Merge dev to master

.gitignore

@@ -18,4 +18,5 @@ proj/templates/__pycache__/
 # not for the smc checker
 # proj/custom/*_custom.py
 
-docker/deploy.sh
+docker
+R/.Rhistory

R/asci.R

@@ -0,0 +1,44 @@
+library(DBI)
+library(dplyr)
+library(RPostgreSQL)
+library(ASCI)
+library(readxl)
+
+args = commandArgs(trailingOnly=TRUE)
+
+dir <- args[1]
+filename <- args[2]
+
+print('Connecting to the database')
+con <- dbConnect(
+  PostgreSQL(),
+  host = Sys.getenv('DB_HOST'),
+  dbname = Sys.getenv('DB_NAME'),
+  user = Sys.getenv('DB_USER'),
+  password = Sys.getenv('DB_PASSWORD')
+)
+print('Created database connection')
+
+alg <- readxl::read_excel(file.path(dir, filename))
+
+# Select from vw_asci_checker_gispredictors since the other view vw_asci_gispredictors only grabs records for stations in unified algae
+# That view is for the sync script
+gis <- dbGetQuery(con, 'SELECT * FROM vw_asci_checker_gispredictors') %>% filter(StationCode %in% alg$stationcode)
+
+alg <- alg %>% 
+  select(c('stationcode','sampledate','replicate','sampletypecode','baresult','result','finalid')) %>% 
+  rename(
+    `StationCode` = stationcode,
+    `SampleDate` = sampledate,
+    `Replicate` = replicate,
+    `SampleTypeCode` = sampletypecode,
+    `BAResult` = baresult,
+    `Result` = result,
+    `FinalID` = finalid                
+  )
+
+
+output <- ASCI(alg, gis) %>% smcify 
+
+write.csv(output, file = file.path(dir, 'ASCI_scores.csv'), row.names = FALSE)
+

R/csci.R

@@ -0,0 +1,70 @@
+library(DBI)
+library(dplyr)
+library(RPostgreSQL)
+library(CSCI)
+library(readxl)
+
+args = commandArgs(trailingOnly=TRUE)
+
+dir <- args[1]
+filename <- args[2]
+
+print('Connecting to the database')
+con <- dbConnect(
+  PostgreSQL(),
+  host = Sys.getenv('DB_HOST'),
+  dbname = Sys.getenv('DB_NAME'),
+  user = Sys.getenv('DB_USER'),
+  password = Sys.getenv('DB_PASSWORD')
+)
+print('Created database connection')
+
+bugs <-  readxl::read_excel(file.path(dir, filename))
+
+# This view does not limit the stations to the ones that are in unified_taxonomy, for some reason
+gis <- dbGetQuery(con, 'SELECT * FROM vw_csci_gispredictors') %>% filter(StationCode %in% bugs$stationcode)
+
+bugs <- bugs %>%
+    mutate(
+        sampleid = paste(stationcode, gsub("[/\\s:]", "", format(sampledate, "%Y%m%d")), fieldreplicate, sep = "_")) %>%
+    select(c('stationcode', 'sampleid' ,'baresult', 'lifestagecode', 'distinctcode', 'finalid')) %>%
+    rename(
+        `StationCode` = stationcode,
+        `SampleID` = sampleid,
+        `FinalID` = finalid,
+        `BAResult` = baresult,
+        `LifeStageCode` = lifestagecode,
+        `Distinct` = distinctcode
+    )
+
+bugs <- cleanData(bugs)
+bugs <- bugs %>% mutate(BAResult = as.numeric(BAResult)) # this can be altered in the view definition
+metadata <- BMIMetrics::loadMetaData()
+namecheck <- paste(bugs$FinalID, bugs$LifeStageCode) %in% paste(metadata$FinalID, metadata$LifeStageCode)
+missing <- which(!namecheck)
+if(length(missing)>0){
+  casenamecheck <- paste(toupper(bugs$FinalID[missing]), bugs$LifeStageCode[missing]) %in% paste(toupper(metadata$FinalID), metadata$LifeStageCode)
+  bugs$FinalID[missing][casenamecheck] <- 
+    as.character(metadata$FinalID[match(toupper(bugs$FinalID[missing][casenamecheck]), toupper(metadata$FinalID))])
+  if(length(namecheck) != (sum(namecheck) + sum(casenamecheck)))
+    warning(c("The following FinalID/LifeStageCode combinations did not match with the internal database:",
+              paste(unique(paste(bugs$FinalID[!namecheck], bugs$LifeStageCode[!namecheck])), collapse=", ")))
+}
+notfound <- bugs %>% filter(!namecheck)
+bugs <- bugs %>% filter(namecheck)
+
+result <- CSCI(bugs, gis)
+
+core <- result$core
+suppl1_grps <- result$Suppl1_grps
+suppl1_mmi <- result$Suppl1_mmi
+suppl2_mmi <- result$Suppl2_mmi
+suppl1_oe <- result$Suppl1_OE
+suppl2_oe <- result$Suppl2_OE
+
+write.csv(core, file = file.path(dir, 'core.csv'), row.names = FALSE)
+write.csv(suppl1_grps, file = file.path(dir, 'suppl1_grps.csv'), row.names = FALSE)
+write.csv(suppl1_mmi, file = file.path(dir, 'suppl1_mmi.csv'), row.names = FALSE)
+write.csv(suppl2_mmi, file = file.path(dir, 'suppl2_mmi.csv'), row.names = FALSE)
+write.csv(suppl1_oe, file = file.path(dir, 'suppl1_oe.csv'), row.names = FALSE)
+write.csv(suppl2_oe, file = file.path(dir, 'suppl2_oe.csv'), row.names = FALSE)

R/phab.R

@@ -0,0 +1,29 @@
+library(PHABMetrics)
+library(PHAB)
+
+
+##########---R Script----##############################
+randomdataframe <- data.frame(testcol1 = c(1,2,3,4,5), testcol2 = c(5,6,7,8,9), testcol3 = c('a','b','c','d','e'))
+print("dataframe: ")
+randomdataframe
+
+args <- commandArgs(trailingOnly=TRUE)
+print("args:")
+args
+dir <- args[1]
+print("dir:")
+dir
+filename <- args[2]
+print("filename:")
+filename
+wbpath <- file.path(dir, filename)
+print("wbpath:")
+wbpath
+output <- (randomdataframe)
+print("Output:")
+output
+
+write.csv(randomdataframe, file = file.path(dir, 'output.csv'), row.names=FALSE)
+
+
+########################################

permissions.sh

@@ -8,6 +8,6 @@ fi
 
 DIRECTORY=$(cd `dirname $0` && pwd)
 chown -R $editor.$editor $DIRECTORY;
-chown -R www-data.$editor $DIRECTORY/files $DIRECTORY/proj/custom $DIRECTORY/proj/static $DIRECTORY/proj/config;
-chmod -R 775 $DIRECTORY/files $DIRECTORY/proj/custom $DIRECTORY/proj/static;
+chown -R www-data.$editor $DIRECTORY/files $DIRECTORY/export $DIRECTORY/proj/custom $DIRECTORY/proj/static $DIRECTORY/proj/config;
+chmod -R 775 $DIRECTORY/files $DIRECTORY/export $DIRECTORY/proj/custom $DIRECTORY/proj/static;
 chmod -R 575 $DIRECTORY/proj/config;

proj/__init__.py

@@ -3,15 +3,19 @@
 from sqlalchemy import create_engine
 import psycopg2
 from psycopg2 import sql
-
+from flask_cors import CORS
 # import blueprints to register them
 from .main import upload
 from .login import homepage
 from .load import finalsubmit
 from .download import download
 from .scraper import scraper
 from .templater import templater # for dynamic lookup lists called into template before output to user
-
+from .process_shapefile import sfprocessing 
+from .load_shapefile import sfloading 
+from .map_check import map_check, get_map_info
+from .admin import admin
+from .query import query
 
 CUSTOM_CONFIG_PATH = os.path.join(os.getcwd(), 'proj', 'config')
 
@@ -26,17 +30,28 @@
 
 
 app = Flask(__name__, static_url_path='/static')
+
+# CORS(app, resources={r"/arcgis/*": {"origins": "https://nexus.sccwrp.org"}})
+
+CORS(app)
+
 app.debug = True # remove for production
 
 
 # does your application require uploaded filenames to be modified to timestamps or left as is
+app.config['APP_SCRIPT_ROOT'] = 'smcchecker'
+
 app.config['CORS_HEADERS'] = 'Content-Type'
 
 app.config['MAIL_SERVER'] = os.environ.get('FLASK_APP_MAIL_SERVER')
 
 app.config['MAX_CONTENT_LENGTH'] = 200 * 1024 * 1024  # 200MB limit
+
+app.config['BACKGROUND_IMAGE'] = BASIC_CONFIG.get("BACKGROUND_IMAGE")
+
 app.secret_key = os.environ.get("FLASK_APP_SECRET_KEY")
 
+
 # set the database connection string, database, and type of database we are going to point our application at
 #app.eng = create_engine(os.environ.get("DB_CONNECTION_STRING"))
 def connect_db():
@@ -138,9 +153,16 @@ def teardown_request(exception):
 # need to assert that the table names are in (SELECT table_name FROM information_schema.tables)
 
 app.register_blueprint(upload)
+app.register_blueprint(sfprocessing)
+app.register_blueprint(sfloading)
 app.register_blueprint(homepage)
 app.register_blueprint(finalsubmit)
+app.register_blueprint(get_map_info)
 app.register_blueprint(download)
 app.register_blueprint(scraper)
 app.register_blueprint(templater)
+app.register_blueprint(map_check)
+app.register_blueprint(admin)
+app.register_blueprint(query)
+