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Module detail: ExperimentChecker.pm |
ArrayExpress::Curator::Config.pm - a module defining general config options.
use ArrayExpress::Curator::Config qw($CONFIG);
This module provides definition of some configuration options used throughout the code. These options may be changed by editing the ArrayExpress/Curator/Config.yml file. If you wish to point your Tab2MAGE installation to an alternate site config YAML file, please edit the $siteconf variable in the ArrayExpress/Curator/Config.pm file. For user-specific configuration, this module will also read any .tab2mage.conf file located in your home directory (i.e., $HOME/.tab2mage.conf).
See the ArrayExpress::Curator::MAGE::Definitions manpage for other MAGE-specific constants.
MIAMExpress data source name or DSN, e.g., ``DBI:mysql:db_name:host:port''.
The username used to connect to the MIAMExpress database.
The password used to connect to the MIAMExpress database.
For local ArrayExpress installations only. This is the ArrayExpress data source name or DSN, e.g., ``DBI:Oracle:db_name:host:port'' used in direct connection to the database. Note that the appropriate DBD::Oracle module must be installed for this to work.
The username used to connect to the ArrayExpress database.
The password used to connect to the ArrayExpress database.
For checking the data warehouse readiness of an experiment submission. This database connection is used in checking that any required array designs have been loaded into the data warehouse. This config value should be the ArrayExpress DW data source name or DSN, e.g., ``DBI:Oracle:db_name:host:port'' used in direct connection to the data warehouse. Note that the appropriate DBD::Oracle module must be installed for this to work.
The username used to connect to the AEDW database.
The password used to connect to the AEDW database.
Remote ArrayExpress array design list web page. Used by Tab2MAGE, MIAMExpress and the experiment checker. This is currently accessible from outside EBI, and so the setting can be left as it is.
The ArrayExpress web page root for retrieving array feature lists. In use, the accession number for the PhysicalArrayDesign is appended to AE_RETRIEVE_FEATURELIST before it is used in an HTTP GET.
The ArrayExpress web page root for retrieving ADFs. In use, the database identifier for the PhysicalArrayDesign is appended to AE_RETRIEVE_ADF before it is used in an HTTP GET.
The path to a directory containing CDF files needed for parsing Affymetrix CHP files. The default value is an empty string, which indicates to the scripts that the CDF files are in the current working directory.
The prefix used to autogenerate reassigned protocol accessions. Default value is ``P-TABM-''. Please note that you should change this to prevent conflicts if you intend to use protocol accession reassignment and submit the resulting MAGE-ML to ArrayExpress.
The prefix used in creating experiment accessions. This is used to check that a valid experiment accession number has been used in conjunction with the protocol reassignment mechanism.
The maximum size of LWP::UserAgent downloads. This applies to ArrayExpress ADF and feature list downloads. Currently set to 40MB.
The maximum size of data file which these scripts will attempt to parse. Currently set to 100MB.
The name of the default font to use in visualization graph creation. This gets passed to the ``dot'' program. Currently set to ``Courier''.
Full path to the file used by autosubs_checkd.pl to track running instances of itself.
Email address of the administrator responsible for managing the checker and exporter daemon processes. Emails will be sent to this address on abnormal termination of the process (e.g. on crashes).
Login for the administrator responsible for managing the checker and exporter daemon processes. Other users are restricted from launching these daemons to aid in process management.
The default domain used in creating MAGE-ML identifiers when exporting experiments using the autosubmissions system. This is set by default to 'ebi.ac.uk'. Note that this does not affect submissions exported from a MIAMExpress database.
The email to which enquiries will be directed from the autosubmissions web form.
The SMTP server used to send notification email from the autosubmissions system.
The DSN to use when connecting to the autosubmissions database system. Typically this will be of the form ``DBI:mysql:dbname:host:port''.
The username to use when connecting to the autosubmissions database.
The password to use when connecting to the autosubmissions database.
The filesystem path to the top-level directory where the autosubmissions system should store uploaded spreadsheets and data files.
The filesystem directory into which new submissions are exported as MAGE-ML. A new directory, named using the automatically assigned experiment accession, will be created and populated.
The filesystem directory where the web submissions form may write temporary files. This is principally used for temporary storage of spreadsheet template files. It is recommended that you run a regular script from e.g. your crontab to delete old files.
The URL pointing to the WEBFORM_TEMPLATE_DIR, used to create links to the temporary template files from the web submissions form.
Full path to the file used by mx_autocheck_daemon.pl to track running instances of itself.
Email address of the administrator responsible for managing the mx_autocheck_daemon.pl process. See notes for AUTOSUBS_ADMIN.
Full command (minus arguments) used to export MAGE-ML from a local MIAMExpress database.
A list of MO ExperimentDesignTypes that indicate an experiment is suitable for the ArrayExpress Data Warehouse.
A list of MO ExperimentDesignTypes that indicate an experiment is not suitable for the ArrayExpress Data Warehouse. This is used to differentiate between experiments known to be of the wrong type from those which are merely under-annotated.
The minimum number of hybridizations required in an experiment for it to be considered for the AE Data Warehouse.
A list of array design accession prefixes (e.g. ``A-AFFY-'') where every design can be assumed to be MIAME compliant, for the purposes of experiment MIAME checking.
These are options we recommend you don't change, unless you know what you're doing.
A hashref, with keys representing data file format type and values as arrayrefs listing the coordinate index columns to be used for parsing those formats. See also the ArrayExpress::Datafile manpage. Current format types are: Generic, GenePix, Affymetrix, ArrayVision, Agilent, Scanalyze, ScanArray, QuantArray, Spotfinder, BlueFuse, UCSF Spot, Illumina, CodeLink, Applied Biosystems, NimbleScan.
Supported data file types for per-hyb parsing and MAGE-ML creation. These tags can appear in the Tab2MAGE spreadsheet as part of a File[] column heading. Currently supported: ``raw'' and ``normalized''.
Supported data file type for FGEM parsing and MAGE-ML creation. These tags can appear in the Tab2MAGE spreadsheet as part of a File[] column heading. Currently supported: ``transformed''.
A list of regular expression which match QTs which are omitted from analyses or MAGE-ML output from non-data matrix files.
Errors returned to the shell by each of the scripts are represented by 8-bit integers; here we map them to the constants used.
Similar to the errors above, this error indicates that the checking process crashed for some reason.
A selection of internal error message texts.
Controls whether extended reporting of sample annotation and factor values is available (only supported for generic MIAMExpress installations).
Name of the file to use as the default source of QT information. This is used to point to a file installed alongside the perl modules, and should not be changed unless you know what you're doing.
Name of the file containing a list of Entrez-approved publication abbreviations. Again, this value should not be changed unless strictly necessary.
Octal number indicating the default permissions to use when creating files using the autosubmission system. This is useful if, for example, your webserver process is in a different group from that of your users. The default is 0555.
Octal number indicating the default directory permissions for the autosubmission system. The default is 0777.
A hashref of parameters used in the MIAMExpress database connection.
A hashref of parameters used in the ArrayExpress database connection.
A hashref of parameters used in the AEDW database connection.
A hashref of parameters used in the autosubmissions database connection.
Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2004.
Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.