search

SD2E / experimental-intent-parser

A tool that combines a word-processing interface with structured tables and assisted linking to definitions to provide a simple interface for incremental codification of experiment designs.
BSD 3-Clause "New" or "Revised" License
4 stars 0 forks source link

Mysteriously missing dictionary entries #87

Closed mwes closed 4 years ago

mwes commented 4 years ago

In GitLab by @nwalczak on Aug 8, 2019, 11:05

I first became clued into this when I opened issue #82. I had noticed that MG1655 was in the dictionary previously, but didn't appear to be in the dictionary later. I got a little confused because originally I wrote MG1665 instead of MG1655 in the ticket but I've since found that that didn't matter.

By comparing the saved copy's of the item_map, that at one point I had an item map that contained slightly fewer entries than the current item_map. When I diffed the json files, this is the result I got:

nwalczak@MIN-nwalczak-L1 ~/workspace/sd2/experimental-intent-parser/intent-parser-server/src $ diff item-map-comp.json item-map-fresh.json  | colordiff
78a79
>   "Ethanol": "https://hub.sd2e.org/user/sd2e/design/CAT_71006_012/1",
593a595
>   "Bacillus subtilis 168 comKS genome": "https://hub.sd2e.org/user/sd2e/design/Bacillus0x20subtilis0x201680x20comKS0x20genome/1",
756a759,797
>   "MG1655": "https://hub.sd2e.org/user/sd2e/design/MG1655/1",
>   "MG1655___with___RPU_Standard_Plasmid": "https://hub.sd2e.org/user/sd2e/design/MG1655___with___RPU_Standard_Plasmid/1",
>   "MG1655_LPV3": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3/1",
>   "MG1655_LPV3_AraC_Sensor": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_AraC_Sensor/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pPhlF_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pPhlF_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_AmeR": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_AmeR/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_AmeR_pPhlF_pAmeR_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_AmeR_pPhlF_pAmeR_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_BM3R1": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_BM3R1/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_BM3R1_pPhlF_pBM3R1_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PhlF_pTac_BM3R1_pPhlF_pBM3R1_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA_pPsrA_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA_pPsrA_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA_pTac_AmeR": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA_pTac_AmeR/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA_pTac_AmeR_pPsrA_pAmeR_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_PsrA_pTac_AmeR_pPsrA_pAmeR_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pBADmin_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pBADmin_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pTac_AmeR": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pTac_AmeR/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pTac_AmeR_pAmeR_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pTac_AmeR_pAmeR_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pTac_BM3R1": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pTac_BM3R1/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pTac_BM3R1_pBM3R1_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pTac_BM3R1_pBM3R1_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors_pTac_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors_pTac_YFP/1",
>   "MG1655_LPV3_LacI_Sensor": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_Sensor/1",
>   "MG1655_LPV3_LacI_Sensor_pTac_AmeR": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_Sensor_pTac_AmeR/1",
>   "MG1655_LPV3_LacI_Sensor_pTac_BM3R1": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_Sensor_pTac_BM3R1/1",
>   "MG1655_LPV3_LacI_Sensor_pTac_PhlF": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_Sensor_pTac_PhlF/1",
>   "MG1655_LPV3_LacI_Sensor_pTac_PsrA": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_Sensor_pTac_PsrA/1",
>   "MG1655_LPV3_pJ23101_High_RBS_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_pJ23101_High_RBS_YFP/1",
>   "MG1655_LPV3_pJ23101_Low_RBS_YFP": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_pJ23101_Low_RBS_YFP/1",
>   "MG1655_LPV3_LacI_AraC_Sensors": "https://hub.sd2e.org/user/sd2e/design/MG1655_LPV3_LacI_AraC_Sensors/1",
>   "Bacillus subtilis 168 Marburg": "https://hub.sd2e.org/user/sd2e/design/Bacillus0x20subtilis0x201680x20Marburg/1",
>   "B. subtilis 168 PmtlA-comKS": "https://hub.sd2e.org/user/sd2e/design/B0x2E0x20subtilis0x201680x20PmtlA0x2DcomKS/1",
>   "State Marker CIS1-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20CIS10x2Dtdtomato/1",
>   "State Marker GPM2-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20GPM20x2Dtdtomato/1",
>   "State Marker GSP2-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20GSP20x2Dtdtomato/1",
>   "State Marker HSP42-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20HSP420x2Dtdtomato/1",
>   "State Marker RGI1-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20RGI10x2Dtdtomato/1",
>   "State Marker UBI4-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20UBI40x2Dtdtomato/1",
>   "State Marker RPL41A-tdtomato": "https://hub.sd2e.org/user/sd2e/design/State0x20Marker0x20RPL41A0x2Dtdtomato/1",
>   "pGPD-tdTomato": "https://hub.sd2e.org/user/sd2e/design/pGPD0x2DtdTomato/1",
>   "S288c_a": "https://hub.sd2e.org/user/sd2e/design/S288c_a/1",

The item-map-fresh.json represents a formatted version of a fresh copy of the item-map pulled from the dictionary. The item-map-comp.json file represents a formatted version from a previous iteration.

mwes commented 4 years ago

In GitLab by @nwalczak on Aug 8, 2019, 11:07

I can't reproduce this issue, but I wanted to create a ticket to keep an eye on it. Initially, I thought maybe there was a problem when it reads the json file to create a copy from cache, but this doesn't seem to be an issue.

This is the dictionary I'm using: https://docs.google.com/spreadsheets/d/1oLJTTydL_5YPyk-wY-dspjIw_bPZ3oCiWiK0xtG8t3g/edit#gid=840133360 While the document has been edited recently, at least the MG1655 entry hasn't been edited since July 3rd. I ran this by @mweston on Slack but he said he hadn't edited any of those entries since early July.

mwes commented 4 years ago

In GitLab by @jakebeal on Nov 19, 2019, 07:20

Since this hasn't come up again, I'm going to close. If it happens again, we can reopen.

mwes commented 4 years ago

In GitLab by @jakebeal on Nov 19, 2019, 07:20

closed