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defaults-cfg.yml
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defaults-cfg.yml
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# TODO: documentation and comments
# This is the datset dir, ie, the place where Knetminer puts all configuration and data by default.
# This is also the host place where the Docker container usually maps its internal dataset dir, by
# means of a volume.
#
# By default, this has one of this values:
# - if the directory where this top-level config file is named /config, then datasetDir is
# dir(<config-file>)/..
# - else, it is dir(<config-file>)
#
# Most of paths below are relative to this directory.
# Additionally, the variables ${mydir} and ${me} for the directory of this config file and the path of
# the file itself.
#
# datasetDir: /alt/path/to/dataset
#dataDir: # <datasetDir>/data as default
#oxl: # <datasetDir>/data/knowledge-network.oxl
# If this is non-empty, the genes used to seed the initial semantic motif graph traverser are taken from this
# file. Its format is very simple, see the example mentioned here.
#
# By default (ie, when this parameter is undefined), all genes from dataset/species (see below) are used as
# seed genes.
#
# WARNING: usually gene accessions are stored in upper case in a Knetminer, hence here you must use upper case
# identifiers in order to match the data.
#
#seedGenesFile: config/seed-genes-example.tsv
# Used to add the number of publications one wants visibly exported in the KnetMiner instance.
# If not defined default is set at 20.
#
defaultExportedPublicationCount: 100
knetSpaceURL: https://knetminer.com/beta/knetspace
# Details about the datset and supported species. Each dataset has its own species to mention here
#
dataset:
# id: aratiny
# title: Aratiny dataset
organization: Rothamsted Research
# # sampleQueries: config/sample-queries.xml # this is a default
# # backgroundImage: config/background.jpg # this is the default
#
# TODO: we had this in the old config, but not used anywhere:
# appKeywords, appDescription
# species:
# - taxId: 3702
# scientificName: Arabidopsis Thaliana
# commonName: Thale cress
# # chromosomeBaseMap: config/species/base-map-3702.xml # this is the default
# - taxId: 4565
# scientificName: Triticum aestivum
# commonName: Bread Wheat
# - taxId: 4577
# scientificName: Zea mays
# commonName: Maize
# Options for the traverser are managed in this subsection and they can't be validated, so be
# careful with typos and alike
graphTraverser:
# When empty, it takes the state machine traverser (net.sourceforge.ondex.algorithm.graphquery.GraphTraverser)
GraphTraverserClass: ""
# ${me} is the absolute path of this hereby file
# ${mydir} is the absolute path of its directory
# Many paths are auto-resolved (eg, sampleQueries, above), but some need an explicit
# specification, since the configuration component isn't aware they are properties about paths
# (since it passes the values downstream)
StateMachineFilePath: "file:///${mydir}/SemanticMotifs.txt"
"knetminer.backend.configPath": "${mydir}/neo4j/config.xml"
# Credentials for Google Analytics, which tracks various requests and events of a Knetminer instance
# If this section isn't defined, no tracking happens.
#
googleAnalyticsAPI:
# If you still have an old (UA-) property, YOU NEED to convert it into a GA4
# (if not already done by Google) and then use its measurement ID here.
measurementId: G-YX04MPYHBG
# You do need to setup one for the API, which uses the GA4 measurement protocol
# See here: https://wiki.resolution.de/doc/gafcc/latest/configure-the-measurement-api-secret
apiSecret: WplJN-diT-a3I0z5wOlrAQ
# This is an ID of the client that sends tracking info. Typically, i's is
# a UUID, but it's arbitrary.
# If not set, the {@link DatasetInfo#getId() dataset ID} is
# used. The Unix command uuidgen can be uses to generate it.
#clientId: 40cdb6ea-e542-4160-a7da-641f6c150d58
# If you want, you can separate the GA credentials used for the API from those used for
# the UI. We don't recommend it and if this is left null, it will use the
# {@link #getGoogleAnalyticsApiConfig() API credentials}.
#
# WARNING: this imply that you need to omit BOTH this and the API credentials if you want to
# disable GA completely. We DO NOT support the setting where the API tracking is enabled and
# the client tracking is not.
#
# Moreover, the only param that is exposed to the UI is
# {@link GoogleAnalyticsConfiguration#getMeasurementId()}, since that's the only one
# that the Google-provided Js library gtag needs.
#
# This also implies that you can omit API secret and measurement ID from the client
# configuration.
googleAnalyticsClient:
measurementId: G-YR7BJVWTNX
# As said above, it's not used.
# clientId: 75507276-c9d5-48ba-bc14-ed7f9cc53698
# MB: these are my personal credentials, which I sometimes use for tests
#googleAnalyticsAPI:
# measurementId: G-31YFKXKSYH
# apiSecret: c9TGJqIBSVuKB1CoRcZ90Q
# clientId: 40cdb6ea-e542-4160-a7da-641f6c150d58
#googleAnalyticsClient:
# measurementId: G-31YFKXKSYH
# clientId: 75507276-c9d5-48ba-bc14-ed7f9cc53698
# TODO: remove, temporarily keeping it to easily remember the old IDs.
#
# The ID for enabling Google Analytics, to track the requests to a Knetminer instance via Google Analytics
# The default for this is the ID that the Knetminer team uses, but you can use your own ID and get your
# instance tracked. If this isn't defined (ie, set to null), then GA is disabled.
# googleAnalyticsIdApi: UA-88753233-2
#
# We used to have two different trackers, but this isn't very much needed and these two values could be
# the same. As above, if this is null, no tracking happens (and no Google code is downloaded).
# googleAnalyticsIdClient: UA-88753233-1
# New GA4, my (MB) test key
# googleAnalyticsIdClient: G-31YFKXKSYH
#
# UA- are the old (universal) API, which is set to be turned off by July 2023 (TODO: migrate)
# G- are for the new GA4, but they don't work with the Java library we're using (both work with the
# Google-provided Js, which appear to be calling the universal API, very confusing).
# Bottom line, we stick to the old API for the time being.
#
# /end: remove
# This enables the CypherDebugger service and corresponding UI interface at TODO.
# It only applies when Neo4j mode is enabled.
# It's normally disabled and enabled for internal test instances.
# It can be enabled via MAVEN_ARGS, see examples in docker-run.sh.
#
# WARNING: THIS allows for completely BREAKING yor Knetminer instance by sending and registering
# arbitrary Cypher queries for the traverser. DO NOT ENABLE in production!!!
# cypherDebuggerEnabled: true
# These are injected into System.getProperties() and made available to other Java components around
# As you can see below, this is used to inject values inside components that use Spring beans
# files (neo4j/config.xml is an example of that).
#
# They can be overridden from the command line (eg, passing -D to Java, via JAVA_TOOL_OPTIONS)
systemProperties:
# You could omit this from your configuration, but it's not a good idea
"knetminer.configDir": "${mydir}"