Merge pull request #4 from bio-oracle/merge-upstream

Merge upstream

.gitignore

@@ -13,3 +13,4 @@ erddap/conf/config.sh
 erddap/content/history/*.xml
 erddap/content/datasets.xml
 erddap/content/setup.xml
+.envrc

GenerateDatasetsXml.sh

@@ -4,5 +4,6 @@ echo $CMD
 docker run --rm -it \
   -v "/data/layers:/datasets" \
   -v "$(pwd)/logs:/erddapData/logs" \
-  axiom/docker-erddap:2.18 \
+   -v $(pwd)/erddap/content:/usr/local/tomcat/content/erddap \
+  axiom/docker-erddap:2.23-jdk17-openjdk \
   bash -c "cd webapps/erddap/WEB-INF/ && $CMD"

docker-compose.yml

@@ -1,18 +1,41 @@
-version: '2'
 services:
   erddap:
     container_name: "bio-oracle-erddap"
-    image: axiom/docker-erddap:2.22-jdk17-openjdk
+    image: axiom/docker-erddap:2.23-jdk17-openjdk
     restart: unless-stopped
     ports:
       - "8080:8080"
-    environment:
-      ERDDAP_MIN_MEMORY: 1G
-      ERDDAP_MAX_MEMORY: 12G
     volumes:
       - "${PWD}/erddap/conf/config.sh:/usr/local/tomcat/bin/config.sh"
       - "${PWD}/erddap/conf/robots.txt:/usr/local/tomcat/webapps/ROOT/robots.txt"
       - "${PWD}/erddap/content:/usr/local/tomcat/content/erddap"
       - "${PWD}/erddap/data:/erddapData"
       - "/data/layers:/datasets"
       - "/tmp/:/usr/local/tomcat/temp/"
+    environment:
+      #note: these can also be set in /usr/local/tomcat/bin/config.sh
+      ERDDAP_MIN_MEMORY: 2G
+      ERDDAP_MAX_MEMORY: 12G
+      ERDDAP_bigParentDirectory: /erddapData/
+      ERDDAP_baseUrl: "http://erddap.bio-oracle.org:8080"
+      ERDDAP_baseHttpsUrl: "http://erddap.bio-oracle.org:8080"
+      ERDDAP_flagKeyKey: "4a0c345f-d494-4edc-b8c7-640c6d99f4b1"
+      ERDDAP_emailEverythingT: [email protected]
+      ERDDAP_emailDailyReportsTo:
+      ERDDAP_emailFromAddress:
+      ERDDAP_emailUserName:
+      ERDDAP_emailPassword:
+      ERDDAP_emailProperties:
+      ERDDAP_emailSmtpHost:
+      ERDDAP_emailSmtpPort:
+      ERDDAP_adminInstitution: Flanders Marine Institute (VLIZ)
+      ERDDAP_adminInstitutionUrl: https://vliz.be/en/
+      ERDDAP_adminIndividualName: VLIZ Data Manager
+      ERDDAP_adminPosition: Data Manager
+      ERDDAP_adminPhone:
+      ERDDAP_adminAddress:
+      ERDDAP_adminCity:
+      ERDDAP_adminStateOrProvince:
+      ERDDAP_adminPostalCode:
+      ERDDAP_adminCountry:
+      ERDDAP_adminEmail:

erddap/conf/config_template.sh

@@ -1,8 +1,9 @@
+ERDDAP_MIN_MEMORY="1G"
+ERDDAP_MAX_MEMORY="12G"
 ERDDAP_bigParentDirectory="/erddapData/"
 ERDDAP_baseUrl="http://erddap.bio-oracle.org:8080"
 ERDDAP_baseHttpsUrl="http://erddap.bio-oracle.org:8080"
 ERDDAP_flagKeyKey="4a0c345f-d494-4edc-b8c7-640c6d99f4b1"
-
 ERDDAP_emailEverythingTo="[email protected]"
 ERDDAP_emailDailyReportsTo=""
 ERDDAP_emailFromAddress=""
@@ -11,15 +12,14 @@ ERDDAP_emailPassword=""
 ERDDAP_emailProperties=""
 ERDDAP_emailSmtpHost=""
 ERDDAP_emailSmtpPort=""
-
-ERDDAP_adminInstitution="Integrated Ocean Observing System (IOOS)"
-ERDDAP_adminInstitutionUrl="https://ioos.github.io/"
-ERDDAP_adminIndividualName="Micah Wengren"
+ERDDAP_adminInstitution="Flanders Marine Institute (VLIZ)"
+ERDDAP_adminInstitutionUrl="https://vliz.be/en/"
+ERDDAP_adminIndividualName="VLIZ Data Manager"
 ERDDAP_adminPosition="Data Manager"
-ERDDAP_adminPhone="240-533-9441"
-ERDDAP_adminAddress="1315 East-West Highway 2nd Floor"
-ERDDAP_adminCity="Silver Spring"
-ERDDAP_adminStateOrProvince="MD"
-ERDDAP_adminPostalCode="20910"
-ERDDAP_adminCountry="USA"
-ERDDAP_adminEmail="[email protected]"
+ERDDAP_adminPhone=""
+ERDDAP_adminAddress=""
+ERDDAP_adminCity=""
+ERDDAP_adminStateOrProvince=""
+ERDDAP_adminPostalCode=""
+ERDDAP_adminCountry=""
+ERDDAP_adminEmail=""

utils/convert_nc_cdl.py

@@ -0,0 +1,30 @@
+from netCDF4 import Dataset
+
+
+def convert_nc_to_cdl(nc_fname):
+    cdl_fname = nc_fname.with_suffix(".cdl")
+    if cdl_fname.exists():
+        print(f"The {cdl_fname} file already exists, not overwriting it.")
+        return
+    with Dataset(nc_fname) as nc:
+        print(f"Converting {nc_fname} to {cdl_fname}.")
+        nc.tocdl(coordvars=True, data=True, outfile=cdl_fname)
+
+def convert_cdl_to_nc(cdl_name):
+    nc_fname = cdl_fname.with_suffix(".nc")
+    if nc_fname.exists():
+        print(f"The {nc_fname} file already exists, not overwriting it.")
+        return
+    print(f"Converting {cdl_fname} to {nc_fname}.")
+    Dataset.fromcdl(cdl_fname)
+
+
+if __name__ == "__main__":
+    from pathlib import Path
+
+    datasets_path = Path("datasets")
+    for nc_fname in datasets_path.glob("*.nc"):
+        convert_nc_to_cdl(nc_fname)
+
+    for cdl_fname in datasets_path.glob("*.cdl"):
+        convert_cdl_to_nc(cdl_fname)