Precision Toxicology Metadata Manager
latest
Project Overview:
1. User Guide
2. Database Model
3. Spreadsheet Creator
4. Data Extraction
5. Email/GMail
6. Creation of Excel spreadsheets
7. Interaction with Google Drive
8. Investigations, Studies And Assays: the ISA format
9. Updater for existing spreadsheets
10. Spreadsheet validation
API Documentation
Precision Toxicology Metadata Manager
Index
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Index
A
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B
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C
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D
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E
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F
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G
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I
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J
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
activation_token (ptmd.database.models.user.User attribute)
activation_token_id (ptmd.database.models.user.User attribute)
add_blanks_to_sample_dataframe() (in module ptmd.lib.creator.dataframes)
add_error() (ptmd.lib.validator.core.ExcelValidator method)
(ptmd.lib.validator.core.ExternalExcelValidator method)
add_node() (ptmd.lib.validator.core.VerticalValidator method)
args (ptmd.lib.updater.batch.BatchError attribute)
author (ptmd.database.models.file.File attribute)
author_id (ptmd.database.models.file.File attribute)
B
batch (ptmd.database.models.file.File attribute)
Batch2ISA (class in ptmd.lib.isa.core)
BatchError
BatchUpdater (class in ptmd.lib.updater.batch)
blanks (ptmd.database.models.file.File attribute)
build_email_core() (in module ptmd.lib.email.core)
build_general_dataframe() (in module ptmd.lib.creator.dataframes)
build_sample_dataframe() (in module ptmd.lib.creator.dataframes)
C
cas (ptmd.database.models.chemical.Chemical attribute)
change_password() (ptmd.database.models.user.User method)
check_if_token_revoked() (in module ptmd.database.models.token_blocklist)
Chemical (class in ptmd.database.models.chemical)
chemical_id (ptmd.database.models.chemical.Chemical attribute)
chemicals (ptmd.database.models.file.File attribute)
common_name (ptmd.database.models.chemical.Chemical attribute)
connect() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
controls (ptmd.database.models.file.File attribute)
convert() (ptmd.lib.isa.core.Batch2ISA method)
create_blank_source() (ptmd.lib.isa.core.Batch2ISA static method)
create_characteristic() (ptmd.lib.isa.core.Batch2ISA static method)
create_confirmation_email_content() (in module ptmd.lib.email.load_templates)
create_directories() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
create_factor_values() (ptmd.lib.isa.core.Batch2ISA method)
create_factors() (ptmd.lib.isa.core.Batch2ISA method)
create_parameter_values() (ptmd.lib.isa.core.Batch2ISA method)
create_protocol() (ptmd.lib.isa.core.Batch2ISA method)
create_protocol_parameters() (ptmd.lib.isa.core.Batch2ISA method)
create_reset_pwd_mail_content() (in module ptmd.lib.email.load_templates)
create_sample() (ptmd.lib.isa.core.Batch2ISA method)
create_samples() (ptmd.lib.isa.core.Batch2ISA method)
create_source() (ptmd.lib.isa.core.Batch2ISA method)
create_treatment_process() (ptmd.lib.isa.core.Batch2ISA method)
create_validated_email_content() (in module ptmd.lib.email.load_templates)
create_validation_mail_content() (in module ptmd.lib.email.load_templates)
created_at (ptmd.database.models.token_blocklist.TokenBlocklist attribute)
D
data (ptmd.database.models.sample.Sample attribute)
DataframeCreator (class in ptmd.lib.creator.core)
delete_file() (ptmd.lib.creator.core.DataframeCreator method)
(ptmd.lib.gdrive.core.GoogleDriveConnector method)
doses (ptmd.database.models.file.File attribute)
download_file() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
(ptmd.lib.validator.core.ExcelValidator method)
(ptmd.lib.validator.core.ExternalExcelValidator method)
E
email (ptmd.database.models.user.User attribute)
end_date (ptmd.database.models.file.File attribute)
ExcelValidator (class in ptmd.lib.validator.core)
expires_on (ptmd.database.models.token.Token attribute)
ExternalExcelValidator (class in ptmd.lib.validator.core)
extract_data_from_spreadsheet() (in module ptmd.lib.data_extractor.core)
F
File (class in ptmd.database.models.file)
file (ptmd.database.models.sample.Sample attribute)
file_id (ptmd.database.models.file.File attribute)
(ptmd.database.models.sample.Sample attribute)
(ptmd.lib.updater.batch.BatchUpdater attribute)
filepath (ptmd.lib.updater.batch.BatchUpdater attribute)
files (ptmd.database.models.timepoint.Timepoint attribute)
find_files_in_folder() (in module ptmd.lib.gdrive.utils)
formula (ptmd.database.models.chemical.Chemical attribute)
G
gdrive_id (ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
get_array_of_unique_chemicals() (ptmd.lib.creator.core.DataframeCreator method)
get_config() (in module ptmd.lib.email.utils)
get_empty_cells_format() (in module ptmd.lib.excel.formats)
get_extra_cells_format() (in module ptmd.lib.excel.formats)
get_file_information() (in module ptmd.lib.gdrive.utils)
get_filename() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
get_folder_id() (in module ptmd.lib.gdrive.utils)
get_header_format() (in module ptmd.lib.excel.formats)
google_drive (ptmd.lib.gdrive.core.GoogleDriveConnector attribute)
GoogleDriveConnector (class in ptmd.lib.gdrive.core)
I
id (ptmd.database.models.token_blocklist.TokenBlocklist attribute)
(ptmd.database.models.user.User attribute)
instance_ (ptmd.lib.gdrive.core.GoogleDriveConnector attribute)
J
jti (ptmd.database.models.token_blocklist.TokenBlocklist attribute)
L
label (ptmd.database.models.timepoint.Timepoint attribute)
lock_file() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
longname (ptmd.database.models.organisation.Organisation attribute)
M
metadata (ptmd.database.models.chemical.Chemical attribute)
(ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
(ptmd.database.models.organism.Organism attribute)
(ptmd.database.models.sample.Sample attribute)
(ptmd.database.models.timepoint.Timepoint attribute)
(ptmd.database.models.token.Token attribute)
(ptmd.database.models.token_blocklist.TokenBlocklist attribute)
(ptmd.database.models.user.User attribute)
modify_in_db() (ptmd.lib.updater.batch.BatchUpdater method)
modify_in_file() (ptmd.lib.updater.batch.BatchUpdater method)
module
ptmd.database.models.chemical
ptmd.database.models.file
ptmd.database.models.organisation
ptmd.database.models.organism
ptmd.database.models.sample
ptmd.database.models.timepoint
ptmd.database.models.token
ptmd.database.models.token_blocklist
ptmd.database.models.user
ptmd.lib.creator.core
ptmd.lib.creator.dataframes
ptmd.lib.data_extractor.core
ptmd.lib.email.const
ptmd.lib.email.core
ptmd.lib.email.load_templates
ptmd.lib.email.utils
ptmd.lib.excel.formats
ptmd.lib.excel.save
ptmd.lib.excel.styles
ptmd.lib.gdrive.const
ptmd.lib.gdrive.core
ptmd.lib.gdrive.utils
ptmd.lib.isa.core
ptmd.lib.isa.ontologies
ptmd.lib.updater.batch
ptmd.lib.validator.core
ptmd.lib.validator.validate_identifier
N
name (ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
O
old_batch (ptmd.lib.updater.batch.BatchUpdater attribute)
Organisation (class in ptmd.database.models.organisation)
organisation (ptmd.database.models.file.File attribute)
(ptmd.database.models.user.User attribute)
organisation_id (ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
(ptmd.database.models.user.User attribute)
organisation_name (ptmd.lib.updater.batch.BatchUpdater attribute)
Organism (class in ptmd.database.models.organism)
organism (ptmd.database.models.file.File attribute)
organism_id (ptmd.database.models.file.File attribute)
(ptmd.database.models.organism.Organism attribute)
P
password (ptmd.database.models.user.User attribute)
ptmd.database.models.chemical
module
ptmd.database.models.file
module
ptmd.database.models.organisation
module
ptmd.database.models.organism
module
ptmd.database.models.sample
module
ptmd.database.models.timepoint
module
ptmd.database.models.token
module
ptmd.database.models.token_blocklist
module
ptmd.database.models.user
module
ptmd.lib.creator.core
module
ptmd.lib.creator.dataframes
module
ptmd.lib.data_extractor.core
module
ptmd.lib.email.const
module
ptmd.lib.email.core
module
ptmd.lib.email.load_templates
module
ptmd.lib.email.utils
module
ptmd.lib.excel.formats
module
ptmd.lib.excel.save
module
ptmd.lib.excel.styles
module
ptmd.lib.gdrive.const
module
ptmd.lib.gdrive.core
module
ptmd.lib.gdrive.utils
module
ptmd.lib.isa.core
module
ptmd.lib.isa.ontologies
module
ptmd.lib.updater.batch
module
ptmd.lib.validator.core
module
ptmd.lib.validator.validate_identifier
module
ptox_biosystem_code (ptmd.database.models.organism.Organism attribute)
ptox_biosystem_name (ptmd.database.models.organism.Organism attribute)
ptx_code (ptmd.database.models.chemical.Chemical attribute)
Q
query (ptmd.database.models.chemical.Chemical attribute)
(ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
(ptmd.database.models.organism.Organism attribute)
(ptmd.database.models.sample.Sample attribute)
(ptmd.database.models.timepoint.Timepoint attribute)
(ptmd.database.models.token.Token attribute)
(ptmd.database.models.token_blocklist.TokenBlocklist attribute)
(ptmd.database.models.user.User attribute)
query_class (ptmd.database.models.chemical.Chemical attribute)
(ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
(ptmd.database.models.organism.Organism attribute)
(ptmd.database.models.sample.Sample attribute)
(ptmd.database.models.timepoint.Timepoint attribute)
(ptmd.database.models.token.Token attribute)
(ptmd.database.models.token_blocklist.TokenBlocklist attribute)
(ptmd.database.models.user.User attribute)
R
receive_date (ptmd.database.models.file.File attribute)
received (ptmd.database.models.file.File attribute)
refresh_connection() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
registry (ptmd.database.models.chemical.Chemical attribute)
(ptmd.database.models.file.File attribute)
(ptmd.database.models.organisation.Organisation attribute)
(ptmd.database.models.organism.Organism attribute)
(ptmd.database.models.sample.Sample attribute)
(ptmd.database.models.timepoint.Timepoint attribute)
(ptmd.database.models.token.Token attribute)
(ptmd.database.models.token_blocklist.TokenBlocklist attribute)
(ptmd.database.models.user.User attribute)
remove() (ptmd.database.models.file.File method)
replicates (ptmd.database.models.file.File attribute)
reset_token (ptmd.database.models.user.User attribute)
reset_token_id (ptmd.database.models.user.User attribute)
role (ptmd.database.models.user.User attribute)
S
Sample (class in ptmd.database.models.sample)
sample_id (ptmd.database.models.sample.Sample attribute)
save_file() (ptmd.lib.creator.core.DataframeCreator method)
save_to_excel() (in module ptmd.lib.excel.save)
scientific_name (ptmd.database.models.organism.Organism attribute)
send_confirmation_mail() (in module ptmd.lib.email.core)
send_email() (in module ptmd.lib.email.core)
send_reset_pwd_email() (in module ptmd.lib.email.core)
send_validated_account_mail() (in module ptmd.lib.email.core)
send_validation_mail() (in module ptmd.lib.email.core)
serialize() (ptmd.lib.updater.batch.BatchError method)
set_common_formats() (in module ptmd.lib.excel.formats)
set_password() (ptmd.database.models.user.User method)
set_role() (ptmd.database.models.user.User method)
ship_date (ptmd.database.models.file.File attribute)
ship_samples() (ptmd.database.models.file.File method)
shipment_was_received() (ptmd.database.models.file.File method)
shipped (ptmd.database.models.file.File attribute)
start_date (ptmd.database.models.file.File attribute)
style_general_sheet() (in module ptmd.lib.excel.styles)
style_sample_sheet() (in module ptmd.lib.excel.styles)
style_sheets() (in module ptmd.lib.excel.styles)
T
Timepoint (class in ptmd.database.models.timepoint)
timepoint_id (ptmd.database.models.timepoint.Timepoint attribute)
timepoints (ptmd.database.models.file.File attribute)
to_dataframe() (ptmd.lib.creator.core.DataframeCreator method)
Token (class in ptmd.database.models.token)
token (ptmd.database.models.token.Token attribute)
token_id (ptmd.database.models.token.Token attribute)
token_type (ptmd.database.models.token.Token attribute)
TokenBlocklist (class in ptmd.database.models.token_blocklist)
U
unit (ptmd.database.models.timepoint.Timepoint attribute)
update_file() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
upload_file() (ptmd.lib.gdrive.core.GoogleDriveConnector method)
used_in_files (ptmd.database.models.chemical.Chemical attribute)
User (class in ptmd.database.models.user)
username (ptmd.database.models.user.User attribute)
V
validate() (ptmd.lib.creator.core.DataframeCreator method)
(ptmd.lib.validator.core.ExcelValidator method)
(ptmd.lib.validator.core.ExternalExcelValidator method)
(ptmd.lib.validator.core.VerticalValidator method)
validate_batch() (in module ptmd.lib.validator.validate_identifier)
validate_compound() (in module ptmd.lib.validator.validate_identifier)
validate_controls() (ptmd.lib.validator.core.VerticalValidator method)
validate_controls_compound() (in module ptmd.lib.validator.validate_identifier)
validate_dose() (in module ptmd.lib.validator.validate_identifier)
validate_file() (ptmd.lib.validator.core.ExcelValidator method)
(ptmd.lib.validator.core.ExternalExcelValidator method)
validate_identifier() (in module ptmd.lib.validator.validate_identifier)
validate_password() (ptmd.database.models.user.User method)
validate_replicate() (in module ptmd.lib.validator.validate_identifier)
validate_replicates_compound() (in module ptmd.lib.validator.validate_identifier)
validate_species() (in module ptmd.lib.validator.validate_identifier)
validate_timepoints() (in module ptmd.lib.validator.validate_identifier)
validate_timepoints_and_timeframe() (ptmd.lib.creator.core.DataframeCreator method)
validate_unique_identifier() (in module ptmd.lib.validator.validate_identifier)
validated (ptmd.database.models.file.File attribute)
value (ptmd.database.models.timepoint.Timepoint attribute)
vehicle (ptmd.database.models.file.File attribute)
vehicle_id (ptmd.database.models.file.File attribute)
VerticalValidator (class in ptmd.lib.validator.core)
W
with_traceback() (ptmd.lib.updater.batch.BatchError method)
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