diff --git a/.docker.test.env b/.docker.test.env deleted file mode 100644 index c6fb25bec..000000000 --- a/.docker.test.env +++ /dev/null @@ -1,26 +0,0 @@ -# APP -FLASK_ENV=development -BEHIND_PROXY=False -SERVICE_VERSION=7d60186f594d420f82901f0514eb3c7e6b6e62d5 -LOGLEVEL=DEBUG -LOGFILE="/var/log/headstart/headstart.log" - -# DB -POSTGRES_USER=testuser -POSTGRES_PASSWORD=postgres -POSTGRES_HOST=db_server -POSTGRES_PORT=5434 -POSTGRES_DATABASE=testdb - -# REDIS -REDIS_HOST=redis-1 -REDIS_PORT=6355 -REDIS_PASSWORD=testredispassword -REDIS_DB=0 - -# R -R_BASE_APIKEY=5812aa4367eb1dc3d366d99fdaaef0e3 - -# ORCID -ORCID_CLIENT_ID="APP-DL8ZAR72EZWW15NX" -ORCID_CLIENT_SECRET="a3389b1a-19c0-4f78-857a-4aba19f5fa46" \ No newline at end of file diff --git a/.gitignore b/.gitignore index c9fbeab53..87d9aa519 100644 --- a/.gitignore +++ b/.gitignore @@ -33,6 +33,7 @@ server/workers/tests/testutils/ local_dev/renv/* local_dev/dev.env local_dev/paper_preview +.docker.test.env # php files /server/classes/headstart/vendor diff --git a/README.md b/README.md index b3fb8de6e..130746988 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Head Start -Head Start is a web-based knowledge mapping software intended to give researchers a head start on their literature review (hence the name). It comes with a powerful backend that is is capable of automatically producing knowledge maps from a variety of data, including text, metadata and references. +Head Start is a web-based knowledge mapping software intended to give anyone a head start on their literature search (hence the name). It comes with a scalable backend that is capable of automatically producing knowledge maps from a variety of data sources. ![Head Start](headstart.png) @@ -9,7 +9,7 @@ Head Start is a web-based knowledge mapping software intended to give researcher ### Client To get started, clone this repository. Next, duplicate the file `config.example.js` in the root folder and rename it to `config.js`. -Make sure to have installed `node` version >= 14.18.1 and `npm` version >=8.1.1 (best way to install is with [nvm](https://github.com/nvm-sh/nvm), `nvm install 14.18.1`) and run the following command to install the Headstart dependencies: +Make sure to have installed `node` version >= 18.20.0 and `npm` version >=10.7.0 (best way to install is with [nvm](https://github.com/nvm-sh/nvm), `nvm install 18.20.0`) and run the following command to install the Headstart dependencies: npm install @@ -19,119 +19,47 @@ We use [webpack](https://webpack.github.io/) to build our client-side applicatio The browser will automatically open a new window with the example. -You can run also different examples - -- `npm run example:pubmed` will run the PubMed example -- `npm run example:triple` will run the GoTriple example -- `npm run example:viper` will run the Viper example -- `npm run example:covis` will run the CoVis example - -If everything has worked out, you should see the example visualization. - -To run Headstart on a different server (e.g. Apache), you need to set the publicPath in `config.js` to the URL of the `dist` directory: -* Dev: specify the full path including protocol, e.g. `http://localhost/headstart/dist` -* Production: specify the full path excluding protocol, e.g. `//example.org/headstart/dist` - -Then build it with the command `npm run prod`. The build will appear in the _dist/_ folder in the root directory. - -You can also set the `skin` property in the config to one of the following values to use the -particular data integration skin: - -- `"covis"` -- `"triple"` -- `"viper"` - -or leave it empty (`""`) for the default project website skin. - -See [client configuration](doc/README.md) for details on adapting the client. - - Also see visualization [options](doc/README.md#visualisation-settings). - -### Server - -See [Installing and configuring the server](doc/server_config.md) for instructions on how to install and configure the server. Also, see [HOWTO: Get the search repos example to work](doc/howto_search_repos.md). - -Make sure to have installed `node` version >= 14.18.1 and `npm` version >=8.1.1 (best way to install is with [nvm](https://github.com/nvm-sh/nvm), `nvm install 14.18.1`) and run the following two commands to build the Headstart client: - - npm install - npm run dev - -We are using [webpack](https://webpack.github.io/) to build our client-side application. `webpack` is started in *watch mode* which means that changes to files are tracked and the created `headstart.js` is automatically updated. - -Now you can run a local dev server: - - npm start - -Note: you can also set the skin in this step as an argument to the `npm start` command (e.g. `npm start -- --env skin=triple`). - -The browser will automatically open a new window with the example specified by the skin. - -Alternatively, you can point your browser to one of the following addresses: - - http://localhost:8080/project_website/base.html - http://localhost:8080/project_website/pubmed.html - http://localhost:8080/local_covis/ - http://localhost:8080/local_triple/map.html - http://localhost:8080/local_triple/stream.html - http://localhost:8080/local_viper/ +You can run also run the PubMed example using `npm run example:pubmed` If everything has worked out, you should see the example visualization. -To run Headstart on a different server (e.g. Apache), you need to set the publicPath in `config.js` to the URL of the `dist` directory: -* Dev: specify the full path including protocol, e.g. `http://localhost/headstart/dist` -* Production: specify the full path excluding protocol, e.g. `//example.org/headstart/dist` - - ## Contributors -Maintainer: [Peter Kraker](https://github.com/pkraker) ([pkraker@openknowledgemaps.org](mailto:pkraker@openknowledgemaps.org)) - -Authors: [Maxi Schramm](https://github.com/tanteuschi), [Christopher Kittel](https://github.com/chreman), [Jan Konstant](https://github.com/konstiman), [Asura Enkhbayar](https://github.com/Bubblbu), [Scott Chamberlain](https://github.com/sckott), [Rainer Bachleitner](https://github.com/rbachleitner), [Yael Stein](https://github.com/jaels), [Thomas Arrow](https://github.com/tarrow), [Mike Skaug](https://github.com/mikeskaug), [Philipp Weissensteiner](https://github.com/wpp), and the [Open Knowledge Maps team](http://openknowledgemaps.org/team) - - -## Features - -* Interactive, web-based knowledge maps based on [D3.js](https://d3js.org), following Shneiderman's principle of "overview first, zoom and filter, then details-on-demand" -* Synchronized list representation of documents complementing the knowledge map -* Integrated PDF viewer and annotation tool, courtesy of [Hypothes.is](https://hypothes.is) -* Powerful server component written in PHP and R for the creation of knowledge maps, including algorithms for clustering, ordination and labelling -* Connectors to a number of academic search engines through [rOpenSci](https://ropensci.org), including [BASE](https://base-search.net), [PubMed](https://www.ncbi.nlm.nih.gov/pubmed), [PLOS](https://plos.org) and [DOAJ](https://doaj.org) -* Persistence and versioning system based on SQLite +Maintainer: [Christopher Kittel](https://github.com/chreman) ([christopher.kittel@openknowledgemaps.org](mailto:christopher.kittel@openknowledgemaps.org)), [Maxi Schramm](https://github.com/tanteuschi) ([maxi@openknowledgemaps.org](mailto:maxi@openknowledgemaps.org)), and [Peter Kraker](https://github.com/pkraker) ([pkraker@openknowledgemaps.org](mailto:pkraker@openknowledgemaps.org)) +Authors: [Thomas Arrow](https://github.com/tarrow), [Andrei Shket](https://github.com/andreishket), [Sergey Krutilin](https://github.com/modsen-hedgehog), [Alexandra Shubenko](https://github.com/vrednyydragon), [Jan Konstant](https://github.com/konstiman), [Asura Enkhbayar](https://github.com/Bubblbu), [Scott Chamberlain](https://github.com/sckott), [Rainer Bachleitner](https://github.com/rbachleitner), [Yael Stein](https://github.com/jaels), [Mike Skaug](https://github.com/mikeskaug), [Philipp Weissensteiner](https://github.com/wpp), and the [Open Knowledge Maps team](http://openknowledgemaps.org/team) ## Showcases -* [Open Knowledge Maps](https://openknowledgemaps.org/): Creates a visualization on the fly based on a user's search in either BASE or PubMed. -* [VIPER - The Visual Project Explorer](https://openknowledgemaps.org/viper/): Provides overviews of research projects indexed by OpenAIRE. -* [CRIS Vis](https://ois.lbg.ac.at/en/cris-I-research-questions): Enables the exploration of crowd-sourced research questions related to mental health. -* [Overview of Educational Technology](https://openknowledgemaps.org/educational-technology): A working prototype for the field of educational technology based on co-readership. -* [OpenUP Dissemination Toolbox](https://www.openuphub.eu/tools): A prototype showcasing an overview of innovative dissemination case studies. -* [Conference Navigator 3](http://halley.exp.sis.pitt.edu/cn3/visualization.php?conferenceID=131) [registration required]: An adaptation of Head Start for the conference scheduling system CN3. This version enables users to schedule papers directly from the visualization. Scheduled papers and recommended papers are highlighted. +* [Open Knowledge Maps Search](https://openknowledgemaps.org/): Creates a visualisation on the fly based on a user's search in either BASE or PubMed. +* [OKMaps Custom Services](https://openknowledgemaps.org/custom): Enable third parties to embed customisable search components and visualisations. +* [VisConnect](https://openknowledgemaps.org/visconnect): Provides an interactive visual profile of a researcher’s work. -## Compatibility +## Browser compatibility -The visualization has been successfully tested with Chrome, Firefox, Safari and Microsoft Edge. Unfortunately, Internet Explorer is not supported due to the fact that it is not possible to insert HTML into a foreignObject. +The frontend has been successfully tested with Chrome, Firefox, Safari and Microsoft Edge. Unfortunately, Internet Explorer is not supported due to the fact that it is not possible to insert HTML into a foreignObject. ## Background More information can be found in the following papers: +Kraker, P., Beardmore, L., Hemila, M., Johann, D., Kaczmirek, L. & Schubert, C. (2024). [Partizipative Modelle im Zusammenspiel von Bibliotheken und KI-Systemen: Drei Fallstudien zur Integration der visuellen Recherche-Plattform Open Knowledge Maps](https://www.b-i-t-online.de/heft/2024-04-fachbeitrag-kraker.pdf). B.I.T. Online, 27(4), 327-335. + +Kraker, P., Goyal, G., Schramm, M., Akin, J., & Kittel, C. (2021). [CoVis: A curated, collaborative & visual knowledge base for COVID-19 research](https://doi.org/10.5281/zenodo.4586079). Zenodo. doi: 10.5281/zenodo.4586079 + Kraker, P., Schramm, M., Kittel, C., Chamberlain, S., & Arrow, T. (2018). [VIPER: The Visual Project Explorer](https://zenodo.org/record/1248119). Zenodo. doi:10.5281/zenodo.2587129 Kraker, P., Kittel, C., & Enkhbayar, A. (2016). [Open Knowledge Maps: Creating a Visual Interface to the World’s Scientific Knowledge Based on Natural Language Processing](https://doi.org/10.12685/027.7-4-2-157). 027.7 Journal for Library Culture, 4(2), 98–103. doi:10.12685/027.7-4-2-157 Kraker, P., Schlögl, C. , Jack, K. & Lindstaedt, S. (2015). [Visualization of Co-Readership Patterns from an Online Reference Management System](http://arxiv.org/abs/1409.0348). Journal of Informetrics, 9(1), 169–182. doi:10.1016/j.joi.2014.12.003 -Kraker, P., Weißensteiner, P., & Brusilovsky, P. (2014). [Altmetrics-based Visualizations Depicting the Evolution of a Knowledge Domain](http://know-center.tugraz.at/download_extern/papers/sti_visualization_evolution_kraker_etal.pdf). In 19th International Conference on Science and Technology Indicators (pp. 330–333). - Kraker, P., Körner, C., Jack, K., & Granitzer, M. (2012). [Harnessing User Library Statistics for Research Evaluation and Knowledge Domain Visualization](http://know-center.tugraz.at/download_extern/papers/user_library_statistics.pdf). Proceedings of the 21st International Conference Companion on World Wide Web (pp. 1017–1024). Lyon: ACM. doi:10.1145/2187980.2188236 ## License Head Start is licensed under [MIT](LICENSE). +## Funding + -## Citation -If you use Head Start in your research, please cite it as follows: - -Peter Kraker, Christopher Kittel, Maxi Schramm, Jan Konstant, Rainer Bachleitner, Thomas Arrow, Scott Chamberlain, Asura Enkhbayar, Yael Stein, Philipp Weissensteiner, Mike Skaug, Katrin Leinweber & Open Knowledge Maps team and contributors. (2019, March 7). Headstart 5 (Version v5). Zenodo. http://doi.org/10.5281/zenodo.2587129 +This project has received funding from the European Union's Horizon 2020 and Horizon Europe research and innovation programmes, under grant agreement nos. 831644, 863420, and 101129751. diff --git a/docker-compose.yml b/docker-compose.yml index 64cae54e6..16336b40d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,13 +1,13 @@ services: - db: - image: 'postgres:12.2-alpine' + image: "postgres:12.2-alpine" hostname: "${POSTGRES_HOSTNAME}" restart: unless-stopped environment: POSTGRES_USER: "${POSTGRES_USER}" POSTGRES_PASSWORD: "${POSTGRES_PASSWORD}" - command: postgres -c config_file=/etc/postgresql.conf -c hba_file=/etc/pg_hba.conf + command: + postgres -c config_file=/etc/postgresql.conf -c hba_file=/etc/pg_hba.conf volumes: - db_data:/var/lib/postgresql/data - ./local_dev/pg_hba.conf:/etc/pg_hba.conf @@ -16,18 +16,26 @@ services: - headstart redis: - image: 'redis:6.0-alpine' + image: "redis:6.0-alpine" restart: unless-stopped hostname: "${REDIS_HOST}" environment: REDIS_HOST: "${REDIS_HOST}" REDIS_PORT: "${REDIS_PORT}" - command: ["redis-server", "/etc/redis/redis.conf", "--bind", "${REDIS_HOST}", "--port", "${REDIS_PORT}"] + command: + [ + "redis-server", + "/etc/redis/redis.conf", + "--bind", + "${REDIS_HOST}", + "--port", + "${REDIS_PORT}", + ] volumes: - - 'redis:/var/lib/redis/data' - - ./local_dev/redis.conf:/etc/redis/redis.conf + - "redis:/var/lib/redis/data" + - ./local_dev/redis.conf:/etc/redis/redis.conf ports: - - "127.0.0.1:${REDIS_PORT}:${REDIS_PORT}" + - "127.0.0.1:${REDIS_PORT}:${REDIS_PORT}" networks: - headstart @@ -80,6 +88,7 @@ services: - ./server/workers/persistence/src:/api depends_on: - redis + - db networks: - headstart @@ -264,7 +273,6 @@ services: networks: - headstart - volumes: redis: db_data: diff --git a/headstart.png b/headstart.png index a927d0d5c..085d33270 100644 Binary files a/headstart.png and b/headstart.png differ diff --git a/local_dev/tools/db-insertion/BASE/81abae6d3af6e47761e2a761a47c2c11.json b/local_dev/tools/db-insertion/BASE/81abae6d3af6e47761e2a761a47c2c11.json new file mode 100644 index 000000000..6e0ff1014 --- /dev/null +++ b/local_dev/tools/db-insertion/BASE/81abae6d3af6e47761e2a761a47c2c11.json @@ -0,0 +1 @@ +{"author":null,"documents":"[]"} \ No newline at end of file diff --git a/local_dev/tools/db-insertion/BASE/config.json b/local_dev/tools/db-insertion/BASE/config.json new file mode 100644 index 000000000..d5ae2dc0e --- /dev/null +++ b/local_dev/tools/db-insertion/BASE/config.json @@ -0,0 +1,15 @@ +{ + "endpoint": "http://127.0.0.1:8081/dev/persistence/createVisualization/dev", + "visualizations": [ + { + "vis_id": "81abae6d3af6e47761e2a761a47c2c11", + "vis_title": "base", + "vis_clean_query": "digital education", + "vis_query": "digital education", + "vis_params": "{\"from\":\"1665-01-01\",\"to\":\"2025-12-03\",\"document_types\":[\"121\"],\"sorting\":\"most-relevant\",\"min_descsize\":\"300\",\"lang_id\":[\"all-lang\"]}", + "data_file": "81abae6d3af6e47761e2a761a47c2c11.json" + } + ] +} + + diff --git a/local_dev/tools/db-insertion/OpenAIRE/9d4dc6b920d1e2cc08a741f7c56821db.json b/local_dev/tools/db-insertion/OpenAIRE/9d4dc6b920d1e2cc08a741f7c56821db.json new file mode 100644 index 000000000..27af992cb --- /dev/null +++ b/local_dev/tools/db-insertion/OpenAIRE/9d4dc6b920d1e2cc08a741f7c56821db.json @@ -0,0 +1 @@ +{"author":null,"documents":"[{\"id\":\"core_ac_uk__::9926a89a2a46d8529f5dcec6b6eb218c\",\"subject\":\"13. Climate action\",\"title\":\"Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests\",\"year\":\"2016-04-28\",\"publisher\":\"European Geosciences Union\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"\",\"link\":\"https:\\/\\/eprints.whiterose.ac.uk\\/100260\\/1\\/BakerClimateseasonalitylimitsleafcarbonassimilation.pdf\",\"fulltext\":\"https:\\/\\/eprints.whiterose.ac.uk\\/100260\\/1\\/BakerClimateseasonalitylimitsleafcarbonassimilation.pdf\",\"paper_abstract\":\"The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is \\u2009\u003C\\u20092000\\u202fmm\\u202fyr\\u22121 (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall \\u2009\u003C\\u20092000\\u202fmm\\u202fyr\\u22121.\",\"doi\":\"\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Wagner, FH; H\\u00e9rault, B; Bonal, D; Stahl, C; Anderson, LO; Baker, TR; Sebastian Becker, G; Beeckman, H; Boanerges Souza, D; Cesar Botosso, P; Bowman, DMJS; Br\\u00e4uning, A; Brede, B; Irving Brown, F; Julio Camarero, J; Camargo, PB; Cardoso, FCG; Carvalho, FA; Castro, W; Koloski Chagas, R; Chave, J; Chidumayo, EN; Clark, DA; Regina Capellotto Costa, F; Couralet, C; Henrique Da Silva Mauricio, P; Dalitz, H; Resende De Castro, V; Milani, JEDF; Consuelo De Oliveira, E; De Souza Arruda, L; Devineau, JL; Drew, DM; D\\u00fcnisch, O; Durigan, G; Elifuraha, E; Fedele, M; Ferreira Fedele, L; Figueiredo Filho, A; Finger, CAG; C\\u00e9sar Franco, A; Jnior, LF; Galv\\u00e3o, F; Gebrekirstos, A; Gliniars, R; Maur\\u00edcio Lima De Alencastro Gra\\u00e7a, P; Griffiths, AD; Grogan, J; Guan, K; Homeier, J; Raquel Kanieski, M; Khoon Kho, L; Koenig, J; Valerio Kohler, S; Krepkowski, J; Lemos-Filho, JP; Lieberman, D; Eugene Lieberman, M; Sergio Lisi, C; Longhi Santos, T; Ayala, JLL; Eijji Maeda, E; Malhi, Y; Maria, VRB; Marques, MCM; Marques, R; Maza Chamba, H; Mbwambo, L; Liana Lisboa Melga\\u00e7o, K; Angela Mendivelso, H; Murphy, BP; O'Brien, JJ; F Oberbauer, S; Okada, N; Plissier, R; Prior, LD; Alejandro Roig, F; Ross, M; Rodrigo Rossatto, D; Rossi, V; Rowland, L; Rutishauser, E; Santana, H; Schulze, M; Selhorst, D; Rodrigues Silva, W; Silveira, M; Spannl, S; Swaine, MD; Toledo, JJ; Miranda Toledo, M; Toledo, M; Toma, T\",\"subject_orig\":\"13. Climate action\",\"oa_state\":1,\"url\":\"core_ac_uk__::9926a89a2a46d8529f5dcec6b6eb218c\",\"cluster_labels\":\"Cycle du carbone, 13. climate action\",\"x\":\"0.395896433436244\",\"y\":\"0.169597229793406\",\"labels\":\"core_ac_uk__::9926a89a2a46d8529f5dcec6b6eb218c\",\"area_uri\":5,\"area\":\"Cycle du carbone, 13. climate action\"},{\"id\":\"doi_dedup___::18be3b76950d65d7355fd20c838eb726\",\"subject\":\"0106 biological sciences\",\"title\":\"Plant Traits Demonstrate That Temperate and Tropical Giant Eucalypt Forests Are Ecologically Convergent with Rainforest Not Savanna\",\"year\":\"2013-12-17\",\"publisher\":\"Public Library of Science (PLoS)\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"PLoS ONE\",\"link\":\"https:\\/\\/doi.org\\/10.1371\\/journal.pone.0084378\",\"fulltext\":\"\",\"paper_abstract\":\"Ecological theory differentiates rainforest and open vegetation in many regions as functionally divergent alternative stable states with transitional (ecotonal) vegetation between the two forming transient unstable states. This transitional vegetation is of considerable significance, not only as a test case for theories of vegetation dynamics, but also because this type of vegetation is of major economic importance, and is home to a suite of species of conservation significance, including the world's tallest flowering plants. We therefore created predictions of patterns in plant functional traits that would test the alternative stable states model of these systems. We measured functional traits of 128 trees and shrubs across tropical and temperate rainforest - open vegetation transitions in Australia, with giant eucalypt forests situated between these vegetation types. We analysed a set of functional traits: leaf carbon isotopes, leaf area, leaf mass per area, leaf slenderness, wood density, maximum height and bark thickness, using univariate and multivariate methods. For most traits, giant eucalypt forest was similar to rainforest, while rainforest, particularly tropical rainforest, was significantly different from the open vegetation. In multivariate analyses, tropical and temperate rainforest diverged functionally, and both segregated from open vegetation. Furthermore, the giant eucalypt forests overlapped in function with their respective rainforests. The two types of giant eucalypt forests also exhibited greater overall functional similarity to each other than to any of the open vegetation types. We conclude that tropical and temperate giant eucalypt forests are ecologically and functionally convergent. The lack of clear functional differentiation from rainforest suggests that giant eucalypt forests are unstable states within the basin of attraction of rainforest. Our results have important implications for giant eucalypt forest management.\",\"doi\":\"10.1371\\/journal.pone.0084378\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Greg J. Jordan; David Y. P. Tng; David M. J. S. Bowman; David M J S Bowman; David Y P Tng; Greg J Jordan; Tng, David Y. P.; Jordan, Greg J.; Bowman, David M. J. S.; David M. J. S. Bowman; David Y. P. Tng; Greg J. Jordan; David Y P, Tng; David M J S, Bowman; Greg J, Jordan\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":1,\"url\":\"doi_dedup___::18be3b76950d65d7355fd20c838eb726\",\"cluster_labels\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\",\"x\":\"0.197639118307433\",\"y\":\"-0.0758870989288165\",\"labels\":\"doi_dedup___::18be3b76950d65d7355fd20c838eb726\",\"area_uri\":2,\"area\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\"},{\"id\":\"doi_dedup___::1ffd696adb19408e4a921e2dfe0030a9\",\"subject\":\"cycle du carbone\",\"title\":\"Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests\",\"year\":\"2016-04-28\",\"publisher\":\"Copernicus GmbH\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Biogeosciences\",\"link\":\"https:\\/\\/hdl.handle.net\\/10067\\/1447620151162165141\",\"fulltext\":\"https:\\/\\/hal.univ-lorraine.fr\\/hal-01557759\\/document\",\"paper_abstract\":\"\u003Cjats:p\u003EAbstract. The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is \\u2009<\\u20092000\\u202fmm\\u202fyr\\u22121 (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall \\u2009<\\u20092000\\u202fmm\\u202fyr\\u22121.\u003C\\/jats:p\u003E\",\"doi\":\"10.5194\\/bg-13-2537-2016\",\"project_id\":\"LP0219425\",\"accessright\":\"Open Access\",\"authors\":\"Hans Beeckman; Vivien Rossi; Fabr\\u00edcio Alvim Carvalho; Simone Aparecida Vieira; Helmut Dalitz; Franziska Volland; Davi Rodrigo Rossatto; J\\u00e9r\\u00f4me Chave; Rapha\\u00ebl P\\u00e9lissier; Marcio Fedele; Hector Maza Maza Chamba; Kaiyu Guan; Kaiyu Guan; Marisol Toledo; Steven F. Oberbauer; Jos\\u00e9 Julio de Toledo; Cl\\u00e9ment Stahl; Cl\\u00e9ment Stahl; Renato Francisco Rodrigues Marques; Michael D. Swaine; J. Julio Camarero; Karina Melga\\u00e7o; Michael S. Ross; Lucy Rowland; Ervan Rutishauser; Fl\\u00e1via R. C. Costa; Fabien Wagner; Franklin Galv\\u00e3o; Oliver D\\u00fcnisch; Foster Brown; Paulo Maur\\u00edcio Lima de Alencastro Gra\\u00e7a; Marcio Lea Bolzan Zanon; Jean-Louis Devineau; Lynda D. Prior; Pl\\u00ednio Barbosa de Camargo; Joseph J. O'Brien; Lawrence Mbwambo; Carolina V. Castilho; Juan Ignacio Valdez Hern\\u00e1ndez; Marcos Miranda Toledo; Mario Tomazello Filho; Hooz Angela Mendivelso; Achim Br\\u00e4uning; Deborah A. Clark; Jos\\u00e9 Luis L\\u00f3pez Ayala; Marcos Silveira; Jennifer Koenig; Gr\\u00e9groire Vincent; Danilo Boanerges Souza; Claudio Sergio Lisi; Claudio Sergio Lisi; James Grogan; Edilson Consuelo de Oliveira; Wendeson Castro; Jan Verbesselt; Williamar Rodrigues Silva; Brett P. Murphy; Eduardo Eijji Maeda; Luciano de Souza Arruda; Fernanda C. G. Cardoso; M\\u00e1rcia C. M. Marques; Martin Worbes; Sintia Valerio Kohler; Bruno H\\u00e9rault; E. N. Chidumayo; Elisha Elifuraha; Maria Raquel Kanieski; Fidel A. Roig; Robert Gliniars; Giselda Durigan; David M. Drew; Ligia Ferreira Fedele; C\\u00e9sar Augusto Guimar\\u00e3es Finger; Lip Khoon Kho; J\\u00fcrgen Homeier; Mark Schulze; Vivian R. B. Maria; Julia Krepkowski; Timothy R. Baker; Vinicius Resende de Castro; Damien Bonal; Milton Eugene Lieberman; Paulo Cesar Botosso; David M. J. S. Bowman; Camille Couralet; Hellen Paredio Santana; Diana Lieberman; Rubens Koloski Chagas; Jos\\u00e9 P. Lemos-Filho; Jo\\u00e3o Lima Freitas J\\u00fanior; Anthony D. Griffiths; Naoki Okada; Aster Gebrekirstos; Luiz E. O. C. Arag\\u00e3o; Luiz E. O. C. Arag\\u00e3o; Gabriel Sebastian Becker; Yadvinder Malhi; Susanne Spannl; Tomaz Longhi Santos; Silva, Williamar Rodrigues; Kanieski, Maria Raquel; Malhi, Yadvinder; Chidumayo, Emmanuel N.; Finger, C\\u00e9sar Augusto Guimar\\u00e3es; Mendivelso, Hooz Angela; Botosso, Paulo Cesar; Lieberman, Milton Eugene; Griffiths, Anthony D.; Devineau, Jean-Louis; Silveira, Marcos; Couralet, Camille; Costa, Flavia Regina Capellotto; Chagas, Rubens Koloski; Vieira, Simone Aparecida; Bonal, Damien; Franco, Augusto C\\u00e9sar; Roig, Fidel Alejandro; Swaine, Michael D.; Becker, Gabriel Sebastian; Verbesselt, Jan; Br\\u00e4uning, Achim; Krepkowski, Julia; Silva, Paulo Henrique; Prior, Lynda D.; Guan, Kaiyu; Galv\\u00e3o, Franklin; Clark, Deborah A.; Marques, Renato; H\\u00e9rault, Bruno; Durigan, Giselda; Gra\\u00e7a, Paulo Maur\\u00edcio Lima de Alencastro; Rossatto, Davi Rodrigo; de Souza Arruda, Luciano; Ferreira Fedele, Ligia; Lemos-Filho, Jos\\u00e9 Pires; Carvalho, Fabr\\u00edcio Alvim; Valdez Hern\\u00e1ndez, Juan Ignacio; Figueiredo Filho, Afonso; Okada, Naoki; Rowland, Lucy; Schulze, Mark; Camarero, Jesus Julio; Volkmer de Castilho, Carolina; Toledo, Marcos Miranda; Anderson, Liana O.; D\\u00fcnisch, Oliver; Rossi, Vivien; Toma, Takeshi; Worbes, Martin; Freitas J\\u00fanior, Jo\\u00e3o Lima; Kohler, Sintia Valerio; Elifuraha, Elisha; Camargo, Pl\\u00ednio Barbosa; Gebrekirstos, Aster; Grogan, James; Selhorst, Diogo; Chave, J\\u00e9rome; Arag\\u00e3o, Luiz E. O. C.; Vincent, Gr\\u00e9goire; L\\u00f3pez Ayala, Jos\\u00e9 Luis; Santana, Hellen; Maza Chamba, Hector; Boanerges Souza, Danilo; Cardoso, Fernanda C. G.; Volland, Franziska; de Castro, Vinicius Resende; Lisi, Claudio Sergio; Gliniars, Robert; Lieberman, Diana; Oberbauer, Steven F.; Dalitz, Helmut; Zanon, Magda Lea Bolzan; Santo, Tomaz, Longhi; Spannl, Susanne; Tomazello Filho, Mario; Bowman, David M.; Toledo, Marisol; Maeda, Eduardo Eijji; de Oliveira, Edilson Consuelo; Murphy, Brett P.; Mbwambo, Lawrence; Wagner, Fabien H.; Brede, Benjamin; Marques, Marcia C. M.; Castro, Wendeson; Ross, Michael; Rutishauser, Ervan; O'Brien, Joseph J.; Beeckman, Hans; Baker, Timothy R.; de Freitas Milani, Ja\\u00e7anan Eloisa; Kho, Lip Khoon; Koenig, Jennifer; Melga\\u00e7o, Karina Liana Lisboa; P\\u00e9lissier, Rapha\\u00ebl; Fedele, Marcio; Homeier, J\\u00fcrgen; Maria, Vivian R. B.; Drew, David M.; Stahl, Cl\\u00e9ment; Brown, Foster Irving; Toledo, Jos\\u00e9 Julio; Mark Schulze; Timothy R. Baker; Jesus Julio Camarero; Oliver D\\u00fcnisch; Simone Aparecida Vieira; Marcos Miranda Toledo; Kaiyu Guan; Jos\\u00e9 Luis L\\u00f3pez Ayala; Michael D. Swaine; Anthony D. Griffiths; Jos\\u00e9 Pires Lemos-Filho; Deborah A. Clark; Vinicius Resende de Castro; Jos\\u00e9 Julio Toledo; Hooz Angela Mendivelso; Lynda D. Prior; Michael Ross; Diana Lieberman; Claudio Sergio Lisi; Carolina Volkmer de Castilho; Emmanuel N. Chidumayo; Rubens Koloski Chagas; Naoki Okada; Paulo Henrique da Silva Mauricio; Takeshi Toma; Karina Liana Lisboa Melga\\u00e7o; C\\u00e9sar Augusto Guimar\\u00e3es Finger; Maria Raquel Kanieski; Damien Bonal; Camille Couralet; Fidel Alejandro Roig; Renato Marques; Magda Lea Bolzan Zanon; Fabien H. Wagner; Aster Gebrekirstos; Yadvinder Malhi; Lucy Rowland; Gr\\u00e9goire Vincent; Danilo Boanerges Souza; Julia Krepkowski; Hector Maza Chamba; Vivian R. B. Maria; Juan Ignacio Valdez Hern\\u00e1ndez; Milton Eugene Lieberman; Foster Irving Brown; Augusto C\\u00e9sar Franco; Steven F. Oberbauer; J\\u00e9rome Chave; Hellen Santana; Marisol Toledo; Robert Gliniars; Davi Rodrigo Rossatto; Afonso Figueiredo Filho; Tomaz Longhi Santos; Marcia C. M. Marques; Paulo Maur\\u00edcio Lima de Alencastro Gra\\u00e7a; Helmut Dalitz; Giselda Durigan; Achim Br\\u00e4uning; Eduardo Eijji Maeda; Hans Beeckman; Williamar Rodrigues Silva; Pl\\u00ednio Barbosa Camargo; Jo\\u00e3o Lima Freitas J\\u00fanior; Rapha\\u00ebl P\\u00e9lissier; Wendeson Castro; Cl\\u00e9ment Stahl; Jennifer Koenig; Joseph J. O'Brien; Benjamin Brede; David M. J. S. Bowman; Luiz E. O. C. Arag\\u00e3o; Jean-Louis Devineau; Marcio Fedele; Fabr\\u00edcio Alvim Carvalho; Paulo Cesar Botosso; Mario Tomazello Filho; Fernanda C. G. Cardoso; Diogo Selhorst; Flavia Regina Capellotto Costa; Ervan Rutishauser; Sintia Valerio Kohler; Lawrence Mbwambo; J\\u00fcrgen Homeier; Liana O. Anderson; Ja\\u00e7anan Eloisa de Freitas Milani; Marcos Silveira; Brett P. Murphy; Edilson Consuelo de Oliveira; Franziska Volland; Franklin Galv\\u00e3o; Luciano de Souza Arruda; Martin Worbes; David M. Drew; Jan Verbesselt; Susanne Spannl; Ligia Ferreira Fedele; Lip Khoon Kho; Elisha Elifuraha; Gabriel Sebastian Becker; Vivien Rossi; Bruno H\\u00e9rault; James Grogan; Silva, Williamar Rodrigues; Kanieski, Maria Raquel; Malhi, Yadvinder; Chidumayo, Emmanuel N.; Finger, C\\u00e9sar Augusto Guimar\\u00e3es; Mendivelso, Hooz Angela; Botosso, Paulo Cesar; Lieberman, Milton Eugene; Griffiths, Anthony D.; Devineau, Jean-Louis; Silveira, Marcos; Couralet, Camille; Costa, Flavia Regina Capellotto; Chagas, Rubens Koloski; Vieira, Simone Aparecida; Bonal, Damien; Franco, Augusto C\\u00e9sar; Roig, Fidel Alejandro; Swaine, Michael D.; Becker, Gabriel Sebastian; Verbesselt, Jan; Br\\u00e4uning, Achim; Krepkowski, Julia; Silva, Paulo Henrique; Prior, Lynda D.; Guan, Kaiyu; Galv\\u00e3o, Franklin; Clark, Deborah A.; Marques, Renato; H\\u00e9rault, Bruno; Durigan, Giselda; Gra\\u00e7a, Paulo Maur\\u00edcio Lima de Alencastro; Rossatto, Davi Rodrigo; de Souza Arruda, Luciano; Ferreira Fedele, Ligia; Lemos-Filho, Jos\\u00e9 Pires; Carvalho, Fabr\\u00edcio Alvim; Valdez Hern\\u00e1ndez, Juan Ignacio; Figueiredo Filho, Afonso; Okada, Naoki; Rowland, Lucy; Schulze, Mark; Camarero, Jesus Julio; Volkmer de Castilho, Carolina; Toledo, Marcos Miranda; Anderson, Liana O.; D\\u00fcnisch, Oliver; Rossi, Vivien; Toma, Takeshi; Worbes, Martin; Freitas J\\u00fanior, Jo\\u00e3o Lima; Kohler, Sintia Valerio; Elifuraha, Elisha; Camargo, Pl\\u00ednio Barbosa; Gebrekirstos, Aster; Grogan, James; Selhorst, Diogo; Chave, J\\u00e9rome; Arag\\u00e3o, Luiz E. O. C.; Vincent, Gr\\u00e9goire; L\\u00f3pez Ayala, Jos\\u00e9 Luis; Santana, Hellen; Maza Chamba, Hector; Boanerges Souza, Danilo; Cardoso, Fernanda C. G.; Volland, Franziska; de Castro, Vinicius Resende; Lisi, Claudio Sergio; Gliniars, Robert; Lieberman, Diana; Oberbauer, Steven F.; Dalitz, Helmut; Zanon, Magda Lea Bolzan; Santo, Tomaz, Longhi; Spannl, Susanne; Tomazello Filho, Mario; Bowman, David M.; Toledo, Marisol; Maeda, Eduardo Eijji; de Oliveira, Edilson Consuelo; Murphy, Brett P.; Mbwambo, Lawrence; Wagner, Fabien H.; Brede, Benjamin; Marques, Marcia C. M.; Castro, Wendeson; Ross, Michael; Rutishauser, Ervan; O'Brien, Joseph J.; Beeckman, Hans; Baker, Timothy R.; de Freitas Milani, Ja\\u00e7anan Eloisa; Kho, Lip Khoon; Koenig, Jennifer; Melga\\u00e7o, Karina Liana Lisboa; P\\u00e9lissier, Rapha\\u00ebl; Fedele, Marcio; Homeier, J\\u00fcrgen; Maria, Vivian R. B.; Drew, David M.; Stahl, Cl\\u00e9ment; Brown, Foster Irving; Toledo, Jos\\u00e9 Julio; Silva, Williamar Rodrigues; Kanieski, Maria Raquel; Malhi, Yadvinder; Chidumayo, Emmanuel N.; Finger, C\\u00e9sar Augusto Guimar\\u00e3es; Mendivelso, Hooz Angela; Botosso, Paulo Cesar; Lieberman, Milton Eugene; Griffiths, Anthony D.; Devineau, Jean-Louis; Silveira, Marcos; Couralet, Camille; Costa, Flavia Regina Capellotto; Chagas, Rubens Koloski; Vieira, Simone Aparecida; Bonal, Damien; Franco, Augusto C\\u00e9sar; Roig, Fidel Alejandro; Swaine, Michael D.; Becker, Gabriel Sebastian; Verbesselt, Jan; Br\\u00e4uning, Achim; Krepkowski, Julia; Silva, Paulo Henrique; Prior, Lynda D.; Guan, Kaiyu; Galv\\u00e3o, Franklin; Clark, Deborah A.; Marques, Renato; H\\u00e9rault, Bruno; Durigan, Giselda; Gra\\u00e7a, Paulo Maur\\u00edcio Lima de Alencastro; Rossatto, Davi Rodrigo; de Souza Arruda, Luciano; Ferreira Fedele, Ligia; Lemos-Filho, Jos\\u00e9 Pires; Carvalho, Fabr\\u00edcio Alvim; Valdez Hern\\u00e1ndez, Juan Ignacio; Figueiredo Filho, Afonso; Okada, Naoki; Rowland, Lucy; Schulze, Mark; Camarero, Jesus Julio; Volkmer de Castilho, Carolina; Toledo, Marcos Miranda; Anderson, Liana O.; D\\u00fcnisch, Oliver; Rossi, Vivien; Toma, Takeshi; Worbes, Martin; Freitas J\\u00fanior, Jo\\u00e3o Lima; Kohler, Sintia Valerio; Elifuraha, Elisha; Camargo, Pl\\u00ednio Barbosa; Gebrekirstos, Aster; Grogan, James; Selhorst, Diogo; Arag\\u00e3o, Luiz E. O. C.; Vincent, Gr\\u00e9goire; Chave, J\\u00e9r\\u00f4me; L\\u00f3pez Ayala, Jos\\u00e9 Luis; Santana, Hellen; Maza Chamba, Hector; Boanerges Souza, Danilo; Cardoso, Fernanda C. G.; Volland, Franziska; de Castro, Vinicius Resende; Lisi, Claudio Sergio; Gliniars, Robert; Lieberman, Diana; Oberbauer, Steven F.; Dalitz, Helmut; Zanon, Magda Lea Bolzan; Santo, Tomaz, Longhi; Spannl, Susanne; Tomazello Filho, Mario; Bowman, David M.; Toledo, Marisol; Maeda, Eduardo Eijji; de Oliveira, Edilson Consuelo; Murphy, Brett P.; Mbwambo, Lawrence; Wagner, Fabien H.; Brede, Benjamin; Marques, Marcia C. M.; Castro, Wendeson; Ross, Michael; Rutishauser, Ervan; O'Brien, Joseph J.; Beeckman, Hans; Baker, Timothy R.; de Freitas Milani, Ja\\u00e7anan Eloisa; Kho, Lip Khoon; Koenig, Jennifer; Melga\\u00e7o, Karina Liana Lisboa; P\\u00e9lissier, Rapha\\u00ebl; Fedele, Marcio; Homeier, J\\u00fcrgen; Maria, Vivian R. B.; Drew, David M.; Stahl, Cl\\u00e9ment; Brown, Foster Irving; Toledo, Jos\\u00e9 Julio; Silva, Williamar Rodrigues; Kanieski, Maria Raquel; Malhi, Yadvinder; Chidumayo, Emmanuel N.; Finger, C\\u00e9sar Augusto Guimar\\u00e3es; Mendivelso, Hooz Angela; Botosso, Paulo Cesar; Lieberman, Milton Eugene; Griffiths, Anthony D.; Devineau, Jean-Louis; Silveira, Marcos; Couralet, Camille; Costa, Flavia Regina Capellotto; Chagas, Rubens Koloski; Vieira, Simone Aparecida; Bonal, Damien; Franco, Augusto C\\u00e9sar; Roig, Fidel Alejandro; Swaine, Michael D.; Becker, Gabriel Sebastian; Verbesselt, Jan; Br\\u00e4uning, Achim; Krepkowski, Julia; Silva, Paulo Henrique; Prior, Lynda D.; Guan, Kaiyu; Galv\\u00e3o, Franklin; Clark, Deborah A.; Marques, Renato; H\\u00e9rault, Bruno; Durigan, Giselda; Gra\\u00e7a, Paulo Maur\\u00edcio Lima de Alencastro; Rossatto, Davi Rodrigo; de Souza Arruda, Luciano; Ferreira Fedele, Ligia; Lemos-Filho, Jos\\u00e9 Pires; Carvalho, Fabr\\u00edcio Alvim; Valdez Hern\\u00e1ndez, Juan Ignacio; Figueiredo Filho, Afonso; Okada, Naoki; Rowland, Lucy; Schulze, Mark; Camarero, Jesus Julio; Volkmer de Castilho, Carolina; Toledo, Marcos Miranda; Anderson, Liana O.; D\\u00fcnisch, Oliver; Rossi, Vivien; Toma, Takeshi; Worbes, Martin; Freitas J\\u00fanior, Jo\\u00e3o Lima; Kohler, Sintia Valerio; Elifuraha, Elisha; Camargo, Pl\\u00ednio Barbosa; Gebrekirstos, Aster; Grogan, James; Selhorst, Diogo; Arag\\u00e3o, Luiz E. O. C.; Vincent, Gr\\u00e9goire; Chave, J\\u00e9r\\u00f4me; L\\u00f3pez Ayala, Jos\\u00e9 Luis; Santana, Hellen; Maza Chamba, Hector; Boanerges Souza, Danilo; Cardoso, Fernanda C. G.; Volland, Franziska; de Castro, Vinicius Resende; Lisi, Claudio Sergio; Gliniars, Robert; Lieberman, Diana; Oberbauer, Steven F.; Dalitz, Helmut; Zanon, Magda Lea Bolzan; Santo, Tomaz, Longhi; Spannl, Susanne; Tomazello Filho, Mario; Bowman, David M.; Toledo, Marisol; Maeda, Eduardo Eijji; de Oliveira, Edilson Consuelo; Murphy, Brett P.; Mbwambo, Lawrence; Wagner, Fabien H.; Brede, Benjamin; Marques, Marcia C. M.; Castro, Wendeson; Ross, Michael; Rutishauser, Ervan; O'Brien, Joseph J.; Beeckman, Hans; Baker, Timothy R.; de Freitas Milani, Ja\\u00e7anan Eloisa; Kho, Lip Khoon; Koenig, Jennifer; Melga\\u00e7o, Karina Liana Lisboa; P\\u00e9lissier, Rapha\\u00ebl; Fedele, Marcio; Homeier, J\\u00fcrgen; Maria, Vivian R. B.; Drew, David M.; Stahl, Cl\\u00e9ment; Brown, Foster Irving; Toledo, Jos\\u00e9 Julio; Beeckman, Hans; Baker, Timothy R.; Bonal, Damien; Wagner, Fabien H.; H\\u00e9rault, Bruno; Becker, Gabriel Sebastian; Botosso, Paulo Cesar; Arag\\u00e3o, Luiz E. O. C.; Anderson, Liana O.; Stahl, Cl\\u00e9ment; Boanerges Souza, Danilo\",\"subject_orig\":\"cycle du carbone\",\"oa_state\":1,\"url\":\"doi_dedup___::1ffd696adb19408e4a921e2dfe0030a9\",\"cluster_labels\":\"Cycle du carbone, 13. climate action\",\"x\":\"0.367382118335057\",\"y\":\"0.397753425114482\",\"labels\":\"doi_dedup___::1ffd696adb19408e4a921e2dfe0030a9\",\"area_uri\":5,\"area\":\"Cycle du carbone, 13. climate action\"},{\"id\":\"doi_dedup___::23e74581e17c81c80e101542938c9c0c\",\"subject\":\"0106 biological sciences\",\"title\":\"Conservative water management in the widespread conifer genus Callitris\",\"year\":\"2013-11-13\",\"publisher\":\"Oxford University Press (OUP)\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"AoB PLANTS\",\"link\":\"https:\\/\\/doi.org\\/10.1093\\/aobpla\\/plt052\",\"fulltext\":\"\",\"paper_abstract\":\"Water management by woody species encompasses characters involved in seeking, transporting and evaporating water. Examples of adaptation of individual characters to water availability are common, but little is known about the adaptability of whole-plant water management. Here we use plant hydration and growth to examine variation in whole-plant water management characteristics within the conifer genus Callitris. Using four species that cover the environmental extremes in the Australian continent, we compare seasonal patterns of growth and hydration over 2 years to determine the extent to which species exhibit adaptive variation to the local environment. Detailed measurements of gas exchange in one species are used to produce a hydraulic model to predict changes in leaf water potential throughout the year. This same model, when applied to the remaining three species, provided a close representation of the measured patterns of water potential gradient at all sites, suggesting strong conservation in water management, a conclusion supported by carbon and oxygen isotope measurements in Callitris from across the continent. We conclude that despite its large range in terms of rainfall, Callitris has a conservative water management strategy, characterized by a high sensitivity of growth to rainfall and a delayed (anisohydric) closure of stomata during soil drying.\",\"doi\":\"10.1093\\/aobpla\\/plt052\",\"project_id\":\"FT100100237\",\"accessright\":\"Open Access\",\"authors\":\"Scott Nichols; David M. J. S. Bowman; Lynda D. Prior; Timothy J. Brodribb; Brett P. Murphy; Brett P. Murphy; Pauline F. Grierson; S. Nichols; T. J. Brodribb; P. F. Grierson; D. M. J. S. Bowman; B. P. Murphy; L. D. Prior; Brodribb, Timothy J.; Nichols, Scott; Bowman, David M. J. S.; Murphy, Brett P.; Grierson, Pauline F.; Prior, Lynda D.\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":1,\"url\":\"doi_dedup___::23e74581e17c81c80e101542938c9c0c\",\"cluster_labels\":\"0106 biological sciences, 0301 basic medicine\",\"x\":\"-0.268025677052877\",\"y\":\"0.18910176812401\",\"labels\":\"doi_dedup___::23e74581e17c81c80e101542938c9c0c\",\"area_uri\":1,\"area\":\"0106 biological sciences, 0301 basic medicine\"},{\"id\":\"doi_dedup___::316e72c784f2d223eca5f1d386a46857\",\"subject\":\"13. Climate action\",\"title\":\"Are giant eucalypt forests rain forest?\",\"year\":\"2023-01-01\",\"publisher\":\"University Of Tasmania\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"\",\"link\":\"https:\\/\\/doi.org\\/10.25959\\/23243075\",\"fulltext\":\"\",\"paper_abstract\":\"Forests dominated by giant eucalypts ( eucalypt species with the potential to attain heights exceeding 70m) occur along the Australian east coast in association with rain forest. These forests contribute significantly to the global carbon budget but their ecological classification suffers from ambiguities around the definition of rain forest. The belief that eucalypts are 'sclerophyllous' and therefore not rain forest is a subjective view that has led to problems with conservation policies and management strategies of giant eucalypt forests. Understanding these forests from a global and functional viewpoint is paramount for their effective management. Eucalyptus grandis-dominated giant eucalypt forests in the Wet Tropics of Australia serve as a case study. Observing that rain forest species continuously regenerate in the understories of these eucalypt forests and believing that rain forest incursion will lead to the local elimination of the giant eucalypts, land managers prescribe frequent, low intensity fires. This management strategy is contentious and not underpinned by robust ecological understanding. To resolve these classificatory problems around eucalypts occurring in rain forest, I take a multidisciplinary approach to address the specific question: Are giant eucalypt forests rain forests? To obtain an in depth understanding of the ecology of giant eucalypts and the forests they dominate, and to provide a global context for these systems, I synthesise over a century's worth of literature on these systems (Chapter 2). Based on these data I propose that giant eucalypts are ecologically akin to rain forest emergent pioneers with a unique dependence on fire for regeneration, and that their habitat should be considered a type of secondary rain forest. Using a GIS-based approach I investigate the landscape scale vegetation dynamics of rain forest and E. grandis forest in the Wet Tropics, where E. grandis forests are considered to be threatened (Chapter 3). Using a environmentally stratified sample of sites, I show that rain forest has expanded over the past 50 years, and that this expansion is most likely a response to a global driver such as increased atmospheric CO2 rather than with local environmental factors. Projective modelling of this rain forest expansion predicts that, even at the fastest estimated rate known for the region, it will be more than 2000 years before rain forest fully engulfs giant eucalypt forests. In Chapter 4, I present a seedling growth experiment to examine if the regeneration niche of E. grandis exhibits ecological convergence with that of well-studied temperate giant eucalypts. I show that E. grandis seedlings grow poorly in unburnt rain forest soils because of the unavailability of phosphorus. The addition of phosphorus lifts phosphorus-deficiency symptoms in seedlings in rain forest soils, and accords well with the idea of E. grandis being a rain forest pioneer with the unique requirement of fire as a disturbance mechanism to create suitable open habitats for regeneration. To contextualize the rain forest- giant eucalypt forest - savanna transitions in Australia from a functional and macroecological perspective, I present a plant functional trait analysis of representative plants across these vegetation transitions in both tropical and temperate Australia (Chapter 5). I show that both tropical and temperate giant eucalypt forest are functionally convergent with rain forest and not with savanna. These results suggest that a classification of giant eucalypt forest based on functional attributes of the whole forest will be more useful for management policy than the established classification based on canopy dominants. In conclusion (Chapter 6), the synthesis ofmy landscape ecology and functional biology data supports my overarching hypothesis that giant eucalypt forests are functionally and ecologically rain forests and should be managed as such. I discuss the implications of my research for the management of Wet Tropics giant eucalypt forest and recommend that E. grandis forest should be managed under a regime of total fire suppression. Given that rare natural fires can be expected to occur under this management, the resulting regime will mimic the inherently long fire return times of these systems.\",\"doi\":\"10.25959\\/23247668.v1\",\"project_id\":\"DP0878177\",\"accessright\":\"not available\",\"authors\":\"Tng, DYP; Tng, DYP; Tng, DYP; Tng, DYP; Tng, DYP\",\"subject_orig\":\"13. Climate action\",\"oa_state\":0,\"url\":\"doi_dedup___::316e72c784f2d223eca5f1d386a46857\",\"cluster_labels\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\",\"x\":\"0.246040628440847\",\"y\":\"-0.167350749419719\",\"labels\":\"doi_dedup___::316e72c784f2d223eca5f1d386a46857\",\"area_uri\":2,\"area\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\"},{\"id\":\"doi_dedup___::42b25a1ae2c99b1997dde4113007d838\",\"subject\":\"0106 biological sciences\",\"title\":\"Humid tropical rain forest has expanded into eucalypt forest and savanna over the last 50 years\",\"year\":\"2011-11-24\",\"publisher\":\"Wiley\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Ecology and Evolution\",\"link\":\"https:\\/\\/doi.org\\/https:\\/\\/doi.org\\/10.1002\\/ece3.70\",\"fulltext\":\"http:\\/\\/hdl.handle.net\\/11343\\/264893\",\"paper_abstract\":\"\u003Cjats:title\u003EAbstract\u003C\\/jats:title\u003E\u003Cjats:p\u003ETropical rain forest expansion and savanna woody vegetation thickening appear to be a global trend, but there remains uncertainty about whether there is a common set of global drivers. Using geographic information techniques, we analyzed aerial photography of five areas in the humid tropics of northeastern Queensland, Australia, taken in the 1950s and 2008, to determine if changes in rain forest extent match those reported for the Australian monsoon tropics using similar techniques. Mapping of the 1950s aerial photography showed that of the combined study area (64,430 ha), 63% was classified as eucalypt forests\\/woodland and 37% as rain forest. Our mapping revealed that although most boundaries remained stable, there was a net increase of 732 ha of the original rain forest area over the study period, and negligible conversion of rain forest to eucalypt forest\\/woodland. Statistical modeling, controlling for spatial autocorrelation, indicated distance from preexisting rain forest as the strongest determinant of rain forest expansion. Margin extension had a mean rate across the five sites of 0.6 m per decade. Expansion was greater in tall open forest types but also occurred in shorter, more flammable woodland vegetation types. No correlations were detected with other local variables (aspect, elevation, geology, topography, drainage). Using a geographically weighted mean rate of rain forest margin extension across the whole region, we predict that over 25% of tall open forest (a forest type of high conservation significance) would still remain after 2000 years of rain forest expansion. This slow replacement is due to the convoluted nature of the rain forest boundary and the irregular shape of the tall open forest patches. Our analyses point to the increased concentration of atmospheric CO\u003Cjats:sub\u003E2\u003C\\/jats:sub\u003Eas the most likely global driver of indiscriminate rain forest expansion occurring in northeastern Australia, by increasing tree growth and thereby overriding the effects of fire disturbance.\u003C\\/jats:p\u003E\",\"doi\":\"10.1002\\/ece3.70\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"David Y. P. Tng; Gregor J. Sanders; Ellen Weber; Grant J. Williamson; Brett P. Murphy; Brett P. Murphy; Jeanette Kemp; David M. J. S. Bowman; Brett P. Murphy; Jeanette Kemp; David M. J. S. Bowman; Gregor Sanders; Grant J. Williamson; Ellen Weber; David Y. P. Tng; David Y P, Tng; David M J S, Bowman; Brett P, Murphy; Ellen, Weber; Grant J, Williamson; Gregor, Sanders; Jeanette, Kemp; Murphy, Brett P; Williamson, Grant J; Tng, David Y P; Sanders, Gregor; Kemp, Jeanette; Bowman, David M J S; Weber, Ellen\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":1,\"url\":\"doi_dedup___::42b25a1ae2c99b1997dde4113007d838\",\"cluster_labels\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\",\"x\":\"0.226080980470218\",\"y\":\"-0.155664175951863\",\"labels\":\"doi_dedup___::42b25a1ae2c99b1997dde4113007d838\",\"area_uri\":2,\"area\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\"},{\"id\":\"doi_dedup___::5348a1734f9efe1cdab94687328e7022\",\"subject\":\"0301 basic medicine\",\"title\":\"Ancestral stomatal control results in a canalization of fern and lycophyte adaptation to drought\",\"year\":\"2013-02-20\",\"publisher\":\"Wiley\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"New Phytologist\",\"link\":\"https:\\/\\/pubmed.ncbi.nlm.nih.gov\\/23421706\\/\",\"fulltext\":\"\",\"paper_abstract\":\"\u003Cjats:title\u003ESummary\u003C\\/jats:title\u003E\u003Cjats:p\u003E \u003Cjats:list list-type=\\\"bullet\\\"\u003E \u003Cjats:list-item\u003E\u003Cjats:p\u003ELittle is known about how a predominantly passive hydraulic stomatal control in ferns and lycophytes might impact water use under stress. Ferns and lycophytes occupy a diverse array of habitats, from deserts to rainforest canopies, raising the question of whether stomatal behaviour is the same under all ecological strategies and imposes ecological or functional constraints on ferns and lycophytes.\u003C\\/jats:p\u003E\u003C\\/jats:list-item\u003E \u003Cjats:list-item\u003E\u003Cjats:p\u003EWe examined the stomatal response of a diverse sample of fern and lycophyte species to both soil and atmospheric water stress, assessing the foliar level of the hormone abscisic acid (\u003Cjats:styled-content style=\\\"fixed-case\\\"\u003EABA\u003C\\/jats:styled-content\u003E) over drought and recovery and the critical leaf water potential (\\u03a8\u003Cjats:sub\u003El\u003C\\/jats:sub\u003E) at which photosynthesis in droughted leaves failed to recover.\u003C\\/jats:p\u003E\u003C\\/jats:list-item\u003E \u003Cjats:list-item\u003E\u003Cjats:p\u003EThe stomata of all ferns and lycophytes showed very predictable responses to soil and atmospheric water deficit via \\u03a8\u003Cjats:sub\u003El\u003C\\/jats:sub\u003E, while stomatal closure was poorly correlated with changes in ABA. We found that all ferns closed stomata at very low levels of water stress and their survival afterwards was limited only by their capacitance and desiccation tolerance.\u003C\\/jats:p\u003E\u003C\\/jats:list-item\u003E \u003Cjats:list-item\u003E\u003Cjats:p\u003EFerns and lycophytes have constrained stomatal responses to soil and atmospheric water deficit as a consequence of a predominantly passive stomatal regulation. This results in a monotypic strategy in ferns and lycophytes under water stress.\u003C\\/jats:p\u003E\u003C\\/jats:list-item\u003E \u003C\\/jats:list\u003E \u003C\\/jats:p\u003E\",\"doi\":\"10.1111\\/nph.12190\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Scott A. M. McAdam; Timothy J. Brodribb; Scott A M, McAdam; Timothy J, Brodribb; Scott A. M. McAdam; Timothy J. Brodribb\",\"subject_orig\":\"0301 basic medicine\",\"oa_state\":1,\"url\":\"doi_dedup___::5348a1734f9efe1cdab94687328e7022\",\"cluster_labels\":\"0301 basic medicine\",\"x\":\"-0.523766748428778\",\"y\":\"0.152693334034553\",\"labels\":\"doi_dedup___::5348a1734f9efe1cdab94687328e7022\",\"area_uri\":4,\"area\":\"0301 basic medicine\"},{\"id\":\"doi_dedup___::5424a60cc6da25220d38f5e334e739d4\",\"subject\":\"0106 biological sciences\",\"title\":\"Aborigine\\u2010managed forest, savanna and grassland: biome switching in montane eastern Australia\",\"year\":\"2014-04-10\",\"publisher\":\"Wiley\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Journal of Biogeography\",\"link\":\"https:\\/\\/doi.org\\/https:\\/\\/doi.org\\/10.1111\\/jbi.12306\",\"fulltext\":\"http:\\/\\/hdl.handle.net\\/1885\\/74078\",\"paper_abstract\":\"\u003Cjats:title\u003EAbstract\u003C\\/jats:title\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EAim\u003C\\/jats:title\u003E\u003Cjats:p\u003ETo assess hypotheses about the role of anthropogenic fire in the maintenance and origin of a fine\\u2010scale vegetation mosaic of rain forest, eucalypt savanna and grassland.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003ELocation\u003C\\/jats:title\u003E\u003Cjats:p\u003EBunya Mountains, subtropical eastern Australia.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EMethods\u003C\\/jats:title\u003E\u003Cjats:p\u003EA time series of vegetation maps was compiled from historical and recent aerial photography and field surveys. Geospatial models were constructed of environmental domains for rain forest, savanna and grassland, and for areas of biome change. Grassland soils were analysed for carbon isotope ratios (\\u03b4\u003Cjats:sup\u003E13\u003C\\/jats:sup\u003EC), and radiocarbon (\u003Cjats:sup\u003E14\u003C\\/jats:sup\u003EC) dates were acquired for bulk samples from a range of depths.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EResults\u003C\\/jats:title\u003E\u003Cjats:p\u003EAnalysis revealed weak associations between topography and the distribution of rain forest, savanna and grassland, and their patterns of recent change. Grassland occupied an environmental domain intermediate between rain forest and savanna and was more than four times as likely to occur within a matrix of rain forest rather than savanna. There was a large proportional reduction in the area of both grassland (\\u221235%) and savanna (\\u221219%) between 1961 and 2006 because of the expansion of rain forest. However, the greater initial extent of savanna meant that the areal loss of savanna was an order of magnitude greater than for grassland (1433 vs. 146\\u00a0ha). There was no evidence of abrupt changes in \\u03b4\u003Cjats:sup\u003E13\u003C\\/jats:sup\u003EC in grassland soil profiles, indicating stability of the vegetation over the last 2000\\u00a0years.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EMain conclusions\u003C\\/jats:title\u003E\u003Cjats:p\u003EThere is no simple gradient in \\u2018tree suitability\\u2019 from rain forest, through savanna, to treeless grassland on the Bunya Mountains. A general absence of fire since the 19th century has greatly reduced the extent of grassy savanna and grassland formations, to the advantage of rain forest. These results support the hypothesis that the vegetation mosaic on the Bunya Mountains is a cultural artefact and testament to millennia of skilful and persistent burning. We could not conclusively reject the hypothesis that the grasslands are Pleistocene relicts that have declined throughout the Holocene; nonetheless, an explanation more consistent with the evidence overall is that the grasslands must have had periods of expansion during the Holocene, probably as a consequence of severe fires that have destroyed patches of rain forest.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\",\"doi\":\"10.1111\\/jbi.12306\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Butler, Don W.; Fensham, Rod; Murphy, Brett P.; Bury, Sarah J.; Bowman, David M. J. S.; Haberle, Simon; Brett P. Murphy; Sarah J. Bury; David M. J. S. Bowman; Simon G. Haberle; Don W. Butler; Roderick J. Fensham\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":1,\"url\":\"doi_dedup___::5424a60cc6da25220d38f5e334e739d4\",\"cluster_labels\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\",\"x\":\"0.214181365281173\",\"y\":\"-0.281557825509733\",\"labels\":\"doi_dedup___::5424a60cc6da25220d38f5e334e739d4\",\"area_uri\":2,\"area\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\"},{\"id\":\"doi_dedup___::5a28071378d0a6878ab94ca168cbff86\",\"subject\":\"0106 biological sciences\",\"title\":\"Alternative stable states and the role of fire\\u2013vegetation\\u2013soil feedbacks in the temperate wilderness of southwest Tasmania\",\"year\":\"2011-11-06\",\"publisher\":\"Springer Science and Business Media LLC\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Landscape Ecology\",\"link\":\"https:\\/\\/doi.org\\/10.1007\\/s10980-011-9677-0\",\"fulltext\":\"\",\"paper_abstract\":\"Two ecological models have been put forward to explain the dynamics of fire-promoting and fire-sensitive vegetation in southwest Tasmania: the alternative stable states model of Jackson (in Proc Ecol Soc Aust 3:9\\u201316, 1968) and the sharpening switch model of Mount (in Search 10:180\\u2013186, 1979). Assessing the efficacy of these models requires high resolution spatio-temporal data on whether vegetation patterns are stable or dynamic across landscapes. We analysed ortho-rectified sequences of aerial photography and satellite imagery from 1948, 1988 and 2010 to detect decadal scale changes in forest and non-forest vegetation cover in southwest Tasmania. There was negligible change from forest to non-forest (\u003C0.05%) and only a modest change from non-forest to forest over the study period. Forest cover increased by 4.1% between 1948 and 1988, apparently due to the recovery of forest vegetation following stand-replacing fire prior to 1948. Forest cover increased by 0.8% between 1988 and 2010, reflecting the limited ability of forest to invade treeless areas. The two models include interactions between vegetation, fire and soil, which we investigated by analysing the chemical (phosphorus, nitrogen) and physical properties (clay, silt) of 128 soil samples collected across 34 forest\\u2013non-forest boundaries. Phosphorus in the upper horizon was typically lower in non-forest vegetation compared to forest vegetation, which is consistent with proposed fire\\u2013vegetation\\u2013soil feedbacks. Mineral horizons were dominated by sand, with low levels of clay under all vegetation types. Available field evidence lends support to the Jackson (1968) alternative stable states model as the most suitable model of vegetation dynamics on nutrient poor substrates in southwest Tasmania although modifications of the timeframes for transitions toward rainforest are required.\",\"doi\":\"10.1007\\/s10980-011-9677-0\",\"project_id\":\"DP0878177\",\"accessright\":\"Closed Access\",\"authors\":\"David M. J. S. Bowman; Samuel W. Wood; David M. J. S. Bowman; Sam W. Wood\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":0,\"url\":\"doi_dedup___::5a28071378d0a6878ab94ca168cbff86\",\"cluster_labels\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\",\"x\":\"0.363903148059666\",\"y\":\"-0.104475505046146\",\"labels\":\"doi_dedup___::5a28071378d0a6878ab94ca168cbff86\",\"area_uri\":2,\"area\":\"0106 biological sciences, 13. climate action, Giant eucalypt forests\"},{\"id\":\"doi_dedup___::7cbcf39e1f8d9712acd1f136fe8ea165\",\"subject\":\"0106 biological sciences\",\"title\":\"Has global environmental change caused monsoon rainforests to expand in the Australian monsoon tropics?\",\"year\":\"2010-06-24\",\"publisher\":\"Springer Science and Business Media LLC\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Landscape Ecology\",\"link\":\"https:\\/\\/doi.org\\/10.1007\\/s10980-010-9496-8\",\"fulltext\":\"\",\"paper_abstract\":\"A large research program in the Australian monsoon tropics has concluded that monsoon rainforests have expanded within the savanna matrix, a trend that has been emulated throughout the tropics worldwide. The driver of the northern Australian trend was not resolved, but it was suggested to be linked to a long-term trend towards wetter climates, atmospheric CO2 enrichment, and changed fire regimes. We review these findings with particular consideration of its analytical and evidentiary basis and plausibility of the global change hypothesis. Field validation has largely demonstrated that the aerial photographic technique that underpinned the previous research is reliable enough to detect rainforest expansion. Statistical modelling demonstrated that the expansion is related to sites with regionally low fire activity, although models are of low explanatory power reflecting the sketchy historical records of fire and feral animal impacts. Field studies show that current fire regimes adjacent to expanding rainforest patches are causing populations of the native conifer Callitris intratropica, an obligate seeder, to crash. Therefore, it is unlikely that changes in fire regimes, which have been deleterious to other fire-sensitive taxa and plant communities in the region, are responsible for the rainforest expansion. We conclude that the expansion of monsoon rainforests is most plausibly linked to the current wetting trend or elevated CO2 concentration. Increases in either water availability or CO2 concentration can potentially overwhelm the negative feedback between fire and rainforest cover that is responsible for the meta-stability of monsoon rainforest boundaries. However, further research at the continental scale, using aerial photography, tree rings and other proxies, is required to evaluate this hypothesis.\",\"doi\":\"10.1007\\/s10980-010-9496-8\",\"project_id\":\"LP0346929\",\"accessright\":\"Closed Access\",\"authors\":\"David M. J. S. Bowman; Daniel S. Banfai; Brett P. Murphy; Brett P. Murphy; Daniel S. Banfai; David M. J. S. Bowman\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":0,\"url\":\"doi_dedup___::7cbcf39e1f8d9712acd1f136fe8ea165\",\"cluster_labels\":\"0106 biological sciences, 0301 basic medicine\",\"x\":\"-0.188262242757116\",\"y\":\"-0.114417703128843\",\"labels\":\"doi_dedup___::7cbcf39e1f8d9712acd1f136fe8ea165\",\"area_uri\":1,\"area\":\"0106 biological sciences, 0301 basic medicine\"},{\"id\":\"doi_dedup___::7f5593e14327f3c66e14520a2667063e\",\"subject\":\"0301 basic medicine\",\"title\":\"Australia\\u2014A Model System for the Development of Pyrogeography\",\"year\":\"2011-04-01\",\"publisher\":\"Springer Science and Business Media LLC\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Fire Ecology\",\"link\":\"https:\\/\\/doi.org\\/10.4996\\/fireecology.0701005\",\"fulltext\":\"\",\"paper_abstract\":\"We define pyrogeography as an integrative, multidisciplinary perspective of landscape fire, its ecological effects, and its relationships with human societies. Like biogeography, this program spans geographic scales from the local to the global, has an evolutionary frame, and thus a geological dimension. And, like other geographic disciplines, pyrogeography has a clear commitment to understanding the interrelationships between cultures and their environment. We illustrate our approach by considering the pyrogeography of Australia. We demonstrate how a long history of fire has had a pervasive influence on the continent\\u2019s biota. While Aborigines coexisted with flammable landscapes for millennia, contemporary Australian society is still learning to live in a land of fire.\",\"doi\":\"10.4996\\/fireecology.0701005\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Brett P. Murphy; David M. J. S. Bowman; Brett P. Murphy; David M. J. S. Bowman\",\"subject_orig\":\"0301 basic medicine\",\"oa_state\":1,\"url\":\"doi_dedup___::7f5593e14327f3c66e14520a2667063e\",\"cluster_labels\":\"0106 biological sciences, 0301 basic medicine\",\"x\":\"-0.0561772020500714\",\"y\":\"0.441696304061327\",\"labels\":\"doi_dedup___::7f5593e14327f3c66e14520a2667063e\",\"area_uri\":1,\"area\":\"0106 biological sciences, 0301 basic medicine\"},{\"id\":\"doi_dedup___::9b6a6075a2a3a6ef4e25a5cdf2c1da53\",\"subject\":\"0106 biological sciences\",\"title\":\"Fire regimes and woody biomass dynamics in Australian savannas\",\"year\":\"2013-08-30\",\"publisher\":\"Wiley\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Journal of Biogeography\",\"link\":\"https:\\/\\/doi.org\\/10.1111\\/jbi.12204\",\"fulltext\":\"\",\"paper_abstract\":\"\u003Cjats:title\u003EAbstract\u003C\\/jats:title\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EAim\u003C\\/jats:title\u003E\u003Cjats:p\u003EMany tropical savannas are undergoing a trend of increasing woody biomass, or \\u2018woody thickening\\u2019. Management to reduce fire frequency and intensity in savannas could substantially increase the amount of carbon stored in woody biomass. We addressed two questions: (1) are northern Australian savannas thickening; and (2) to what extent, and by what demographic processes, does fire affect woody biomass accumulation?\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003ELocation\u003C\\/jats:title\u003E\u003Cjats:p\u003EThree large national parks, covering 24,000\\u00a0km\u003Cjats:sup\u003E2\u003C\\/jats:sup\u003E, in monsoonal northern Australia.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EMethods\u003C\\/jats:title\u003E\u003Cjats:p\u003EWe examined changes in woody biomass carbon stocks \\u2013 inferred from tree basal area and the density of woody understorey plants \\u2013 over a 10\\u2010year period in 136 savanna monitoring plots. We statistically assessed these changes in relation to fire frequency and severity. We used a meta\\u2010analysis to identify general trends in woody cover in Australian savannas over the last half\\u2010century.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EResults\u003C\\/jats:title\u003E\u003Cjats:p\u003EWoody biomass carbon stocks were relatively stable across the three national parks, but rates of change were statistically indistinguishable from earlier findings of a weak thickening trend. Change was negatively correlated with fire frequency, particularly the frequency of severe fires. High frequencies of severe fires decreased rates of accumulation of biomass by existing trees (through reductions in tree growth and death of individual stems), rather than whole\\u2010tree mortality and suppression of recruitment. However, across northern Australia, our meta\\u2010analysis identified a general, albeit weak, trend of woody thickening.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\u003Cjats:sec\u003E\u003Cjats:title\u003EMain conclusions\u003C\\/jats:title\u003E\u003Cjats:p\u003EThe drivers of northern Australia's weak thickening trend are uncertain, but likely candidates include increasing atmospheric \u003Cjats:styled-content style=\\\"fixed-case\\\"\u003ECO\u003C\\/jats:styled-content\u003E\u003Cjats:sub\u003E2\u003C\\/jats:sub\u003E concentration and water availability, and pastoral intensification. We demonstrate that changes to fire management have the potential to either increase or decrease rates of woody thickening relative to any underlying trend. Understanding how savanna fires affect woody biomass, and how fire effects are mediated by climate and \u003Cjats:styled-content style=\\\"fixed-case\\\"\u003ECO\u003C\\/jats:styled-content\u003E\u003Cjats:sub\u003E2\u003C\\/jats:sub\u003E, are essential research priorities to predict the fate of savannas.\u003C\\/jats:p\u003E\u003C\\/jats:sec\u003E\",\"doi\":\"10.1111\\/jbi.12204\",\"project_id\":\"DP0878177\",\"accessright\":\"Closed Access\",\"authors\":\"Michael J. Lawes; Jeremy Russell-Smith; Caroline E. R. Lehmann; Caroline E. R. Lehmann; Brett P. Murphy; Brett P. Murphy; Caroline E. R. Lehmann; Jeremy Russell\\u2010Smith; Michael J. Lawes\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":0,\"url\":\"doi_dedup___::9b6a6075a2a3a6ef4e25a5cdf2c1da53\",\"cluster_labels\":\"0106 biological sciences\",\"x\":\"-0.250484439327965\",\"y\":\"-0.37778601916065\",\"labels\":\"doi_dedup___::9b6a6075a2a3a6ef4e25a5cdf2c1da53\",\"area_uri\":3,\"area\":\"0106 biological sciences\"},{\"id\":\"doi_dedup___::9d67f67aece20a8e050eb2742c68b198\",\"subject\":\"0106 biological sciences\",\"title\":\"Population collapse of a Gondwanan conifer follows the loss of Indigenous fire regimes in a northern Australian savanna\",\"year\":\"2022-05-31\",\"publisher\":\"Springer Science and Business Media LLC\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Scientific Reports\",\"link\":\"https:\\/\\/doi.org\\/https:\\/\\/doi.org\\/10.1038\\/s41598-022-12946-3\",\"fulltext\":\"http:\\/\\/purl.org\\/au-research\\/grants\\/arc\\/DP150101777\",\"paper_abstract\":\"\u003Cjats:title\u003EAbstract\u003C\\/jats:title\u003E\u003Cjats:p\u003EColonialism has disrupted Indigenous socioecological systems around the globe, including those supported by intentional landscape burning. Because most disruptions happened centuries ago, our understanding of Indigenous fire management is largely inferential and open to debate. Here, we investigate the ecological consequences of the loss of traditional Aboriginal fire management on fire-exposed savannas on the Arnhem Plateau, northern Australia, using the fire-sensitive conifer \u003Cjats:italic\u003ECallitris intratropica\u003C\\/jats:italic\u003E as a bio-indicator. We contrast Kakadu National Park, where traditional Aboriginal fire management was severely disrupted during the early twentieth century following Aboriginal relocation to surrounding settlements, and an adjacent Aboriginal estate where traditional Aboriginal fire management endures. Since 2006, traditional Aboriginal fire management at this site has been overlaid by a program of broad-scale institutionalized burning in the early dry season, designed to reduce greenhouse emissions. Using remote sensing, field survey, and dendrochronology, we show that on the Aboriginal estate, \u003Cjats:italic\u003EC. intratropica\u003C\\/jats:italic\u003E populations depend on the creation of a shifting patch mosaic of long unburned areas necessary for the recruitment of \u003Cjats:italic\u003EC. intratropica.\u003C\\/jats:italic\u003E However, the imposition of broad-scale fire management is disrupting this population patch dynamic. In Kakadu, there have been extreme declines of \u003Cjats:italic\u003EC. intratropica\u003C\\/jats:italic\u003E associated with widespread fires since the mid twentieth century and consequent proliferation of grass fuels. Fire management in Kakadu since 2007, designed to increase the size and abundance of patches of unburned vegetation, has not been able to reverse the population collapse of \u003Cjats:italic\u003EC. intratropica\u003C\\/jats:italic\u003E. Our study demonstrates that colonial processes including relocation of Indigenous people and institutional fire management can have deleterious consequences that are nearly irreversible because of hysteresis in \u003Cjats:italic\u003EC. intratropica\u003C\\/jats:italic\u003E population dynamics.\u003C\\/jats:p\u003E\",\"doi\":\"10.1038\\/s41598-022-12946-3\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Bowman, DMJS; Williamson, GJ; Johnston, FH; Bowman, CJW; Murphy, BP; Roos, CI; Trauernicht, C; Rostron, J; Prior, LD; Bowman, DMJS; Prior, LD; Haverkamp, C; Rann, KD; Donald C. Franklin; Sean M. Bellairs; Pascale Taplin; Michael J. Lawes; Brook, B.; Prior, L.; Bowman, D.; Walsh, Angie; Bowman, David M. J. S.; Whitehead, Peter J.; Price, Owen; Rosanne D'Arrigo; Jonathan G. Palmer; Patrick J. Baker; Brittany Dahl; Declan Norrie; Kathryn Allen; Lynda D. Prior; David J. M. S. Bowman; Scott Nichols; Jonathan G. Palmer; Matthew Brookhouse; Ben J. French; David M. J. S. Bowman; David M. J. S. Bowman; Owen Price; Nichols, SC; MacDermott, HJ; Bowman, DMJS; Murphy, BP; Russell-Smith, Jeremy; Yibarbuk, D.; Cooke, P; Bowman, David M. J. S.; Jackson, DM; Whitehead, Peter J.; Fisher, Alaric; Godjuwa, C; Choquenot, D; David M. J. S. Bowman; Stuart Pearson; Kathryn Allen; Quan Hua; Brett P. Murphy; David M. J. S. Bowman; Talia E. Portner; Clay Trauernicht; Wanner, J\\u00fcrgen; Buchbauer, Gerhard; Jirovetz, Leopold; Schmidt, Erich; Bowman, David M. J. S.; Murphy, Brett P.; Roos, Christopher I.; Rostron, Joshua; Williamson, Grant J.; Johnston, Fay H.; Bowman, Clarence J. W.; Trauernicht, Clay; Prior, Lynda D.; Brett P. Murphy; Christopher I. Roos; Fay H. Johnston; Clarence J. W. Bowman; David M. J. S. Bowman; Grant J. Williamson; Clay Trauernicht; Lynda D. Prior; Joshua Rostron; Brett P. Murphy; Christopher I. Roos; Fay H. Johnston; Clarence J. W. Bowman; David M. J. S. Bowman; Grant J. Williamson; Clay Trauernicht; Lynda D. Prior; Joshua Rostron; David M J S, Bowman; Christopher I, Roos; Fay H, Johnston; Brett P, Murphy; Joshua, Rostron; Lynda D, Prior; Grant J, Williamson; Clay, Trauernicht; Clarence J W, Bowman\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":1,\"url\":\"doi_dedup___::9d67f67aece20a8e050eb2742c68b198\",\"cluster_labels\":\"0106 biological sciences, 0301 basic medicine\",\"x\":\"-0.0231958227792847\",\"y\":\"0.278514210389028\",\"labels\":\"doi_dedup___::9d67f67aece20a8e050eb2742c68b198\",\"area_uri\":1,\"area\":\"0106 biological sciences, 0301 basic medicine\"},{\"id\":\"doi_dedup___::af584b153c2cdb958ac3d065f932fb5f\",\"subject\":\"0301 basic medicine\",\"title\":\"Unique Responsiveness of Angiosperm Stomata to Elevated CO2 Explained by Calcium Signalling\",\"year\":\"2013-11-20\",\"publisher\":\"Public Library of Science (PLoS)\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"PLoS ONE\",\"link\":\"https:\\/\\/doi.org\\/10.1371\\/journal.pone.0082057\",\"fulltext\":\"\",\"paper_abstract\":\"Angiosperm and conifer tree species respond differently when exposed to elevated CO2, with angiosperms found to dynamically reduce water loss while conifers appear insensitive. Such distinct responses are likely to affect competition between these tree groups as atmospheric CO2 concentration rises. Seeking the mechanism behind this globally important phenomenon we targeted the Ca(2+)-dependent signalling pathway, a mediator of stomatal closure in response to elevated CO2, as a possible explanation for the differentiation of stomatal behaviours. Sampling across the diversity of vascular plants including lycophytes, ferns, gymnosperms and angiosperms we show that only angiosperms possess the stomatal behaviour and prerequisite genetic coding, linked to Ca(2+)-dependent stomatal signalling. We conclude that the evolution of Ca(2+)-dependent stomatal signalling gives angiosperms adaptive benefits in terms of highly efficient water use, but that stomatal sensitivity to high CO2 may penalise angiosperm productivity relative to other plant groups in the current era of soaring atmospheric CO2.\",\"doi\":\"10.1371\\/journal.pone.0082057\",\"project_id\":\"DP0878177\",\"accessright\":\"Open Access\",\"authors\":\"Scott A. M. McAdam; Timothy J. Brodribb; Scott A M, McAdam; Timothy J, Brodribb; Scott A. M. McAdam; Timothy J. Brodribb; Brodribb, Timothy J.; McAdam, Scott A. M.; Timothy J Brodribb; Scott A M McAdam\",\"subject_orig\":\"0301 basic medicine\",\"oa_state\":1,\"url\":\"doi_dedup___::af584b153c2cdb958ac3d065f932fb5f\",\"cluster_labels\":\"0301 basic medicine\",\"x\":\"-0.543985837479226\",\"y\":\"0.0858289826142518\",\"labels\":\"doi_dedup___::af584b153c2cdb958ac3d065f932fb5f\",\"area_uri\":4,\"area\":\"0301 basic medicine\"},{\"id\":\"doi_dedup___::bdb359a4581133463ee3ce28d1fc83f5\",\"subject\":\"0106 biological sciences\",\"title\":\"Are the eucalypt and non-eucalypt components of Australian tropical savannas independent?\",\"year\":\"2010-11-10\",\"publisher\":\"Springer Science and Business Media LLC\",\"resulttype\":\"publication\",\"language\":\"\",\"published_in\":\"Oecologia\",\"link\":\"https:\\/\\/espace.cdu.edu.au\\/view\\/cdu:37682\",\"fulltext\":\"\",\"paper_abstract\":\"Eucalypts (Eucalyptus and Corymbia spp.) dominate (60%) the tree biomass of Australia's tropical savannas but account for only a fraction (28%) of the tree diversity. Because of their considerable biomass and adaptation to environmental stressors, such as fire, the eucalypts may drive tree dynamics in these savannas, possibly to the exclusion of non-eucalypts. We evaluated whether the eucalypt and non-eucalypt components in tropical savannas are dependent so that changes in one component are matched by opposite trends in the other. Using tree inventory data from 127 savanna sites across the rainfall and fire frequency gradients, we found that eucalypt and non-eucalypt basal area and species richness had a negative relationship. This relationship was maintained across the rainfall gradient, with rainfall having a positive effect on the basal area and species richness of both components, but with a greater effect in non-eucalypts. Fire frequency negatively affected basal area, but not species richness, although basal area and species richness of eucalypts and non-eucalypts did not differ in their response to fire. Rainfall appears to set the upper bounds to woody biomass in these mesic savannas, while fire maintains woody biomass below carrying capacity and facilitates coexistence of the components. The magnitude of the component responses, particularly for non-eucalypts, is determined by rainfall, but their dependence is likely due to their differential response to both rainfall and fire, but not to competition for resources. Thus, while eucalypts dominate biomass overall, at high rainfall sites non-eucalypt basal area and diversity are highest, especially where fire frequency is low.\",\"doi\":\"10.1007\\/s00442-010-1829-4\",\"project_id\":\"DP0878177\",\"accessright\":\"Closed Access\",\"authors\":\"Michael J. Lawes; Jeremy Russell-Smith; Jeremy J. Midgley; Brett P. Murphy; J. Russell-Smith; M. J. Lawes; B. P. Murphy; J. J. Midgley; B P, Murphy; J, Russell-Smith; J J, Midgley; M J, Lawes\",\"subject_orig\":\"0106 biological sciences\",\"oa_state\":0,\"url\":\"doi_dedup___::bdb359a4581133463ee3ce28d1fc83f5\",\"cluster_labels\":\"0106 biological sciences\",\"x\":\"-0.157225822455321\",\"y\":\"-0.438046176985289\",\"labels\":\"doi_dedup___::bdb359a4581133463ee3ce28d1fc83f5\",\"area_uri\":3,\"area\":\"0106 biological sciences\"}]"} \ No newline at end of file diff --git a/local_dev/tools/db-insertion/OpenAIRE/config.json b/local_dev/tools/db-insertion/OpenAIRE/config.json new file mode 100644 index 000000000..42c109d91 --- /dev/null +++ b/local_dev/tools/db-insertion/OpenAIRE/config.json @@ -0,0 +1,15 @@ +{ + "endpoint": "http://127.0.0.1:8081/dev/persistence/createVisualization/dev", + "visualizations": [ + { + "vis_id": "9d4dc6b920d1e2cc08a741f7c56821db", + "vis_title": "openaire", + "vis_clean_query": "DP0878177", + "vis_query": "DP0878177", + "vis_params": "{\"project_id\":\"DP0878177\",\"funder\":\"ARC\",\"acronym\":\"\",\"title\":\"Understanding the impact of global environmental change on Australian forests and woodlands using rainforest boundaries and Callitris growth as bio-indicators\",\"start_date\":\"2008-01-01\",\"end_date\":\"2011-12-31\",\"special_clause\":\"false\",\"oa_mandate\":\"false\",\"organisations\":[],\"openaire_link\":\"http:\\/\\/purl.org\\/au-research\\/grants\\/arc\\/DP0878177\",\"obj_id\":\"arc_________::fe52f7d04f4139c2c80b4144c294f12d\",\"call_id\":\"\",\"funding_tree\":[null,null,\"Discovery Projects\"]}", + "data_file": "9d4dc6b920d1e2cc08a741f7c56821db.json" + } + ] +} + + diff --git a/local_dev/tools/db-insertion/README.md b/local_dev/tools/db-insertion/README.md new file mode 100644 index 000000000..1652abfd7 --- /dev/null +++ b/local_dev/tools/db-insertion/README.md @@ -0,0 +1,21 @@ +# About that folder + +This folder contains code that allows adding visualization information to the database. + +> [!TIP] +> This can be useful when, for example, due to errors on the part of other services (not ours), we are unable to create a visualization, but such visualization is necessary for testing or development. To avoid stopping work and blocking the task, visualisation can be added to the database using this code. + +## How does it all work? + +To work with this functionality, it is important to understand two main entities: `insert.py` and configuration files for each service. + +The `insert.py` file is universal code that can write visualization information to the database for any service. To do this, you only need to specify the desired service in the `insert.py` file (or, in other words, connect the necessary configuration). + +Services and their configurations are stored in folders such as `./BASE/` or `./OpenAIRE/`. These folders contain two files: `.json` and `config.json`: +- The `.json` file stores visualization data that will be used to build the visualization on the client; +- The `config.json` file stores the rest of the information that is important for creating a database record and will also be partially used on the client. + +To connect the required service, simply make a change in line 7 in the `insert.py` file - this is the line where the path to a configuration (variable `CONFIG_PATH`) is created. You need to replace the service name with the required one. + +> [!IMPORTANT] +> The name of the service must match the name of the folder where its configurations are stored. Pay attention to the case of the characters! diff --git a/local_dev/tools/db-insertion/insert.py b/local_dev/tools/db-insertion/insert.py new file mode 100644 index 000000000..e9f5f1ad4 --- /dev/null +++ b/local_dev/tools/db-insertion/insert.py @@ -0,0 +1,47 @@ +import json +import requests + +from pathlib import Path + +BASE_DIR = Path(__file__).resolve().parent +CONFIG_PATH = BASE_DIR / "OpenAIRE" / "config.json" + +VISUALIZATION_DATA = [] +ENDPOINT_URL = "http://127.0.0.1:8081/dev/persistence/createVisualization/dev" + + +def insert_from_config(config_path: Path) -> None: + """Insert visualizations described in the given config JSON file.""" + with open(config_path, "r") as f: + config = json.load(f) + + endpoint = config.get("endpoint", ENDPOINT_URL) + visualizations = config.get("visualizations", VISUALIZATION_DATA) + + for vis in visualizations: + data_file = config_path.parent / vis["data_file"] + with open(data_file, "r") as df: + data = df.read() + + payload = { + "vis_id": vis["vis_id"], + "vis_title": vis["vis_title"], + "vis_clean_query": vis["vis_clean_query"], + "vis_query": vis["vis_query"], + "vis_params": vis["vis_params"], + "data": data, + } + + res = requests.post(endpoint, json=payload) + print(f"Inserted {vis['vis_id']}: {res.status_code}") + print(res.text) + + +def main() -> None: + insert_from_config(CONFIG_PATH) + + +if __name__ == "__main__": + main() + + diff --git a/server/workers/README.md b/server/workers/README.md deleted file mode 100644 index c0c42fbca..000000000 --- a/server/workers/README.md +++ /dev/null @@ -1,164 +0,0 @@ -## This documentation is not up-to-date and following it will not result in a running server backend for Headstart. We apologize for any inconvenience this may cause and ask for patience until the public documentation has been updated. - - -## Folder structure - -Following backend component containers are currently in `workers`: - -* dataprocessing: Executing the machine learning and natural language processing -* services: a Flask-based API, providing endpoints for each integrated data source - -Each comes with a docker file (ending on `.docker`), which is used for creating a container, and a source code folder. - -## Setup - -### Install docker and docker-compose - -Please follow the install instructions for your OS: - -* Mac: https://docs.docker.com/docker-for-mac/install/ -* Ubuntu: https://docs.docker.com/docker-for-mac/install/ (also available for other Linux) - -Please follow the install instructions for docker-compose for your OS: https://docs.docker.com/compose/install/ - -### Setting up the Apache2 reverse proxy - -Following Apache2 mods have to be installed and enabled: - -* ssl -* proxy -* proxy_balancer -* proxy_http - -Possibly also following modules need to be installed and enabled: -* mod_slotmem_shm - -The following lines have to be added to the appropriate sites-available config of Apache2 webserver: - -``` - - # - # other config - - # Proxy server settings for Head Start API - - Deny from all - Allow from 127.0.0.1 - ProxyPass http://127.0.0.1:8080/ - ProxyPassReverse http://127.0.0.1/api - - - -``` - -After that, restart the Apache2 service. - -## Configuration - -Setting up configurations for each backend service: - -Dataprocessing: -* In `server/workers/dataprocessing` copy `example_dataprocessing.env` to `dataprocessing.env` and set the desired loglevel. - -Services: -* In `server/workers/services/src/config` copy `example_settings.py` to `settings.py` and change the values for `ENV` (`development` or `production`) and `DEBUG` (`TRUE` or `FALSE`). -* In `settings.py` you can also configure databases. - -Secure Redis: -* In `server/workers` copy `example_redis.conf` to `redis.conf` and replace "long_secure_password" with a long, secure password (Line 507 in redis.conf, parameter `requirepass`). - -Secure Postgres: -* In `server/workers` duplicate `example_pg_hba.conf` to `pg_hba.conf` and review the settings. The default values should be ok for a default deployment (host connections are only allowed for user "headstart" with an md5-hashed password), but you may want to change access rights. - - -Overall deployment environment variables: -PostgreSQL service: -* In `server/workers/flavorconfigs` folder create a new `flavorname.env` from the `example.env` and fill in the environment variables with the correct login data. - * This includes Postgresql and redis settings - - -* Manual database creation for Postgres: - -Enter container: `docker exec -it VARYINGNAME_db_1 psql -U headstart` - -Execute command: `CREATE DATABASE databasename;` - -Exit the container and re-enter it as normal user: `docker exec -it VARYINGNAME_persistence_1 /bin/bash` - -Execute command: `python manage.py` - -* In `preprocessing/conf/config_local.ini` change "databasename" to the dev/production database name for the specific integration. This should be in line with the database names provided in `settings.py` - - -* Running backup processes for postgres-volumes: - -https://hub.docker.com/p/loomchild/volume-backup - -### Adding a new versioned "flavor" of the backend - - -1. Make changes to code in `server/workers` (any API /integration, …) -1. Commit changes -1. Checkout commit (make note of commit hash) -1. Run `server/workers/build_docker_images.sh` -1. Create new {flavor}.env in `server/workers/flavorconfigs/` using `example.env` as template. Set the “COMPOSE_PROJECT_NAME={flavor}” and the SERVICE_VERSION={commit hash} to the values from step 3. -1. Run `docker-compose up --env-file server/workers/flavorconfigs/flavor.env -d` to start the services -1. Add new entry to `server/workers/proxy/templates/default.conf.templates` -1. Add flavored networks to `server/workers/proxy/docker-compose.yml` so that the Nginx-proxy knows where to find the specific versioned services -1. Down and up the proxy service from `server/workers/proxy` working directory -1. Test by e.g. `curl -vvvv localhost/api/{flavor}/base/service_version` - - -### Starting a specific versioned "flavor" of the backend services with docker-compose - -Following commands have to be executed from the root folder of the repository, where `docker-compose.yml` is located. - -**Start services and send them to the docker daemon** - -``` -docker-compose --env-file server/workers/flavorconfigs/flavor.env up -d -``` - - -**Shutting service down** - -``` -docker-compose --env-file server/workers/flavorconfigs/flavor.env down -``` - - -### Adding a new service to the backend - -1. Add service configuration in docker-compose.yml - 1. Add required environment variables that need to be passed from .env to container in docker-compose.yml -1. Add service related changes in build-docker-images.sh - 1. Add service to build list -1. Add service source code and Dockerfile in a new folder in `server/workers` -1. Add new env variables to .env files - - -### Integrating with clients - -In `server/preprocessing/conf/config_local.ini` change the following configs: -``` -# URL to OKMaps API -api_url = "http://127.0.0.1/api/" -# flavor of API, default: "stable" -api_flavor = "stable" -# The persistence backend to use - either api or legacy -persistence_backend = "api" -# The processing backend to use - either api or legacy -processing_backend = "api" -``` - - -## Updating R dependencies - -1. start rstudio -2. navigate to folder of worker file, e.g. /workers/base: setwd("~/projects/OpenKnowledgeMaps/Headstart/server/workers/base") -3. initiate renv with renv::activate() -4. check if dependencies.R is up to date -5. make any updates to packages as required, e.g. installing remotes::install_github('OpenKnowledgeMaps/rbace', force=TRUE) -6. update renv.lock file with renv::snapshot() -7. review lock file -8. if OK, commit lockfile diff --git a/server/workers/tests/README.md b/server/workers/tests/README.md index 73d1ef340..4f80d964c 100644 --- a/server/workers/tests/README.md +++ b/server/workers/tests/README.md @@ -69,6 +69,8 @@ listen_addresses = 'localhost,headstart_db_1,headstart-db-1' Run tests +Create a `.docker.test.env` file first, then run the following command: + ``` docker compose -f docker-compose-integration-tests.yml --env-file .docker.test.env run integration_tests ```