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import csv
import sql_utils as su
from tqdm.notebook import tqdm_notebook
def create_characterization_dt_tables(connection):
CharacterizationInfo_str = "CREATE TABLE IF NOT EXISTS " + \
"CharacterizationInfo " + \
"(ID INT, CharType VARCHAR(150), CharName VARCHAR(150), " + \
"AssayType VARCHAR(150), Protocol TEXT, " + \
"DesignDescription TEXT, AnalysisAndConclusion TEXT);"
CharExpConfig_str = "CREATE TABLE IF NOT EXISTS " + \
"CharExpConfig " + \
"(ID INT, CharType VARCHAR(150), CharName VARCHAR(150), " + \
"AssayType VARCHAR(150), ExpConfigTechnique TEXT, " + \
"ExpConfigInstruments TEXT, ExpConfigDescription TEXT);"
CharResultDescriptions_str = "CREATE TABLE IF NOT EXISTS " + \
"CharResultDescriptions " + \
"(ID INT, CharType VARCHAR(150), CharName VARCHAR(150), " + \
"AssayType VARCHAR(150), CharResultDescription TEXT);"
CharResultKeywords_str = "CREATE TABLE IF NOT EXISTS " + \
"CharResultKeywords " + \
"(ID INT, CharType VARCHAR(150), CharName VARCHAR(150), " + \
"AssayType VARCHAR(150), CharResultKeyword VARCHAR(150)); "
CharResultTables_str = "CREATE TABLE IF NOT EXISTS " + \
"CharResultTables " + \
"(ID INT, CharType VARCHAR(150), CharName VARCHAR(150), " + \
"AssayType VARCHAR(150), CharTable TEXT); "
table_creation_querys = [
CharacterizationInfo_str,
CharExpConfig_str,
CharResultDescriptions_str,
CharResultKeywords_str,
CharResultTables_str
]
for query in table_creation_querys:
results = su.simple_querry(
connection,
query
)
if len(results) == 0:
print("Table Exists")
else:
print(results)
su.show_tables(connection)
def characterization_to_sql(
characterization_dt,
connection
):
total_ids = len(characterization_dt)
no_sample_list = []
with tqdm_notebook(
total=total_ids,
desc='Processing',
unit='ID'
) as progress_bar:
cursor = connection.cursor()
for ID in characterization_dt:
sample_info = characterization_dt[ID]
for CharType_info in sample_info:
if 'type' not in CharType_info:
print('There is no characterization with your sample.')
no_sample_list.append([ID, CharType_info])
continue
CharType = CharType_info['type']
CharType_Info_Assay = CharType_info['charsByAssayType']
for CharName in CharType_Info_Assay:
CharName_infos = CharType_Info_Assay[CharName]
for charname_info in CharName_infos:
displayableItems = charname_info['displayableItems']
# Create a cursor object
for item in displayableItems:
if item['name'] == 'Assay Type':
AssayType = item['value']
if item['name'] == 'Protocol':
Protocol = item['value']
if item['name'] == 'Design Description':
DesignDescription = item['value']
if item['name'] == 'Experiment Configurations':
exp_config_list = item['value']
if item['name'] == 'Characterization Results':
char_results = item['value']
if item['name'] == 'Analysis and Conclusion':
AnalysisAndConclusion = item['value']
n_row = len(exp_config_list[0]['Technique'])
for i in range(n_row):
ExpConfigTechnique = exp_config_list[
0
]['Technique'][i]
ExpConfigInstruments = exp_config_list[
1
]['Instruments'][i]
ExpConfigDescription = exp_config_list[
2
]['Description'][i]
# Write to NanoEntDes
CharExpConfig_insert = (
ID,
CharType,
CharName,
AssayType,
ExpConfigTechnique,
ExpConfigInstruments,
ExpConfigDescription
)
# Execute a SELECT statement to check
# if the entry already exists
search_query = "SELECT COUNT(*) FROM " + \
"CharExpConfig" + \
" WHERE ID = ?" + \
" AND CharType = ?" + \
" AND CharName = ?" + \
" AND AssayType = ?" + \
" AND ExpConfigTechnique = ?" + \
" AND ExpConfigInstruments = ?;"
cursor.execute(
search_query,
CharExpConfig_insert[:6]
)
count = cursor.fetchone()[0]
# Check the count to determine
# if the entry exists
if count == 0:
# Entry does not exist, proceed
# with insertion
insert_query = "INSERT INTO " + \
"CharExpConfig " + \
"(ID, " + \
"CharType, " + \
"CharName, " + \
"AssayType, " + \
"ExpConfigTechnique, " + \
"ExpConfigInstruments, " + \
"ExpConfigDescription) " + \
"VALUES (?, ?, ?, ?, ?, ?, ?)"
cursor.execute(
insert_query,
CharExpConfig_insert
)
connection.commit()
for char_result in char_results:
if 'Data and Conditions' in char_result:
table_list = char_result[
'Data and Conditions'
]
CharTable = ""
for item in table_list:
tsc = ",".join(
item[
'value'
]
)
CharTable += tsc
CharTable += ";"
# Write to NanoEntDes
CRTables_insert = (
ID,
CharType,
CharName,
AssayType,
CharTable
)
# Execute a SELECT
# statement to check
# if the entry already exists
search_query = "SELECT " + \
"COUNT(*) FROM " + \
"CharResultTables" + \
" WHERE ID = ?" + \
" AND CharType = ?" + \
" AND CharName = ?" + \
" AND AssayType = ?;"
cursor.execute(
search_query,
CRTables_insert[:4]
)
count = cursor.fetchone()[0]
# Check the count to determine
# if the entry exists
if count == 0:
# Entry does not exist, proceed
# with insertion
insert_query = "INSERT " + \
"INTO " + \
"CharResultTables " + \
"(ID, " + \
"CharType, " + \
"CharName, " + \
"AssayType, " + \
"CharTable) " + \
"VALUES (?, ?, ?, ?, ?)"
cursor.execute(
insert_query,
CRTables_insert
)
connection.commit()
if 'Files' in char_result:
file_list = char_result[
'Files'
]
for char_file in file_list:
if 'description' in char_file:
CRDes = char_file[
'description'
]
else:
CRDes = "None"
if 'keywordsString' in char_file:
CRKWstr_ls = char_file[
'keywordsString'
].split(",")
else:
CRKWstr_ls = list("None")
CRDes_insert = (
ID,
CharType,
CharName,
AssayType,
CRDes
)
# Execute a SELECT
# statement to check
# if the entry already exists
search_query = "SELECT " + \
"COUNT(*) FROM " + \
"CharResultDescriptions" + \
" WHERE ID = ?" + \
" AND CharType = ?" + \
" AND CharName = ?" + \
" AND AssayType = ?;"
cursor.execute(
search_query,
CRDes_insert[:4]
)
count = cursor.fetchone()[0]
# Check the count to determine
# if the entry exists
if count == 0:
# Entry does not exist, proceed
# with insertion
insert_query = "INSERT " + \
"INTO " + \
"CharResultDescriptions" +\
" (ID, " + \
"CharType, " + \
"CharName, " + \
"AssayType, " + \
"CharResultDescription" + \
") " + \
"VALUES (?, ?, ?, ?, ?)"
cursor.execute(
insert_query,
CRDes_insert
)
connection.commit()
for CRKW in CRKWstr_ls:
CRKW_insert = (
ID,
CharType,
CharName,
AssayType,
CRKW
)
# Execute a SELECT
# statement to check
# if the entry already exists
search_query = "SELECT " + \
"COUNT(*) FROM " + \
"CharResultKeywords" + \
" WHERE ID = ?" + \
" AND CharType = ?" + \
" AND CharName = ?" + \
" AND AssayType = ?" + \
" AND " + \
"CharResultKeyword = ?;"
cursor.execute(
search_query,
CRKW_insert
)
count = cursor.fetchone()[0]
# Check the count to determine
# if the entry exists
if count == 0:
# Entry does not exist,
# proceed
# with insertion
insert_query = "INSERT " +\
"INTO " + \
"CharResultKeywords" +\
" (ID, " + \
"CharType, " + \
"CharName, " + \
"AssayType, " + \
"CharResultKeyword" + \
") " + \
"VALUES (?, ?, " + \
"?, ?, ?)"
cursor.execute(
insert_query,
CRKW_insert
)
connection.commit()
# Write to NanoEntDes
CharacterizationInfo_insert = (
ID,
CharType,
CharName,
AssayType,
Protocol,
DesignDescription,
AnalysisAndConclusion
)
# Execute a SELECT statement to check
# if the entry already exists
search_query = "SELECT COUNT(*) FROM " + \
"CharacterizationInfo" + \
" WHERE ID = ?" + \
" AND CharType = ?" + \
" AND CharName = ?" + \
" AND AssayType = ?" + \
" AND Protocol = ?;"
cursor.execute(
search_query,
CharacterizationInfo_insert[:5]
)
count = cursor.fetchone()[0]
# Check the count to determine if the entry exists
if count == 0:
# Entry does not exist, proceed with insertion
insert_query = "INSERT INTO " + \
"CharacterizationInfo " + \
"(ID, " + \
"CharType, " + \
"CharName, " + \
"AssayType, " + \
"Protocol, " + \
"DesignDescription, " + \
"AnalysisAndConclusion) " + \
"VALUES (?, ?, ?, ?, ?, ?, ?)"
cursor.execute(
insert_query,
CharacterizationInfo_insert
)
connection.commit()
progress_bar.update(1)
cursor.close()
no_sample_csv = 'no_characterization.csv'
# Specify the filename for the CSV file
with open(no_sample_csv, 'w', newline='') as file:
writer = csv.writer(file)
writer.writerows(no_sample_list)
print(f"CSV file '{no_sample_csv}' has been created.")
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