New topic showing no data on the dashboard

[Abdouzster]

I am currently using the default topics file. However, more than week ago, I added lately unknown hepatitis topic to the file. When I try to see the topic on the dashboard, it shows no data available. However, when I search it in data protection tab, it is collecting data for the topic. I am not sure why it is not displaying it in the dashboard.

[forchard]

Hi @Abdouzster Do you see your topics on the dashboard drop down list?

Also what is the name of the new topic?

Can you please share the output of the following code?

epitweetr::setup_config("your_home_folder_here") codes <- unique(sapply(epitweetr:::conf$topics, function(t) t$topic)) labels <- epitweetr:::get_topics_labels() codes labels

Thanks! Francisco

[Abdouzster]

Hi Francisco, I see the topics on the dropdown list. Here is the result of this run:

library(epitweetr) epitweetr::setup_config("your_home_folder_here") codes <- unique(sapply(epitweetr:::conf$topics, function(t) t$topic)) labels <- epitweetr:::get_topics_labels() codes [1] "Measles"
[2] "Rubella"
[3] "Mumps"
[4] "Dengue"
[5] "Haemorrhagic fever"
[6] "Avian influenza"
[7] "Chikungunya"
[8] "Poliomyelitis"
[9] "Tuberculosis"
[10] "Anthrax"
[11] "West Nile virus"
[12] "Crimean-Congo haemorrhagic fever" [13] "Botulism"
[14] "Ebola"
[15] "Tularaemia"
[16] "Rabies"
[17] "Tetanus"
[18] "Brucellosis"
[19] "Chickenpox"
[20] "Dihphteria"
[21] "Lyme disease"
[22] "Plague"
[23] "Pertussis"
[24] "Meningococcal disease"
[25] "Antimicrobial resistance"
[26] "Campylobacteriosis"
[27] "Chlamydiosis"
[28] "Cholera"
[29] "Creutzfeld-Jakob disease"
[30] "Cryptosporidiosis"
[31] "Echinococcosis"
[32] "Giardiasis"
[33] "Gonorrhea"
[34] "Haemophilus influenzae"
[35] "Hantavirus"
[36] "Clostridium difficile"
[37] "Hepatitis A"
[38] "Hepatitis B-C"
[39] "HIV-AIDS"
[40] "Seasonal influenza"
[41] "Lassa fever"
[42] "Legionnaires disease"
[43] "Leptospirosis"
[44] "Listeriosis"
[45] "Lymphogranuloma venereum"
[46] "Malaria"
[47] "Pneumococcal disease"
[48] "Q fever"
[49] "Rift Valley fever"
[50] "Salmonellosis"
[51] "Shigellosis"
[52] "Syphillis"
[53] "Tick-borne encephalitis"
[54] "Toxoplasmosis"
[55] "Trichinellosis"
[56] "Typhoid fever"
[57] "Yellow fever"
[58] "Yersiniosis"
[59] "Zika"
[60] "Bioterrorism"
[61] "Infectious diseases"
[62] "MERS-CoV"
[63] "COVID-19"
[64] "COVID-19 outbreaks"
[65] "SARS"
[66] "Smallpox"
[67] "Healthcare-associated infections" [68] "Zoonoses"
[69] "Vectorborne diseases"
[70] "Foodborne diseases"
[71] "Waterborne diseases"
[72] "STEC-VTEC"
labels Anthrax "Anthrax" Antimicrobial resistance "Antimicrobial resistance" Avian influenza "Avian influenza" Bioterrorism "Bioterrorism" Botulism "Botulism" Brucellosis "Brucellosis" Campylobacteriosis "Campylobacteriosis" Chickenpox "Chickenpox" Chikungunya "Chikungunya" Chlamydiosis "Chlamydiosis" Cholera "Cholera" Clostridium difficile "Clostridium difficile" COVID-19 "COVID-19" COVID-19 outbreaks "COVID-19 outbreaks" Creutzfeld-Jakob disease "Creutzfeld-Jakob disease" Crimean-Congo haemorrhagic fever "Crimean-Congo haemorrhagic fever" Cryptosporidiosis "Cryptosporidiosis" Dengue "Dengue" Dihphteria "Dihphteria" Ebola "Ebola" Echinococcosis "Echinococcosis" Foodborne diseases "Foodborne diseases" Giardiasis "Giardiasis" Gonorrhea "Gonorrhea" Haemophilus influenzae "Haemophilus influenzae" Haemorrhagic fever "Haemorrhagic fever" Hantavirus "Hantavirus" Healthcare-associated infections "Healthcare-associated infections" Hepatitis A "Hepatitis A" Hepatitis B-C "Hepatitis B-C" HIV-AIDS "HIV-AIDS" Infectious diseases "Infectious diseases" Lassa fever "Lassa fever" Legionnaires disease "Legionnaires disease" Leptospirosis "Leptospirosis" Listeriosis "Listeriosis" Lyme disease "Lyme disease" Lymphogranuloma venereum "Lymphogranuloma venereum" Malaria "Malaria" Measles "Measles" Meningococcal disease "Meningococcal disease" MERS-CoV "MERS-CoV" Mumps "Mumps" Pertussis "Pertussis" Plague "Plague" Pneumococcal disease "Pneumococcal disease" Poliomyelitis "Poliomyelitis" Q fever "Q fever" Rabies "Rabies" Rift Valley fever "Rift Valley fever" Rubella "Rubella" Salmonellosis "Salmonellosis" SARS "SARS" Seasonal influenza "Seasonal influenza" Shigellosis "Shigellosis" Smallpox "Smallpox" STEC-VTEC "STEC-VTEC" Syphillis "Syphillis" Tetanus "Tetanus" Tick-borne encephalitis "Tick-borne encephalitis" Toxoplasmosis "Toxoplasmosis" Trichinellosis "Trichinellosis" Tuberculosis "Tuberculosis" Tularaemia "Tularaemia" Typhoid fever "Typhoid fever" Vectorborne diseases "Vectorborne diseases" Waterborne diseases "Waterborne diseases" West Nile virus "West Nile virus" Yellow fever "Yellow fever" Yersiniosis "Yersiniosis" Zika "Zika" Zoonoses "Zoonoses"

[Abdouzster]

The new topic did not appear in the results of this code

[forchard]

Is the new topic appearing on?

topics_path <- epitweetr:::get_topics_path() df <- readxl::read_excel(topics_path) df$Topic df$Label

Best, Francisco

[Abdouzster]

the new topics appearing on the dashboard that is how I select it and it give me no data. Monkeypox and hepatitis-unknown topics_path <- epitweetr:::get_topics_path()

df <- readxl::read_excel(topics_path) df$Topic [1] "Measles" "Rubella"
[3] "Mumps" "Dengue"
[5] "Haemorrhagic fever" "Avian influenza"
[7] "Chikungunya" "Poliomyelitis"
[9] "Tuberculosis" "Anthrax"
[11] "West Nile virus" "West Nile virus"
[13] "Crimean-Congo haemorrhagic fever" "Botulism"
[15] "Botulism" "Ebola"
[17] "Tularaemia" "Rabies"
[19] "Rabies" "Tetanus"
[21] "Brucellosis" "Chickenpox"
[23] "Dihphteria" "Lyme disease"
[25] "Plague" "Pertussis"
[27] "Meningococcal disease" "Antimicrobial resistance"
[29] "Campylobacteriosis" "Chlamydiosis"
[31] "Cholera" "Creutzfeld-Jakob disease"
[33] "Cryptosporidiosis" "Echinococcosis"
[35] "Giardiasis" "Gonorrhea"
[37] "Haemophilus influenzae" "Hantavirus"
[39] "Clostridium difficile" "Hepatitis A"
[41] "Hepatitis B-C" "HIV-AIDS"
[43] "HIV-AIDS" "Seasonal influenza"
[45] "Lassa fever" "Legionnaires disease"
[47] "Leptospirosis" "Listeriosis"
[49] "Lymphogranuloma venereum" "Malaria"
[51] "Pneumococcal disease" "Q fever"
[53] "Rift Valley fever" "Salmonellosis"
[55] "Shigellosis" "Syphillis"
[57] "Tick-borne encephalitis" "Tick-borne encephalitis"
[59] "Toxoplasmosis" "Trichinellosis"
[61] "Typhoid fever" "Yellow fever"
[63] "Yersiniosis" "Zika"
[65] "Bioterrorism" "Infectious diseases"
[67] "Infectious diseases" "MERS-CoV"
[69] "MERS-CoV" "COVID-19"
[71] "COVID-19 outbreaks" "COVID-19 outbreaks"
[73] "COVID-19 outbreaks" "COVID-19 outbreaks"
[75] "SARS" "Smallpox"
[77] "Yersiniosis" "Healthcare-associated infections" [79] "Healthcare-associated infections" "Zoonoses"
[81] "Vectorborne diseases" "Foodborne diseases"
[83] "Waterborne diseases" "STEC-VTEC"
[85] "STEC-VTEC" "Hepatitis-Unknown"
[87] "Hepatitis-Unknown" "Hepatitis-Unknown"
[89] "Hepatitis-Unknown" "Hepatitis-Unknown"
[91] "Hepatitis-Unknown" "Hepatitis-Unknown"
[93] "Hepatitis-Unknown" "Hepatitis-Unknown"
[95] "Hepatitis-Unknown" "Hepatitis-Unknown"
[97] "Hepatitis-Unknown" "Hepatitis-Unknown"
[99] "Hepatitis-Unknown" "Hepatitis-Unknown"
[101] "Hepatitis-Unknown" "Monkeypox"
df$Label [1] "Measles" "Rubella"
[3] "Mumps" "Dengue"
[5] "Haemorrhagic fever" "Avian influenza"
[7] "Chikungunya" "Poliomyelitis"
[9] "Tuberculosis" "Anthrax"
[11] "West Nile virus" "West Nile virus"
[13] "Crimean-Congo haemorrhagic fever" "Botulism"
[15] "Botulism" "Ebola"
[17] "Tularaemia" "Rabies"
[19] "Rabies" "Tetanus"
[21] "Brucellosis" "Chickenpox"
[23] "Dihphteria" "Lyme disease"
[25] "Plague" "Pertussis"
[27] "Meningococcal disease" "Antimicrobial resistance"
[29] "Campylobacteriosis" "Chlamydiosis"
[31] "Cholera" "Creutzfeld-Jakob disease"
[33] "Cryptosporidiosis" "Echinococcosis"
[35] "Giardiasis" "Gonorrhea"
[37] "Haemophilus influenzae" "Hantavirus"
[39] "Clostridium difficile" "Hepatitis A"
[41] "Hepatitis B-C" "HIV-AIDS"
[43] "HIV-AIDS" "Seasonal influenza"
[45] "Lassa fever" "Legionnaires disease"
[47] "Leptospirosis" "Listeriosis"
[49] "Lymphogranuloma venereum" "Malaria"
[51] "Pneumococcal disease" "Q fever"
[53] "Rift Valley fever" "Salmonellosis"
[55] "Shigellosis" "Syphillis"
[57] "Tick-borne encephalitis" "Tick-borne encephalitis"
[59] "Toxoplasmosis" "Trichinellosis"
[61] "Typhoid fever" "Yellow fever"
[63] "Yersiniosis" "Zika"
[65] "Bioterrorism" "Infectious diseases"
[67] "Infectious diseases" "MERS-CoV"
[69] "MERS-CoV" "COVID-19"
[71] "COVID-19 outbreaks" "COVID-19 outbreaks"
[73] "COVID-19 outbreaks" "COVID-19 outbreaks"
[75] "SARS" "Smallpox"
[77] "Yersiniosis" "Healthcare-associated infections" [79] "Healthcare-associated infections" "Zoonoses"
[81] "Vectorborne diseases" "Foodborne diseases"
[83] "Waterborne diseases" "STEC-VTEC"
[85] "STEC-VTEC" "Hepatitis-Unknown"
[87] "Hepatitis-Unknown" "Hepatitis-Unknown"
[89] "Hepatitis-Unknown" "Hepatitis-Unknown"
[91] "Hepatitis-Unknown" "Hepatitis-Unknown"
[93] "Hepatitis-Unknown" "Hepatitis-Unknown"
[95] "Hepatitis-Unknown" "Hepatitis-Unknown"
[97] "Hepatitis-Unknown" "Hepatitis-Unknown"
[99] "Hepatitis-Unknown" "Hepatitis-Unknown"
[101] "Hepatitis-Unknown" "Monkeypox"

[Abdouzster]

error in the database processing: 2022-06-21 11:28:36[INFO]---->Delaying commit request to finish before. Waiting geolocation: true. Waiting aggregation true 2022-06-21 11:28:37[INFO]---->Error during geolocalisation: key not found: Monkeypox: scala.collection.MapLike.default(MapLike.scala:235)

[forchard]

Hi @Abdouzster We manage to replicate the issue and find a solution. A fix will be included on next epitweetr release.

In the meantime there is also a way so you can solve it on your installation.

You have to open an R interpreter and run:

epitweetr::setup_config('full path to your epitweetr_home folder here') epitweetr:::update_topic_keywords()

After a while aggregations will start to be calculated. Unfortunately aggregations before this will not be produced.

Please let us know if this fix your issue.

Best, Francisco

[Abdouzster]

Thanks Francisco! New topic now is showing on the dashboard.

Abdelhamid

[forchard]

Already fixed on DEV. To be included on next CRAN release