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PoonLab / covizu

Rapid analysis and visualization of coronavirus genome variation
https://filogeneti.ca/CoVizu/
MIT License
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Transfer compressed JSON #208

Closed ArtPoon closed 3 years ago

ArtPoon commented 3 years ago

It should be possible to transfer a compressed version of clusters.JSON, but this may require reconfiguring the server in addition to modifying the jQuery request by index.html.

ArtPoon commented 3 years ago

See #108 and #166

ArtPoon commented 3 years ago

There are some low-hanging fruit in terms of shrinking the clusters JSON file. For example:

> clusters[0]
{nodes: {…}, edges: Array(1522), lineage: "B", region: "Europe", allregions: {…}, …}
allregions: {China: 579, Asia: 444, Europe: 1189, North America: 535, Oceania: 58, …}
country: (2914) ["Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Beijing", "Thailand", "Beijing", "Thailand", "Thailand", "Nepal", "Thailand", "Thailand", "Thailand", "Guangdong", "Zhejiang", "Guangdong", "Chongqing", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Guangdong", "Guangzhou", "Foshan", "Foshan", "Hangzhou", "Vietnam", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Guangdong", "Beijing", "Guangdong", "France", "France", "Chongqing", "Japan", "France", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Canada", "Guangdong", "Jiangsu", "Hangzhou", "Malaysia", "Hangzhou", "Sichuan", "Sichuan", "Singapore", "Australia", "Japan", "Taiwan", "Hangzhou", "Australia", "Hangzhou", "Hangzhou", "Hangzhou", "Hangzhou", "Guangdong", "Thailand", "Thailand", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Xinyu", "Wuhan", "Changzhou", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Wuhan", "Singapore", "Guangdong", "Guangzhou", …]
edges: (1522) [Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), Array(3), …]
label1: "Wuhan/IVDC-HB-01"
lineage: "B"
nodes: {EPI_ISL_402119: Array(1080), EPI_ISL_462450: Array(1), EPI_ISL_419226: Array(1), EPI_ISL_415641: Array(1), EPI_ISL_415486: Array(1), …}
region: "Europe"
searchtext: "Wuhan/IVDC-HB-01,Wuhan/WIV04,Wuhan/WIV06,Wuhan/IPBCAMS-WH-04,Wuhan/HBCDC-HB-03,Wuhan/IME-WH02,Wuhan/IME-WH04,Wuhan/IME-WH05,Wuhan/Hu-1,Wuhan/IVDC-HB-04,Wuhan/WH03,Wuhan/WHU01,Wuhan/WHU02,Beijing/Beijing-01,Thailand/61,Beijing/WH-09,Thailand/SI200040-NT,Thailand/74,Nepal/61,Thailand/Nonthaburi_59,Thailand/Nonthaburi_68,Thailand/NIH-59,Guangdong/20SF028,Zhejiang/WZ-02,Guangdong/20SF040,Chongqing/IVDC-CQ-001,Hangzhou/HZCDC0001,Hangzhou/HZ-1,Hangzhou/HZ48,Hangzhou/HZ49,Hangzhou/HZ79,Hangzhou/HZ90,Hangzhou/HZ91,Hangzhou/HZCDC0091L,Hangzhou/HZCDC0090L,Hangzhou/HZCDC0049L,Hangzhou/HZCDC0048L,Hangzhou/HZCDC0048,Guangdong/20SF174,Guangzhou/20SF206,Foshan/20SF210,Foshan/20SF211,Hangzhou/ZJU-05,Vietnam/19-01S,Hangzhou/HZ60,Hangzhou/HZ62,Hangzhou/HZCDC0135,Hangzhou/HZCDC0119,Guangdong/20SF198,Beijing/IME-HZ01,Guangdong/20SF201,France/IDF-0372,France/IDF-0373,Chongqing/ZX01,Japan/OS-20-07-1,France/IDF-0372-isl,Hangzhou/HZ162,Hangzhou/HZ178,Hangzhou/HZ185,Hangzhou/HZCDC0162,Canada/ON_ON-VIDO-01-2,Guangdong/20SF200,Jiangsu/JS03,Hangzhou/ZJU-04,Malaysia/MKAK-CL-2020-5047,Hangzhou/HZ477,Sichuan/SC-PHCC2-041,Sichuan/SC-WCH4-290,Singapore/2,Australia/NSW03,Japan/NA-20-05-1,Taiwan/CGMH-CGU-01,Hangzhou/ZJU-01,Australia/VIC03,Hangzhou/HZ481,Hangzhou/HZ551,Hangzhou/HZ576,Hangzhou/HZ638,Guangdong/20SF602,Thailand/SI200433-NT,Thailand/Phuket_247,Wuhan/YB012504,Wuhan/YB012506,Wuhan/0125-A137,Wuhan/0125-A145,Wuhan/0125-A153,Wuhan/0125-A164,Wuhan/0125-A182,Xinyu/JX124,Wuhan/YB012602,Changzhou/JS27,Wuhan/0126-C12,Wuhan/0126-C47,Wuhan/0126-C77,Wuhan/0126-C93,Wuhan/0126-C94,Wuhan/0126-C100,Singapore/7,Guangdong/20SF665,Guangzhou/GZMU0058,Guangzhou/GZMU0059,Sichuan/SC-MY-053,Sichuan/SC-MY-054,Sichuan/SC-NJ-090,Sichuan/SC-PHCC1-032,Sichuan/SC-WCH-311,Sichuan/SC-WCH4-285,France/IDF-0386-islP1,France/IDF-0386-islP3,Taiwan/4,Finland/1,USA/CA-CDC-5,Italy/LAZ-INMI-SPL1,Singapore/3Clin,Nanchang/JX176,Nanchang/JX155,Guangzhou/GZMU0051,Guangzhou/GZMU0052,Guangzhou/GZMU0054,Guangzhou/GZMU0055,Sichuan/SC-PHCC2-043,Sichuan/SC-PHCC2-046,Guangdong/2020XN4433-P0040,Guangdong/20SF1136,Italy/LAZ-INMI2-N,Sichuan/SC-GA-063,Sichuan/SC-GA-064,Italy/LAZ-INMI1-cs,Sichuan/SC-NJ-095,Sichuan/SC-YA-088,Sichuan/SC-YB-085,Shaoxing/05,Singapore/3,South 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Kong/HKU-908a,Hong Kong/HKU-908b,USA/CA-CZB0107,Guangdong/20SF273,USA/WI-UW-234,USA/WI-UW-231,USA/WI-UW-229,Scotland/CVR80,Iceland/431,Netherlands/NoordBrabant_94,Netherlands/NoordBrabant_87,Netherlands/NA_67,Wales/PHWC-2707C,England/20139024204,England/201361012,Pingxiang/JX151,Hangzhou/HZCDC0013,Hangzhou/HZCDC0012,Wales/PHWC-24F36,Singapore/24nan,Singapore/24,Singapore/50nan,Singapore/50,Australia/VIC102,Australia/VIC78,Hong Kong/HKPU60-0802,Portugal/PT0041,Portugal/PT0056,France/ARA-06573,England/20110097506,Japan/DP0743,Japan/DP0687,Japan/DP0290,Japan/DP0158,Shanghai/SH0054,Shanghai/SH0053,Shanghai/SH0028,Shandong/LY005-2,Shandong/LY007-2,Shandong/LY008-2,Guangzhou/GZMU0030,Hong Kong/VM20002849,Hong Kong/HKU-200723-017,Netherlands/ZuidHolland_7,Hong Kong/HKU-907a,Hong Kong/HKU-907b,Guangdong/2020XN4475-P0042,USA/CruiseA-10,Jiangsu/IVDC-JS-001,Jiangxi/IVDC-JX-002,Pingxiang/JX5,France/IDF-0626,Singapore/1,Zhejiang/WZ-01,Wuhan/IPBCAMS-WH-03,USA/MN-MDH-1333,United Arab Emirates/0988,United Arab Emirates/0090,Sichuan/SC-PHCC1-026,United Arab Emirates/0219,United Arab Emirates/0166,United Arab Emirates/0314,Uganda/UG059,United Arab Emirates/0112,Uganda/UG119,Sichuan/SC-WCH4-293,India/OR-ILC-RMRC123,Mali/M002672,Saudi Arabia/KAUST-Madinah57,Turkey/HSGM-5770,Wuhan/HB-WHCM2-283,Wuhan/HB-WH1-126,England/EXET-135872,Wuhan/HB-WH1-129,Wuhan/HB-WH1-132,United Arab Emirates/0266,USA/CA-CZB-1687,Scotland/EDB015,Iceland/141,Wuhan/HB-WH4-202,Wuhan/HB-WH2-146,Wuhan/HB-WH5-230,Wuhan/HB-WHCM-107,Saudi Arabia/KAUST-Madinah211,SaudiArabia/KAUST-JEDDAH1001,India/WB-IICB-005,Hong Kong/HKPU-0291,Turkey/HSGM-6204,SaudiArabia/KAUST-JEDDAH720,France/ARA-SC088,Saudi Arabia/KAUST-MAKKAH1610,Sweden/RV-FOI-1,Belgium/MSE-0324121,Australia/QLD1154,Shanghai/SH0060,Guangdong/GD2020080-P0010,Denmark/ALAB-SSI-1250,Sichuan/SC-WCH2-017,Singapore/187,USA/CruiseA-18,Portugal/PT0278,Wuhan/HB-WH1-134,Canada/MB-NML-841,Zhejiang/CN3,Jiangsu/JS01,Shanghai/SH0031,Singapore/485,Taiwan/NTU27,Georgia/Tb-537,Georgia/Tb-468,Scotland/EDB6448,England/NORT-295C64,Switzerland/BL-UHB-42191605,Netherlands/ZuidHolland_142,Netherlands/NA_191,Australia/SAP309,Italy/VEN-UniVR-83,Italy/VEN-UniVR-106,USA/CA-QRTP-Donor15,USA/CA-QRTP-Donor17,USA/NY-QDX-108,Taiwan/2,Spain/AR-IBV-005035,Singapore/913,Spain/AR-ISCIII-201779,Spain/AR-IBV-2421,Scotland/EDB5709,Scotland/GCVR-172387,Spain/AR-IBV-2445,Scotland/GCVR-17179B,Scotland/CVR1669,England/NORW-E737F,England/NORW-E9049,England/NORW-E9AB4,England/NORT-2848BF,USA/FL-BPHL-1848,England/EXET-1356F0,England/EXET-1353EA,USA/NY-PV09061,USA/NY-SURV0166,USA/NY-SURV0168,USA/NY-PV09063,USA/NY-PV09067,Scotland/EDB157,Iceland/484,Iceland/480,England/20134016802,England/20134025704,England/201061453,England/201160261,England/LOND-124F738,Austria/CeMM0906,England/CAMB-789BD,England/CAMB-7E058,Israel/990300681,Beijing/ICDC-DT005,Gansu/NPRC0003,England/LIVE-A5832,England/LIVE-AA2E4,England/LIVE-A9BDB,England/LIVE-A9CD8,England/LIVE-AA79A,England/LIVE-A8617,Scotland/EDB821,Iceland/496,Spain/PV-IBV-005156,Singapore/417,Spain/NC-IBV-001382,England/CAMB-82F81,Brazil/SP02cc,USA/NJ-QDX-1957,Netherlands/NA_238,Hong Kong/HKPU42-0302,Hong Kong/VM20002493-2,Spain/MD-IBV-004906,Wales/PHWC-26EDD,Wales/PHWC-30007,Wales/PHWC-2B281,Ireland/D-NVRL-20G41451,Hangzhou/ZJU-011,England/OXON-B0F3F,England/OXON-ACD4B,Jian/JX169,Wales/PHWC-33B7C,Sweden/20-02114,Sweden/01,England/NORT-28B26F,Iceland/457,Iceland/275,Netherlands/NA_35,Netherlands/GE-RIVM-10314,England/20139029304,Spain/VC-IBV-98003103,Spain/VC-FISABIO-151,Spain/VC-FISABIO-144,Netherlands/ZuidHolland_108,England/BRIS-130EA2,England/NORW-EC85D,England/NORW-E9E7C,Scotland/CVR1377,Scotland/CVR2876,Spain/VC-FISABIO-105,England/LIVE-A9D02,Germany/HH-hpi-p2048,England/LIVE-A8750,England/NORT-295BD0,USA/CA-QDX-1437,Spain/AR-ISCIII-201778,Spain/AR-IBV-2453,England/CAMB-7C227,Thailand/Bangkok_2972,England/20132080004,Spain/MD-IBV-003662,France/PAC02003,Poland/PL_P42,Poland/PL_P39,Spain/MD-IBV-004907,Spain/MD-IBV-005281,Belgium/rega-0411452,Belgium/Rega-0330251,Belgium/JJC-0325165,Belgium/DC-0322355,England/20144023304,England/LOND-D5D49,England/201180067,Finland/29M11S3,England/LOND-12611BA,England/LOND-124C3CE,England/NORT-295A6A,Wales/PHWC-25BC8,Australia/VIC668,England/NORT-295CA0,Netherlands/Utrecht_18,Netherlands/NoordBrabant_73,Netherlands/ZuidHolland_33,Netherlands/NoordBrabant_147,Germany/BY-MVP-0044,England/ALDP-951F82,England/ALDP-951C6D,England/OXON-AC6F5,England/PORT-2D21A8,England/CAMB-74025,USA/VA-DCLS-0056,Slovenia/751,Singapore/180,Singapore/1037,Singapore/231,Indonesia/JK-EIJK-2444,Indonesia/YO-UGM-200927,Indonesia/JK-EIJK-43,Indonesia/JK-EIJK44,Indonesia/JK-EIJK48,Uganda/UG038,USA/CA-CZB-1400,USA/CA-CZB-9560,Slovenia/V0-15921,Hangzhou/HZCDC6224,Hangzhou/HZCDC6789,Greece/150,USA/CA-CZB-9714,USA/CA-QDX-2203,Portugal/PT0549,Portugal/PT0202,England/EXET-136FB8,England/EXET-135818,USA/TX-HMH-MCoV-11119,USA/TX-HMH-MCoV-9721,Canada/ON-S906,England/LIVE-A68B9,England/ALDP-9EE01E,England/LIVE-A5F2E,England/LIVE-A696B,England/LIVE-A638B,England/SHEF-C6C11,England/SHEF-CD315,Australia/QLDID922,United Arab Emirates/skmc-0532497,Lithuania/MR-LUHS-Eilnr25,United Arab Emirates/0252,United Arab Emirates/0536,USA/WA-UW-4243,South Korea/KCDC2074,South Korea/KCDC2030,Australia/QLD1115,USA/CA-SR0195,Portugal/PT0596,Portugal/PT0598,Portugal/PT0599,Germany/HH-hpi-p1987,Shanghai/CH-02,Shanghai/SH0027,Vietnam/PIHCM-503,Vietnam/PIHCM-507-4H,Ireland/LD-NVRL-20G49957,Wuhan/HB-WHCM-108,England/20126003406,England/20129025404,England/CWAR-24FDAFF,Shaoxing/09,Shanghai/SH0041,Shanghai/SH0026,Singapore/990,Taiwan/NTU07,England/20128035406,Australia/VIC396,Wales/PHWC-28EAE,Wales/PHWC-27917,Wales/PHWC-27BC6,South Korea/IHC1215,Shangrao/JX1974,USA/CruiseA-14,Indonesia/PA-NIHRD-C0710684,Indonesia/PA-NIHRD-C0710717,Spain/AN-IBV-002043,Australia/WA11,England/LOND-D6D39,Sichuan/SC-NJ-093,England/BRIS-123F45,England/BRIS-130103,England/LEED-2AA121,England/LEED-2AA491,England/LEED-2AA67D,England/LIVE-A7539,England/LEED-2AA22E,USA/CA-CDPH-UC3,England/ALDP-9ED695,England/MILK-4C2BF6,England/ALDP-9ED62C,Czech Republic/NRL-1753,Austria/CeMM0097,Sweden/20-08136,Austria/CeMM0897,Latvia/02,Shanghai/SH0039,Guangdong/2020XN4448-P0002,England/OXON-B15C3,England/OXON-B148A,Sichuan/SC-WCH-315,Sichuan/SC-NC-069,Guangzhou/IQTC05,Guangzhou/IQTC03,Guangzhou/GZMU0079,Wuhan/HB-WH4-209,Wuhan/HB-WH4-208,USA/CA-CZB-1343,USA/CA-CZB-1348,USA/CA-CZB-1276,USA/CA-CZB-1410,USA/CA-CHLA-PLM20127810,USA/CA-CHLA-PLM41214732,USA/CA-CHLA-PLM47560065,Indonesia/JI-ITDua-1006NTv,Indonesia/JI-ITD-1238Sp,Indonesia/JK-EIJK47,Indonesia/JK-EIJK37,Indonesia/JK-EIJK20,Singapore/130,Indonesia/JK-EIJK-04,Shanghai/SH0107,Shanghai/SH0114,USA/CA-CZB-1175,Japan/PG-0139,USA/CruiseA-7,Japan/DP0037,Singapore/516,Singapore/318,Singapore/538,Singapore/1173,USA/CruiseA-24,Shangrao/JX1177,Shangrao/JX1176,Beijing/BJ53,Beijing/BJ54,Beijing/BJ252,Beijing/BJ251,Malaysia/MKAK-CL-2020-7554,Malaysia/IMR_WC413,Malaysia/IMR_WC458,Malaysia/IMR_WC627,Guangdong/20SF316,USA/MA1,USA/CA-CHLA-PLM73393837,USA/CA-CHLA-PLM86862197,Spain/AN-ISCIII-201614,Shanghai/SH0069,Wuhan/HB-WH5-231,Wuhan/HB-WH6-246,Thailand/Bangkok_168,Thailand/SI200615-NT,Beijing/DT-WH02,Beijing/DT-travelUK04,USA/WI-QDX-782,United Arab Emirates/0021,Hunan/HN-CIDC-P11,Hunan/HN-CIDC-P6,USA/WI-WSLH-200230,USA/WI-UW-210,Yichun/JX2391,Spain/CM-ISCIII-201329,Spain/CM-ISCIII-201368,Spain/MD-IBV-004917,Guangzhou/IQTC04,Belgium/KWA-0323410,England/BIRM-5F15A,Scotland/CVR1710,USA/FL-BPHL-2127,USA/CA-CZB088,Scotland/CVR2777,USA/CA-CZB-2043,USA/CA-CZB-1591,Japan/DP0481,Scotland/EDB4006,Wuhan/HB-WH2-156,Wuhan/WHUH021,Shenzhen/SZTH-004,Oman/RESP-20-B-15703,USA/CA-CZB046,Wales/PHWC-2B2EB,USA/CA-CSMC111,South Africa/Tygerberg-430,Japan/DP0457,England/NOTT-10DFF6,England/NOTT-10E089,Sichuan/SC-WCH4-301,Wuhan/0125-A192,Spain/AR-IBV-2388,USA/WI-WSLH-200159,Scotland/EDB5794,Scotland/EDB5918,Wuhan/0125-A160,Wuhan/0125-A163,Wuhan/0125-A142,Wuhan/0125-A168,England/CAMB-79AB9,Shanghai/SH0020,USA/UT-QDX-1880,USA/CA-CZB-1223,USA/DE-DHSS-F918677,Guangdong/MZ02,Guangdong/MZ01,Malaysia/UNIMAS-0694,Indonesia/SA-EIJK-06,Wales/PHWC-2E1AF,Shanghai/SH0067,Shanghai/SH0076,England/BRIS-18547EF,England/BRIS-1265D7,Taiwan/CGMH-CGU-22,USA/WI-WSLH-200214,USA/WI-UW-216,USA/WI-UW-408,Taiwan/8,Indonesia/JI-ITD-3101NT,Guangdong/20SF812,Japan/KY-V-029,Wuhan/YB012605,Wuhan/YB012611,Sichuan/SC-PHCC2-048,USA/WI-UW-266,USA/WI-UW-183,Japan/PG-0119,Scotland/EDB1173,Wuhan/WIV02,Scotland/CVR157,Japan/DP0278,USA/CruiseA-21,Japan/DP0236,USA/CruiseA-2,USA/CruiseA-17,USA/CA-SCCPHD-UC108,Singapore/25,Netherlands/NA_240,Netherlands/NA_234,Wuhan/HB-WHCM2-272,Wuhan/HB-WHCM2-268,Shanghai/SH0047,USA/CA-CZB-13091,England/2,England/20238034404,England/01,England/02,England/MILK-45DD72,England/MILK-45CE8F,England/204161234,England/204221328,England/204261202,England/204290933,Scotland/EDB5511,Scotland/EDB5065,England/NORW-EB94C,England/NORW-E7193,Israel/CVL-n-5826,Singapore/486,Singapore/1052,England/BRIS-1853FE8,Singapore/1017,Japan/DP0190,Singapore/182,India/MH-1-31,Sichuan/SC-WCH3-254,Wuhan/HB-WH1-144,Wuhan/HB-WH3-174,SaudiArabia/KAUST-JEDDAH919,USA/CA-QRTP-Donor21,Spain/AR-IBV-2454,Spain/AR-IBV-2464,Spain/AR-IBV-2444,USA/FL-BPHL-0473,USA/FL-BPHL-1837,USA/FL-BPHL-1990,USA/NY-SURV0165,Australia/VIC01,Australia/VIC2387,Germany/BE-ChVir-D900-8163,England/OXON-B2191,South Korea/KUMC02,South Korea/KUMC01,England/LIVE-A90AF,England/20139071104,France/BRE-2340,France/BRE-2334,England/NOTT-10E57B,England/NOTT-10EFB9,England/NOTT-10F2FB,USA/AZ-TG268188,Malaysia/5056,Singapore/280,Greece/236_31815,USA/CT-UW-3845,USA/WA-UW275,USA/NY-PV09335,Canada/ON-S950,India/TG-GMC-RK100,United Arab Emirates/L6599,Portugal/PT1125,Portugal/PT0597,Wuhan/HB-WHCM-117,Wuhan/HB-WHCM-099,England/NORW-EAF4B,England/NORW-EB812,England/NORW-EB6B1,South Korea/IHC1217,Indonesia/PA-NIHRD-PME4306,Scotland/GCVR-173034,Scotland/CVR3030,England/LEED-2AA2B5,England/QEUH-5DAF1C,England/QEUH-5DABDC,Sweden/20-08157,Austria/CeMM0557,Germany/HH-hpi-p1459,USA/CA-CZB-1404,USA/CA-CZB-1347,USA/CA-CZB-1349,USA/CA-CZB-1393,USA/CA-CZB-1412,USA/CA-CZB-1110,Singapore/707,Singapore/707nan,Singapore/706,Guangdong/20SF1152,Germany/HE-FFM1,Netherlands/NoordHolland_10011,Spain/VC-FISABIO-92,Scotland/CVR2151,Scotland/EDB4044,Singapore/980,USA/CA-CZB-1512,Wuhan/0125-A148,USA/WI-CDC-0952,Taiwan/5,USA/WI-UW-318,Japan/DP0065,Australia/VIC8344,England/PORT-2D0DB5,England/NORW-EB548,England/NORW-EB135,England/NORW-EBB46,England/NORW-EBC8F,England/NORW-EBAD0,England/MILK-4C2C8A,Sweden/20-08532,England/NORT-284891,England/NORT-2818A3,USA/WI-UW-344,USA/CruiseA-23"
__proto__: Object
ArtPoon commented 3 years ago

Shoot, I forgot that the country and searchtext fields are being generated client-side. Still we should be more efficient about this data structure.

ArtPoon commented 3 years ago

Modified beadplot.py to generate simplified JSON data structures. Run on testdata.xz, noting that the current JSON has filesize 5400069 bytes. See #213

ArtPoon commented 3 years ago

clusters.{}.json with new data structure is 3531514 bytes

ArtPoon commented 3 years ago

Putative fix - before merging into dev branch need to notify @PoonLab/everyone that this refactor is not back-compatible with previous version of JSON data!

ArtPoon commented 3 years ago

Compressed searchtext attribute

ArtPoon commented 3 years ago

Countries now entabulated client-side

ArtPoon commented 3 years ago 
{nodes: {…}, edges: Array(56), lineage: "B", region: "China", allregions: {…}, …}
allregions: {China: 31, Europe: 15, Asia: 15, Oceania: 3, North America: 8}
country: {Jiangxi: 1, France: 10, Wuhan: 11, Foshan: 3, Guangzhou: 1, …}
edges: (56) [Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4), Array(4)]
label1: "Jiangxi/IVDC-JX-002"
lineage: "B"
nodes: {unsampled0: Array(0), EPI_ISL_408486: Array(1), EPI_ISL_408431: Array(1), EPI_ISL_402132: Array(1), EPI_ISL_402120: Array(1), …}
region: "China"
searchtext: "Jiangxi,IVDC-JX-002,France,IDF-0626,Wuhan,HBCDC-HB-01,IVDC-HB-04,Foshan,20SF210,20SF211,WIV05,Guangzhou,20SF206,IDF-0515,IDF-0515-isl,IDF-0571,WH01,IPBCAMS-WH-05,Taiwan,NTU02,Australia,NSW02,USA,CA-CDC-3,CA-CDC-4,20SF207,Shenzhen,SZTH-003,Nepal,61,ARA-739,Cambodia,0012,Beijing,WH-09,CA-CDC-6,Jiangsu,IVDC-JS-001,Japan,AI-I-004,Singapore,2,6,IPBCAMS-WH-03,IVDC-HB-05,1,IPBCAMS-WH-01,Guangdong,20SF028,20SF040,20SF174,CA-CDC-5,Zhejiang,WZ-01,WIV07,Hong Kong,VB20026565-2,20SF014,IPBCAMS-WH-02,Shandong,IVDC-SD-001,IDF-0372,IDF-0373,IDF-0372-isl,NSW03,IDF-0386-islP1,IDF-0386-islP3,Italy,LAZ-INMI1-cs,JS01,CA-CDC-8,England,01,Fujian,13,11,WI1,KY-V-029,MA1,JS02,SZTH-004,LAZ-INMI1-isl,VIC01,ICDC-DT005,7,Sweden,9,10,5,8,CA2,WIV02,02"
__proto__: Object

Much more compact!

ArtPoon commented 3 years ago

Ran Chrome Lighthouse, looks like this would really be worth doing: https://web.dev/uses-text-compression/?utm_source=lighthouse&utm_medium=devtools

ArtPoon commented 3 years ago

@gopigugan would you be able to figure how to configure the client request to have the server send gzipped clusters.json, to be expanded client-side? I created a test file on the webserver at covizu/data/temp.json.gz but haven't been able to get this to work:

> req = $.getJSON("data/temp.json.gz", function(data) {
  clusters = data;
});
{readyState: 1, getResponseHeader: ƒ, getAllResponseHeaders: ƒ, setRequestHeader: ƒ, overrideMimeType: ƒ, …}
abort: ƒ ( statusText )
always: ƒ ()
catch: ƒ ( fn )
done: ƒ ()
fail: ƒ ()
getAllResponseHeaders: ƒ ()
getResponseHeader: ƒ ( key )
overrideMimeType: ƒ ( type )
pipe: ƒ ( /* fnDone, fnFail, fnProgress */ )
progress: ƒ ()
promise: ƒ ( obj )
readyState: 4
responseText: "���`temp.json���rG�%�+2=w>��};8�Ip�T�"
setRequestHeader: ƒ ( name, value )
state: ƒ ()
status: 200
statusCode: ƒ ( map )
statusText: "OK"
then: ƒ ( onFulfilled, onRejected, onProgress )
arguments: (...)
caller: (...)
length: 3
name: "then"
prototype: {constructor: ƒ}
__proto__: ƒ ()
[[FunctionLocation]]: jquery.js:3746
[[Scopes]]: Scopes[4]
__proto__: Object
> $.ajaxSetup({
    scriptCharset: "utf-8",
    contentType: "application/json; charset=utf-8"
});
{url: "http://filogeneti.ca/covizu/", type: "GET", isLocal: false, global: true, processData: true, …}
accepts:
*: "*/*"
html: "text/html"
json: "application/json, text/javascript"
script: "text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"
text: "text/plain"
xml: "application/xml, text/xml"
__proto__: Object
async: true
contentType: "application/json; charset=utf-8"
contents: {xml: /\bxml\b/, html: /\bhtml/, json: /\bjson\b/, script: /\b(?:java|ecma)script\b/}
converters: {text html: true, * text: ƒ, text json: ƒ, text xml: ƒ, text script: ƒ}
flatOptions: {url: true, context: true}
global: true
isLocal: false
jsonp: "callback"
jsonpCallback: ƒ ()
processData: true
responseFields: {xml: "responseXML", text: "responseText", json: "responseJSON"}
scriptCharset: "utf-8"
type: "GET"
url: "http://filogeneti.ca/covizu/"
xhr: ƒ ()
__proto__: Object
GopiGugan commented 3 years ago

Sure. I can look into this

ArtPoon commented 3 years ago

Thanks - I've confirmed that mod_deflate is enabled on the webserver.

GopiGugan commented 3 years ago

Image of the response header (for the GET request for "data/temp.json.gz"):

GET_request

A few others ran into a similar problem: https://stackoverflow.com/questions/20859246/no-auto-decompression-of-gzipped-json-on-browsers-side-when-using-angulars-htt?noredirect=1&lq=1 https://stackoverflow.com/questions/19308318/ajax-loadin-file-json-gz-from-server-without-compresion-enabled-how-set-heade

It seems like modifications to ".htaccess" on the server-side resolved their issue. In the first link, the user created their own .jsongz extension, but I think we can try adding the following (as mentioned in the second link):

AddEncoding gzip gz 
<FilesMatch "\.gz$">
ForceType text/plain
Header set Content-Encoding: gzip
</FilesMatch>

If the above modification doesn't fix the issue, I found some resources which explain how to manually decompress gz files on the client-side using resources like "zlib" and I can look further into this.

ArtPoon commented 3 years ago

Currently we don't have an .htaccess file in /var/www/html or /var/www/html/covizu - should we make a new one in the latter location?

ArtPoon commented 3 years ago

Those forums are pretty old, we should verify this .htaccess configuration in more recent documentation or forum threads.

ArtPoon commented 3 years ago

Also it should be possible to have the server compress the JSON file (uncompressed) while transmitting it to client, but the documentation I've seen so far would compress everything and I'd rather focus on this one file.

GopiGugan commented 3 years ago

Okay. I'll double-check documentation on .htaccess

ArtPoon commented 3 years ago

I created a file .htaccess at /var/www/html/covizu with the following content:

art@coreceptor:/var/www/html/covizu$ cat .htaccess
AddEncoding gzip gz
<FilesMatch "\.json\.gz$">
ForceType text/plain
Header set Content-Encoding: gzip
</FilesMatch>

and then navigated to http://filogeneti.ca/covizu/ and ran this in the console:

> req = $.getJSON("data/temp.json.gz", function(data) {
  temp = data;
});
> req.getAllResponseHeaders()
"accept-ranges: bytes
content-length: 5927650
content-type: application/x-gzip
date: Fri, 29 Jan 2021 17:17:20 GMT
etag: "5a72e2-5b9f7b3e72c7e"
last-modified: Thu, 28 Jan 2021 15:40:09 GMT
server: Apache/2.4.18 (Ubuntu)
"

so this doesn't seem to be working so far - maybe we haven't set the request headers correctly? @gopigugan

GopiGugan commented 3 years ago

I tried making changes to the request headers:

> $.ajax({
    type: "GET",
    url: "http://filogeneti.ca/covizu/data/temp.json.gz",
    beforeSend: function(xhr) {
        xhr.setRequestHeader('Content-Type', 'application/json');
        xhr.setRequestHeader('Accept', 'application/json');
        xhr.setRequestHeader('Accept-Encoding', 'gzip');
    },
    success: function(data) {
        alert(data);
    },
});

But this didn't seem to work.

I think we need to make some changes to the response header.

I've quickly set up a local apache server so I'm going to try making some changes and see if I can get it to work.

GopiGugan commented 3 years ago

I looked into documentation for mod_deflate and figured out how to configure it: https://httpd.apache.org/docs/trunk/mod/mod_deflate.html

"mod_deflate provides the DEFLATE output filter that allows output from your server to be compressed before being sent to the client over the network"

If we look into /etc/apache2/mods-enabled/deflate.conf, by default when mod_deflate is enabled, HTML, CSS and Javascript files are compressed before being sent to the client:

Screen Shot 2021-01-30 at 7 55 00 PM

We need to add the following to the file to compress JSON files:

AddOutputFilterByType DEFLATE application/json

Once this is done and we restart the server, the Content-Length for ALL JSON files are smaller. Below I've attached screenshots for dbstats.json:

Screen Shot 2021-01-30 at 7 47 54 PM

Before modifying /etc/apache2/mods-enabled/deflate.conf:

Screen Shot 2021-01-30 at 7 48 54 PM

After modifying the file:

Screen Shot 2021-01-30 at 8 04 14 PM

But we only want to compress the clusters.json file, right?

ArtPoon commented 3 years ago

I would prefer to just compress clusters.json, but I don't think we're serving any other JSON files on the webserver...

ArtPoon commented 3 years ago

@gopigugan ok let's test this Monday, I'll make the modification to the config then and then can you please run some quick tests at the same time? Let's coordinate.

GopiGugan commented 3 years ago

Sure, sounds good

ArtPoon commented 3 years ago

Made the above change and restarted the server. Transfer time for clusters.json is down from 8.8 seconds to about 2 seconds. Additional changes (simplification of data structure) should make for further improvements in page load time.