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isabelrem / 2023-Software-Development-Assessment

MIT License
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64 modify sql functions so app will continue to run even if database cannot be found #65

Closed isabelrem closed 8 months ago

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jess789550 commented 8 months ago

Enter 1 to search for new panel information. Enter 2 to browse existing PanelSearch records. 1 If you would like to search by R-code, enter 1. If you would like to enter a disease description, enter 2. 1 Enter your search term: (e.g., R128 or pneumothorax) R128 Which genome build would you like to use? Enter 1 for GRCh37. Enter 2 for GRCh38. 2 GRch38 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Mane_Select_Transcript HGNC:10593 SCN5A 3:38548057-38649673 NM_000335.5 HGNC:6251 KCNH2 7:150944961-150978315 NM_000238.4 HGNC:60 ABCC9 12:21797401-21942529 NM_020297.4 HGNC:493 ANK2 4:112818109-113383740 NM_001148.6 HGNC:1390 CACNA1C 12:1970786-2697950 NM_000719.7 HGNC:1399 CACNA2D1 7:81946444-82443798 NM_000722.4 HGNC:1402 CACNB2 10:18140677-18541869 NM_201596.3 HGNC:1529 CAV3 3:8733800-8841808 NM_033337.3 HGNC:2900 DLG1 3:197042560-197299300 NM_001366207.1 HGNC:28956 GPD1L 3:32105689-32168713 NM_015141.4 HGNC:16882 HCN4 15:73319859-73369264 NM_005477.3 HGNC:6239 KCND3 1:111770662-111989155 NM_001378969.1 HGNC:6243 KCNE3 11:74454841-74467729 NM_005472.5 HGNC:6241 KCNE5 X:109623700-109625172 NM_012282.4 HGNC:6269 KCNJ8 12:21764955-21775581 NM_004982.4 HGNC:9024 PKP2 12:32790745-32896840 NM_001005242.3 HGNC:17679 RANGRF 17:8288497-8290092 NM_016492.5 HGNC:10582 SCN10A 3:38696802-38794010 NM_006514.4 HGNC:10586 SCN1B 19:35030466-35040449 NM_001037.5 HGNC:10589 SCN2B 11:118161951-118176673 NM_004588.5 HGNC:20665 SCN3B 11:123629187-123655244 NM_001040151.2 HGNC:16643 SLMAP 3:57755450-57929168 NM_001377540.1 HGNC:17993 TRPM4 19:49157741-49211836 NM_017636.4 Generate BED file? (Y/N) N Would you like to save this search against a patient ID? (Y/N) Y What patient ID would you like to save this search against? rdhgfhgj Brugada syndrome and cardiac sodium channel disease GRch38 GRch38 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Mane_Select_Transcript HGNC:10593 SCN5A 3:38548057-38649673 NM_000335.5 HGNC:6251 KCNH2 7:150944961-150978315 NM_000238.4 HGNC:60 ABCC9 12:21797401-21942529 NM_020297.4 HGNC:493 ANK2 4:112818109-113383740 NM_001148.6 HGNC:1390 CACNA1C 12:1970786-2697950 NM_000719.7 HGNC:1399 CACNA2D1 7:81946444-82443798 NM_000722.4 HGNC:1402 CACNB2 10:18140677-18541869 NM_201596.3 HGNC:1529 CAV3 3:8733800-8841808 NM_033337.3 HGNC:2900 DLG1 3:197042560-197299300 NM_001366207.1 HGNC:28956 GPD1L 3:32105689-32168713 NM_015141.4 HGNC:16882 HCN4 15:73319859-73369264 NM_005477.3 HGNC:6239 KCND3 1:111770662-111989155 NM_001378969.1 HGNC:6243 KCNE3 11:74454841-74467729 NM_005472.5 HGNC:6241 KCNE5 X:109623700-109625172 NM_012282.4 HGNC:6269 KCNJ8 12:21764955-21775581 NM_004982.4 HGNC:9024 PKP2 12:32790745-32896840 NM_001005242.3 HGNC:17679 RANGRF 17:8288497-8290092 NM_016492.5 HGNC:10582 SCN10A 3:38696802-38794010 NM_006514.4 HGNC:10586 SCN1B 19:35030466-35040449 NM_001037.5 HGNC:10589 SCN2B 11:118161951-118176673 NM_004588.5 HGNC:20665 SCN3B 11:123629187-123655244 NM_001040151.2 HGNC:16643 SLMAP 3:57755450-57929168 NM_001377540.1 HGNC:17993 TRPM4 19:49157741-49211836 NM_017636.4 Unfortunately the SQL database cannot be accessed at this time. Your search was not saved. Thank you for using PanelSearch. Goodbye.

jess789550 commented 8 months ago

Enter 1 to search for new panel information. Enter 2 to browse existing PanelSearch records. 2 Please enter the patient ID here. If you wish to see all saved records, press Return/Enter: successful connection to sql database

Patients table

id patient_id search_id 0 1 Bucket 1 1 2 grdfcv 2

Searches table

id panel_id panel_name panel_version ... r_code transcript genome_build bed_file 0 1 1331 Factor XI deficiency 1.1 ... R120 a really good one GRch37 transcript start end label score ... 1 2 13 Brugada syndrome and cardiac sodium channel di... 3.6 ... R128 a really good one GRch37 placeholder

[2 rows x 10 columns] Would you like to save these tables locally? (Y/N) N Thank you for using PanelSearch. Goodbye.

jess789550 commented 8 months ago

Works well - just need to change "transcript" in SQL db parsing

jess789550 commented 8 months ago

Also could we update docs to include SQL database examples please? Thanks :)