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Merge pull request #7 from jlab/auth_oidc_wellknown
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using the well-known json dict instead of manually providing multiple…
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sjanssen2 authored Jun 5, 2024
2 parents 33f2879 + d96bbae commit a491870
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31 changes: 28 additions & 3 deletions .github/workflows/qiita-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -154,8 +154,6 @@ jobs:
echo "5. Setting up qiita"
conda activate qiita
# adapt environment_script for private qiita plugins from travis to github actions.
sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile; conda #' -i qiita_db/support_files/patches/54.sql
qiita-env make --no-load-ontologies
qiita-test-install
qiita plugins update
Expand Down Expand Up @@ -203,7 +201,34 @@ jobs:
QIITA_PID=`cat /tmp/supervisord.pid`
kill $QIITA_PID
sleep 10
if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then test_data_studies/commands.sh; all-qiita-cron-job; fi
# due to qiita_db tests being more complex and taking longer than
# the other tests we will only add some extra tests to the run that is
# not testing qiita_db
if [[ "$COVER_PACKAGE" != *"qiita_db"* ]]; then
# 1. testing that we can add some "dummy" studies to the db via
# CLI
test_data_studies/commands.sh;
# 2. making sure that all qiita cron jobs complete as expected
all-qiita-cron-job;
# 3. making sure than a production system has the expected rows
# in all our tables; steps: a. drop test db, b. change $QIITA_CONFIG_FP
# c. create new production system, c. count rows in the db.
qiita-env drop;
cp $QIITA_CONFIG_FP ${QIITA_CONFIG_FP}.bk
sed 's/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/g' ${QIITA_CONFIG_FP}.bk > $QIITA_CONFIG_FP;
qiita-env make --no-load-ontologies;
export PGPASSWORD=postgres
pgport=${{ job.services.postgres.ports[5432] }}
row_counts=`psql -h localhost -U postgres -d qiita_test -p $pgport -c "SELECT SUM(c.reltuples) FROM pg_class c JOIN pg_namespace n on n.oid = c.relnamespace WHERE n.nspname = 'qiita' AND c.relkind = 'r' AND n.nspname NOT IN ('information_schema', 'pg_catalog');"`
if [[ `echo $row_counts` != *" 0 "* ]]; then
echo "***********";
echo "The number of rows in a production system is not what's expected:";
echo $row_counts;
echo "***********";
exit 1
fi
fi
- name: Submit coveralls
uses: AndreMiras/coveralls-python-action@develop
Expand Down
11 changes: 11 additions & 0 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,17 @@ After the initial production release of Qiita, changes to the database schema wi
2. We keep fully patched versions of the DBS and HTML files in the repository
3. We keep a patch file for each patch as required in the `qiita_db/support_files/patches` directory. Note that **the patches will be applied in order based on the natural sort order of their filename** (e.g., `2.sql` will be applied before `10.sql`, and `10.sql` will be applied before `a.sql`)

### Patch 91.sql

In May 2024 we decided to:
* Merge all patches into the main database schema, this means that there are no patches younger than 92.sql.
* Added a new folder `patches/test_db_sql/` where we can store sql files that will only be applied for the test environment.
* Added a test to the GitHub actions to test that the production database has an expected number of rows.

Note that these changes mean:
1. 92.sql is the current first sql file to patch the database.
2. If you need to make changes (like INSERTS) _only_ to the tests database you need to add a patch to `patches/test_db_sql/`.

### Developer Workflow

1. Load the fully patched DBS file (e.g., `qiita-db.dbs`) in [DBSchema](http://www.dbschema.com/)
Expand Down
5 changes: 4 additions & 1 deletion INSTALL.md
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ You can reboot the system with `sudo reboot` in case any packages were updated.
Next, we need to add the Postgres repository to our system:
```bash
sudo apt update
sudo apt install curl gpg gnupg2 software-properties-common apt-transport-https lsb-release ca-certificates
sudo apt install curl gpg gnupg2 software-properties-common apt-transport-https lsb-release ca-certificates git
curl -fsSL https://www.postgresql.org/media/keys/ACCC4CF8.asc|sudo gpg --dearmor -o /etc/apt/trusted.gpg.d/postgresql.gpg
echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" |sudo tee /etc/apt/sources.list.d/pgdg.list
```
Expand Down Expand Up @@ -238,6 +238,9 @@ If you are using [NGINX](https://www.nginx.com/) via conda, you are going to nee
mkdir -p ${CONDA_PREFIX}/var/run/nginx/
```

Note that the shipped nginx version from conda, does **not** contain the mod_zip module: https://github.com/evanmiller/mod_zip
This leads to unexpected behaviour when generating a download link for anonymous artefact sharing, i.e. Qiita returns a flat file listing artifact filepaths instead of generating a ZIP archive that contains those files. You need to compile nginx with the additional mod_zip module yourself. (I've invested multiple hours to realize that the configure routine does not properly link shared libraries to the nginx binary. Try adding `--with-ld-opt=" -Wl,-rpath,/home/foo/lib "` to the `./auto/configure` call.)

## Start Qiita

Start postgres (instructions vary depending on operating system and install method).
Expand Down
40 changes: 25 additions & 15 deletions qiita_core/configuration_manager.py
Original file line number Diff line number Diff line change
Expand Up @@ -137,16 +137,22 @@ class ConfigurationManager(object):
redirect_endpoint : str
The internal Qiita endpoint the IdP shall redirect the user after
logging in
authorize_url : str
The URL of the IdP to obtain a code (step 1)
accesstoken_url : str
The URL of the IdP to exchange the code from step 1 for an access
token (step 2)
userinfo_url : str
The URL of the IdP to obtain information about the user, like email,
username, ...
wellknown_uri : str
The URL of the well-known json document, specifying how API end points
like 'authorize', 'token' or 'userinfo' are defined. See e.g.
https://swagger.io/docs/specification/authentication/
openid-connect-discovery/
label : str
A speaking label for the Identity Provider
scope : str
The scope, i.e. fields about a user, which Qiita requests from the
Identity Provider, e.g. "profile email eduperson_orcid".
Will be automatically extended by the scope "openid", to enable the
"authorize_code" OIDC flow.
logo : str
Optional. Name of a file in qiita_pet/static/img that shall be
displayed for login through Service Provider, instead of a plain
button
Raises
------
Expand Down Expand Up @@ -410,7 +416,7 @@ def _get_portal(self, config):
raise ValueError(msg % (name, val, 'larger than 180°'))

def _iframe(self, config):
self.iframe_qiimp = config.get('iframe', 'QIIMP')
self.iframe_qiimp = config.get('iframe', 'QIIMP', fallback=None)

def _get_oidc(self, config):
"""Get the configuration of the open ID connect section(s)
Expand All @@ -436,14 +442,18 @@ def _get_oidc(self, config):
if provider['redirect_endpoint'].endswith('/'):
provider['redirect_endpoint'] = provider[
'redirect_endpoint'][:-1]
provider['authorize_url'] = config.get(
section_name, 'AUTHORIZE_URL')
provider['accesstoken_url'] = config.get(
section_name, 'ACCESS_TOKEN_URL')
provider['userinfo_url'] = config.get(
section_name, 'USERINFO_URL')
provider['wellknown_uri'] = config.get(
section_name, 'WELLKNOWN_URI')
provider['label'] = config.get(section_name, 'LABEL')
if not provider['label']:
# fallback, if no label is provided
provider['label'] = section_name[len(PREFIX):]
self.oidc[section_name[len(PREFIX):]] = provider
provider['scope'] = config.get(
section_name, 'SCOPE', fallback=None)
if not provider['scope']:
provider['scope'] = 'openid'
if 'openid' not in provider['scope']:
provider['scope'] = 'openid %s' % provider['scope']
provider['logo'] = config.get(
section_name, 'LOGO', fallback=None)
7 changes: 7 additions & 0 deletions qiita_core/support_files/cert.conf
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
authorityKeyIdentifier=keyid,issuer
basicConstraints=CA:FALSE
keyUsage = digitalSignature, nonRepudiation, keyEncipherment, dataEncipherment
subjectAltName = @alt_names

[alt_names]
DNS.1 = localhost
32 changes: 16 additions & 16 deletions qiita_core/support_files/ci_rootca.crt
Original file line number Diff line number Diff line change
@@ -1,20 +1,20 @@
-----BEGIN CERTIFICATE-----
MIIDSzCCAjOgAwIBAgIUMpJXCX29kpvz+72BzsmGaOl8+TowDQYJKoZIhvcNAQEL
MIIDSzCCAjOgAwIBAgIUNZa06QPa5si7H/HCG2E4s0opIO0wDQYJKoZIhvcNAQEL
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7Hxn0nKlwIBYD1zvoxqqL2YUHa4wp2fOp1jJ9H3zNA==
-----END CERTIFICATE-----
28 changes: 28 additions & 0 deletions qiita_core/support_files/ci_rootca.key
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
-----BEGIN PRIVATE KEY-----
MIIEvAIBADANBgkqhkiG9w0BAQEFAASCBKYwggSiAgEAAoIBAQDC1vjTsLU7DajT
nfeoib2B6tzVpg+iKDR5Wb3WyjkiO1suRJlgZFRqgIX+agWXCfQlZhjvjbbB8OG+
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4+5t5RSoyHDQeIc4OKiCdA==
-----END PRIVATE KEY-----
2 changes: 1 addition & 1 deletion qiita_core/support_files/ci_rootca.srl
Original file line number Diff line number Diff line change
@@ -1 +1 @@
2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4B
2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4C
34 changes: 17 additions & 17 deletions qiita_core/support_files/ci_server.crt
Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
-----BEGIN CERTIFICATE-----
MIIDoTCCAomgAwIBAgIUL7lGt6ryH9wDh7qntav12R4Nn0swDQYJKoZIhvcNAQEL
MIIDoTCCAomgAwIBAgIUL7lGt6ryH9wDh7qntav12R4Nn0wwDQYJKoZIhvcNAQEL
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Q/uy5CFcuPA1ZCfs0jwDpdBjcUm0
-----END CERTIFICATE-----
24 changes: 12 additions & 12 deletions qiita_core/support_files/ci_server.csr
Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,17 @@
MIIC4DCCAcgCAQAwbjELMAkGA1UEBhMCVVMxEzARBgNVBAgMCkNhbGlmb3JuaWEx
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YK+3NzntO3H+LD0kmKTW9AzafNU=
-----END CERTIFICATE REQUEST-----
52 changes: 26 additions & 26 deletions qiita_core/support_files/ci_server.key
Original file line number Diff line number Diff line change
@@ -1,28 +1,28 @@
-----BEGIN PRIVATE KEY-----
MIIEvgIBADANBgkqhkiG9w0BAQEFAASCBKgwggSkAgEAAoIBAQC8E/2iNfoklCRl
D9rDHjkEOKoIlN2CAJUyEIXV0PBgek0gANZUupeixQ6aXaU+nxAAPcyuSUH5uWk8
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LdHIPBlkgwKLVL6fqmQ3cfwQV82jIoesiEMvvHOyAvPYQkkYTZK46vl4XH52+WTr
LEluqA2De7Zc9mdvWENRT00=
-----END PRIVATE KEY-----
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