            #                    self.set_attrs_from_json(json_obj, self.SAMPLE)
            ##        stage_name == 'upload'
            #        stage_name_list = json_obj[self.SEQUENCESET_ID_ARRAY]
            #        sequence_file_names = []
            #        sequence_file_names = [x['file_name'] for x in stage_name_list if x['stage_name'] == 'upload']
            #
            mobedac_logger.info("preparing the submission detail object")
            # now create the submission details objects
            new_details = SubmissionDetailsORM(None)

            # new_details.project_id = project_id
            new_details.project_id = "XX_ID"
            vamps_project_name = "MOBEDAC_TEST_" + new_details.project_id
            new_details.vamps_project_name = vamps_project_name

            new_details.library_id = lib_id

            new_details.sample_id = sample_id

            # new_details.region = curr_library_region.lower()
            new_details.region = ""

            new_details.sequence_file_url = curr_library.sequence_set_names

            detail_objs.append(new_details)

            # mobedac uses periods...we don't want them
            dataset_name = str(curr_library.id).replace(".", "_")
            new_details.vamps_dataset_name = dataset_name
            new_details.sequenceset_id = curr_library.get_sequence_set_id_array()[0]  # just take the first one for now
            mobedac_logger.info("new_details has sequence set id: " + new_details.sequenceset_id)
            # this is the starting value for next_action....call mobedac and download the sequence data
            new_details.next_action = SubmissionDetailsORM.ACTION_DOWNLOAD
            mobedac_logger.info("DONE preparing the submission detail object")

        try:
            # make sure to write this submission out before anything
            sess_obj.add(self)
            mobedac_logger.info("committing all submission detail objects")
            sess_obj.commit()
            # now set the submission id into each of these submission_detail objects since everything worked out ok
            # because only now do we have a submission id (self)
            for new_detail in detail_objs:
                new_detail.submission_id = self.id
                sess_obj.add(new_detail)
            sess_obj.commit()
            mobedac_logger.info("committing submission object got id: " + str(self.id))
        except Exception as e:
            raise SubmissionException("There was an error during submission: %s" % e)
 def __init__(self, value):
     super(SubmissionException, self).__init__(value)
     self.value = value
     mobedac_logger.info(value)
     mobedac_logger.exception(value)
    def initialize_for_processing(self, sess_obj):
        
        # need to call back to mobedac and figure out all the other objects etc
        libraries = self.library_ids
        # now loop and gather all info
        project_hash = {}
        sample_hash = {}
        library_hash = {}
        detail_objs = []
        for lib_id in libraries:
            try:
                mobedac_logger.info("\nRetrieving remote library: " + str(lib_id));
                library_hash[lib_id] = curr_library = LibraryORM.getFromMOBEDAC(lib_id, None, sess_obj)
            except Exception as e:
                # some kind of error 
                raise SubmissionException("There was an error retrieving library: " + str(lib_id) + " error: " + str(e))
                
            mobedac_logger.info("sample: " + str(curr_library.sample) );  
            
            sample_id = str(curr_library.sample)
            mobedac_logger.info('file_name(s) '+str(curr_library.sequence_set_names))
            
            
#             
#             # THIS DOESN'T WORK 2013-3-27
#             try:
#                 mobedac_logger.info("Retrieving remote sample: " + str(sample_id));
#                 # getFromMOBEDAC is in basmobedac.py
#                 sample_hash[sample_id] = curr_sample = SampleORM.getFromMOBEDAC(sample_id, None, sess_obj)
#             except Exception as e:
#                 # some kind of error 
#                 raise SubmissionException("There was an error retrieving sample: " + str(sample_id) + " error: " + str(e))
#             
#             project_id = curr_sample.project
#             try:
#                 mobedac_logger.info("Retrieving remote project: " + str(project_id));
#                 project_hash[project_id] = curr_project = ProjectORM.getFromMOBEDAC(project_id, None, sess_obj)
#                 mobedac_logger.info("done Retrieving remote project: " + str(project_id));
#             except Exception as e:
#                 # some kind of error 
#                 raise SubmissionException("There was an error retrieving project: " + str(project_id) + " error: " + str(e))

            # do some sanity check/validation on the library and project information
            #mobedac_logger.info("library domain: " + curr_library.get_domain())
            #mobedac_logger.info("library run_key: " + curr_library.get_run_key())
            #mobedac_logger.info("library region: " + curr_library.get_region())
            #mobedac_logger.info("project metadatastr: " + curr_project.mbd_metadata)
#             if not(curr_library.get_run_key()):
#                 raise SubmissionException("The library: " + str(lib_id) + " is missing a run key")
#             if not(curr_library.get_domain()):
#                 raise SubmissionException("The library: " + str(lib_id) + " is missing a domain")
#             if not(curr_library.get_region()):
#                 raise SubmissionException("The library: " + str(lib_id) + " is missing a region")
#             #if not(curr_project.get_metadata_json()['vamps_id']):
#                 raise SubmissionException("The project: " + str(lib_id) + " is missing a vamps_id")
            #check the primers
#            primers = curr_library.get_primers()
            # if only 1 primer and it isn't a BOTH direction then complain
#            forward_found = False
#            reverse_found = False
            mobedac_logger.info("done Retrieving remote objects");
#             for primer in primers:
#                 dir = primer['direction'].lower()
#                 if dir == 'f':
#                     forward_found = True
#                 elif dir == 'r':
#                     reverse_found = True
#             if not(forward_found) or not(reverse_found):
#                 raise SubmissionException("You must supply at least 1 forward primer and 1 reverse primer.")
#             mobedac_logger.info("done with primers");
            
            # now what will the official project name be in vamps for this library?
#            curr_library_domain = curr_library.get_domain()
#            curr_library_region = curr_library.get_region()
#            domain_region_suffix = '_' + curr_library_domain[0].upper() + curr_library_region.lower()
#            vamps_project_name = curr_project.get_metadata_json()['vamps_id']['value'] + domain_region_suffix
            
#                    self.set_attrs_from_json(json_obj, self.SAMPLE)
##        stage_name == 'upload'
#        stage_name_list = json_obj[self.SEQUENCESET_ID_ARRAY]
#        sequence_file_names = []
#        sequence_file_names = [x['file_name'] for x in stage_name_list if x['stage_name'] == 'upload']
#            
            mobedac_logger.info("preparing the submission detail object");
            # now create the submission details objects
            new_details = SubmissionDetailsORM(None)
            
            
            #new_details.project_id = project_id
            new_details.project_id = "XX_ID"
            vamps_project_name = "MOBEDAC_TEST_"+new_details.project_id
            new_details.vamps_project_name = vamps_project_name
            
            new_details.library_id = lib_id
            
            new_details.sample_id = sample_id
            
            #new_details.region = curr_library_region.lower()
            new_details.region = ''
            
            
            
            new_details.sequence_file_url = curr_library.sequence_set_names
            
            detail_objs.append(new_details)
            
            # mobedac uses periods...we don't want them
            dataset_name = str(curr_library.id).replace('.', '_')
            new_details.vamps_dataset_name = dataset_name
            new_details.sequenceset_id = curr_library.get_sequence_set_id_array()[0] # just take the first one for now
            mobedac_logger.info("new_details has sequence set id: " + new_details.sequenceset_id)
            # this is the starting value for next_action....call mobedac and download the sequence data
            new_details.next_action = SubmissionDetailsORM.ACTION_DOWNLOAD
            mobedac_logger.info("DONE preparing the submission detail object");

        try:
            # make sure to write this submission out before anything
            sess_obj.add(self)
            mobedac_logger.info("committing all submission detail objects");
            sess_obj.commit()
            # now set the submission id into each of these submission_detail objects since everything worked out ok
            # because only now do we have a submission id (self)
            for new_detail in detail_objs:
                new_detail.submission_id = self.id
                sess_obj.add(new_detail)
            sess_obj.commit()
            mobedac_logger.info("committing submission object got id: " + str(self.id));
        except Exception as e:
            raise SubmissionException("There was an error during submission: %s" % e)