IGVF Utils package

Installation and configuration instructions are provided on the project’s GitHub wiki.

Examples

• Connection class
  • Imports
  • Connecting to the production and development Portals
  • Log Files
  • GET Request
  • Search
  • PATCH Request
  • POST Request
  • Removing properties from a record

Scripts

• registration
• iu_check_not_posted
• iu_create_gcp_url_list
• iu_generate_upload_creds.py
• iu_get_aliases
• iu_get_accessions

Client API Modules

• igvf_utils.aws_storage
  • S3Upload
    • S3Upload.upload()
  • S3Object
    • S3Object.md5sum()
    • S3Object.size()
• igvf_utils.connection
  • LOG_DIR
  • Connection
    • Connection.IGVFID_KEY
    • Connection.PROFILE_KEY
    • Connection.POST
    • Connection.PATCH
    • Connection.debug_logger
    • Connection.igvf_modes
    • Connection.dry_run
    • Connection.error_logger
    • Connection.post_logger
    • Connection.auth
    • Connection.set_submission()
    • Connection.check_dry_run()
    • Connection.set_dry_run()
    • Connection.set_live_run()
    • Connection.log_error()
    • Connection.add_alias_prefix()
    • Connection.get_aliases()
    • Connection.indexing()
    • Connection.make_search_url()
    • Connection.search()
    • Connection.get_profile_from_payload()
    • Connection.get_lookup_ids_from_payload()
    • Connection.get()
    • Connection.set_attachment()
    • Connection.after_submit_file_cloud_upload()
    • Connection.after_submit_hooks()
    • Connection.before_submit_alias()
    • Connection.before_submit_attachment()
    • Connection.before_post_file()
    • Connection.before_post_fastq_file()
    • Connection.before_submit_hooks()
    • Connection.post()
    • Connection.patch()
    • Connection.remove_props()
    • Connection.remove_and_patch()
    • Connection.get_fastqfiles_on_exp()
    • Connection.get_fastqfile_replicate_hash()
    • Connection.extract_aws_upload_credentials()
    • Connection.get_upload_credentials()
    • Connection.regenerate_aws_upload_creds()
    • Connection.gcp_transfer_urllist()
    • Connection.gcp_transfer_from_aws()
    • Connection.upload_file()
    • Connection.get_platforms_on_experiment()
    • Connection.post_document()
    • Connection.download()
    • Connection.s3_object_path()
• igvf_utils
  • AWARD_PROP_NAME
  • ALIAS_PROP_NAME
  • LAB_PROP_NAME
  • LAB
  • LAB_PREFIX
  • AWARD
  • PROFILES_URL
  • IGVF_MODES
  • TIMEOUT
  • DEBUG_LOGGER_NAME
  • ERROR_LOGGER_NAME
  • POST_LOGGER_NAME
  • debug_logger
  • error_logger
• igvf_utils.profiles
  • DEBUG_LOGGER
  • ERROR_LOGGER
  • UnknownProfile
  • Profiles
    • Profiles.FILE_PROFILE_ID
    • Profiles.SUBMITTED_FILE_PROP_NAME
    • Profiles.MD5SUM_NAME_PROP_NAME
    • Profiles.FILE_SIZE_PROP_NAME
    • Profiles.profiles
    • Profiles.profiles_with_property()
    • Profiles.get_profile_from_id()
    • Profiles.remove_duplicate_associations()
• igvf_utils.utils
  • REQUEST_HEADERS_JSON
  • is_jpg_or_tiff()
  • orient_jpg()
  • url_join()
  • get_record_id()
  • err_context()
  • calculate_md5sum()
  • calculate_file_size()
  • print_format_dict()
  • truncate_long_strings_in_objects()
  • clean_aliases()
  • create_subprocess()
  • strip_alias_prefix()
  • add_to_set()
  • remove_duplicate_objects()

Unit Tests

• igvf_utils.tests.test_utils
• igvf_utils.tests.test_connection

Indices and tables

• Index

• Module Index

• Search Page