Technical report

Item: Web development (improvement of web interface and of interoperability of database for volcanic/non volcanic CO2 emissions in the mediterranean area.

PI. Carlo Cardellini, Dipartimento di Fisica e Geologia, Università degli Studi di Perugia (Italy)Start date: 9 July 2014 – order 62355

Report.

The product of the work done consist in the development an improved version of MaGa batabase and its web interface concerning:

1) tools for the on-line, server-side, visualization and download of the data stored in the database;2) user-manual.3) ingestion of data from worldwide distributed volcanic emissions4) interoperability.5) specific tool to insert large amount of data for a single gas emissions

1) Tools for the on-line, server-side, visualization and download of the data stored in the databaseThe specific activities on this item included:a) migration of the database to a new domain that is the starting point for the transition from a development version to a production version. The new database URL is http://www.magadb.net for the visualization of the data. The user interface for the ingestion of new data is http://www.magadb.net/admin and the access to this section is restricted to authorised user trough an ID and Password that can be requested.b) An improved interactive map for the visualization of the location of the site catalogued in the database and to access to data has been developed (fig. 1). The new tool allow a “global view” where are displayed the number the number of sites per area until there is no overlapping between sites at the scale of the displayed map, zoom in, by double clicking or shift-select, allow to select the single gas emission site and to browse the data stored.

Figure 1.

c) Development of the tool to download all the data in to KML format file (fig. 2) that can be used to locate the emission site and browse the data on MaGa by Google Earth (fig. 3).

Figure. 2

Figure. 3

2) User-manualThe user manuals including the instructions for users to upload data in to the database. The user manual is reported in the Annex 1.

3) Ingestion of data from worldwide distributed volcanic emissionsThe database has been populated with new data about 54 gas emission sites located in 40 volcanoes worldwide distribute (Table 1). This activity has been supported also by a fellowship financed by INGV-DPC project “V2 precursori di eruzioni”. The list of the all the emission sites can be found at http://www.magadb.net/locations/. This can be “searched” using the search tool or sorted by volcano name or country.

Table 1. List of the new data ingested in to MaGa.

Country Volcano Emission site Degassing Type n. of CO2

flux

Alaska

Fourpeaked Fourpeaked volcanic plume 3Mageik Mageik volcanic plume 1Martin Martin volcanic plume 1

Ukinrek Ukinrek volcanic plume 1 Antarctica Mt. Erebus Erebus volcano plume volcanic plume 3

ChileLastarria volcano Lastarria plume volcanic plume 1Lascar volcano Lascar plume volcanic plume 1

Congo Nyiragongo Nyiragongo volcanic plume 1

Costa RicaTurialba Turialba plume volcanic plume 1

Irazù volcano Irazù degassing area soil diffuse emission 1 El Salvador Santa Ana complex Santa Ana complex soil diffuse emission 1

Hawaii Kilauea volcano Kilauea-Pu'u 'O'o crater volcanic plume 1 Indonesia Merapi volcano Merapi degassing area soil diffuse emission 1

Nicaragua Masaya Masaya volcanic plume 1Cerro Negro Cerro Negro soil diffuse emission 1

New Zeland White IslandWhite Island plume volcanic plume 3White Island crater floor soil diffuse emission 1

NicaraguaTelica volcano Telica volcanic plume 1

San Cristobal volcano San Cristobal volcanic plume 1 Japan Iwojima volcano Iwojima volcano soil diffuse emission

Miyakejima volcano Miyakejima soil diffuse emission 2Tarumae volcano Tarumae soil diffuse emission 1Showa-Shinzan

volcano Showa-Shinzan soil diffuse emission 1

Usu volcano Usu soil diffuse emission 3Hakkoda volcano Hakkoda soil diffuse emission 1Kusatsu-Shirane

volcano Kusatsu-Shirane soil diffuse emission 1

Izu-Oshima volcano Izu-Oshima soil diffuse emission 1Ioutou volcano Ioutou soil diffuse emission 1Aso volcano Aso soil diffuse emission 1

Satsuma-Iwoshima volcano Satsuma-Iwoshima soil diffuse emission 1

Aogashima

Funakoyama Fumarole Field fumarole -Maruyama Volcano Central Cone fumarole -

Misone Fumarole Field fumarole -

Hachijojima

Hachijojima well -Kashidate Hot Spring Well well -Ogoshi Hot Spring Well well -Sueyoshi Hot Spring Well well -Yasuragi Hot Spring Well well -

Hakone Complex

Owakdani Fumarole Field fumarole -Sounjigoku Fumarole Field fumarole -Yunohanazawa Fumarole Field fumarole -

Iwojima Iwojima volcano soil diffuse emission 1

Niijima Jinata Hot Springs spring -Mamashita Hot Spring Well well -

Oshima Hotel Onsen Well well -

Koshimizu Well well -Ohtsu Well well -Univ. of Tokyo Obs. Well well -

Mariana Isl. Agrigan Summit Crater, Agrigan fumarole -Pagan Old Crater, Pagan fumarole -

Mexico Popocatepetl Popocatepetl, Plume volcanic plume 6

Russia Bezymianny Bezymianny plume volcanic plume 5Bezymiznny dome fumaroles fumarole -

Tanzania Oldoinyo Lengai Oldoinyo Lengai plume volcanic plume 3

4) Interoperability.An operative meeting with Kerstin Lehernet Lehnert, (Lamont-Doherty Earth Observatory of Columbia University), Jason Ash (University of Kansas), Alessandro Frigeri (IAPS, Italy) and Brendan McCormick (Smithsonian Institution - Global Volcanism Program) has been done at Lamont-Doherty Earth Observatory, after a general meeting including also Tobias Fischer (University of New Mexico), to explore the interoperability between MaGa, EarthChem and GVP databases. A road map has been discussed to create a first version of DECADE portal to search data in the 3 repositories. A first development of WFS service, which allows the DECADE portal to access the MaGa datadbase, has been done to explore the realization of the interoperability. A specific further work it is necessary to put in to production the WFS service.

5) Development a specific tool to insert large amount of data for a single gas emissions A collaboration with a team of the Dipartimento di Fisica and Geologia, has been settled up to explore possible solutions to create a tool for uploading large dataset. The first activities concerned the creation of an XML (Xtensible Markup Language) schema for the data in the database to use this for the applications to be developed. A GitHup space for collaboration, code review, and code management has been created to make possible a multi users access to the MaGa code to improve and test the new applications. Possible solutions have been explored. The coding of the final tool will be the target of future activities.

Annex 1. MaGa User Manual.

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MaGa user manual

Maga uses Object-relational model, thought to translate the experience of field surveyors/researcher

into the database schema. The web interface of MaGa allows to insert interactively and dynamically

into the database. The data entry can be fully performed by two main pages, one for the “Location”

and one for the “Gas flux/Composition measurement”.

The “Location” includes the general information on a particular gas emission site and it is

univocally identified by its geographic position (i.e. geographic coordinates), while the

“measurements” are the numerous measurements that can be done in a gas emission including

fluxes, compositions that can be performed by different researchers or in different times.

How to insert data into MaGa

To start in using MaGa database the User has to log in to the website www.magadb.net/admin/

which will lead the User to the Site Administration Page (Fig. 1). Here all the functions which can

be changed and/or added in the database are shown as well as the current and past User Actions.

Figure 1 Site Administration page of MaGa database.

1. The Location

The “Location” page is used to ingest the general information on a particular gas emission site

which is univocally identified by its geographic position (i.e., geographic coordinates). Before

creating a location, the User has to check if the gas emissions he has measured just exist in the

database. This can be done by browsing the list of sites (in the catalogue) or consulting the

interactive map at www.magadb.net (Fig. 2). Numbers in blue circles reported in the global view of

the interactive map are the number of sites per area, zoom in (by double clicking or shift-select) to

select the single gas emission site.

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Figure 2 (a) list of sites and (b) interactive map of gas emissions.

If the location does not exist a new one can be created by logging to the website

www.magadb.net/admin/, and select “Add Locations” in the Site Administration page (Fig. 3).

(a)

(b)

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Figure 3. Site Administration page to add a Location

Creating a new Location requires to provide several information (Fig. 4):

Site Name: is the name of the gas emission site (e.g. a gas vent, a fumarole, a crater’s plume). The

local name or that used most frequently should be chosen.

Type: is the type of the gas emission and one of the given option can be selected: fumarole,

volcanic plume, spring, well, lake, cold vent, soil diffuse emission, bubbling water.

Name of the volcano: is, the case of a volcanic gas emission, the name of the volcanic apparatus

where the gas emission is located. The volcano name can be selected from a list. If the Volcano of

interest is not in the list the name and the associated ID form the Smithsonian Institution GVP can

be

Description of the site: a brief description of the site including relevant indications that are

considered relevant to characterize the site and that can be useful to identify on the field the

sampling-measuring site.

Hazard description: the User has to report notes (if any) about the just existing literature

information on previous documented cases of gas hazard related to the added location. The User can

specify if there are reported cases of “Accidents to Humans” (if any) and/or “Accidents to

Animals” by selecting “Unknown, Yes or Not” from the drop-down menu (Fig. 5).

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Figure 4. How to add a Location

Figure 5. How to specify eventual cases of accidents to humans and/or animals.

Geometry: the position of a “Location” can be defined interactively by moving the place mark on

the interactive map (Fig. 6). Latitude and Longitude can be directly typed and refreshing the page

the place mark in the interactive map will move automatically to the position.

Figure 6. How to insert geographic coordinates for a given Location.

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Picture of the location displayed on the web map: for each “Location”, the User can provide a

Picture of the location which will be displayed on the web page as main image for the Location.

To add a “picture of the location”, the user has to click on the green cross and provides all the

required information appearing in the “Add picture” box, such as “Image” source, “Caption” of the

picture, “Image credits”, “author”, and eventually to flag the “Creative Commons License” (Fig. 7).

Image: the User has to upload a file which will be loaded by the system.

Caption: the User has to provide a short explanation, or description accompanying the image.

Image credits, author: the User has to provide the name of the author of the uploaded image.

Creative Commons License: the User has to indicate if the author of the image has given the

permission to share and use it by flagging the box.

Contact: insert the contact details of expert researcher/s of the site. To add a “contact” of an expert

researcher of the location, the User has to click on the green cross and provide all the information

required in the opening “Add contact” box, such as “First Name” of the contact, “Family Name”,

research “Role”, “Institution”, “Address” and “e-mail” (Fig. 8).

Figure 8. How to add the contact of an expert researcher of the site.

Figure 7. How to add a picture of the location.

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First Name: is the name of the expert researcher of the location.

Family Name: is the surname of the expert researcher of the location.

Role: is the position occupied by the expert researcher at a given institution.

Institution: is the name of the Institution where the expert researcher works.

Address: is the address of the Institution.

E-mail address: is the e-mail address of the expert researcher .

Bibliographic references: are the literature sources related to the data uploaded by the User within

the database. For each location, the User can to report one or more “Bibliographic references”, at

first by consulting the just existing reference list of the database. If the reference is not present in

the database list, the User can add a new reference article, by clicking on the green cross and

providing all the required information needed by the system (Fig. 9), such as “Authors”, “Title”,

“Journal”, “Volume”, “Issue No.”, “Pages”, “Year”, “DOI”.

Authors: are the authors of the reported research article.

Title: is the full title the reported research article.

Journal: is the name of the journal where the reported research article has been published.

Volume: is the volume number of the journal where the reported research article has been

published.

Issue No.: the User has to provide the Issue number only if the particular journal starts

pagination over at page 1 at the beginning of each issue.

Figure 9. How to add a bibliographic reference for a location.

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Pages: are the page numbers which give the range of pages for the journal article

Year: is the year of publication.

DOI: is the “digital object identifier”, which is used to uniquely identify a research article.

File: the User has to upload a file which will be loaded by the system. Other “Aux files regarding

the measurement” can be added by the User (Fig. 10), such as a map of the measurements

distribution, a poster presented at congress, tables, etc etc. To add “Aux files” the User has to

provide:

Figure 10. How to add auxiliary files.

Description: the User has to provide a brief description of the uploaded file.

Once uploaded all of these information related to a Location, the User can “Save and add an other”

location, “Save and continue editing” and/or “Save” at all. At this moment the “Location” will be

finally created.

2. The Gas Flux/Composition Measurements

The “Gas flux/Composition measurement” page is used to ingest the different types of

“measurements” (i.e., gas fluxes, chemical and isotopic compositions of gases; etc..) that were

performed on a “Location” in a specific time. This allow to record, properly and in a structured

way, different data sets produced in different periods for a specific gas emission.

To add a new “Gas flux/Composition measurement”, the user has to log in to the website

www.magadb.net/admin/, and select “Add Gas Flux/Composition Measurements” in the Site

Administration page (Fig.11).

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Figure 11. How to add a new Gas Flux/Composition measurement

Inserting a new “Gas flux/Composition measurement” requires to provide several information:

Location: is the location where the measurement has been carried out. The User can select a

location from a list of available ones or create a new one (Fig. 12), as explained in the previous

section.

Name: is the specific name of the measurement (for example: Etna Bocca Nuova crater).

Day: is the day to which the measurement refers.

Month: is the month to which the measurement refers.

Year: is the year to which the measurement refers.

Time: it refers to hh:mm:ss which is taken at the end of the measurement, if the measurement is

averaged over a time-span, the time-span ends with this time

Time-averaging: is the averaged time to which a measurement refers (Fig. 13). In detail, the User

has to select:

- exact measurement: if the measurement has been done in a precise time as for example,

when sampling a fumarole and/or collecting gases from a plume by filterpack

methodology, etc etc;

- daily mean: if measurement is the average of all measurements collected during an

whole sampling day;

- weekly mean: if measurement is averaged between measurements collected during a

seven days survey (as for example data obtained by a continuous gas acquisition

sampling by a permanent multi-GAS station, remote sensing, etc…);

- biweekly mean: if measurement is averaged between measurements collected during a

14 days survey (as for example data obtained by a continuous gas acquisition sampling

by a permanent multi-GAS station, remote sensing, etc…);

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- monthly mean: if measurement is averaged between the totality of measurements

collected in one month (as for example data obtained by a continuous gas acquisition

sampling by a permanent multi-GAS station, remote sensing, etc…).

Area: is the area in square meters covered by the soil diffuse emission; the box has to be left blank

for a point source.

Notes: are brief annotations which the User can enter referred to the time, the measurements, the

location, and so on.

Figure 12. How to select a just existing location in the list of the database.

Figure 13. Time averaging to select for each reported new measurement.

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Gas species concentration

To add a “Gas species concentration” the User has to provide different information:

Name: is the name of the gas species or gas species ratio (Fig.14).

Concentr: is the concentration value of the gas species or the value of the ratio.

Uom: is the measurement unit, which is actually fixed and the User has to select among those

reported in the list (Fig. 14).

Sampmethod: is the sampling method adopted to collect gas species in the field; actually it is

fixed and the User has to select the sampling method among those reported in the list (Fig. 15).

Figure 15. Sampling Method list just existing in the database.

Concentration measurement method: is the method adopted to measure gas concentration. The

User can select a method just present in the list of the database, or to create a new one. To create a

new “Concentration measurement method”, the User has to click on the green cross and provide

all the required parameters in the box “Add meas method” (Fig. 16):

Figure 16. How to add a new concentration measurement method.

Name: is the name of the concentration measurement method.

Descr: the User has to provide a brief description of the adopted method.

Figure 14. How to add a Gas concentration.

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Type: the User has to specify the use of the method adopted, that is if it is useful for

estimating Gas concentration, isotopes, flux, etc...

Instrument: is the instrument used to detect the concentration of the gas species. The User can

select an instrument just present in the list of the database, or to create a new one. To add a new

“Instrument” the User has to click on the green cross, and to fill the required information listed in

the opening box “Add Instrument”.

Brand: is the commercial brand of the instrument.

Model: is the specific model of the instrument.

Serial Number: is the serial number that characterizes the uniqueness of the instrument.

Instrument type: is a parameter describing the type of the instrument, i.e. if it is an

electrochemical sensor, or a Correlation Spectrometer, or an UV-camera, etc etc.

Description: the User has to provide a brief description about the operational schemes of the

instrument, detection limit, particular requirements, etc….

Picture: the User can eventually provide a picture illustrating the instrument.

Figure 18. How to add a new instrument or

consult the list.

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Gas Fluxes

To add a “Gas Fluxes” data, the user has to enter requested parameters, such as:

Figure 19. How to add a gas flux measurement.

Name: is the name of the gas species (Fig. 19).

Flux: is the value of the estimated flux.

Standard Deviation: Standard deviation related to the flux value reported.

Lower Confidence Limit/ Upper Confidence Limit: of the flux value reported

Uom flux: is the measurement unit of the flux value reported.

Flux measurement method: refers to the method used to measure the gas flux in the field. If the

“Flux measurement method” is not present in the database list the User can create a new “Flux

measurement method”, by clicking on the green cross and providing all the required information

reported in the “Add meas method” opening box (Fig. 20), such as:

Name: is the name of the flux measurement method (for example like those just reported

actually in the database: Accumulation chamber, UV-camera, etc…).

Descr: the User has to provide a brief description of the adopted method.

Type: the User has to specify the use of the method adopted, that is if it is useful for

estimating Gas concentration, isotopes, flux, etc...In this case the User has to select “Flux”.

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Instrument: As well as for “Gas concentration”, also for the “Gas Fluxes”, the User can select an

“Instrument” used to measure the flux just from the reported list, or by adding a new one (Fig.21).

To add a new “Instrument” the User has to click on the green cross, and to provide all the required

information listed in the opening box “Add Instrument” (Fig. 21), as explained previously.

Flux estimation method: refers to the method used to finally calculate/estimate the gas Flux

reported. If the “Flux estimation method” proposed by the User is not present in the database, he

can add a new “Flux estimation method” by clicking on the green cross, and providing all the

required information listed in the box “Add flux estimation method” (Fig. 22):

Name: is the name of the new created Flux estimation method.

Decr: is a brief description of the method.

Figure 20. How to add a new flux measurement method.

Figure 21. How to add a new instrument for gas fluxes measurements.

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Figure 22. How to add a new Flux estimation method and/or consult a just existing list.

Article: each measurement flux needs of a bibliographic reference, that is an “Article”, which can

be selected by the just reported list in the database (Fig. 23a) or to create a new one. To add a

reference article, the User has to click on the green cross and provide all the required information

needed by the system (Fig. 23b), such as “Authors”, “Title”, “Journal”, “Volume”, “Issue No.”,

“Pages”, “Year”, “DOI”, as explained in the previous section.

Figure 23. How to add a new article in the Gas Flux measurements

.

(a)

(b)

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Gas isotopic composition

To include a “Gas Isotope” data, the User has to enter the “Name” of the gas isotope, the

“Aboundance”, the measurement unit (“Uom”), the “Isotope measurement method”, the

“Instrument” and the reference “Article” (Fig. 24). In detail:

Name: is the name of the gas isotope.

Aboundance: is the amount of the entered isotope.

Uom: Is the measurement unit.

Isotope measurement method: is the method adopted to estimate the isotopic aboundance in the

collected gas.

Instrument: is the instrument used to measure the isotopic aboundance.

Article: is the bibliographic reference referred to the gas isotope aboundance entered by the User

into the database.

The User can select an Isotope measurement method just from the existing list or to create a new

one. To create a new “Isotope measurement method”, the User has to click on the green cross and

provide all the required information which characterize the method listed in the opening box “Add

meas method”, such as the “Name” of the method, a brief description (“Desc”) and specify the use

of the method (“Type”), that is it is for “isotopic composition” (Fig. 25). Also in this case, the User

has to provide a bibliographic reference for the inserted data.

Gas temperatures

For each measurement the User can also include the “Gas temperatures” (Fig. 26), by specifying

the unit of measurement (“Unit”), the “Temperature measurement method” and the “Instrument”

adopted.

Temperature: is the gas temperature measured in the field.

Uom: is the measurement unit.

Figure 25. How to add a new Isotope measurement method.

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Figure 26. Snapshots of the MAGA “Measurements” form to insert temperature.

Temperature measurement method: is the method adopted to estimate the gas temperature in the

field. As regard the “Temperature measurement method”, the User can select a method just

present in the Database list, and/or create a new one. To create a new “Temperature measurement

method”, the User has to click on the green cross and provide all the required information which

characterize the method listed in the opening box “Add meas method”, such as the “Name” of the

method, a brief description (“Desc”) and specify the use of the method (“Type”), in this case is

“temperature” (Fig. 27). Also in this case, the User has to provide a bibliographic reference for the

inserted data.

Figure 27. How to add a new temperature measurement method.

Instrument: is the instrument used to measure gas temperature.

Article: is the bibliographic reference referred to the gas temperature entered by the User into the

database.

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Picture of the measurement

For each measurement, the User can provide a “Picture of the measurement” by clicking on the

green cross and providing all the required information appearing in the opening “Add picture” box,

such as “Image” source, “Caption” of the picture, “Image credits”, “author”, and eventually to flag

the Creative Commons License (Fig. 28).

Figure 28. How to add a new picture.

Image: the User has to upload a file which will be loaded by the system.

Caption: the User has to provide a short explanation, or description accompanying the image.

Image credits, author: the User has to provide the name of the author of the uploaded image.

Creative Commons License: the User has to indicate if the author of the image has given the

permission to share and use it by flagging the box.

Auxiliary files

Auxiliary files (“Aux files”) regarding the measurement can be added by the User (Fig. 29)., such

as a map of the measurements distribution, poster presented at congress, tables, etc etc.

Finally, once uploaded all of these information related to a measurement, the User can “Save and

add an other” measurement, “Save and continue editing” and/or “Save” at all.

Figure 29. How to add auxiliary

files to the measurement page.