Prepare Release 1.1.1 (#512)

* Bump version 1.1.1

* add module for tween factories
add maintenance mode tween factory

* fix variable

* add test for maintenance mode

* add settings for maintenance mode

* Revert "add settings for maintenance mode"

This reverts commit ba2ad3f.

* Revert "add test for maintenance mode"

This reverts commit feb0f15.

* Revert "fix variable"

This reverts commit 29d03ca.

* Revert "add module for tween factories"

This reverts commit a67241a.

* Revert "Bump version 1.1.1"

This reverts commit dd790b6.

* Bump version 1.1.1 (#510)

* Update README (instructions and animation) (#508)

* Update deployment instructions

* update # CHANGEME tag to # CHANGE THIS

* Update deploy/compose_minimal/docker-compose.yml

Co-authored-by: Camill Kaipf <[email protected]>

* update compose files
TFA related settings were not added yet

---------

Co-authored-by: Camill Kaipf <[email protected]>
Co-authored-by: ckaipf <[email protected]>

* Handle MetaDatum unique but not mandatory (#509)

* remove not used argument

* don't count values which are `None` while ensuring
unique constraint
if MetaDatum is not mandatory
several MetaDatumRecord will have
value set to `None`

* add empty line

* add fixtures for test unique but not mandatory MetaDatum

* rename file

* add simplified submission test, to submit MetaDataSets
with a unique and
not mandatory MetaDatum

* mypy is not happy here with reassigning this
variable,
refactored it

* fix var name
wrote too often None in the last hour

* one MetaDataSet should be in an other Submission for global constraint

* list to generator

Co-authored-by: Leon Kuchenbecker <[email protected]>

* flatten nested if

---------

Co-authored-by: Leon Kuchenbecker <[email protected]>

---------

Co-authored-by: Leon Kuchenbecker <[email protected]>

Author: ckaipf

README.md

@@ -10,9 +10,20 @@ users!
 
 ## Quick Installation
 
+1. Create a directory for the datameta configuration (of your choice)
+   ```
+   mkdir /usr/local/lib/datameta
+   cd /usr/local/lib/datameta
+   ```
+
+1. Edit the configuration file
+
+   The fields that require changing are marked with `# CHANGE THIS`. You may want
+   to perform additional adjustments to the compose file to fit your needs.
+
 1. Download the Docker compose file
    ```
-   curl -LO https://raw.githubusercontent.com/ghga-de/datameta/main/datameta.compose.yml
+   curl -LO https://datameta.org/minimal/docker-compose.yml
    ```
 
 1. Create the Docker volumes for persistent file and database storage
@@ -23,13 +34,5 @@ users!
 
 1. Start up your DataMeta Instance
    ```
-   docker stack deploy --compose-file datameta.compose.yml datameta
+   docker-compose up -d
    ```
-
-1. Connect to your DataMeta instance at http://localhost:9950 and log in with the default
-   account `[email protected]`. The initial password can be obtained using
-   `docker logs {your_app_container_id}`.
-
-## Full Installation Instructions
-
-Detailed installation instructions can be found [here](./docs).

datameta/validation.py

@@ -21,6 +21,7 @@
 from .security import authz
 from .api.metadata import get_all_metadata
 from .utils import get_record_from_metadataset
+from typing import Dict
 
 
 def validate_submission_access(db, db_files, db_msets, auth_user):
@@ -120,11 +121,14 @@ def validate_submission_association(db_files, db_msets, ignore_submitted_metadat
     return f_names_obj, ref_fnames, errors
 
 
-def validate_submission_uniquekeys(db, db_files, db_msets):
+def validate_submission_uniquekeys(
+        db,
+        db_msets: Dict[str, MetaDataSet],
+        ):
     errors = []
 
     # Submission unique keys (includes those that are globally unique)
-    keys_submission_unique  = [ md.name for md in db.query(MetaDatum).filter(or_(MetaDatum.submission_unique.is_(True), MetaDatum.site_unique.is_(True))) ]
+    keys_submission_unique = [ md.name for md in db.query(MetaDatum).filter(or_(MetaDatum.submission_unique.is_(True), MetaDatum.site_unique.is_(True))) ]
     # Globally unique keys
     keys_site_unique        = [ md.name for md in db.query(MetaDatum).filter(MetaDatum.site_unique.is_(True)) ]
 
@@ -134,20 +138,20 @@ def validate_submission_uniquekeys(db, db_files, db_msets):
         # Associate all values for that key with the metadatasets it occurs in
         for db_mset in db_msets.values():
             for mdatrec in db_mset.metadatumrecords:
-                if mdatrec.metadatum.name == key:
+                if mdatrec.metadatum.name == key and mdatrec.value:
                     value_msets[mdatrec.value].append(db_mset)
         # Reduce to those values that occur in more than one metadatast
-        value_msets = { k: v for k, v in value_msets.items() if len(v) > 1 }
+        not_unique = ( v for v in value_msets.values() if len(v) > 1 )
         # Produce errrors
-        errors += [ (db_mset, key, "Violation of intra-submission unique constraint") for msets in value_msets.values() for db_mset in msets ]
+        errors += [ (db_mset, key, "Violation of intra-submission unique constraint") for msets in not_unique for db_mset in msets ]
 
     # Validate the set of metadatasets with regard to site-wise unique key constraints
     for key in keys_site_unique:
         value_msets = defaultdict(list)
         # Associate all values for that key with the metadatasets it occurs in
         for db_mset in db_msets.values():
             for mdatrec in db_mset.metadatumrecords:
-                if mdatrec.metadatum.name == key:
+                if mdatrec.metadatum.name == key and mdatrec.value:
                     value_msets[mdatrec.value].append(db_mset)
 
         # Query the database for the supplied values
@@ -196,7 +200,7 @@ def validate_submission(request, auth_user):
         val_errors += [ (db_msets[mset_id], mset_error['field'], mset_error['message']) for mset_error in mset_errors ]
 
     # Validate unique field constraints
-    val_errors += validate_submission_uniquekeys(db, db_files, db_msets)
+    val_errors += validate_submission_uniquekeys(db, db_msets)
 
     # If we collected any val_errors, raise 400
     if val_errors:

deploy/compose_minimal/docker-compose.yml

@@ -17,19 +17,21 @@ services:
   appserver:
     image: "datameta/datameta:dev"
     restart: "always"
+    volumes:
+      - datameta-filestorage:/var/datameta/storage
     environment:
       SQLALCHEMY_URL: postgresql://datameta:datameta@dbserver/datameta
       SESSION_URL: sessionserver:11211
       SESSION_KEY: datameta
-      SESSION_SECRET: dummy # TODO: Insert 64 character random string here
+      SESSION_SECRET: dummy # CHANGE THIS: Insert 64 character random string here
       DATAMETA_STORAGE_PATH: /var/datameta/storage
 
       # The initial values can be changed once the DataMeta instance was
       # deployed.
-      DATAMETA_INITIAL_FULLNAME: Joe user # TODO: Insert initial user fullname here
-      DATAMETA_INITIAL_EMAIL: joe@user # TODO: Insert initial user email address here
-      DATAMETA_INITIAL_PASS: j03us3r # TODO: Insert initial user password here
-      DATAMETA_INITIAL_GROUPNAME: Joe's lab # TODO: Insert intial user group name here
+      DATAMETA_INITIAL_FULLNAME: Joe User # CHANGE THIS: Insert initial user fullname here
+      DATAMETA_INITIAL_EMAIL: joe@user # CHANGE THIS: Insert initial user email address here
+      DATAMETA_INITIAL_PASS: j03us3r # CHANGE THIS: Insert initial user password here
+      DATAMETA_INITIAL_GROUPNAME: Joe's lab # CHANGE THIS: Insert intial user group name here
 
       # The maximum number of days an API key can be valid
       DATAMETA_API_KEYS_MAX_EXPIRE_DAYS: 365
@@ -45,12 +47,12 @@ services:
       # DataMeta sends out emails for password forgot tokens, registration
       # confirmations and to notify admins about new registrations. Configure
       # an SMTP server for outgoing email below.
-      DATAMETA_SMTP_HOST: # TODO: Insert SMTP server address here
+      DATAMETA_SMTP_HOST: # CHANGE THIS: Insert SMTP server address here
       DATAMETA_SMTP_PORT: 587 # Adjust if needed
-      DATAMETA_SMTP_USER: # TODO: Insert SMTP user here
-      DATAMETA_SMTP_PASS: # TODO: Insert SMTP password here
+      DATAMETA_SMTP_USER: # CHANGE THIS: Insert SMTP user here
+      DATAMETA_SMTP_PASS: # CHANGE THIS: Insert SMTP password here
       DATAMETA_SMTP_TLS: "true"
-      DATAMETA_SMTP_FROM: # TODO: Specify SMTP FROM header here, format 'Example Support <[email protected]>'
+      DATAMETA_SMTP_FROM: # CHANGE THIS: Specify SMTP FROM header here, format 'Example Support <[email protected]>'
 
       # Site ID prefixes and lengths
       # The entites 'user', 'group', 'submission', 'metadataset' and 'file' are
@@ -71,6 +73,11 @@ services:
       DATAMETA_SITE_ID_PREFIX_FILES: "DMF-"
       DATAMETA_SITE_ID_PREFIX_SERVICES: "DMP-"
 
+      # Two factor authentication settings
+      DATAMETA_TFA_ENABLED: # CHANGE THIS: Insert bool to enable
+      DATAMETA_TFA_ENCRYPT_KEY: # CHANGE THIS: Insert secret here
+      DATAMETA_TFA_OTP_ISSUER: # CHANGE THIS: Insert OTP issuer name here
+
       GUNICORN_WORKERS: 4 # Adjust to your needs. 2-4x #CPUs
       GUNICORN_PROC_NAME: datameta
       GUNICORN_FORWARDED_ALLOW_IPS: "*"
@@ -82,4 +89,6 @@ services:
 
 volumes: # TODO: Create external volumes before first launch
   datameta-db:
-    external: false
+    external: true
+  datameta-filestorage:
+    external: true

deploy/compose_multiprocess/docker-compose.yml

@@ -71,6 +71,11 @@ services:
       DATAMETA_SITE_ID_PREFIX_FILES: "DMF-"
       DATAMETA_SITE_ID_PREFIX_SERVICES: "DMP-"
 
+      # Two factor authentication settings
+      DATAMETA_TFA_ENABLED: # CHANGE THIS: Insert bool to enable
+      DATAMETA_TFA_ENCRYPT_KEY: # CHANGE THIS: Insert secret here
+      DATAMETA_TFA_OTP_ISSUER: # CHANGE THIS: Insert OTP issuer name here
+      
       GUNICORN_WORKERS: 75 # Adjust to your needs. 2-4x #CPUs
       GUNICORN_PROC_NAME: datameta
       GUNICORN_FORWARDED_ALLOW_IPS: "*"

deploy/compose_scale/docker-compose.yml

@@ -16,6 +16,11 @@ services:
       # The maximum number of days an API key can be valid
       DATAMETA_API_KEYS_MAX_EXPIRE_DAYS: 365
 
+      # Two factor authentication settings
+      DATAMETA_TFA_ENABLED: # CHANGE THIS: Insert bool to enable
+      DATAMETA_TFA_ENCRYPT_KEY: # CHANGE THIS: Insert secret here
+      DATAMETA_TFA_OTP_ISSUER: # CHANGE THIS: Insert OTP issuer name here
+
       LETSENCRYPT_HOST:   # Picked up by nginx-proxy / letsencrypt. Comma separated list of hostnames.
       VIRTUAL_HOST:       # Picked up by nginx-proxy / letsencrypt. Comma separated list of hostnames. Every hostname in LETSENCRYPT_HOST must appear also here, otherwise cert acquisition will fail
       WAITRESS_MAX_REQUEST_BODY_SIZE: 10737418240 # 10 GB

deploy/compose_testing/docker-compose.yml

@@ -68,6 +68,11 @@ services:
       DATAMETA_SITE_ID_PREFIX_FILES: "DMF-"
       DATAMETA_SITE_ID_PREFIX_SERVICES: "DMP-"
 
+      # Two factor authentication settings
+      DATAMETA_TFA_ENABLED: # CHANGE THIS: Insert bool to enable
+      DATAMETA_TFA_ENCRYPT_KEY: # CHANGE THIS: Insert secret here
+      DATAMETA_TFA_OTP_ISSUER: # CHANGE THIS: Insert OTP issuer name here
+
       GUNICORN_WORKERS: 4 # Adjust to your needs. 2-4x #CPUs
       GUNICORN_PROC_NAME: datameta
       GUNICORN_FORWARDED_ALLOW_IPS: "*"

img/datameta.demo.gif

@@ -67,7 +67,7 @@
 
 setup(
     name                   = 'datameta',
-    version                = '1.1.0',
+    version                = '1.1.1',
     description            = 'DataMeta - submission server for data and associated metadata',
     long_description       = README + '\n\n' + CHANGES,
     author                 = 'Leon Kuchenbecker',

setup.py

@@ -0,0 +1,61 @@
+# Copyright 2021 Universität Tübingen, DKFZ and EMBL for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+metadataset_unique_not_mandatory_0:
+  class: MetaDataSet
+  attributes:
+    site_id: metadataset_unique_not_mandatory_0
+    records:
+      unique_not_mandatory_id: null
+  references:
+    user:
+      fixtureset: users
+      name: user_a
+    submission:
+      fixtureset: submissions
+      name: submission_a
+  fixtureOnly:
+    - records
+
+metadataset_unique_not_mandatory_1:
+  class: MetaDataSet
+  attributes:
+    site_id: metadataset_unique_not_mandatory_1
+    records:
+      unique_not_mandatory_id: null
+  references:
+    user:
+      fixtureset: users
+      name: user_a
+    submission:
+      fixtureset: submissions
+      name: submission_a
+  fixtureOnly:
+    - records
+
+metadataset_unique_not_mandatory_2:
+  class: MetaDataSet
+  attributes:
+    site_id: metadataset_unique_not_mandatory_2
+    records:
+      unique_not_mandatory_id: null
+  references:
+    user:
+      fixtureset: users
+      name: user_a
+    submission:
+      fixtureset: submissions
+      name: submission_b
+  fixtureOnly:
+    - records

tests/integration/fixtures/metadatasets_unique_not_mandatory.yaml

@@ -0,0 +1,24 @@
+# Copyright 2021 Universität Tübingen, DKFZ and EMBL for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+unique_not_mandatory_id:
+  class: MetaDatum
+  attributes:
+    name: unique_not_mandatory_id
+    mandatory: false
+    example: "ID123"
+    order: 101
+    isfile: false
+    submission_unique: true
+    site_unique: true