Tool by tool

Harmonize your data¶

Run QCV harmonizer (What is it?) for creating the harmonized in format and vocabulary input data file(s) by following these instructions :

• Click on Tools just below Upload on the Galaxy action list vertical panel on the left (see a in the Figure 1) . A new vertical panel called Tools appears next to the Galaxy action list vertical panel.

• Search QCV harmonizer in the top search bar (Figure 1)

• Select the tool. Its parametrization page appears on the center (Figure 1)

• In the blue box and below Input the Netcdf data files (Figure 1)

  • for a dataset collection such as 4903881,

    • Select {Dataset collection} then click on Select Value. A window with files listed in your history opens.

    • Select 4903881

  • for WOA,

    • Select {Single dataset}

    • Then click on Select Value. A window with files listed in your history opens.

    • Select woa###.nc file

• Run the tool by clicking on the corresponding button below (see b in the Figure 1).

Once the QCV harmonizer outputs are ready, the harmonized file is available in the history section (green color)

Qualify your data¶

Step1 : Creation of the ODV collection¶

Run ODV collection manager (What is it?) for creating Ocean Data View (ODV) spreadsheet collection and qualifying the dataset. Please, follow the instructions :

• Click on Tools just below Upload on the Galaxy action list vertical panel on the left (see a in the Figure 2). A new vertical panel appears.

• Search ODV collection manager in the top search bar (Figure 2)

• Select the tool. Its parametrization page appears on the center (Figure 2)

• For Input raw data,

  • Select {Multiple Datasets}, then click on Select Value (Figure 2)

  • A window with files listed in your history opens

  • Select 4903881_harm.nc

• (optional) It is possible to change the ODV collection manager default parametrization by selecting Yes, I to write my own configuration file at the question Select if you want to write your own configuration file or not (see c in the Figure 2) :

  • operator name = Enter your name

  • QC convention for the output file = Select one QC flag scale understanding by ODV

  • Subsetting = 1 (yes it is), 0 (no), -1 (for float crossing 180°E/W)

  • plt = 0 (no plot), 1( yes)

• Run the tool by clicking on the corresponding button below (see d on Figure 2).

Once the ODV collection manager outputs are ready, files are available in the history section (green color) (Figure 2) through :

• the galaxy collection ODV tool collection (include all outputs)

• the galaxy file ODV collection manager output (= odv_collection.txt)

Step 2 : Launch ODV automatically¶

For launching ODV interactive tool automatically, follow the instructions :

• Click on Tools just below Upload (see a in the Figure 3) or Interactive Tools just above (see b in the Figure 3) in the Galaxy action list vertical panel on the left. A new vertical panel appears.

• Search ODV interactive tool in the top search bar (Figure 3)

• Select the tool. Its parametrization page appears on the center (Figure 3)

• At the question Do you want your data to be automatically load when ODV is launched? (see c in the Figure 3), answer Yes, I want my data to be loaded directly. This is useful to open directly the odv collection, and with a specific view if this last one is available.

• At the question Netcdf or tabular text file. For text file, odv format is recommanded (see d in the Figure 3),

  • select {Dataset collection}, then ODV collection manager output

  • or select {single dataset}, drag and drog odv_collection.txt from odv tool collection available in the history section

• At the question Do you have a view? (see e in the Figure 3), answer Yes, I have my own view. A Data view selection panel appears (see f in the Figure 3).

• Click on ODV tool collection in the history section

• Drag and Drop qualification_startingPoint_nitrate.xview in the Data view panel

• Run the tool (see g in the Figure 3)

When the ODV interactive tool is ready,

• Open odv interactive tool

Step3 : Qualify the dataset with ODV¶

Many useful information are available the How to use ODV section

Step4 : Export history once qualification is finished.¶

To export history information,

• Click on the top left Export > History

• The Export station history opens, with a default name history_from_odv_collection.txt with our example;

• Go to working/Documents/ODV/galaxy/outputs

• Save > OK > OK

• close ODV by clicking on top left File > exit

Once the ODV interactive tool closed, the 3 potential odv outputs are now available (green color) in the History section (Figure 3). Only 2 are useful for the next steps:

• The galaxy collection ODV all outputs that includes :

  • data_odv_collection.zip (all odv output files in a zip)

  • history_from_odv_collection.txt

  • odv_collection.odv

  • odv_collection.txt (creating with odv collection manager)

• The file ODV history extracted with the history txt files (same as history_from_odv_collection.txt).

Step5 : (optional) Report QC & Data changes¶

For reporting your QC flags & data changes into the harmonized dataset before calibrating the nitrate sensor, run ODV history manager tool (What is it?). For that, please :

• Click on Tools just below Upload on the vertical panel Galaxy action list on the left (see a in the Figure 6). A new vertical panel appears.

• Search ODV history manager in the top search bar (Figure 6)

• Select the tool. Its configuration page appears on the center (Figure 6)

Please below, select the odv collection spreadsheet open with ODV to have futher instructions

• (optional) It is possible to change the Default parametrization by selecting Yes, I to write my own configuration file for the question Select if you want your own configuration file (see e in the Figure 6) :

  • QC convention for the ODV output file = Select one QC flag scale understanding by ODV

  • ODV edits to be reported:

    • EDITFLAGS (report QC changes from the history to the data collection)

    • EDITDATA (report data changes from the history to the data collection).

• Run the tool by clicking on the corresponding button below (see f in the Figure 6).

At the end of the process, the tool outputs are distributed by Galaxy in 3 collections :

• One for NetCDF files, called ODV history manager netcdf collection

• One for csv files, called ODV history manager csv collection

• One for log files, called ODV history manager log files

All of these are now available (green color) in the History section (Figure 6) and ready for running the Biogechemical Calibration tool but before,

• Check the tool logs (YYYY-MM-DDTHHMM_galaxy_odv-history-manager_history) to be sure that everythink is reported in the extended harmonized file by clicking on the “eye” icon on the right of the file. If you encounter issues, make sure you respect the file name conventions at step 4. If you still don’t find why it does not work, send an email to the contact point.

Calibrate your data¶

Nitrate¶

Run Biogeochemical calibration (What is it?) for calibrating the nitrate sensor by following these instructions :

• Click on Tools just below Upload on the vertical panel on the left of Galaxy action list vertical panel on the left (see a in the Figure 7). A new vertical panel appears.

• Search Biogeochemical calibration in the top search bar (Figure 7)

• Select the tool. Its parametrization page appears on the center (Figure 7)

• In Tool Parameters section, select for each input (see b in the Figure 7):

  • Input harmonized netcdf data: Select the 4903881 harmonized NetCDF file(s) with QC report, named ###_harm_qced.nc. The selection is easier by clicking on the 3 dots {Browse or Upload datasets}

  • Input reference data : (optional) Select woa_###_harm.nc if you want to estimate the reference nitrate from climatology (see for getting it)

• (optional) Change the default QC flag configuration (see d in the Figure 7), if :

  • you work with platforms that do not follow the argo flag scale convention

  • you want to fix adjusted value at QC flag 2 (potentially good)

• (optional) Change the default calibration method parametrization or add new parametrizations for comparison. For that, at the question Select if you want to write your own configuration file or not (see e in the Figure 7) , answer Yes, I want to write my own configuration file.

  • Change the first configuration if needed

  • Click on the Insert Configurations button to add new parametrization as many time as needed

• (optional for argo floats) The tool gives the possibility to fill directly original argo nc files with DM information (coefficient, equation, comment, dm operator …) using DM filler tools from C. Schmechtig. For that, in the section Do you want to use DMfiller option (see f in the Figure 7), change to Yes, I want to use it. Then, fill sections :

  • Input original raw netcdf data with the dataset collection 4903881 built at the beginning of the work (Manage your data). This collection includes indeed all original argo nc files useful for reporting DM information

  • Input csv files with the csv created by odv history manager tool.

for the next sections, report all information that are mandatories regarding the

• institution managing your ago data set

• BGC contact point

• BGC DM operator for this action

• Click on Run

At the end of the process, the tool outputs are distributed by Galaxy in 3 collections:

• One for NetCDF files, called BGC calibration netcdf collection

• One for figures files, called BGC calibration figure collection

• One for log files, called BGC calibration log files

If your are a DM Argo operator and activate DM filler option, DM filler outputs are also distributed in a 4^rd galaxy collection called BGC calibration tar.gz collection

All of these are now available (green color) in the History section (Figure 7) and ready for comparison and validation but before,

• Check the tool logs (YYYY-MM-DDTHHMM_galaxy_odv-calibration-methods_nitrate_c) to be sure that everythink is ajdusted and reported in the ARGO BD files (if DMfiller is activated) by clicking on the “eye” icon on the right of the file. If you encounter issues, make sure you respect all the instruction. If you still don’t find why it does not work, send an email to the contact point.

Validate your data¶

We suggest to compare your adjustement with ODV for validating one of the parametrization tested. For that,

• Repeat Step1 of Qualify your data and create the ODV collection including all NetCDF creating during the Calibrate your data phase.