From a8f6f9bec050394d60273824940103ad27cd051f Mon Sep 17 00:00:00 2001
From: James Runnalls <james.runnalls@eawag.ch>
Date: Tue, 27 Oct 2020 15:53:22 +0100
Subject: [PATCH] Initial data upload
---
.gitignore | 3 +
.idea/.gitignore | 3 +
.idea/inspectionProfiles/Project_Default.xml | 80 ++++++++++++++
.../inspectionProfiles/profiles_settings.xml | 6 ++
.idea/lake-greifen-profiles.iml | 8 ++
.idea/misc.xml | 4 +
.idea/modules.xml | 8 ++
.idea/vcs.xml | 6 ++
data/Level0/Lake_Greifen_CTD_W_2020-01-27.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-02-03.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-02-10.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-02-17.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-02-24.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-03-02.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-03-09.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-03-16.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-03-23.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-03-30.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-04-06.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-04-13.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-04-20.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-04-27.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-05-04.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-05-11.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-05-18.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-05-25.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-06-01.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-06-08.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-06-15.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-06-22.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-06-29.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-07-06.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-07-13.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-07-20.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-07-27.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-08-03.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-08-10.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-08-17.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-08-24.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-08-31.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-09-07.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-09-14.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-09-21.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-09-28.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-10-05.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-10-12.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-10-19.txt | 3 +
data/Level0/Lake_Greifen_CTD_W_2020-10-26.txt | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-01-27.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-02-03.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-02-10.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-02-17.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-02-24.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-03-02.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-03-09.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-03-16.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-03-23.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-03-30.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-04-06.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-04-13.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-04-20.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-04-27.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-05-04.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-05-11.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-05-18.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-05-25.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-06-01.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-06-08.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-06-15.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-06-22.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-06-29.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-07-06.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-07-13.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-07-20.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-07-27.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-08-03.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-08-10.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-08-17.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-08-24.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-08-31.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-09-07.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-09-14.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-09-21.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-09-28.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-10-05.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-10-12.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-10-19.nc | 3 +
data/Level1A/Lake_Greifen_CTD_W_2020-10-26.nc | 3 +
notebooks/automate.sh | 9 ++
notebooks/functions.py | 102 ++++++++++++++++++
notebooks/lastupdated.ini | 3 +
notebooks/main.py | 49 +++++++++
92 files changed, 521 insertions(+)
create mode 100644 .idea/.gitignore
create mode 100644 .idea/inspectionProfiles/Project_Default.xml
create mode 100644 .idea/inspectionProfiles/profiles_settings.xml
create mode 100644 .idea/lake-greifen-profiles.iml
create mode 100644 .idea/misc.xml
create mode 100644 .idea/modules.xml
create mode 100644 .idea/vcs.xml
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-01-27.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-02-03.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-02-10.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-02-17.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-02-24.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-03-02.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-03-09.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-03-16.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-03-23.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-03-30.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-04-06.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-04-13.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-04-20.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-04-27.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-05-04.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-05-11.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-05-18.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-05-25.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-06-01.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-06-08.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-06-15.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-06-22.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-06-29.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-07-06.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-07-13.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-07-20.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-07-27.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-08-03.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-08-10.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-08-17.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-08-24.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-08-31.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-09-07.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-09-14.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-09-21.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-09-28.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-10-05.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-10-12.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-10-19.txt
create mode 100644 data/Level0/Lake_Greifen_CTD_W_2020-10-26.txt
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-01-27.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-02-03.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-02-10.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-02-17.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-02-24.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-03-02.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-03-09.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-03-16.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-03-23.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-03-30.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-04-06.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-04-13.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-04-20.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-04-27.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-05-04.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-05-11.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-05-18.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-05-25.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-06-01.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-06-08.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-06-15.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-06-22.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-06-29.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-07-06.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-07-13.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-07-20.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-07-27.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-08-03.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-08-10.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-08-17.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-08-24.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-08-31.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-09-07.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-09-14.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-09-21.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-09-28.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-10-05.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-10-12.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-10-19.nc
create mode 100644 data/Level1A/Lake_Greifen_CTD_W_2020-10-26.nc
create mode 100644 notebooks/automate.sh
create mode 100644 notebooks/functions.py
create mode 100644 notebooks/lastupdated.ini
create mode 100644 notebooks/main.py
diff --git a/.gitignore b/.gitignore
index 7112dacd..67049215 100644
--- a/.gitignore
+++ b/.gitignore
@@ -378,3 +378,6 @@ tags
.renku.lock
.renku/tmp
.renku/cache
+
+# Database
+/notebooks/database.ini
\ No newline at end of file
diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 00000000..26d33521
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 00000000..ae5d44ba
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,80 @@
+<component name="InspectionProjectProfileManager">
+ <profile version="1.0">
+ <option name="myName" value="Project Default" />
+ <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+ <option name="ignoredPackages">
+ <value>
+ <list size="67">
+ <item index="0" class="java.lang.String" itemvalue="nose" />
+ <item index="1" class="java.lang.String" itemvalue="jpy" />
+ <item index="2" class="java.lang.String" itemvalue="pandas" />
+ <item index="3" class="java.lang.String" itemvalue="netCDF4" />
+ <item index="4" class="java.lang.String" itemvalue="PyYAML" />
+ <item index="5" class="java.lang.String" itemvalue="numpy" />
+ <item index="6" class="java.lang.String" itemvalue="traitlets" />
+ <item index="7" class="java.lang.String" itemvalue="jupyter-core" />
+ <item index="8" class="java.lang.String" itemvalue="ptyprocess" />
+ <item index="9" class="java.lang.String" itemvalue="georaster" />
+ <item index="10" class="java.lang.String" itemvalue="pickleshare" />
+ <item index="11" class="java.lang.String" itemvalue="wcwidth" />
+ <item index="12" class="java.lang.String" itemvalue="PyQt5-sip" />
+ <item index="13" class="java.lang.String" itemvalue="affine" />
+ <item index="14" class="java.lang.String" itemvalue="ipython-genutils" />
+ <item index="15" class="java.lang.String" itemvalue="Pygments" />
+ <item index="16" class="java.lang.String" itemvalue="PyQt5" />
+ <item index="17" class="java.lang.String" itemvalue="pyzmq" />
+ <item index="18" class="java.lang.String" itemvalue="prompt-toolkit" />
+ <item index="19" class="java.lang.String" itemvalue="snuggs" />
+ <item index="20" class="java.lang.String" itemvalue="six" />
+ <item index="21" class="java.lang.String" itemvalue="rio-mucho" />
+ <item index="22" class="java.lang.String" itemvalue="parso" />
+ <item index="23" class="java.lang.String" itemvalue="sphinx-rtd-theme" />
+ <item index="24" class="java.lang.String" itemvalue="cligj" />
+ <item index="25" class="java.lang.String" itemvalue="rio-rgbify" />
+ <item index="26" class="java.lang.String" itemvalue="ipython" />
+ <item index="27" class="java.lang.String" itemvalue="jupyter-client" />
+ <item index="28" class="java.lang.String" itemvalue="pexpect" />
+ <item index="29" class="java.lang.String" itemvalue="click" />
+ <item index="30" class="java.lang.String" itemvalue="ipykernel" />
+ <item index="31" class="java.lang.String" itemvalue="jedi" />
+ <item index="32" class="java.lang.String" itemvalue="rasterio" />
+ <item index="33" class="java.lang.String" itemvalue="cftime" />
+ <item index="34" class="java.lang.String" itemvalue="backcall" />
+ <item index="35" class="java.lang.String" itemvalue="virtualenv" />
+ <item index="36" class="java.lang.String" itemvalue="mercantile" />
+ <item index="37" class="java.lang.String" itemvalue="pytz" />
+ <item index="38" class="java.lang.String" itemvalue="click-plugins" />
+ <item index="39" class="java.lang.String" itemvalue="idna" />
+ <item index="40" class="java.lang.String" itemvalue="Pillow" />
+ <item index="41" class="java.lang.String" itemvalue="sphinxcontrib-applehelp" />
+ <item index="42" class="java.lang.String" itemvalue="decorator" />
+ <item index="43" class="java.lang.String" itemvalue="haversine" />
+ <item index="44" class="java.lang.String" itemvalue="Babel" />
+ <item index="45" class="java.lang.String" itemvalue="python-dateutil" />
+ <item index="46" class="java.lang.String" itemvalue="MarkupSafe" />
+ <item index="47" class="java.lang.String" itemvalue="requests" />
+ <item index="48" class="java.lang.String" itemvalue="Jinja2" />
+ <item index="49" class="java.lang.String" itemvalue="snowballstemmer" />
+ <item index="50" class="java.lang.String" itemvalue="sphinxcontrib-devhelp" />
+ <item index="51" class="java.lang.String" itemvalue="alabaster" />
+ <item index="52" class="java.lang.String" itemvalue="certifi" />
+ <item index="53" class="java.lang.String" itemvalue="sphinxcontrib-qthelp" />
+ <item index="54" class="java.lang.String" itemvalue="docutils" />
+ <item index="55" class="java.lang.String" itemvalue="urllib3" />
+ <item index="56" class="java.lang.String" itemvalue="pyparsing" />
+ <item index="57" class="java.lang.String" itemvalue="scipy" />
+ <item index="58" class="java.lang.String" itemvalue="tornado" />
+ <item index="59" class="java.lang.String" itemvalue="sphinxcontrib-serializinghtml" />
+ <item index="60" class="java.lang.String" itemvalue="imagesize" />
+ <item index="61" class="java.lang.String" itemvalue="packaging" />
+ <item index="62" class="java.lang.String" itemvalue="snappy" />
+ <item index="63" class="java.lang.String" itemvalue="sphinxcontrib-htmlhelp" />
+ <item index="64" class="java.lang.String" itemvalue="attrs" />
+ <item index="65" class="java.lang.String" itemvalue="Sphinx" />
+ <item index="66" class="java.lang.String" itemvalue="sphinxcontrib-jsmath" />
+ </list>
+ </value>
+ </option>
+ </inspection_tool>
+ </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 00000000..105ce2da
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+ <settings>
+ <option name="USE_PROJECT_PROFILE" value="false" />
+ <version value="1.0" />
+ </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/lake-greifen-profiles.iml b/.idea/lake-greifen-profiles.iml
new file mode 100644
index 00000000..2c68311e
--- /dev/null
+++ b/.idea/lake-greifen-profiles.iml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+ <component name="NewModuleRootManager">
+ <content url="file://$MODULE_DIR$" />
+ <orderEntry type="jdk" jdkName="Python 3.7 (rs)" jdkType="Python SDK" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 00000000..e40478af
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7 (rs)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 00000000..bcea194f
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectModuleManager">
+ <modules>
+ <module fileurl="file://$PROJECT_DIR$/.idea/lake-greifen-profiles.iml" filepath="$PROJECT_DIR$/.idea/lake-greifen-profiles.iml" />
+ </modules>
+ </component>
+</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 00000000..94a25f7f
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="$PROJECT_DIR$" vcs="Git" />
+ </component>
+</project>
\ No newline at end of file
diff --git a/data/Level0/Lake_Greifen_CTD_W_2020-01-27.txt b/data/Level0/Lake_Greifen_CTD_W_2020-01-27.txt
new file mode 100644
index 00000000..31bca842
--- /dev/null
+++ b/data/Level0/Lake_Greifen_CTD_W_2020-01-27.txt
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diff --git a/notebooks/automate.sh b/notebooks/automate.sh
new file mode 100644
index 00000000..685b10e7
--- /dev/null
+++ b/notebooks/automate.sh
@@ -0,0 +1,9 @@
+cd /home/ubuntu/lake-greifen-platform
+
+git pull
+
+python3 /home/ubuntu/lake-greifen-platform/notebooks/main.py
+
+git add --all
+git commit -m "Auto upload"
+git push
diff --git a/notebooks/functions.py b/notebooks/functions.py
new file mode 100644
index 00000000..94a1ebaa
--- /dev/null
+++ b/notebooks/functions.py
@@ -0,0 +1,102 @@
+import netCDF4
+import pandas as pd
+import numpy as np
+import requests
+from os import path, remove
+
+from sqlalchemy import create_engine
+import pymysql
+
+
+def mysql_netcdf(database, start, end, Level0, Level1A):
+ db_connection_str = 'mysql+pymysql://'+database["user"]+':'+database["password"]+'@'+database["host"]+'/'+database["db"]
+ db_connection = create_engine(db_connection_str)
+ df = pd.read_sql("SELECT * FROM ctd WHERE timestamp BETWEEN '"+start+"' AND '"+end+"';", con=db_connection)
+ df.to_csv(Level0, index=False)
+ timestamps = df.groupby('profile_id').first()["timestamp"]
+ df = df.drop(['timestamp'], axis=1)
+ df = pd.merge(df, timestamps, how='left', on='profile_id')
+ profile_ids = list(df["profile_id"].sort_values(ascending=True).unique())
+ press = df.press.sort_values(ascending=True).unique()
+ press_temp = pd.DataFrame(press, columns=["press"])
+ profiles = []
+ for index, value in enumerate(profile_ids):
+ profile = df.loc[df['profile_id'] == value]
+ profiles.append(pd.merge(press_temp, profile.drop_duplicates(subset=['press']), how='left', on='press'))
+
+ data = {}
+ data["press"] = list(press)
+ data["time"] = list(df.timestamp.sort_values(ascending=True).unique().astype(int) / 10 ** 9)
+
+ att = {
+ "institution": "EAWAG",
+ "source": "Lake Greifen CTD Data",
+ "history": "See history on Renku",
+ "conventions": "CF 1.7",
+ "comment": "Data from CTD profiler on platform in Lake Greifen",
+ "title": "Lake Greifen CTD Data"
+ }
+
+ dim_dict = {
+ 'time': {'dim_name': 'time', 'dim_size': None},
+ 'press': {'dim_name': 'press', 'dim_size': None}
+ }
+
+ dim_var_dict = {
+ 'time': {'var_name': 'time', 'dim': ('time',), 'unit': 'seconds since 1970-01-01 00:00:00', 'longname': 'time'},
+ 'press': {'var_name': 'pressure', 'dim': ('press',), 'unit': 'm', 'longname': 'pressure'}
+ }
+
+ var_dict = {
+ 'temp': {'var_name': 'temperature', 'dim': ('press', 'time',), 'unit': 'degC',
+ 'longname': 'Water Temperature'},
+ 'cond': {'var_name': 'conductivity', 'dim': ('press', 'time',), 'unit': 'mS/cm',
+ 'longname': 'Conductivity'},
+ 'sal': {'var_name': 'conductivity_20', 'dim': ('press', 'time',), 'unit': 'mS/cm',
+ 'longname': 'Conductivity 20deg'},
+ 'o2_percent': {'var_name': 'o2_percent', 'dim': ('press', 'time',), 'unit': '%',
+ 'longname': 'Percentage Oxygen Concentration'},
+ 'o2_ppm': {'var_name': 'o2_ppm', 'dim': ('press', 'time',), 'unit': 'mg/L',
+ 'longname': 'Oxygen Concentration'},
+ 'ph': {'var_name': 'ph', 'dim': ('press', 'time',), 'unit': '',
+ 'longname': 'pH'},
+ 'chl': {'var_name': 'chla', 'dim': ('press', 'time',), 'unit': 'μg/L',
+ 'longname': 'Chlorophyll A'},
+ 'turb': {'var_name': 'turb', 'dim': ('press', 'time',), 'unit': 'NTU',
+ 'longname': 'Turbidity'},
+ 'phy': {'var_name': 'phycocyanin', 'dim': ('press', 'time',), 'unit': 'μg/L',
+ 'longname': 'Phycocyanin'},
+ 'par': {'var_name': 'par', 'dim': ('press', 'time',), 'unit': 'μE',
+ 'longname': 'Photosynthetically Active Radiation'},
+ }
+
+ # Create new NetCDF file
+ ncfile = netCDF4.Dataset(Level1A, mode='w', format='NETCDF4')
+
+ # Add global attributes
+ for key in att:
+ setattr(ncfile, key, att[key])
+
+ # Create Dimensions
+ for key, values in dim_dict.items():
+ ncfile.createDimension(values['dim_name'], values['dim_size'])
+
+ # Create Dimensions Variables
+ for key, values in dim_var_dict.items():
+ var = ncfile.createVariable(values["var_name"], np.float64, values["dim"])
+ var.units = values["unit"]
+ var.long_name = values["longname"]
+ var[:] = data[key]
+
+ # Create Dimensions Variables
+ for key, values in var_dict.items():
+ var = ncfile.createVariable(values["var_name"], np.float64, values["dim"])
+ var.units = values["unit"]
+ var.long_name = values["longname"]
+ for index, value in enumerate(data["time"]):
+ var[:, index] = list(profiles[index][key])
+
+ # Close NetCDF file
+ ncfile.close()
+
+
diff --git a/notebooks/lastupdated.ini b/notebooks/lastupdated.ini
new file mode 100644
index 00000000..1b084a6a
--- /dev/null
+++ b/notebooks/lastupdated.ini
@@ -0,0 +1,3 @@
+[Updated]
+datetime = 2020-10-27T00:00:00Z
+
diff --git a/notebooks/main.py b/notebooks/main.py
new file mode 100644
index 00000000..61d85fc5
--- /dev/null
+++ b/notebooks/main.py
@@ -0,0 +1,49 @@
+from datetime import datetime, date, timedelta
+from os import path, remove
+import configparser
+from functions import mysql_netcdf
+
+# Output folders
+base = "/media/jamesrunnalls/JamesSSD/Eawag/EawagRS/git/lake-greifen-profiles"
+#base = "/home/ubuntu/lake-greifen-profiles"
+
+Level0 = base + "/data/Level0"
+Level1A = base + "/data/Level1A"
+params_file = base + "/notebooks/lastupdated.ini"
+db_file = base + "/notebooks/database.ini"
+
+# Get last updated date
+params = configparser.ConfigParser()
+params.read(params_file)
+last_update = date_time_obj = datetime.strptime(params['Updated']['datetime'], r"%Y-%m-%dT%H:%M:%SZ")
+
+db = configparser.ConfigParser()
+db.read(db_file)
+
+def tofirstdayinisoweek(year, week):
+ ret = datetime.strptime('%04d-%02d-1' % (year, week), '%Y-%W-%w')
+ if date(year, 1, 4).isoweekday() > 4:
+ ret -= timedelta(days=7)
+ return ret
+
+# Start and End Date
+process_date = tofirstdayinisoweek(last_update.year, last_update.isocalendar()[1])
+end_date = datetime.today()
+
+while process_date < end_date:
+ date_string = process_date.strftime(r"%Y-%m-%d")
+ end_week = process_date + timedelta(days=7)
+ outfilename1A = "Lake_Greifen_CTD_W" + "_" + date_string + ".nc"
+ outfile1A = path.join(Level1A, outfilename1A)
+ outfilename0 = "Lake_Greifen_CTD_W" + "_" + date_string + ".txt"
+ outfile0 = path.join(Level0, outfilename0)
+ if path.exists(outfile1A):
+ remove(outfile1A)
+ mysql_netcdf(db["Database"], process_date.strftime(r"%Y-%m-%d"), end_week.strftime(r"%Y-%m-%d"), outfile0, outfile1A)
+ process_date = end_week
+
+new_update = date.today().strftime(r"%Y-%m-%dT%H:%M:%SZ")
+params['Updated']['datetime'] = new_update
+with open(params_file, "w") as f:
+ params.write(f)
+
--
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