Drop parent repository code (peskas.timor.pipeline), add infrastructu…

…re to download WCS survey data and upload it to cloud storage providers
WorldFishCenter · Oct 30, 2023 · dfa915d · dfa915d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
-Package: peskas.kenya.data.pipeline
-Title: Functions to Implement the kenya Small Scale Fisheries
+Package: peskas.zanzibar.data.pipeline
+Title: Functions to Implement the Zanzibar Small Scale Fisheries
     Data Pipeline
-Version: 3.0.0
+Version: 5.0.0
 Authors@R: 
     c(person(given = "Lorenzo",
              family = "Longobardi",
@@ -16,64 +16,37 @@ License: GPL-3
 Imports:
     config,
     dplyr,
-    digest,
     git2r,
-    glmmTMB,
     googleAuthR,
     googleCloudStorageR,
     googledrive,
     httr,
     jsonlite,
     logger,
+    lubridate,
     magrittr,
     purrr,
     readr,
+    stringr,
+    tibble,
     tidyr,
-    rlang (>= 0.1.2),
-    googlesheets4,
-    reticulate,
-    tools,
-    readxl
+    rlang,
+    KoboconnectR
 Suggests: 
     covr,
-    pkgdown,
-    remotes,
-    sessioninfo,
-    testthat,
-    RCurl,
-    roxygen2,
-    geosphere,
-    tidyselect,
-    textclean,
-    tinytest,
-    dataverse,
-    rmarkdown,
-    cowplot,
-    broom,
-    zoo,
-    sf,
-    ggplot2,
-    ggpubr,
-    lubridate,
-    stringr,
-    tibble,
-    furrr,
-    future,
-    rfishbase,
-    taxize,
-    univOutl,
-    zip,
-    leaflet,
-    htmltools,
-    imputeTS,
-    Amelia,
-    mice,
-    blastula,
-    glue,
-    mime,
-    janitor,
-    reactable,
-    kableExtra
+    pkgdown, 
+    sessioninfo, 
+    testthat, 
+    roxygen2, 
+    tidyselect, 
+    textclean, 
+    rmarkdown, 
+    taxize, 
+    tinytest, 
+    remotes, 
+    tidytext, 
+    htmltools, 
+    reticulate
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

diff --git a/Dockerfile b/Dockerfile
@@ -14,13 +14,11 @@ RUN install2.r --error --skipinstalled \
     lubridate \
     magrittr \
     purrr \
-    RCurl \
     readr \
     stringr \
     tibble \
     tidyr \
-    rlang \
-    googlesheets4
+    rlang
 
 # Install suggests
 RUN install2.r --error --skipinstalled \
@@ -31,35 +29,12 @@ RUN install2.r --error --skipinstalled \
     roxygen2 \
     tidyselect \
     textclean \
-    dataverse \
     rmarkdown \
-    geosphere \
-    rmarkdown \
-    ggplot2 \
-    bookdown \
-    broom \
-    zoo \
-    ggpubr \
-    cowplot \
-    kableExtra \
-    furrr \
-    future \
-    univOutl \
     taxize \
     tinytest \
     remotes \
     tidytext \
-    zip \
-    leaflet \
     htmltools \
-    Amelia \
-    mice \
-    blastula \
-    glue \
-    mime \
-    janitor \
-    reactable \
-    kableExtra \
     reticulate
 
 # Install GitHub packages

diff --git a/Dockerfile.prod b/Dockerfile.prod
@@ -27,13 +27,11 @@ RUN install2.r --error --skipinstalled \
     lubridate \
     magrittr \
     purrr \
-    RCurl \
     readr \
     stringr \
     tibble \
     tidyr \
-    rlang \
-    googlesheets4
+    rlang
 
 # Install suggests
 RUN install2.r --error --skipinstalled \
@@ -44,35 +42,12 @@ RUN install2.r --error --skipinstalled \
     roxygen2 \
     tidyselect \
     textclean \
-    dataverse \
-    rmarkdown \
-    geosphere \
-    broom \
-    zoo \
-    kableExtra \
-    ggplot2 \
-    bookdown \
     cowplot \
-    broom \
-    ggpubr \
-    furrr \
-    future \
-    univOutl \
     taxize \
     tinytest \
     remotes \
     tidytext \
-    zip \
-    leaflet \
     htmltools \
-    Amelia \
-    mice \
-    blastula \
-    glue \
-    mime \
-    janitor \
-    reactable \
-    kableExtra \
     reticulate
 
 

diff --git a/NAMESPACE b/NAMESPACE
@@ -5,107 +5,29 @@ export("%||%")
 export(":=")
 export(.data)
 export(add_version)
-export(air_get_records)
-export(air_records_to_tibble)
-export(air_tibble_to_records)
-export(air_upload_records)
 export(as_label)
 export(as_name)
-export(authenticate_google_drive)
-export(calculate_weights)
-export(clean_catches)
-export(clean_legacy_landings)
-export(clean_updated_landings)
 export(cloud_object_name)
 export(cloud_storage_authenticate)
-export(coalist)
-export(convert_taxa_names)
-export(delete_dataset)
-export(delete_dataverse)
 export(download_cloud_file)
 export(enquo)
 export(enquos)
 export(expr)
-export(fill_missing_regions)
-export(format_public_data)
-export(generate_description)
-export(generate_metadata)
-export(get_catch_types)
-export(get_distance)
-export(get_fish_length)
 export(get_full_tracks)
 export(get_full_trips)
-export(get_host_url)
-export(get_merged_landings)
 export(get_models)
-export(get_nutrients_table)
 export(get_preprocessed_metadata)
 export(get_sync_tracks)
-export(get_tracks_descriptors)
 export(get_tracks_ids)
 export(get_tracks_map)
 export(get_validated_landings)
 export(get_validation_sheet)
-export(ingest_complete_tracks)
-export(ingest_kepler_tracks)
-export(ingest_landings)
-export(ingest_legacy_landings)
-export(ingest_metadata_tables)
-export(ingest_pds_map)
-export(ingest_pds_matched_trips)
-export(ingest_pds_tracks)
-export(ingest_pds_trips)
-export(ingest_rfish_table)
-export(ingest_updated_landings)
-export(ingest_validation_tables)
-export(insistent_download_cloud_file)
-export(insistent_upload_cloud_file)
-export(join_weights)
-export(kepler_mapper)
-export(merge_consecutive_trips)
-export(merge_landings)
-export(merge_trips)
-export(model_indicators)
-export(preprocess_landings_step_1)
-export(preprocess_landings_step_2)
-export(preprocess_legacy_landings)
-export(preprocess_metadata_tables)
-export(preprocess_pds_tracks)
-export(preprocess_pds_trips)
-export(preprocess_updated_landings)
 export(pt_nest_attachments)
 export(pt_nest_species)
-export(pt_validate_boats)
-export(pt_validate_devices)
-export(pt_validate_flags)
-export(pt_validate_vms_installs)
-export(publish_dataverse)
-export(publish_last_dataset)
 export(read_config)
-export(retrieve_lengths)
-export(retrieve_pds_tracks)
-export(retrieve_pds_tracks_data)
-export(retrieve_pds_trips)
-export(retrieve_pds_trips_data)
-export(retrieve_survey)
-export(retrieve_survey_data)
-export(retrieve_survey_metadata)
-export(send_sites_report)
-export(send_validation_mail)
 export(sym)
 export(syms)
 export(upload_cloud_file)
-export(upload_dataverse)
-export(upload_files)
-export(validate_catch_params)
-export(validate_catch_price)
-export(validate_landings)
-export(validate_pds_data)
-export(validate_pds_trips)
-export(validate_price_weight)
-export(validate_surveys_time)
-importFrom(digest,digest)
-importFrom(glmmTMB,glmmTMB)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(magrittr,"%T>%")
@@ -119,7 +41,4 @@ importFrom(rlang,enquos)
 importFrom(rlang,expr)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
-importFrom(stats,mad)
-importFrom(stats,na.omit)
-importFrom(stats,predict)
 importFrom(utils,globalVariables)