Merge branch 'dev' of github.com:biocore/qiita

Author: antgonza

.github/workflows/qiita-ci.yml

@@ -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
@@ -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

.gitignore

@@ -72,3 +72,6 @@ qiita_pet/*.conf
 
 # jupyter notebooks input data
 notebooks/*/*.tsv.gz
+
+# jupyter notebooks input data
+notebooks/resource-allocation/data

CHANGELOG.md

@@ -1,5 +1,24 @@
 # Qiita changelog
 
+Version 2024.07
+---------------
+
+Deployed on July 15th, 2024
+
+* On June 14th, 2024 we modified the SPP to use ["fastp & minimap2 against GRCh38.p14 + Phi X 174 + T2T-CHM13v2.0, then Movi against GRCh38.p14, T2T-CHM13v2.0 + Human Pangenome Reference Consortium release 2023"](https://github.com/cguccione/human_host_filtration) to filter human-reads.
+* Full refactor of the [DB patching system](https://github.com/qiita-spots/qiita/blob/master/CONTRIBUTING.md#patch-91sql) to make sure that a new production deployment has a fully empty database.
+* Fully removed Qiimp from Qiita.
+* Users can now add `ORCID`, `ResearchGate` and/or `GoogleScholar` information to their profile and the creation (registration) timestamp is kept in the database. Thank you @jlab.
+* Admins can now track and purge non-confirmed users from the database via the GUI (`/admin/purge_users/`). Thank you @jlab.
+* Added `qiita.slurm_resource_allocations` to store general job resource usage, which can be populated by `qiita_db.util.update_resource_allocation_table`.
+* Added `qiita_db.util.resource_allocation_plot` to generate different models to allocate resources from a given software command based on previous jobs, thank you @Gossty !
+* The stats page map can be centered via the configuration file; additionally, the Help and Admin emails are defined also via the configuration files, thank you @jlab !
+* ``Sequel IIe``, ``Revio``, and ``Onso`` are now valid instruments for the ``PacBio_SMRT`` platform.
+* Added `current_human_filtering` to the prep-information and `human_reads_filter_method` to the artifact to keep track of the method that it was used to human reads filter the raw artifact and know if it's up to date with what is expected via the best practices.
+* Added `reprocess_job_id` to the prep-information so we keep track if a preparation has been reprocessed with another job.
+* Other general fixes, like [#3385](https://github.com/qiita-spots/qiita/pull/3385), [#3397](https://github.com/qiita-spots/qiita/pull/3397), [#3399](https://github.com/qiita-spots/qiita/pull/3399), [#3400](https://github.com/qiita-spots/qiita/pull/3400), [#3409](https://github.com/qiita-spots/qiita/pull/3409), [#3410](https://github.com/qiita-spots/qiita/pull/3410).
+
+
 Version 2024.02
 ---------------
 

CONTRIBUTING.md

@@ -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/)

INSTALL.md

@@ -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
 ```
@@ -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).

notebooks/resource-allocation/generate-allocation-summary-arrays.py

@@ -1,4 +1,4 @@
-from qiita_core.util import MaxRSS_helper
+from qiita_db.util import MaxRSS_helper
 from qiita_db.software import Software
 import datetime
 from io import StringIO

notebooks/resource-allocation/generate-allocation-summary.py

@@ -5,7 +5,7 @@
 from json import loads
 from os.path import join
 
-from qiita_core.util import MaxRSS_helper
+from qiita_db.util import MaxRSS_helper
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.processing_job import ProcessingJob
 from qiita_db.software import Software

qiita_core/configuration_manager.py

@@ -109,6 +109,12 @@ class ConfigurationManager(object):
         The portal subdirectory used in the URL
     portal_fp : str
         The filepath to the portal styling config file
+    stats_map_center_latitude : float
+        The center latitude of the world map, shown on the Stats map.
+        Defaults to 40.01027 (Boulder, CO, USA)
+    stats_map_center_longitude : float
+        The center longitude of the world map, shown on the Stats map.
+        Defaults to -105.24827 (Boulder, CO, USA)
     qiita_env : str
         The script used to start the qiita environment
     private_launcher : str
@@ -117,6 +123,10 @@ class ConfigurationManager(object):
         The script used to start the plugins
     plugin_dir : str
         The path to the directory containing the plugin configuration files
+    help_email : str
+        The email address a user should write to when asking for help
+    sysadmin_email : str
+        The email address, Qiita sends internal notifications to a sys admin
 
     Raises
     ------
@@ -234,6 +244,32 @@ def _get_main(self, config):
             self.key_file = join(install_dir, 'qiita_core', 'support_files',
                                  'ci_server.key')
 
+        self.help_email = config.get('main', 'HELP_EMAIL')
+        if not self.help_email:
+            raise ValueError(
+                "You did not specify the HELP_EMAIL address in the main "
+                "section of Qiita's config file. This address is essential "
+                "for users to ask for help as it is displayed at various "
+                "location throughout Qiita's web pages.")
+        if (self.help_email == '[email protected]') and \
+           (self.test_environment is False):
+            warnings.warn(
+                "Using the github fake email for HELP_EMAIL, "
+                "are you sure this is OK?")
+
+        self.sysadmin_email = config.get('main', 'SYSADMIN_EMAIL')
+        if not self.sysadmin_email:
+            raise ValueError(
+                "You did not specify the SYSADMIN_EMAIL address in the main "
+                "section of Qiita's config file. Serious issues will "
+                "automatically be reported to a sys admin, an according "
+                "address is therefore required!")
+        if (self.sysadmin_email == '[email protected]') and \
+           (self.test_environment is False):
+            warnings.warn(
+                "Using the github fake email for SYSADMIN_EMAIL, "
+                "are you sure this is OK?")
+
     def _get_job_scheduler(self, config):
         """Get the configuration of the job_scheduler section"""
         self.job_scheduler_owner = config.get(
@@ -317,5 +353,40 @@ def _get_portal(self, config):
         else:
             self.portal_dir = ""
 
+        msg = ("The value %s for %s you set in Qiita's configuration file "
+               "(section 'portal') for the Stats world map cannot be "
+               "intepreted as a float! %s")
+        lat_default = 40.01027  # Boulder CO, USA
+        try:
+            self.stats_map_center_latitude = config.get(
+                'portal', 'STATS_MAP_CENTER_LATITUDE', fallback=lat_default)
+            if self.stats_map_center_latitude == '':
+                self.stats_map_center_latitude = lat_default
+            self.stats_map_center_latitude = float(
+                self.stats_map_center_latitude)
+        except ValueError as e:
+            raise ValueError(msg % (self.stats_map_center_latitude,
+                                    'STATS_MAP_CENTER_LATITUDE', e))
+
+        lon_default = -105.24827  # Boulder CO, USA
+        try:
+            self.stats_map_center_longitude = config.get(
+                'portal', 'STATS_MAP_CENTER_LONGITUDE', fallback=lon_default)
+            if self.stats_map_center_longitude == '':
+                self.stats_map_center_longitude = lon_default
+            self.stats_map_center_longitude = float(
+                self.stats_map_center_longitude)
+        except ValueError as e:
+            raise ValueError(msg % (self.stats_map_center_longitude,
+                                    'STATS_MAP_CENTER_LONGITUDE', e))
+        for (name, val) in [('latitude', self.stats_map_center_latitude),
+                            ('longitude', self.stats_map_center_longitude)]:
+            msg = ("The %s of %s you set in Qiita's configuration file "
+                   "(section 'portal') for the Stats world map cannot be %s!")
+            if val < -180:
+                raise ValueError(msg % (name, val, 'smaller than -180°'))
+            if val > 180:
+                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)

qiita_core/support_files/cert.conf

@@ -0,0 +1,7 @@
+authorityKeyIdentifier=keyid,issuer
+basicConstraints=CA:FALSE
+keyUsage = digitalSignature, nonRepudiation, keyEncipherment, dataEncipherment
+subjectAltName = @alt_names
+
+[alt_names]
+DNS.1 = localhost

qiita_core/support_files/ci_rootca.crt

@@ -1,20 +1,20 @@
 -----BEGIN CERTIFICATE-----
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 -----END CERTIFICATE-----

qiita_core/support_files/ci_rootca.key

@@ -0,0 +1,28 @@
+-----BEGIN PRIVATE KEY-----
+MIIEvAIBADANBgkqhkiG9w0BAQEFAASCBKYwggSiAgEAAoIBAQDC1vjTsLU7DajT
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+4+5t5RSoyHDQeIc4OKiCdA==
+-----END PRIVATE KEY-----

qiita_core/support_files/ci_rootca.srl

@@ -1 +1 @@
-2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4B
+2FB946B7AAF21FDC0387BAA7B5ABF5D91E0D9F4C

qiita_core/support_files/ci_server.crt

@@ -1,22 +1,22 @@
 -----BEGIN CERTIFICATE-----
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 -----END CERTIFICATE-----