Package : via_DMS

Module : DMSDatabase

class src.data_access.via_DMS.DMSDatabase.DMSDatabase(config)

Bases: object

Database connection class

open_connection()

Connection to DMS MS sqlserver i.e DMS5 or DMS_Data_Package

run_query(query)

Execute SQL query.

Module : FileOperations

class src.data_access.via_DMS.FileOperations.FileOperations(analysis_jobs=None, parent_folder=None, job_info=None)

Bases: object

Grab locations of the MSGF+ & MASIC analysis tools using analysis_jobs object

create_dir(folder)

Parameters

folder –

Returns

write_to_disk(url: str)

Parameters

url – Job’s file path on DMS.

Returns

check_url(url)

Parameters

url –

Returns

download_over_http()

Given a url, copy files from DMS to disk! :return:

parse_fileserverpath_to_web_url(file_server_path)

Converts Windows FileSever path to webURL. :param file_server_path: windows server file path. :return:

download_msgf_jobs(df)

Parameters

df –

Returns

download_masic_jobs(df)

Parameters

df –

Returns

download_raw_files(df, path_or_url)

download_fasta_param_files()

Returns

use_df(df)

Called for each dataset in the dataFrame! :param df: reference to analysis_jobs object. :return:

get_files(**kw)

Module : Input

class src.data_access.via_DMS.Input.Input

Bases: object

Handle & validate User input

other_input(InputType, UserInput)

changes input string to list of numbers.

user_input()

Returns

Module : Query

class src.data_access.via_DMS.Query.Query

Bases: object

SQL queries to access data from DMS

DATASET_MSFG = " SELECT A.Dataset_ID,\n A.MSGFPlusJob,\n B.MasicJob\n FROM ( SELECT Dataset_ID,\n Job AS MSGFPlusJob\n FROM DMS_Data_Package.dbo.V_Data_Package_Analysis_Jobs_List_Report\n WHERE ID = {} AND\n Tool LIKE 'msgf%' ) A\n LEFT OUTER JOIN\n ( SELECT Dataset_ID,\n Job AS MasicJob\n FROM DMS_Data_Package.dbo.V_Data_Package_Analysis_Jobs_List_Report\n WHERE ID = {} AND\n Tool LIKE 'masic%' ) B\n ON A.Dataset_ID = B.Dataset_ID\n "

MSGF_loc = 'SELECT JobNum As MSGFPlusJob, [Data Folder Link] As MSGFplus_loc\n FROM V_Analysis_Job_Detail_Report_2\n WHERE JobNum IN ({})'

DATASET_MASIC = " SELECT Dataset_ID, Max(Job) As NewestMasicJob\n FROM V_Analysis_Job_List_Report_2\n WHERE Dataset_ID In ({})\n And Tool Like 'masic%'\n Group by Dataset_ID"

MASIC_loc = 'SELECT JobNum AS NewestMasicJob , [Results Folder Path] As MASIC_loc\n FROM V_Analysis_Job_Detail_Report_2\n WHERE JobNum IN ({})'

DATASET = " SELECT Dataset_ID, Job As MSGFPlusJob, [Results Folder Path] As MSGFplus_loc\n FROM V_Analysis_Job_List_Report_2\n WHERE Job IN ( SELECT Max(Job)\n FROM V_Analysis_Job_List_Report_2\n WHERE [Tool] LIKE 'msgf%' AND\n Dataset_ID IN ({})\n GROUP BY dataset_id )"

MSGF = 'SELECT Dataset_ID, Job As MSGFPlusJob,[Results Folder Path] As MSGFplus_loc \n FROM V_Analysis_Job_List_Report_2\n WHERE Job IN ({})'

JOB_INFO = 'SELECT Job, Dataset, Experiment, OrganismDBName, ProteinCollectionList, ParameterFileName\n FROM V_Analysis_Job_Export\n Where Job In ({}) \n Order By Dataset, job'

Module : QueryBuilder

class src.data_access.via_DMS.QueryBuilder.QueryBuilder(user_input=None, storage=None, project_name=None)

Bases: object

1. Build MS-SQl Queries.

2. Execute them

3. create a dataFrame that holds all Information

   Dataset_ID | MSGFPlusJob | Data Folder Link | NewestMasicJob | Results Folder Path |

save_to_disk(data, data_path, msgf_job_list, id)

Parameters

• data –

• data_path –

• msgf_job_list –

• id –

Returns

start_with_datapackage_id(id)

Given a ID —-Find out the Dataset_ID , MSGFPlusJob ——–Using MSGFPlusJob, findout “Data Folder Link” ——–Using Dataset_ID, findout NewestMasicJob ————Using NewestMasicJob findout “Results Folder Path” Merge results to create “analysis_jobs”.

Parameters

id – datapackage_id

Returns

start_with_dataset_ids(id_list)

Given set of dataset-IDs —-findout MSGFPlusJob, “Results Folder Path” ——–Using Dataset_ID, findout NewestMasicJob ————Using NewestMasicJob findout “Results Folder Path” Merge results to create “analysis_jobs”.

Parameters

id_list – set of dataset-IDs

Returns

start_with_job_nums(id_list)

Given set of MSGFJobs —-Find the Dataset_ID, & “Results Folder Path” ——–Using Dataset_ID, findout MASIC ————Using MASIC, findout “Results Folder Path” Merge results to create “analysis_jobs”.

Parameters

id_list – set of JobNums

Returns

execute()

Design queries here & set it

Module : secure

class src.data_access.via_DMS.secure.Config

Bases: object

db_user = None

db_password = None

db_server = None

db_name = None