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MoTrPAC / MotrpacBicQC

R package for the MoTrPAC community
https://motrpac.github.io/MotrpacBicQC/index.html
MIT License
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Date format #206

Closed araskind closed 1 year ago

araskind commented 1 year ago

I was validating the updated manifest and this was in QC file:

Why is it reported as incorrect format The format you propose in guidlines document is MM/DD/YYYY HH:MM:SS AM/PM which seems to be not valid, at least not in Java, HH stands for 24 hour format which can not be AM/PM at the same time and SS stands for milliseconds, while ss - for seconds. Could you please clarify?

PS. I just looked in the code and the validation function includes these:

parsed_datetimes <- lubridate::parse_date_time(datetime_values, orders = c("mdy HM", "mdy HMp", "m/d/y h:M:s a", "m/d/y h:M a"), quiet = TRUE)

None of these formats corresponds to one suggested in the guidelines document

biodavidjm commented 1 year ago

Hi @araskind

The current data format was determined in alignment with the feedback from the metabolomics groups during our one-on-one consultations. As you've observed, we have extended our support to include a variety of additional formats, in an effort to foster flexibility.

We have rigorously validated each of these formats using simulated data. However, in the dynamic realm of software development, some discrepancies might still sneak through our checks.

To better address this situation, may we kindly request a test case? Specifically, we would appreciate a metadata sample file (with about 10 lines of data) that you have encountered this issue. This will significantly aid our debugging process and help us in pinpointing the issue more effectively.

We appreciate your cooperation. Thank you!

araskind commented 1 year ago

Please find the sample file enclosed.

I know that there are hundred ways to format date/time, but in the text in the guidelines document is this one:

● “acquisition_date”: (data type: date), required: date for the process of collecting and recording mass spectral data from samples. Two possible formats:

       *   Preferred: MM/DD/YYYY HH:MM:SS AM/PM
       *   Alternative: YYYY-MM-DD (with no time provided)

I think the conventions for formatting are universal across programming languages (although I am not sure). In Java the “Preferred” format is not valid and it is not one of specified in your validation R code, that is why I don’t know which one to use.

From: David JM @.> Date: Thursday, June 15, 2023 at 3:56 PM To: MoTrPAC/MotrpacBicQC @.> Cc: Sasha Raskind @.>, Mention @.> Subject: Re: [MoTrPAC/MotrpacBicQC] Date format (Issue #206) External Email - Use Caution

Hi @araskindhttps://github.com/araskind

The current data format was determined in alignment with the feedback from the metabolomics groups during our one-on-one consultations. As you've observed, we have extended our support to include a variety of additional formats, in an effort to foster flexibility.

We have rigorously validated each of these formats using simulated data. However, in the dynamic realm of software development, some discrepancies might still sneak through our checks.

To better address this situation, may we kindly request a test case? Specifically, we would appreciate a metadata sample file (with about 10 lines of data) that you have encountered this issue. This will significantly aid our debugging process and help us in pinpointing the issue more effectively.

We appreciate your cooperation. Thank you!

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sample_id sample_type sample_order ms_mode raw_file extraction_date acquisition_date lc_column_id MRC2 sample ID Injection time Sample Position Sample Name Comment Method Inj Vol (ul) CS00000SB-01-B01 QC-Blank 1 IONPNEG 20220107-EX01190-A049-IN0030-CS00000SB-01-N 2022-01-06 01/07/2022 05:43:00 Agilent-759700-902_US00000000-B00011 CS00000SB 1/7/2022 17:43 P3-F6 CS00000SB-01 Solvent Blank D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS00000SB-02-B01 QC-Blank 2 IONPNEG 20220107-EX01190-A049-IN0030-CS00000SB-02-N 2022-01-06 01/07/2022 06:17:00 Agilent-759700-902_US00000000-B00011 CS00000SB 1/7/2022 18:17 P3-F6 CS00000SB-02 Solvent Blank D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 R00CHRPL1-01-B01 QC-InternalStandard 3 IONPNEG 20220107-EX01190-A049-IN0030-R00CHRPL1-01-N 2022-01-06 01/07/2022 06:51:00 Agilent-759700-902_US00000000-B00011 R00CHRPL1 1/7/2022 18:51 P3-F2 R00CHRPL1-01 Reference 1 - plasma D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 R00CHRPL1-02-B01 QC-InternalStandard 4 IONPNEG 20220107-EX01190-A049-IN0030-R00CHRPL1-02-N 2022-01-06 01/07/2022 07:25:00 Agilent-759700-902_US00000000-B00011 R00CHRPL1 1/7/2022 19:25 P3-F2 R00CHRPL1-02 Reference 1 - plasma D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS00000SB-03-B01 QC-Blank 5 IONPNEG 20220107-EX01190-A049-IN0030-CS00000SB-03-N 2022-01-06 01/07/2022 07:59:00 Agilent-759700-902_US00000000-B00011 CS00000SB 1/7/2022 19:59 P3-F6 CS00000SB-03 Solvent Blank D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CSMR81040-01-B01 QC-Reference 6 IONPNEG 20220107-EX01190-A049-IN0030-CSMR81040-01-N 2022-01-06 01/07/2022 08:32:00 Agilent-759700-902_US00000000-B00011 CSMR81040 1/7/2022 20:32 P3-F3 CSMR81040-01 MoTrPAC - Plasma-Human: Male D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CSMR81040-02-B01 QC-Reference 7 IONPNEG 20220107-EX01190-A049-IN0030-CSMR81040-02-N 2022-01-06 01/07/2022 09:06:00 Agilent-759700-902_US00000000-B00011 CSMR81040 1/7/2022 21:06 P3-F3 CSMR81040-02 MoTrPAC - Plasma-Human: Male D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CSMR81030-01-B01 QC-Reference 8 IONPNEG 20220107-EX01190-A049-IN0030-CSMR81030-01-N 2022-01-06 01/07/2022 09:40:00 Agilent-759700-902_US00000000-B00011 CSMR81030 1/7/2022 21:40 P3-F4 CSMR81030-01 MoTrPAC - Plasma-Human: Female D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CSMR81030-02-B01 QC-Reference 9 IONPNEG 20220107-EX01190-A049-IN0030-CSMR81030-02-N 2022-01-06 01/07/2022 10:14:00 Agilent-759700-902_US00000000-B00011 CSMR81030 1/7/2022 22:14 P3-F4 CSMR81030-02 MoTrPAC - Plasma-Human: Female D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS00000MP-01-B01 QC-DriftCorrection 10 IONPNEG 20220107-EX01190-A049-IN0030-CS00000MP-01-N 2022-01-06 01/07/2022 10:47:00 Agilent-759700-902_US00000000-B00011 CS00000MP 1/7/2022 22:47 P3-F1 CS00000MP-01 Master Pool D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS000QCMP-01-B01 QC-Pooled 11 IONPNEG 20220107-EX01190-A049-IN0030-CS000QCMP-01-N 2022-01-06 01/07/2022 11:21:00 Agilent-759700-902_US00000000-B00011 CS000QCMP 1/7/2022 23:21 P3-F1 CS000QCMP-01 Master Pool.QCMP D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11169010204 Sample 12 IONPNEG 20220107-EX01190-A049-IN0030-S00054705-11169010204-N 2022-01-06 01/07/2022 11:55:00 Agilent-759700-902_US00000000-B00011 S00054705 1/7/2022 23:55 P2-D9 S00054705 090_11169010204 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11449020211 Sample 13 IONPNEG 20220107-EX01190-A049-IN0030-S00054659-11449020211-N 2022-01-06 01/08/2022 12:29:00 Agilent-759700-902_US00000000-B00011 S00054659 1/8/2022 0:29 P1-E8 S00054659 044_11449020211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11007070211 Sample 14 IONPNEG 20220107-EX01190-A049-IN0030-S00054646-11007070211-N 2022-01-06 01/08/2022 01:03:00 Agilent-759700-902_US00000000-B00011 S00054646 1/8/2022 1:03 P1-D4 S00054646 031_11007070211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11442050211 Sample 15 IONPNEG 20220107-EX01190-A049-IN0030-S00054694-11442050211-N 2022-01-06 01/08/2022 01:37:00 Agilent-759700-902_US00000000-B00011 S00054694 1/8/2022 1:37 P2-C7 S00054694 079_11442050211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11283040211 Sample 16 IONPNEG 20220107-EX01190-A049-IN0030-S00054679-11283040211-N 2022-01-06 01/08/2022 02:11:00 Agilent-759700-902_US00000000-B00011 S00054679 1/8/2022 2:11 P2-B1 S00054679 064_11283040211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11151020211 Sample 17 IONPNEG 20220107-EX01190-A049-IN0030-S00054620-11151020211-N 2022-01-06 01/08/2022 02:45:00 Agilent-759700-902_US00000000-B00011 S00054620 1/8/2022 2:45 P1-A5 S00054620 005_11151020211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11327040211 Sample 18 IONPNEG 20220107-EX01190-A049-IN0030-S00054681-11327040211-N 2022-01-06 01/08/2022 03:19:00 Agilent-759700-902_US00000000-B00011 S00054681 1/8/2022 3:19 P2-B3 S00054681 066_11327040211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11205060211 Sample 19 IONPNEG 20220107-EX01190-A049-IN0030-S00054658-11205060211-N 2022-01-06 01/08/2022 04:27:00 Agilent-759700-902_US00000000-B00011 S00054658 1/8/2022 4:27 P1-E7 S00054658 043_11205060211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS00000MP-02-B01 QC-DriftCorrection 20 IONPNEG 20220107-EX01190-A049-IN0030-CS00000MP-02-N 2022-01-06 01/08/2022 05:01:00 Agilent-759700-902_US00000000-B00011 CS00000MP 1/8/2022 5:01 P3-F1 CS00000MP-02 Master Pool D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11320040211 Sample 21 IONPNEG 20220107-EX01190-A049-IN0030-S00054652-11320040211-N 2022-01-06 01/08/2022 05:35:00 Agilent-759700-902_US00000000-B00011 S00054652 1/8/2022 5:35 P1-E1 S00054652 037_11320040211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11055010204 Sample 22 IONPNEG 20220107-EX01190-A049-IN0030-S00054706-11055010204-N 2022-01-06 01/08/2022 06:42:00 Agilent-759700-902_US00000000-B00011 S00054706 1/8/2022 6:42 P2-E1 S00054706 091_11055010204 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11038040211 Sample 23 IONPNEG 20220107-EX01190-A049-IN0030-S00054665-11038040211-N 2022-01-06 01/08/2022 07:16:00 Agilent-759700-902_US00000000-B00011 S00054665 1/8/2022 7:16 P1-F5 S00054665 050_11038040211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11007010204 Sample 24 IONPNEG 20220107-EX01190-A049-IN0030-S00054707-11007010204-N 2022-01-06 01/08/2022 07:50:00 Agilent-759700-902_US00000000-B00011 S00054707 1/8/2022 7:50 P2-E2 S00054707 092_11007010204 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11283050211 Sample 25 IONPNEG 20220107-EX01190-A049-IN0030-S00054680-11283050211-N 2022-01-06 01/08/2022 08:24:00 Agilent-759700-902_US00000000-B00011 S00054680 1/8/2022 8:24 P2-B2 S00054680 065_11283050211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11003050211 Sample 26 IONPNEG 20220107-EX01190-A049-IN0030-S00054632-11003050211-N 2022-01-06 01/08/2022 09:32:00 Agilent-759700-902_US00000000-B00011 S00054632 1/8/2022 9:32 P1-B8 S00054632 017_11003050211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11151040211 Sample 27 IONPNEG 20220107-EX01190-A049-IN0030-S00054622-11151040211-N 2022-01-06 01/08/2022 10:06:00 Agilent-759700-902_US00000000-B00011 S00054622 1/8/2022 10:06 P1-A7 S00054622 007_11151040211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS00000MP-03-B01 QC-DriftCorrection 28 IONPNEG 20220107-EX01190-A049-IN0030-CS00000MP-03-N 2022-01-06 01/08/2022 10:40:00 Agilent-759700-902_US00000000-B00011 CS00000MP 1/8/2022 10:40 P3-F1 CS00000MP-03 Master Pool D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 CS000QCMP-02-B01 QC-Pooled 29 IONPNEG 20220107-EX01190-A049-IN0030-CS000QCMP-02-N 2022-01-06 01/08/2022 11:14:00 Agilent-759700-902_US00000000-B00011 CS000QCMP 1/8/2022 11:14 P3-F1 CS000QCMP-02 Master Pool.QCMP D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11151030211 Sample 30 IONPNEG 20220107-EX01190-A049-IN0030-S00054621-11151030211-N 2022-01-06 01/08/2022 11:48:00 Agilent-759700-902_US00000000-B00011 S00054621 1/8/2022 11:48 P1-A6 S00054621 006_11151030211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11327070211 Sample 31 IONPNEG 20220107-EX01190-A049-IN0030-S00054684-11327070211-N 2022-01-06 01/08/2022 12:22:00 Agilent-759700-902_US00000000-B00011 S00054684 1/8/2022 12:22 P2-B6 S00054684 069_11327070211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11169050211 Sample 32 IONPNEG 20220107-EX01190-A049-IN0030-S00054636-11169050211-N 2022-01-06 01/08/2022 12:56:00 Agilent-759700-902_US00000000-B00011 S00054636 1/8/2022 12:56 P1-C3 S00054636 021_11169050211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11020020211 Sample 33 IONPNEG 20220107-EX01190-A049-IN0030-S00054624-11020020211-N 2022-01-06 01/08/2022 01:30:00 Agilent-759700-902_US00000000-B00011 S00054624 1/8/2022 13:30 P1-A9 S00054624 009_11020020211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7 11283030211 Sample 34 IONPNEG 20220107-EX01190-A049-IN0030-S00054678-11283030211-N 2022-01-06 01/08/2022 02:04:00 Agilent-759700-902_US00000000-B00011 S00054678 1/8/2022 14:04 P2-A9 S00054678 063_11283030211 D:\MassHunter\Methods\MoTrPAC\precovid human\M001_30min_centroid_MS1_7ul_WBsensON.m 7

biodavidjm commented 1 year ago

Thanks. The current version, as explained in the guideilnes, supports the AM/PM format. But it makes sense to also support the 24 hours format. We will release a new version very soon supporting the 24 hours format as well.

biodavidjm commented 1 year ago

HI @araskind A new version 0.8.8 is out. Please, reinstall it and try again and let me know. Thanks!