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Changelog for clarity_scripts

0.17 (unreleased)

  • Nothing changed yet.

0.16 (2019-11-05)

  • Bug fixes in generate_hamilton_input_make_cst.py and populate_batch_id.py

0.15 (2019-10-01)

  • New script for generating Human Tissue Storage Reports
    • Details on samples recorded in the LIMS as being currently stored in the lab
    • New config: human_tissue.recipients

0.14 (2019-09-13)

  • Remove tracking letter from customer manifest

0.13 (2019-07-26)

  • Updating EGCG-Core to v0.11.1
  • New pooling and CST workflow scripts:
    • autoplacement_8_well.py
    • check_index_compatibility.py
    • check_plates_libraries_indexes.py
    • generate_hamilton_input_make_cst.py
    • generate_hamilton_input_make_pdp.py
    • generate_hamilton_input_make_pdp_mix.py
    • populate_batch_id.py
    • populate_pool_batch_and_pools.py
    • transfer_udf_input_output.py

0.12.3 (2019-07-10)

  • 'gender' API key renamed to 'sex'

0.12.2 (2019-05-30)

  • copy_samples.py: “Comments” step UDF in “Remove from processing” step now populated with description “Repeat samples requested.”

0.12.1 (2019-05-09)

  • common.py - Bugfix to allow naming of SGP tube racks

0.12 (2019-05-09)

New scripts:

  • copy_samples.py : Create new samples from the ones in the step
  • generate_hamilton_input_qpcr_dilution.py: Generate Hamilton input file for the the QPCR dilution
  • next_step_assignment_spectramax.py: Set next step after spectramax step Other changes:
  • next_step_assignment_sample_receipt.py: Change Step UDF name
  • common.py: Add finish_step function to safely finish an "in progress" step

0.11.2 (2019-04-11)

  • assign_workflow_post_receive_sample.py: routing FluidX tubes to FluidX receipt/transfer workflow
  • create_samples.py: fixing container name regexes
  • create_sample_tracking_letter.py: removing single input container constraint
  • generate_hamilton_input_UPL.py: fixing blank lines in output file
  • generate_manifest.py: fixing UDF parsing - reverting refactor
  • parse_fluidx_scan.py: adding container name check -milton_input_make_cst.py fixing StepEPP max_nb_input_container_typea

0.11.1 (2019-04-02)

  • Fix for unexpected NotImplementedError in spectramax.py
  • Configurable workflow stage names for assigning samples to PCR-free/Nano/KAPA/Quant
  • Fixed KAPA workflow stage name
  • Fixed autoplacement input columns
  • Binary file support
  • Customer manifest email template
  • New scripts:
    • assign_workflow_post_receive_sample.py
    • create_sample_tracking_letter.py
    • create_samples.py
    • email_container_dispatched.py
    • email_container_ready_for_dispatch.py
    • email_manifest_tracking_letter_customer.py
    • email_sample_review.py
    • generate_sample_manifest.py
    • next_step_assignment_sample_receipt.py
    • next_step_assignment_udf.py
    • parse_fluidx_scan.py
    • parse_manifest.py
    • project_udfs_to_step_udfs.py
    • step_udf_completion_check.py

0.11 (2019-03-25)

  • EPP common: Generic Autoplacement class
  • autoplacement_96_well.py: place all input from up to 27 input plate to 1 output plate. (input plate are ordered by name)
  • generate_hamilton_input_quant_studio.py : create one to three hamilon input files from up to load sample from up to 27 input plates
  • normalisation.py: look up the udf from artifact or sample when normalising concentration

0.10 (2019-03-15)

  • EPP common:
    • New validation framework that check step parameters before the _run function is used.
    • generic GenerateHamiltonInputEPP and ParseSpectramaxEPP class
  • Test common: new class to generate Fake entities within a step or a process.
  • KAPA library prep support scripts that helps:
    • with autoplacement in plates (autoplacement_24_imp_gx, autoplacement_24_in_96, autoplacement_qpcr_384)
    • Hamilton worklist generation (generate_hamilton_input_cfp, generate_hamilton_input_imp_ssqc, generate_hamilton_input_ntp, generate_hamilton_input_qpcr_1to24, generate_hamilton_input_seq_quant_plate, generate_hamilton_input_uct)
    • next step assignment (next_step_assignment_gx, next_step_assignment_imp_ssqc, next_step_assignment_kapa_qc, next_step_assignment_kapa_qpcr, next_step_assignment_seq_pico
    • out of workflow routing (assign_workflow_kapa_qc, assign_workflow_preseqlab, assign_workflow_seqlab_quantstudio)
    • normalisation: used to calculate volume of sample and buffer
    • qc_check: generic script to check specific UDF values
    • check_container_name: Ensure the name of container follows a specific format
  • Spectramax parsing: spectramax_sample_quant spectramax_seq_plate_quant both parse spectramax output file at different time

0.9.1 (2018-11-13)

  • Enabled multiple projects for sample disposal emails

0.9 (2018-10-04)

  • PEP8 refactor
  • Boilerplate reduction
    • EPPs are now initialised without arguments, rather than step_uri, username, password, log_file
    • For adding extra arguments, EPPs can define the method add_args(argparser)
  • Adding email_sample_disposal_notification.py
  • Adding email_sample_disposal_review.py
  • Fixing mean coverage query in populate_review_step.py
  • Expanding valid container names in prepare_discard_plate.py
  • Rewriting remove_from_freezer.py

0.8 (2018-06-13)

  • apply_freezer_location.py: is for updating Freezer/Shelf UDFs for samples
  • update email_receive_sample.py to support user prepared libraries
  • next_step_assignment_user_prepared_plate_receipt.py assigns the Next Step for user prepared libraries
  • assign_workflow_user_library.py assigns artifacts that pass through the step to qPCR step and updates required UDF "SSQC Result" to "Passed".
  • check_container_name.py checks that the container names have the correct naming convention.
  • update assign_workflow_receive_sample.py to assign samples to User Prepared Library receipt based on UDF
  • generate_hamilton_input_UPL.py: create hamilton input for the UPL batching step
  • Multiple bug fixes.

0.7 (2018-05-01)

  • populate_review_step: Change the criteria for reviewing run elements so that it is more in line with SOP.
  • assign_sample_review: New script that assign sample after review
  • check_step_UDFs: New script that check if UDFs are present and exist with errors if not.
  • email_data_release_facility_manager: sent data release step notification to facility manager.
  • next_step_assignment_quantstudio_data_import: assign next step after Quantstudio import
  • convert_and_dispatch_genotypes:
    • support for new format.
    • match all samples in the step with sample in the genotyping.
    • adds new UDFs in submitted sample and output artifacts.

0.6.2 (2018-03-26)

  • Updated EGCG-Core to 0.8.1
  • PEP8 refactor
  • New scripts: next_step_assignment, remove_from_freezer

0.6.1 (2018-02-02)

  • New email notification for Data release, Sample receipt, FluidX receipt

0.6 (2017-10-23)

  • Populate steps with review metrics from the Reporting App database for samples and run elements
  • Generate email requesting data release

0.5 (2017-08-30)

  • Added assign_container_name

0.4.1 (2017-07-14)

  • Made Spectramax able to tolerate incomplete plates

0.4 (2017-06-27)

  • Moved automatic file closing to StepEPP superclass
  • Added temporary copy of pyclarity_lims.lims.Lims.get_file_contents to StepEPP
  • Added assign_workflow_receive_sample, assign_workflow_user_library, spectramax

0.3 (2017-06-09)

  • Import of scripts from production server (cleanup and migration to python3)
  • added and tested assign_workflow_preseqlab.py and assign_workflow_seqlab_quantstudio.py

0.2 (2017-04-27)

  • add accufill check in convert_and_dispatch_genotypes
  • Support for installing via setup.py

0.1.1