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pieterprovoost/csvreader 5

Index and query large CSV files

iobis/ebsa 2

R code to calculate biodiversity indices and other metrics in support of the CBD EBSA process

iobis/worms 2

R package for consuming the WoRMS webservice

pieterprovoost/comfort 2

Calculation of the PMV and PPD indices and local thermal comfort criteria (ISO 7730:2006)

GLOMICON/asvBiomXchange 1

A repository to develop an exchange format for molecular biodiversity data

iobis/woa2-fish 1

WOA2 fish biodiversity

pieterprovoost/datetimepicker 1

Angular directive for XDSoft's DateTimePicker jQuery plugin

iobis/benchmarking 0

Server IOPS benchmarking

iobis/eov-macroalgae 0

Repository for the second macroalgal EOV workshop

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[Backport to 3.2.x][Fixes #7895] File upload fails with 400 Bad Request (#7898) * [Fixes #7895] File upload fails with 400 Bad Request (cherry picked from commit 84a1228b72049e967eb333e8b6907b9621e7131e) * [Fixes #7895] File upload fails with 400 Bad Request

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[Fixes #7739] An empty map cannot be saved (#7806) (#7917) (cherry picked from commit 246d7b6bc47324b04f04276a1cd5cdb1bbdbe56f) # Conflicts: # geonode/thumbs/thumbnails.py (cherry picked from commit d3e38b49a7c80bb60fd57590a589f848a89abca8) Co-authored-by: NAGGINDA MARTHA <marthamareal@gmail.com>

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afabiani

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[Performance] Update GeoFence security rules only if the DB transaction is successful (cherry picked from commit 5bf6bea218cc720c8da0e4df62a19d7f266761e3)

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[Fixes #7835] The first time a map is saved thumbnail is created using the default style instead of the selected one (#7846)

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[Fixes #7958] OSM refuses to return tiles while generating thumbnails (#7978) (#7986) Co-authored-by: Giovanni Allegri <giohappy@gmail.com> Co-authored-by: mattiagiupponi <51856725+mattiagiupponi@users.noreply.github.com> Co-authored-by: Giovanni Allegri <giohappy@gmail.com>

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[Backport to 3.3.x][Fixes #7957] RuntimeError not handled in sync_geonode_layers (#7993) (#7994) Co-authored-by: Alessio Fabiani <alessio.fabiani@geo-solutions.it>

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[Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources re… (#7996) (#7997) * [Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources requiring further user inputs * [Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources requiring further user inputs * [Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources requiring further user inputs Co-authored-by: Alessio Fabiani <alessio.fabiani@geo-solutions.it>

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[Backport to 3.2.x][Fixes #7948] Error handling monitoring module (#7998) (#8001) (cherry picked from commit dea24e245b3dedc195a0b15913bbfd1268af9f58) # Conflicts: # pavement.py

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afabiani

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[3.2.x][Fixes #7999] Set bulk permissions from resources list pages (#8000) * [Fixes #7999] Set bulk permissions from resources list pages * fix tests and form errors * fix form errors * - add submit loader * create a base perm update modal

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Jose Caceres

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[Backport to 3.3.x][Fixes #6631] Remote Service does not use GetMap url as given in capabilities-document (#8040) (#8050) * [Backport to 3.3.x][Fixes #6631] Remote Service does not use GetMap url as given in capabilities-document * [Backport to 3.3.x][Fixes #6631] Remote Service does not use GetMap url as given in capabilities-document * [CircleCI] Fix test cases * [CircleCI] Fix test cases * [CircleCI] Fix test cases * [CircleCI] Fix test cases * [CircleCI] Fix test cases Co-authored-by: Alessio Fabiani <alessio.fabiani@geo-solutions.it>

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Alessio Fabiani

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[Backport to 3.2.x][Fixes #7895] File upload fails with 400 Bad Request (#7898) * [Fixes #7895] File upload fails with 400 Bad Request (cherry picked from commit 84a1228b72049e967eb333e8b6907b9621e7131e) * [Fixes #7895] File upload fails with 400 Bad Request

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[Fixes #7739] An empty map cannot be saved (#7806) (#7917) (cherry picked from commit 246d7b6bc47324b04f04276a1cd5cdb1bbdbe56f) # Conflicts: # geonode/thumbs/thumbnails.py (cherry picked from commit d3e38b49a7c80bb60fd57590a589f848a89abca8) Co-authored-by: NAGGINDA MARTHA <marthamareal@gmail.com>

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afabiani

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[Fixes #7835] The first time a map is saved thumbnail is created using the default style instead of the selected one (#7846)

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[Performance] Update GeoFence security rules only if the DB transaction is successful (cherry picked from commit 5bf6bea218cc720c8da0e4df62a19d7f266761e3)

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commit sha 28452fdcefe6ce784907accbb4b5b586734fbde9

[Fixes #7958] OSM refuses to return tiles while generating thumbnails (#7978) (#7986) Co-authored-by: Giovanni Allegri <giohappy@gmail.com> Co-authored-by: mattiagiupponi <51856725+mattiagiupponi@users.noreply.github.com> Co-authored-by: Giovanni Allegri <giohappy@gmail.com>

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[Backport to 3.3.x][Fixes #7957] RuntimeError not handled in sync_geonode_layers (#7993) (#7994) Co-authored-by: Alessio Fabiani <alessio.fabiani@geo-solutions.it>

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commit sha 311e7a88ab0bee8580e9ff4fc488931398cfe182

[Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources re… (#7996) (#7997) * [Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources requiring further user inputs * [Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources requiring further user inputs * [Backport to 3.3.x][Fixes #7989] Misbehavior with upload resources requiring further user inputs Co-authored-by: Alessio Fabiani <alessio.fabiani@geo-solutions.it>

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[Backport to 3.2.x][Fixes #7948] Error handling monitoring module (#7998) (#8001) (cherry picked from commit dea24e245b3dedc195a0b15913bbfd1268af9f58) # Conflicts: # pavement.py

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afabiani

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[Fixes #7948] Error handling monitoring module (#7995) (cherry picked from commit fa9a924b5a405726b33b75771ef4e7941a7dff95)

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[3.2.x][Fixes #7999] Set bulk permissions from resources list pages (#8000) * [Fixes #7999] Set bulk permissions from resources list pages * fix tests and form errors * fix form errors * - add submit loader * create a base perm update modal

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Jose Caceres

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[Fixes #8003] Update Spanish Translation (#8029) Update django.po and djangojs.po to include complete Spanish translation.

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[Backport to 3.3.x][Fixes #6631] Remote Service does not use GetMap url as given in capabilities-document (#8040) (#8050) * [Backport to 3.3.x][Fixes #6631] Remote Service does not use GetMap url as given in capabilities-document * [Backport to 3.3.x][Fixes #6631] Remote Service does not use GetMap url as given in capabilities-document * [CircleCI] Fix test cases * [CircleCI] Fix test cases * [CircleCI] Fix test cases * [CircleCI] Fix test cases * [CircleCI] Fix test cases Co-authored-by: Alessio Fabiani <alessio.fabiani@geo-solutions.it>

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Pieter Provoost

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save eovs

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meliezer

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Updated URL

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Pieter Provoost

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Merge pull request #5 from meliezer/patch-2 Updated URL

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issue commentgbif/ipt

Unable to run setup on HTTPS + proxy'd sub-path

I tested with Tomcat 8.5 on Java 8 before, but I did a quick check with a (Dockerized) Tomcat 7.0.76 on OpenJDK 8 and that worked fine as well. If you do not need your Tomcat for other purposes you may want to look into the IPT Docker image, it works like a charm.

vollmerk

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issue commentnvs-vocabs/OBISVocabs

eMoF for 'Reproductive condition of biological entity specified elsewhere'

@meliezer We currently do not populate/modify any occurrence values from eMoF, and usually recommend populating the occurrence fields in addition to creating eMoF records (although that's not reflected in the manual). If you would like to have this option discussed in the SG or QC task team please create an issue in https://github.com/iobis/obis-issues

meliezer

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issue commentropensci/spocc

error with the limitation extractign data from OBIS

@hannahlowens The size parameter is limited to 10000, subsequent pages need to be fetched using the after parameter. See https://github.com/iobis/robis/blob/master/R/occurrence.R#L121

haniehsaeedi

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issue commentgbif/ipt

Unable to run setup on HTTPS + proxy'd sub-path

@vollmerk I tried with the latest version (2.5.1) using Docker, as well as in a Tomcat subfolder like you did. For the latter case I had to change my config to proxy_pass http://localhost:8080/ipt/;.

This is what the POST request looks like, so the setup2.do request redirects to setup3.do taking into account the public URL.

Screen Shot 2021-09-16 at 15 34 19

vollmerk

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issue commentiobis/manual

Missing information: Which DwC terms would 'arrive' to the OBIS format?

@meliezer That information can be found on the data access page: https://obis.org/manual/access/. In summary we keep all fields but some are quality controlled and may be modified.

meliezer

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meliezer

commit sha 9106bdc16dc226f146f9dd251563e0e5e6ab630f

Adding Sex to measurementValueID section

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Pieter Provoost

commit sha 1109fb444c8abf18eb0b2ecb57fa8f9ac55ed24d

Merge pull request #4 from meliezer/patch-1 Adding Sex to measurementValueID section

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Adding Sex to measurementValueID section
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issue commentiobis/obis-issues

Update extended measurement or fact extension to follow existing dwciri namespace

Does anyone know if this would work with IPT? As far as I know there's no indication of namespace in the mapping panel?

albenson-usgs

comment created time in 6 days

issue commentgbif/ipt

Unable to run setup on HTTPS + proxy'd sub-path

The config below works for me, as long as I complete the setup on http://example.com:8080. You may need to change proxy_pass if you are not using Docker or deploying in the Tomcat root.

server {
    server_name ipttest.obis.org;

    location /ipt {
        proxy_set_header X-Real-IP  $remote_addr;
        proxy_set_header X-Forwarded-For $remote_addr;
        proxy_set_header Host $host;
        proxy_pass http://localhost:8080/;
    }

    listen [::]:443 ssl ipv6only=on; # managed by Certbot
    listen 443 ssl; # managed by Certbot
    ssl_certificate /etc/letsencrypt/live/ipttest.obis.org/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/ipttest.obis.org/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
}

server {
    if ($host = ipttest.obis.org) {
        return 301 https://$host$request_uri;
    } # managed by Certbot
    listen 80 default_server;
    listen [::]:80 default_server;
    server_name ipttest.obis.org;
    return 404; # managed by Certbot
}
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root

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heading fix

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Helen Lillis

commit sha 7e406d46126cbfc2c351226826d452ea6dd4a99c

Update dataformat.md

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Helen Lillis

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Update dataformat.md

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Helen Lillis

commit sha 8d2918f3e02eb070f3b1936b90cc601afd520334

Update dataformat.md

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Helen Lillis

commit sha 80ec564d631e47b824821b35c24eab6d998af628

Update dataformat.md as discussed, the new 'A special case: habitat types' section has been updated to draw more attention to the fact that it is Europe-specific and not a globally agreed standard.

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Pieter Provoost

commit sha 456036de398a5014a231cac32f993d2e155ba155

Merge pull request #2 from helen-lillis/master new section added: A special case: habitat types

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new section added: A special case: habitat types
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PR opened cloudyr/aws.s3

Fix DigitalOcean get_bucket pagination

This PR fixes get_bucket() pagination for DigitalOcean Spaces, see https://github.com/cloudyr/aws.s3/issues/393. This solution has not been tested with AWS.

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Pieter Provoost

commit sha 47c2ef72d7ecd2a21dd4d782117aaf4414cf7a1e

updated description and news

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issue openedcloudyr/aws.s3

get_bucket() pagination not working with DigitalOcean Spaces

get_bucket() does not work with DigitalOcean Spaces when there are more than 1000 objects (around 4000 in my case). Setting max at a value over 1000 results in duplicate objects, and setting max at Inf results in an infinite loop.

library("aws.s3")

## code goes here
objects <- get_bucket(
  bucket = "my-bucket",
  prefix = "pipeline",
  max = 10000
)

## session info for your system
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] aws.s3_0.3.22

loaded via a namespace (and not attached):
[1] httr_1.4.2          compiler_4.0.2      R6_2.5.0            tools_4.0.2         base64enc_0.1-3     curl_4.3            aws.signature_0.6.0 xml2_1.3.2          digest_0.6.27

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