Throwaway #20
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Throwaway #20
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Allow to find a runfolder in 'analysis' or 'outgoing' in the presence of a duplicate runfolder in 'incoming'. The duplicates in 'incoming' are sometimes created by instruments well after the run was mirrored and the runfolder moved to 'analysis'.
Recently, the default LIMS driver type in samplesheet generation was changed to 'ml_warehouse'. Following this change, the code for auto-generation of MiSeq default samplesheets is now simplified to exclude an explicit creation of LIMS objects.
…ates Ability to disregard duplicate runfolders.
Simplified samplesheet auto-generation code.
* Samplesheet generation tests - move to mlwh driver. Previously the tests uses XML feeds as a source of LIMS data. All production code is using mlwh database as a source of LIMS data. Amend tests to use mlwh data and the default ml_warehouse lims driver. Amended how an undefined sample public name is dealt with, i.e. converted an error to a warning and assigned a sensible fall-back value. Some samplesheets are generated without names of study owners, followers, etc. This is due to the fact that some studies do not have fixtures for user data. The database fixtures were generated from the current data, this explains multiple differences between the old and new content of the generated samplesheets. In some tests newer production batches were used instead of hand-crafted data. Deleted tests for old scenarios that do not exist in production any longer. Deleted tests that are duplicated by similar tests with more contemporary test data. * Deleted now redundant XML test fixtures
Use correct name instrument name pattern in docs.
* Deleted the xml driver for st::api::lims. * Simplified code for insert size and restored is tests. * Restored previously available tests. Used existing test fixtures, which had to be changed in a few places.
* Improved and extended basic tests for tag zero * Extended tests for study and sample properties
Deleted low-level LIMS XML API
Remove lims xml fixtures
Changes are due to the MySQL database server upgrade to v8.+
Updated DBIx classes from the prod database.
st::api::lims - drop deprecated methods
Dropped unused constants
Dropped project_id, project_name, request_id accessors from st::api::lims since this data is not represented in ml warehouse. project_ids method is dropped as well.
Dropped lims accessors for which no data exist.
In practice we never automatically merged rapid runs, this flag was reverted to false for them by the pipeline. Instruments on which rapid runs were performed are no longer in use.
Restricted automatically meargeable to NovaSeq.
This was used for Tradis runs when no LIMS support was available. Was not needed for the last 7 years.
Created a parent class for two existing samplesheet generators. Moved common methods to this class. Through this inheritance the NovaSeqX samplesheet generator gets a standard method for setting a configurable path for a samplesheet.
An option to read the value from the configuration file is not used.
Ability to set a path for NovaSeqX samplesheet
Added a test to test the correctness of passing the option to teh samplesheet generator.
The object used the ml_warehouse driver. This tests demonstrates that the children of such object are created correctly, their sample properties can be accessed.
Tests moved from t/40-st-lims.t to t/40-st-lims-merge.t since similar functionality for creating a lane object is tested in t/40-st-lims-merge.t t/40-st-lims.t is now left to test methods for retrieving LIMS data using the samplesheet driver.
... to use copy_init_args method instead of _driver_arguments method mostly in order to be consistent. Since this method is called in the run-level object, it does not suffer from the same problems as other methods, which had to be updated in this pr. All new tests for this commit passed without changing the code.
Was needed when we used the xml driver. No current lims driver is using this argument. Existing production code does not pass batch_id to st::api::lims constructor. st::api::lims documentation updated.
The old samplesheet generator had this ability. Rearranged the code so that the samplesheet generator for NovaSeqX also has this ability, which simplifies the code in the samplesheet daemon. NovaSeqX samplesheet generator retains ability to generate a samplesheet when neither id_run nor the run db record is set via the constructor.
Correctly propagate driver details for mlwh driver
Removed st::api::lims batch_id constructor arg.
Daemon4novaseqx samplesheet
Recorded recent changes
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