INDRA Database modules

• The Client
  • The Principal Database Client
    • Access Readings and Text Content (indra_db.client.principal.content)
    • Submit and Retrieve Curations (indra_db.client.principal.curation)
    • Get Raw Statements (indra_db.client.principal.raw_statements)
  • The Readonly Client
    • Construct composable queries (indra_db.client.readonly.query)
  • Miscellaneous Client APIs (Mostly Deprecated)
    • Get Datasets (indra_db.client.datasets)
    • Get Statements (indra_db.client.statements)
• Pipeline Management CLI
  • indra-db
    • content
    • dump
    • kb
    • pa
    • pipeline-stats
    • reading
    • xdd
• Pipeline CLI Implementations
  • Content (indra_db.cli.content)
    • UploadError
    • ContentManager
    • Pubmed
    • PmcManager
    • PmcOA
    • Manuscripts
    • Elsevier
  • Reading (indra_db.cli.reading)
    • ReadingUpdateError
    • ReadingManager
    • BulkReadingManager
    • BulkAwsReadingManager
    • BulkLocalReadingManager
  • PreAssembly (indra_db.cli.preassembly)
    • list_last_updates()
    • list_latest_raw_stmts()
    • run_preassembly()
  • Knowledge Bases (indra_db.cli.knowledgebase)
    • TasManager
    • CBNManager
    • HPRDManager
    • SignorManager
    • BiogridManager
    • BelLcManager
    • PathwayCommonsManager
    • RlimspManager
    • TrrustManager
    • PhosphositeManager
    • CTDManager
    • VirHostNetManager
    • PhosphoElmManager
    • DrugBankManager
  • Static Dumps (indra_db.cli.dump)
    • list_dumps()
    • get_latest_dump_s3_path()
    • DumpOrderError
    • Start
    • PrincipalStats
    • Belief
    • Readonly
    • SourceCount
    • ResiduePosition
    • FullPaStmts
    • FullPaJson
    • Sif
    • StatementHashMeshId
    • End
    • dump()
    • DumperChild
• Database Integrated Reading Tools
  • The Database Readers (indra_db.reading.read_db)
    • ReadDBError
    • generate_reading_id()
    • DatabaseResultData
    • DatabaseStatementData
    • DatabaseMeshRefData
    • DatabaseReader
    • process_content()
    • construct_readers()
    • read()
    • run_reading()
  • The Database Script for Running on AWS (indra_db.reading.read_db_aws)
    • is_trips_datestring()
  • A Class to Manage and Monitor AWS Batch Jobs (indra_db.reading.submitter)
• Database Integrated Preassembly Tools
  • Database Preassembly (indra_db.preassembly.preassemble_db)
    • IndraDBPreassemblyError
    • UserQuit
    • DbPreassembler
    • shash()
    • make_graph()
  • A Class to Manage and Monitor AWS Batch Jobs (indra_db.preassembly.submitter)
• Database Schemas
  • Principal Database Schema (indra_db.schemas.principal_schema)
    • The Principal Schema
    • PrincipalSchema
  • Readonly Database Schema (indra_db.schemas.readonly_schema)
    • ReadonlySchema
  • Class Mix-ins (indra_db.schemas.mixins)
    • DbIndexError
    • IndraDBTableMetaClass
    • IndraDBRefTable
    • Schema
  • Indexes (indra_db.schemas.indexes)
• Utilities
  • Database Session Constructors (indra_db.util.constructors)
    • get_db()
    • get_primary_db()
    • get_ro()
    • get_ro_host()
  • Scripts to Get Content (indra_db.util.content_scripts)
    • get_stmts_with_agent_text_like()
    • get_text_content_from_stmt_ids()
  • Distilling Raw Statements (indra_db.util.distill_statements)
    • delete_raw_statements_by_id()
    • distill_stmts()
    • get_filtered_db_stmts()
    • get_filtered_rdg_stmts()
    • get_reading_stmt_dict()
  • Script to Create a SIF Dump (indra_db.util.dump_sif)
    • dump_sif()
    • get_source_counts()
    • load_db_content()
    • load_res_pos()
    • make_dataframe()
  • General Helper Functions (indra_db.util.helpers)
    • get_raw_stmts_frm_db_list()
    • get_statement_object()
  • Routines for Inserting Statements and Content (indra_db.util.insert)
    • extract_agent_data()
    • insert_db_stmts()
    • insert_pa_stmts()
    • insert_raw_agents()
    • regularize_agent_id()
• Some Miscellaneous Modules
  • Low Level Database Interface (indra_db.databases)
    • DatabaseManager
    • IndraDbException
    • readers
    • reader_versions
    • PrincipalDatabaseManager
    • ReadonlyDatabaseManager
  • Belief Calculator (indra_db.belief)
    • LoadError
    • MockEvidence
    • MockStatement
    • load_mock_statements()
    • populate_support()