Merge pull request #96 from melofton/eco_apps_release

fixing gitignore omission in data publication folder

9_Data_publication/.gitignore

@@ -4,4 +4,5 @@
 !.gitignore
 !9A_rename_hindcast_files.R
 !9B_create_netcdfs.R
-!9C_MakeEMLHindcasts_NLDAS_PRISM
+!9C_MakeEMLHindcastsNLDASPRISM.R
+!readme.txt

9_Data_publication/9C_MakeEMLHindcastsNLDASPRISM.R

@@ -0,0 +1,232 @@
+##MakeEMLNLDASPRISM
+##Author: Mary Lofton
+##Date: 10MAY20
+
+#good site for step-by-step instructions
+#https://ediorg.github.io/EMLassemblyline/articles/overview.html
+#and links therein
+
+#load packages
+library(tidyverse)
+
+#read in final data files to check format
+nldas <- read_csv("C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM/NLDAS_solar_radiation_2009-2016.csv")
+prism <- read_csv("C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM/PRISM_precipitation_2009-2016.csv")
+
+# (install and) Load EMLassemblyline #####
+# install.packages('devtools')
+
+devtools::install_github("EDIorg/EMLassemblyline")
+library(EMLassemblyline)
+
+
+#Step 1: Create a directory for your dataset
+#in this case, our directory is C:\Users\Mary Lofton\Dropbox\Ch5\EDI.hindcasts.NLDAS.PRISM
+
+#Step 2: Move your dataset to the directory
+
+#Step 3: Identify an intellectual rights license
+#ours is CCBY
+
+#Step 4: Identify the types of data in your dataset
+#we have two tables and one zip file
+
+#Step 5: Import the core metadata templates
+
+#for our application, we will need to generate all types of metadata
+#files except for taxonomic coverage, as we have both continuous and
+#categorical variables and want to report our geographic location
+
+# View documentation for these functions
+?template_core_metadata
+?template_table_attributes
+?template_geographic_coverage
+?template_taxonomic_coverage
+
+# Import templates for our dataset licensed under CCBY, with 2 tables.
+template_core_metadata(path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                 license = "CCBY",
+                 file.type = ".txt",
+                 write.file = TRUE)
+
+template_table_attributes(path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                       data.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                       data.table = "NLDAS_solar_radiation_2009-2016.csv",
+                       write.file = TRUE)
+
+template_table_attributes(path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                          data.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                          data.table = "PRISM_precipitation_2009-2016.csv",
+                          write.file = TRUE)
+
+#we want empty to be true for this because we don't include lat/long
+#as columns within our dataset but would like to provide them
+#only have to do this once even if have multiple data tables
+template_geographic_coverage(path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                          data.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+                          data.table = "NLDAS_solar_radiation_2009-2016.csv",
+                          empty = TRUE,
+                          write.file = TRUE)
+
+
+#for this project we also need taxonomic coverage for G. echinulata
+#however, I am using a file created for a different Gloeo pub
+#so we are not going to create a new file in this script
+
+#Step 6: Script your workflow
+#that's what this is.
+
+#Step 7: Abstract
+#copy-paste the abstract from your Microsoft Word document into abstract.txt
+#if you want to check your abstract for non-allowed characters, go to:
+#https://pteo.paranoiaworks.mobi/diacriticsremover/
+#paste text and click remove diacritics
+
+#Step 8: Methods
+#copy-paste the methods from your Microsoft Word document into methods.txt
+#if you want to check your abstract for non-allowed characters, go to:
+#https://pteo.paranoiaworks.mobi/diacriticsremover/
+#paste text and click remove diacritics
+
+#Step 9: Additional information
+#refs to other data pubs associated with the GLEON Bayes Gloeo project are in here
+
+#Step 10: Keywords
+#DO NOT EDIT KEYWORDS FILE USING A TEXT EDITOR!! USE EXCEL!!
+#good sources for keyword thesauri:
+#lter controlled vocabulary
+#cuahsi controlled vocabulary
+
+#Step 11: Personnel
+#copy-paste this information in from your metadata document
+#Typically, the lead PI needs to be listed several times; that person has to be listed separately for his/her roles as
+#PI, creator, and contact, and also separately for each separate funding source (!!)
+
+#Step 12: Attributes
+#you will need to edit the attributes files for each data table you are publishing
+#grab attribute names and definitions from your metadata Google doc
+#for units....
+# View and search the standard units dictionary
+view_unit_dictionary()
+
+#Step 13: Custom Units
+#if units are not in the unit dictionary, you need to fill them out in the
+#custom_units.txt file
+#in our case, this is lnColoniesPerLiter, wattsPerMeterSquared, and millimetersPerDay
+
+#Step 14: Close files
+#if all your files aren't closed, sometimes functions don't work
+
+#Step 15: Categorical variables
+#we don't have any - hooray! :-)
+
+#Step 16: Geographic coverage
+#fill in the text file with the appropriate bounding box for your site
+#we added both a bounding box for Lake Sunapee as well as
+#point coordinates for the South Herrick Cove sampling site
+
+#Step 17: Taxonomic coverage
+#again, got this file from Bethel so no need to edit here - thx, Bethel! :-)
+
+## Step 18: Obtain a package.id. ####
+# Go to the EDI staging environment (https://portal-s.edirepository.org/nis/home.jsp),
+# then login using your username and password.
+
+# Select Tools --> Data Package Identifier Reservations and click
+# "Reserve Next Available Identifier"
+# A new value will appear in the "Current data package identifier reservations"
+# table (e.g., edi.123)
+# Make note of this value, as it will be your package.id below
+
+#Step 19: Make EML
+# View documentation for this function
+?make_eml
+
+# Run this function
+make_eml(
+  path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+  data.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+  eml.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+  dataset.title = "Lake Sunapee Gloeotrichia echinulata density near-term hindcasts from 2015-2016 and meteorological model driver data, including shortwave radiation and precipitation from 2009-2016",
+  temporal.coverage = c("2009-05-29", "2016-09-28"), #needs edited!!
+  maintenance.description = 'completed', #ongoing or completed if we don't ever plan on updating this
+  data.table = c("NLDAS_solar_radiation_2009-2016.csv","PRISM_precipitation_2009-2016.csv"),
+  data.table.name = c("NLDAS solar radiation data","PRISM precipitation data"),
+  data.table.description = c("NLDAS solar radiation data","PRISM precipitation data"),
+  other.entity = "Gechinulata_hindcasts.zip",
+  other.entity.name = "Lake Sunapee G. echinulata density hindcast NetCDF files",
+  other.entity.description = "Lake Sunapee G. echinulata density hindcast NetCDF files",
+  user.id = '', #you need credentials for this part
+  user.domain = 'EDI',
+  package.id = 'edi.18.5') #will need to change this
+
+## Step 20: Check your data product! ####
+# Return to the EDI staging environment (https://portal-s.edirepository.org/nis/home.jsp),
+# then login using your username and password
+
+# Select Tools --> Evaluate/Upload Data Packages, then under "EML Metadata File",
+# choose your metadata (.xml) file (e.g., edi.270.1.xml), check "I want to
+# manually upload the data by selecting files on my local system", then click Upload.
+
+# Now, Choose File for each file within the data package (e.g., each zip folder),
+# then click Upload. Files will upload and your EML metadata will be checked
+# for errors. If there are no errors, your data product is now published!
+# If there were errors, click the link to see what they were, then fix errors
+# in the xml file.
+# Note that each revision results in the xml file increasing one value
+# (e.g., edi.270.1, edi.270.2, etc). Re-upload your fixed files to complete the
+# evaluation check again, until you receive a message with no errors.
+
+## Step 21: PUBLISH YOUR DATA! ####
+# Reserve a package.id for your error-free data package.
+# NEVER ASSIGN this identifier to a staging environment package.
+# Go to the EDI Production environment (https://portal.edirepository.org/nis/home.jsp)
+# and login using your permanent credentials.
+
+# Select Tools --> Data Package Identifier Reservations and click "Reserve Next
+# Available Identifier". A new value will appear in the "Current data package
+# identifier reservations" table (e.g., edi.518)
+# This will be your PUBLISHED package.id
+
+# In the make_eml command below, change the package.id to match your
+# PUBLISHED package id. This id should end in .1 (e.g., edi.518.1)
+
+# ALL OTHER entries in the make_eml() command should match what you ran above,
+# in step 19
+
+make_eml(
+  path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+  data.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+  eml.path = "C:/Users/Mary Lofton/Dropbox/Ch5/EDI.hindcasts.NLDAS.PRISM",
+  dataset.title = "Lake Sunapee Gloeotrichia echinulata density near-term hindcasts from 2015-2016 and meteorological model driver data, including shortwave radiation and precipitation from 2009-2016",
+  temporal.coverage = c("2009-05-29", "2016-09-28"), #needs edited!!
+  maintenance.description = 'completed', #ongoing or completed if we don't ever plan on updating this
+  data.table = c("NLDAS_solar_radiation_2009-2016.csv","PRISM_precipitation_2009-2016.csv"),
+  data.table.name = c("NLDAS solar radiation data","PRISM precipitation data"),
+  data.table.description = c("NLDAS solar radiation data","PRISM precipitation data"),
+  other.entity = "Gechinulata_hindcasts.zip",
+  other.entity.name = "Lake Sunapee G. echinulata density hindcast NetCDF files",
+  other.entity.description = "Lake Sunapee G. echinulata density hindcast NetCDF files",
+  user.id = '', #you need credentials for this part
+  user.domain = 'EDI',
+  package.id = 'edi.18.5') #will need to change this
+
+# Once your xml file with your PUBLISHED package.id is Done, return to the
+# EDI Production environment (https://portal.edirepository.org/nis/home.jsp)
+
+# Select Tools --> Preview Your Metadata, then upload your metadata (.xml) file
+# associated with your PUBLISHED package.id. Look through the rendered
+# metadata one more time to check for mistakes (author order, bounding box, etc.)
+
+# Select Tools --> Evaluate/Upload Data Packages, then under "EML Metadata File",
+# choose your metadata (.xml) file associated with your PUBLISHED package.id
+# (e.g., edi.518.1.xml), check "I want to manually upload the data by selecting
+# files on my local system", then click Upload.
+
+# Now, Choose File for each file within the data package (e.g., each zip folder),
+# then click Upload. Files will upload and your EML metadata will be checked for
+# errors. Since you checked for and fixed errors in the staging environment, this
+# should run without errors, and your data product is now published!
+
+# Click the package.id hyperlink to view your final product! HOORAY!
+# Have a cookie or a beer, whichever you feel is more appropriate. :-)

9_Data_publication/readme.txt

@@ -0,0 +1,9 @@
+9_Data_publication
+
+Scripts to compile hindcast .csvs into NetCDF format and create EML metadata for hindcasts, NLDAS, and PRISM data for publication at the Environmental Data Initiative (EDI).
+
+Guide to files:
+
+9A_rename_hindcast_files.R: renames hindcast .csv files to be compatible with 9B_create_netcdfs.R
+9B_create_netcdfs.R: converts hindcasts .csv files to NetCDF format and generates an EML file for each NetCDF following Ecological Forecasting Initiative (EFI) standards
+9C_MakeEMLHindcastsNLDASPRISM.R: script documenting workflow for creation of EML for data publication to EDI.