Source code for pybel.constants

# -*- coding: utf-8 -*-

"""Constants for PyBEL.

This module maintains the strings used throughout the PyBEL codebase to promote consistency.
"""

from .config import connection


[docs]def get_cache_connection() -> str: """Get the preferred RFC-1738 database connection string. 1. Check the environment variable ``PYBEL_CONNECTION`` 2. Check the ``PYBEL_CONNECTION`` key in the config file ``~/.config/pybel/config.json``. Optionally, this config file might be in a different place if the environment variable ``PYBEL_CONFIG_DIRECTORY`` has been set. 3. Return a default connection string using a SQLite database in the ``~/.pybel``. Optionally, this directory might be in a different place if the environment variable ``PYBEL_RESOURCE_DIRECTORY`` has been set. """ return connection
PYBEL_CONTEXT_TAG = 'pybel_context' PYBEL_AUTOEVIDENCE = 'Automatically added by PyBEL' CITATION_TYPE_BOOK = 'Book' CITATION_TYPE_PUBMED = 'PubMed' CITATION_TYPE_PMC = 'PubMed Central' CITATION_TYPE_JOURNAL = 'Journal' CITATION_TYPE_ONLINE = 'Online Resource' CITATION_TYPE_URL = 'URL' CITATION_TYPE_DOI = 'DOI' CITATION_TYPE_OTHER = 'Other' #: The valid citation types #: .. seealso:: https://wiki.openbel.org/display/BELNA/Citation CITATION_TYPES = { CITATION_TYPE_BOOK: None, CITATION_TYPE_PUBMED: 'pmid', CITATION_TYPE_PMC: 'pmc', CITATION_TYPE_JOURNAL: None, CITATION_TYPE_ONLINE: None, CITATION_TYPE_URL: None, CITATION_TYPE_DOI: 'doi', CITATION_TYPE_OTHER: None, } NAMESPACE_DOMAIN_BIOPROCESS = 'BiologicalProcess' NAMESPACE_DOMAIN_CHEMICAL = 'Chemical' NAMESPACE_DOMAIN_GENE = 'Gene and Gene Products' NAMESPACE_DOMAIN_OTHER = 'Other' #: The valid namespace types #: .. seealso:: https://wiki.openbel.org/display/BELNA/Custom+Namespaces NAMESPACE_DOMAIN_TYPES = { NAMESPACE_DOMAIN_BIOPROCESS, NAMESPACE_DOMAIN_CHEMICAL, NAMESPACE_DOMAIN_GENE, NAMESPACE_DOMAIN_OTHER, } #: Represents the key for the citation date in a citation dictionary CITATION_DATE = 'date' #: Represents the key for the citation authors in a citation dictionary CITATION_AUTHORS = 'authors' #: Represents the key for the citation comment in a citation dictionary CITATION_JOURNAL = 'journal' #: Represents the key for the optional PyBEL citation volume entry in a citation dictionary CITATION_VOLUME = 'volume' #: Represents the key for the optional PyBEL citation issue entry in a citation dictionary CITATION_ISSUE = 'issue' #: Represents the key for the optional PyBEL citation pages entry in a citation dictionary CITATION_PAGES = 'pages' #: Represents the key for the optional PyBEL citation first author entry in a citation dictionary CITATION_FIRST_AUTHOR = 'first' #: Represents the key for the optional PyBEL citation last author entry in a citation dictionary CITATION_LAST_AUTHOR = 'last' # Used during BEL parsing MODIFIER = 'modifier' EFFECT = 'effect' FROM_LOC = 'fromLoc' TO_LOC = 'toLoc' LOCATION = 'location' ACTIVITY = 'Activity' DEGRADATION = 'Degradation' TRANSLOCATION = 'Translocation' CELL_SECRETION = 'CellSecretion' CELL_SURFACE_EXPRESSION = 'CellSurfaceExpression' INTRACELLULAR = 'intracellular' EXTRACELLULAR = 'extracellular space' CELL_SURFACE = 'cell surface' # Internal node data format keys #: The node data key specifying the node's function (e.g. :data:`GENE`, :data:`MIRNA`, :data:`BIOPROCESS`, etc.) FUNCTION = 'function' #: The key specifying a concept CONCEPT = 'concept' #: The key specifying an identifier dictionary's namespace. Used for nodes, activities, and transformations. NAMESPACE = 'namespace' #: The key specifying an identifier dictionary's name. Used for nodes, activities, and transformations. NAME = 'name' #: The key specifying an identifier dictionary IDENTIFIER = 'identifier' #: The key specifying an optional label for the node LABEL = 'label' #: The key specifying an optional description for the node DESCRIPTION = 'description' #: The key specifying xrefs XREFS = 'xref' #: They key representing the nodes that are a member of a composite or complex MEMBERS = 'members' #: The key representing the nodes appearing in the reactant side of a biochemical reaction REACTANTS = 'reactants' #: The key representing the nodes appearing in the product side of a biochemical reaction PRODUCTS = 'products' #: The node data key specifying a fusion dictionary, containing :data:`PARTNER_3P`, :data:`PARTNER_5P`, # :data:`RANGE_3P`, and :data:`RANGE_5P` FUSION = 'fusion' #: The key specifying the identifier dictionary of the fusion's 3-Prime partner PARTNER_3P = 'partner_3p' #: The key specifying the identifier dictionary of the fusion's 5-Prime partner PARTNER_5P = 'partner_5p' #: The key specifying the range dictionary of the fusion's 3-Prime partner RANGE_3P = 'range_3p' #: The key specifying the range dictionary of the fusion's 5-Prime partner RANGE_5P = 'range_5p' FUSION_REFERENCE = 'reference' FUSION_START = 'left' FUSION_STOP = 'right' FUSION_MISSING = 'missing' #: The key specifying the node has a list of associated variants VARIANTS = 'variants' #: The key representing what kind of variation is being represented KIND = 'kind' #: The value for :data:`KIND` for an HGVS variant HGVS = 'hgvs' #: The value for :data:`KIND` for a protein modification PMOD = 'pmod' #: The value for :data:`KIND` for a gene modification GMOD = 'gmod' #: The value for :data:`KIND` for a fragment FRAGMENT = 'frag' #: The allowed values for :data:`KIND` PYBEL_VARIANT_KINDS = { HGVS, PMOD, GMOD, FRAGMENT, } #: The group of all BEL-provided keys for node data dictionaries, used for hashing. PYBEL_NODE_DATA_KEYS = { FUNCTION, NAMESPACE, NAME, IDENTIFIER, VARIANTS, FUSION, MEMBERS, REACTANTS, PRODUCTS, } #: Used as a namespace when none is given when lenient parsing mode is turned on. Not recommended! DIRTY = 'dirty' #: Represents the BEL abundance, abundance() ABUNDANCE = 'Abundance' #: Represents the BEL abundance, geneAbundance() #: .. seealso:: http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#Xabundancea GENE = 'Gene' #: Represents the BEL abundance, rnaAbundance() RNA = 'RNA' #: Represents the BEL abundance, microRNAAbundance() MIRNA = 'miRNA' #: Represents the BEL abundance, proteinAbundance() PROTEIN = 'Protein' #: Represents the BEL function, biologicalProcess() BIOPROCESS = 'BiologicalProcess' #: Represents the BEL function, pathology() PATHOLOGY = 'Pathology' #: Represents the BEL function, populationAbundance() POPULATION = 'Population' #: Represents the BEL abundance, compositeAbundance() COMPOSITE = 'Composite' #: Represents the BEL abundance, complexAbundance() COMPLEX = 'Complex' #: Represents the BEL transformation, reaction() REACTION = 'Reaction' #: A set of all of the valid PyBEL node functions PYBEL_NODE_FUNCTIONS = { ABUNDANCE, GENE, RNA, MIRNA, PROTEIN, BIOPROCESS, PATHOLOGY, COMPOSITE, COMPLEX, REACTION, POPULATION, } #: The mapping from PyBEL node functions to BEL strings rev_abundance_labels = { ABUNDANCE: 'a', GENE: 'g', MIRNA: 'm', PROTEIN: 'p', RNA: 'r', BIOPROCESS: 'bp', PATHOLOGY: 'path', COMPLEX: 'complex', COMPOSITE: 'composite', POPULATION: 'pop', } # Internal edge data keys #: The key for an internal edge data dictionary for the relation string RELATION = 'relation' #: The key for an internal edge data dictionary for the citation dictionary CITATION = 'citation' CITATION_DB = NAMESPACE # for backwards compatibility CITATION_IDENTIFIER = IDENTIFIER # for backwards compatibility #: The key for an internal edge data dictionary for the evidence string EVIDENCE = 'evidence' #: The key for an internal edge data dictionary for the annotations dictionary ANNOTATIONS = 'annotations' SOURCE = 'source' SUBJECT = SOURCE # for backwards compatibility TARGET = 'target' OBJECT = TARGET # for backwards compatibility #: The key for an internal edge data dictionary for the source modifier dictionary SOURCE_MODIFIER = 'source_modifier' #: The key for an internal edge data dictionary for the target modifier dictionary TARGET_MODIFIER = 'target_modifier' #: The key or an internal edge data dictionary for the line number LINE = 'line' #: The key representing the hash of the other HASH = 'hash' #: The group of all BEL-provided keys for edge data dictionaries, used for hashing. PYBEL_EDGE_DATA_KEYS = { RELATION, CITATION, EVIDENCE, ANNOTATIONS, SOURCE_MODIFIER, TARGET_MODIFIER, } #: The group of all PyBEL-specific keys for edge data dictionaries, not used for hashing. PYBEL_EDGE_METADATA_KEYS = { LINE, HASH, } #: The group of all PyBEL annotated keys for edge data dictionaries PYBEL_EDGE_ALL_KEYS = PYBEL_EDGE_DATA_KEYS | PYBEL_EDGE_METADATA_KEYS #: A BEL relationship HAS_REACTANT = 'hasReactant' #: A BEL relationship HAS_PRODUCT = 'hasProduct' #: A BEL relationship HAS_VARIANT = 'hasVariant' #: A BEL relationship #: :data:`GENE` to :data:`RNA` is called transcription TRANSCRIBED_TO = 'transcribedTo' #: A BEL relationship #: :data:`RNA` to :data:`PROTEIN` is called translation TRANSLATED_TO = 'translatedTo' #: A BEL relationship INCREASES = 'increases' #: A BEL relationship DIRECTLY_INCREASES = 'directlyIncreases' #: A BEL relationship DECREASES = 'decreases' #: A BEL relationship DIRECTLY_DECREASES = 'directlyDecreases' #: A BEL relationship CAUSES_NO_CHANGE = 'causesNoChange' #: A BEL relationship REGULATES = 'regulates' #: A BEL relationship BINDS = 'binds' #: A BEL relationship CORRELATION = 'correlation' #: A BEL relationship NO_CORRELATION = 'noCorrelation' #: A BEL relationship NEGATIVE_CORRELATION = 'negativeCorrelation' #: A BEL relationship POSITIVE_CORRELATION = 'positiveCorrelation' #: A BEL relationship ASSOCIATION = 'association' #: A BEL relationship ORTHOLOGOUS = 'orthologous' #: A BEL relationship ANALOGOUS_TO = 'analogousTo' #: A BEL relationship IS_A = 'isA' #: A BEL relationship RATE_LIMITING_STEP_OF = 'rateLimitingStepOf' #: A BEL relationship SUBPROCESS_OF = 'subProcessOf' #: A BEL relationship BIOMARKER_FOR = 'biomarkerFor' #: A BEL relationship PROGONSTIC_BIOMARKER_FOR = 'prognosticBiomarkerFor' #: A BEL relationship, added by PyBEL EQUIVALENT_TO = 'equivalentTo' #: A BEL relationship, added by PyBEL PART_OF = 'partOf' #: A set of all causal relationships that have an increasing effect CAUSAL_INCREASE_RELATIONS = {INCREASES, DIRECTLY_INCREASES} #: A set of all causal relationships that have a decreasing effect CAUSAL_DECREASE_RELATIONS = {DECREASES, DIRECTLY_DECREASES} #: A set of direct causal relations DIRECT_CAUSAL_RELATIONS = {DIRECTLY_DECREASES, DIRECTLY_INCREASES} #: A set of direct causal relations INDIRECT_CAUSAL_RELATIONS = {DECREASES, INCREASES, REGULATES} #: A set of causal relationships that are polar CAUSAL_POLAR_RELATIONS = CAUSAL_INCREASE_RELATIONS | CAUSAL_DECREASE_RELATIONS #: A set of all causal relationships CAUSAL_RELATIONS = CAUSAL_INCREASE_RELATIONS | CAUSAL_DECREASE_RELATIONS | {REGULATES} APOLAR_CORRELATIVE_RELATIONS = { CORRELATION, NO_CORRELATION, } POLAR_CORRELATIVE_RELATIONS = { POSITIVE_CORRELATION, NEGATIVE_CORRELATION, } #: A set of all correlative relationships CORRELATIVE_RELATIONS = APOLAR_CORRELATIVE_RELATIONS | POLAR_CORRELATIVE_RELATIONS #: A set of polar relations POLAR_RELATIONS = CAUSAL_POLAR_RELATIONS | POLAR_CORRELATIVE_RELATIONS #: A set of all relationships that are inherently directionless, and are therefore added to the graph twice TWO_WAY_RELATIONS = CORRELATIVE_RELATIONS | { ASSOCIATION, ORTHOLOGOUS, ANALOGOUS_TO, EQUIVALENT_TO, BINDS, } #: A list of relationship types that don't require annotations or evidence UNQUALIFIED_EDGES = { HAS_REACTANT, HAS_PRODUCT, HAS_VARIANT, TRANSCRIBED_TO, TRANSLATED_TO, IS_A, EQUIVALENT_TO, PART_OF, ORTHOLOGOUS, } # BEL Keywords BEL_KEYWORD_SET = 'SET' BEL_KEYWORD_DOCUMENT = 'DOCUMENT' BEL_KEYWORD_DEFINE = 'DEFINE' BEL_KEYWORD_NAMESPACE = 'NAMESPACE' BEL_KEYWORD_ANNOTATION = 'ANNOTATION' BEL_KEYWORD_AS = 'AS' BEL_KEYWORD_URL = 'URL' BEL_KEYWORD_LIST = 'LIST' BEL_KEYWORD_OWL = 'OWL' BEL_KEYWORD_PATTERN = 'PATTERN' BEL_KEYWORD_UNSET = 'UNSET' BEL_KEYWORD_STATEMENT_GROUP = 'STATEMENT_GROUP' BEL_KEYWORD_CITATION = 'Citation' BEL_KEYWORD_EVIDENCE = 'Evidence' BEL_KEYWORD_SUPPORT = 'SupportingText' BEL_KEYWORD_ALL = 'ALL' BEL_KEYWORD_METADATA_NAME = 'Name' BEL_KEYWORD_METADATA_VERSION = 'Version' BEL_KEYWORD_METADATA_DESCRIPTION = 'Description' BEL_KEYWORD_METADATA_AUTHORS = 'Authors' BEL_KEYWORD_METADATA_CONTACT = 'ContactInfo' BEL_KEYWORD_METADATA_LICENSES = 'Licenses' BEL_KEYWORD_METADATA_COPYRIGHT = 'Copyright' BEL_KEYWORD_METADATA_DISCLAIMER = 'Disclaimer' BEL_KEYWORD_METADATA_PROJECT = 'Project' # Internal metadata representation. See BELGraph documentation, since these are shielded from the user by properties. #: The key for the document metadata dictionary. Can be accessed by :code:`graph.graph[GRAPH_METADATA]`, or by using #: the property built in to the :class:`pybel.BELGraph`, :func:`pybel.BELGraph.document` GRAPH_METADATA = 'document_metadata' GRAPH_NAMESPACE_URL = 'namespace_url' GRAPH_NAMESPACE_PATTERN = 'namespace_pattern' GRAPH_ANNOTATION_URL = 'annotation_url' GRAPH_ANNOTATION_MIRIAM = 'annotation_miriam' GRAPH_ANNOTATION_CURIE = 'annotation_curie' GRAPH_ANNOTATION_PATTERN = 'annotation_pattern' GRAPH_ANNOTATION_LIST = 'annotation_list' GRAPH_WARNINGS = 'warnings' GRAPH_PYBEL_VERSION = 'pybel_version' GRAPH_PATH = 'path' #: The key for the document name. Can be accessed by :code:`graph.document[METADATA_NAME]` or by using the property #: built into the :class:`pybel.BELGraph` class, :func:`pybel.BELGraph.name` METADATA_NAME = 'name' #: The key for the document version. Can be accessed by :code:`graph.document[METADATA_VERSION]` METADATA_VERSION = 'version' #: The key for the document description. Can be accessed by :code:`graph.document[METADATA_DESCRIPTION]` METADATA_DESCRIPTION = 'description' #: The key for the document authors. Can be accessed by :code:`graph.document[METADATA_NAME]` METADATA_AUTHORS = 'authors' #: The key for the document contact email. Can be accessed by :code:`graph.document[METADATA_CONTACT]` METADATA_CONTACT = 'contact' #: The key for the document licenses. Can be accessed by :code:`graph.document[METADATA_LICENSES]` METADATA_LICENSES = 'licenses' #: The key for the document copyright information. Can be accessed by :code:`graph.document[METADATA_COPYRIGHT]` METADATA_COPYRIGHT = 'copyright' #: The key for the document disclaimer. Can be accessed by :code:`graph.document[METADATA_DISCLAIMER]` METADATA_DISCLAIMER = 'disclaimer' #: The key for the document project. Can be accessed by :code:`graph.document[METADATA_PROJECT]` METADATA_PROJECT = 'project' #: Provides a mapping from BEL language keywords to internal PyBEL strings DOCUMENT_KEYS = { BEL_KEYWORD_METADATA_AUTHORS: METADATA_AUTHORS, BEL_KEYWORD_METADATA_CONTACT: METADATA_CONTACT, BEL_KEYWORD_METADATA_COPYRIGHT: METADATA_COPYRIGHT, BEL_KEYWORD_METADATA_DESCRIPTION: METADATA_DESCRIPTION, BEL_KEYWORD_METADATA_DISCLAIMER: METADATA_DISCLAIMER, BEL_KEYWORD_METADATA_LICENSES: METADATA_LICENSES, BEL_KEYWORD_METADATA_NAME: METADATA_NAME, BEL_KEYWORD_METADATA_VERSION: METADATA_VERSION, BEL_KEYWORD_METADATA_PROJECT: METADATA_PROJECT, } #: The keys to use when inserting a graph to the cache METADATA_INSERT_KEYS = { METADATA_NAME, METADATA_VERSION, METADATA_DESCRIPTION, METADATA_AUTHORS, METADATA_CONTACT, METADATA_LICENSES, METADATA_COPYRIGHT, METADATA_DISCLAIMER, } #: Provides a mapping from internal PyBEL strings to BEL language keywords. Is the inverse of :data:`DOCUMENT_KEYS` INVERSE_DOCUMENT_KEYS = {v: k for k, v in DOCUMENT_KEYS.items()} #: A set representing the required metadata during BEL document parsing REQUIRED_METADATA = { METADATA_NAME, METADATA_VERSION, METADATA_DESCRIPTION, METADATA_AUTHORS, METADATA_CONTACT, } # Modifier parser constants #: The key for the starting position of a fragment range FRAGMENT_START = 'start' #: The key for the stopping position of a fragment range FRAGMENT_STOP = 'stop' #: The key signifying that there is neither a start nor stop position defined FRAGMENT_MISSING = 'missing' #: The key for any additional descriptive data about a fragment FRAGMENT_DESCRIPTION = 'description' #: The order for serializing gene modification data GMOD_ORDER = [KIND, IDENTIFIER] #: The key for the reference nucleotide in a gene substitution. #: Only used during parsing since this is converted to HGVS. GSUB_REFERENCE = 'reference' #: The key for the position of a gene substitution. #: Only used during parsing since this is converted to HGVS GSUB_POSITION = 'position' #: The key for the effect of a gene substitution. #: Only used during parsing since this is converted to HGVS GSUB_VARIANT = 'variant' #: The key for the protein modification code. PMOD_CODE = 'code' #: The key for the protein modification position. PMOD_POSITION = 'pos' #: The order for serializing information about a protein modification PMOD_ORDER = [KIND, IDENTIFIER, PMOD_CODE, PMOD_POSITION] #: The key for the reference amino acid in a protein substitution. #: Only used during parsing since this is concerted to HGVS PSUB_REFERENCE = 'reference' #: The key for the position of a protein substitution. Only used during parsing since this is converted to HGVS. PSUB_POSITION = 'position' #: The key for the variant of a protein substitution.Only used during parsing since this is converted to HGVS. PSUB_VARIANT = 'variant' #: The key for the position at which a protein is truncated TRUNCATION_POSITION = 'position' #: The mapping from BEL namespace codes to PyBEL internal abundance constants #: ..seealso:: https://wiki.openbel.org/display/BELNA/Assignment+of+Encoding+%28Allowed+Functions%29+for+BEL+Namespaces belns_encodings = { 'G': {GENE}, 'R': {RNA, MIRNA}, 'P': {PROTEIN}, 'M': {MIRNA}, 'A': {ABUNDANCE, RNA, MIRNA, PROTEIN, GENE, COMPLEX}, 'B': {PATHOLOGY, BIOPROCESS}, 'O': {PATHOLOGY}, 'C': {COMPLEX}, } BELNS_ENCODING_STR = ''.join(sorted(belns_encodings)) PYBEL_REMOTE_HOST = 'PYBEL_REMOTE_HOST' PYBEL_REMOTE_USER = 'PYBEL_REMOTE_USER' PYBEL_REMOTE_PASSWORD = 'PYBEL_REMOTE_PASSWORD' # noqa: S105 PYBEL_PUBMED = '29048466' SET_CITATION_FMT = 'SET Citation = {{"{}", "{}"}}'