From fb4849688de375b26df832cc4f3f148635b8875d Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Sun, 8 Nov 2020 19:54:37 +0100 Subject: [PATCH 01/26] minor bugfix layout --- frontend/src/components/Home.vue | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/frontend/src/components/Home.vue b/frontend/src/components/Home.vue index b6259c74..697f9a3b 100644 --- a/frontend/src/components/Home.vue +++ b/frontend/src/components/Home.vue @@ -15,8 +15,10 @@ pharmacokinetics data enriched with the required meta-information for computational modeling and data integration.

- - + - - + PK-DB: pharmacokinetics database for individualized and stratified computational modeling
- Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Barthorscht F, Köller A, Ke DYJ, De Angelis S, König M.
+ Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Barthorscht F, Köller A, Ke DYJ, De Angelis S, König M.
Nucleic Acids Res. 2020 Nov 5:gkaa990. doi: 10.1093/nar/gkaa990. Epub ahead of print. PMID: 33151297 - - + +

Data

From c9e87b2cc2e0ba0de5b6b2c016b3571e09dca15d Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Sun, 8 Nov 2020 23:41:44 +0100 Subject: [PATCH 02/26] updated server configuration for webroot authentification --- nginx/alpha.pk-db.com_proxy | 28 +++++++++++++++++++----- nginx/develop.pk-db.com_proxy | 40 ----------------------------------- nginx/pk-db.com | 11 +++++++++- 3 files changed, 33 insertions(+), 46 deletions(-) delete mode 100644 nginx/develop.pk-db.com_proxy diff --git a/nginx/alpha.pk-db.com_proxy b/nginx/alpha.pk-db.com_proxy index da3dbb66..649761f1 100644 --- a/nginx/alpha.pk-db.com_proxy +++ b/nginx/alpha.pk-db.com_proxy @@ -1,8 +1,6 @@ # ------------------ # alpha.pk-db.com # ------------------ -# sudo ln -s /etc/nginx/sites-available/alpha.pk-db.com /etc/nginx/sites-enabled/ -# ------------------ access_log /var/www/logs/alpha.pk-db.com_access.log; error_log /var/www/logs/alpha.pk-db.com_error.log; @@ -10,7 +8,27 @@ server { listen 80; listen [::]:80; - server_name alpha.pk-db.com; + server_name alpha.pk-db.com develop.pk-db.com; + + # letsencrypt webroot authenticator + location /.well-known/acme-challenge/ { + root /usr/share/nginx/letsencrypt; + } + + # https redirects + location = / { + return 301 https://alpha.pk-db.com$request_uri; + } +} + +server { + listen 443 ssl http2; + listen [::]:443 ssl http2; + + server_name develop.pk-db.com; + ssl_certificate /etc/letsencrypt/live/alpha.pk-db.com/fullchain.pem; + ssl_certificate_key /etc/letsencrypt/live/alpha.pk-db.com/privkey.pem; + return 301 https://alpha.pk-db.com$request_uri; } @@ -20,8 +38,8 @@ server { server_name alpha.pk-db.com; - ssl_certificate /etc/letsencrypt/live/pk-db.com/fullchain.pem; - ssl_certificate_key /etc/letsencrypt/live/pk-db.com/privkey.pem; + ssl_certificate /etc/letsencrypt/live/alpha.pk-db.com/fullchain.pem; + ssl_certificate_key /etc/letsencrypt/live/alpha.pk-db.com/privkey.pem; include /etc/nginx/snippets/ssl.conf; client_max_body_size 100m; diff --git a/nginx/develop.pk-db.com_proxy b/nginx/develop.pk-db.com_proxy deleted file mode 100644 index 14b2628c..00000000 --- a/nginx/develop.pk-db.com_proxy +++ /dev/null @@ -1,40 +0,0 @@ -# ------------------ -# develop.pk-db.com -# ------------------ -access_log /var/www/logs/develop.pk-db.com_access.log; -error_log /var/www/logs/develop.pk-db.com_error.log; - -server { - listen 80; - listen [::]:80; - - server_name develop.pk-db.com; - return 301 https://develop.pk-db.com$request_uri; -} - -server { - listen 443 ssl http2; - listen [::]:443 ssl http2; - - server_name develop.pk-db.com; - - ssl_certificate /etc/letsencrypt/live/pk-db.com/fullchain.pem; - ssl_certificate_key /etc/letsencrypt/live/pk-db.com/privkey.pem; - include /etc/nginx/snippets/ssl.conf; - - client_max_body_size 100m; - proxy_connect_timeout 600; - proxy_send_timeout 600; - proxy_read_timeout 600; - send_timeout 600; - - location / { - # return 200 "ssl on proxy"; - proxy_pass http://172.107.0.1:8888; - proxy_set_header HOST $host; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-for $remote_addr; - proxy_set_header X-Forwarded-Proto https; - port_in_redirect off; - } -} \ No newline at end of file diff --git a/nginx/pk-db.com b/nginx/pk-db.com index 01efea5b..3c759087 100644 --- a/nginx/pk-db.com +++ b/nginx/pk-db.com @@ -9,7 +9,16 @@ server { listen [::]:80; server_name pk-db.com pk-db.de www.pk-db.com www.pk-db.de; - return 301 https://pk-db.com$request_uri; + + # letsencrypt webroot authenticator + location /.well-known/acme-challenge/ { + root /usr/share/nginx/letsencrypt; + } + + # https redirects + location = / { + return 301 https://pk-db.com$request_uri; + } } server { From b7480667a86459a4580b28e4ac6883bcca802ab7 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Tue, 10 Nov 2020 11:21:00 +0100 Subject: [PATCH 03/26] closes #683 --- backend/pkdb_app/studies/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/pkdb_app/studies/views.py b/backend/pkdb_app/studies/views.py index b0bf088f..5b3fe3a0 100644 --- a/backend/pkdb_app/studies/views.py +++ b/backend/pkdb_app/studies/views.py @@ -593,7 +593,7 @@ def _pks(self, view_class: DocumentViewSet, query_dict: Dict, pk_field: str = "p def data_by_query_dict(self, query_dict, viewset, serializer, boost): view = viewset(request=self.request) - queryset = view.filter_queryset(view.get_queryset()) + queryset = view.get_queryset() if boost: queryset = queryset.filter("terms", **query_dict).source(serializer.Meta.fields) return [hit.to_dict() for hit in queryset.params(size=5000).scan()] From 77eec3590d09c6a83a36c8953b5bf6d56e9d7ea9 Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Tue, 10 Nov 2020 12:47:45 +0100 Subject: [PATCH 04/26] updated info closes issues --- release-notes/0.9.5.md | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 release-notes/0.9.5.md diff --git a/release-notes/0.9.5.md b/release-notes/0.9.5.md new file mode 100644 index 00000000..e66cbe2f --- /dev/null +++ b/release-notes/0.9.5.md @@ -0,0 +1,8 @@ +# Release notes for pkdb 0.9.5 + +## New features + +## Fixes +- interventions were missing in download (#683) + + From 0f1d4eef90cc3b16f229957cf2793a34113b2d35 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Thu, 12 Nov 2020 15:16:12 +0100 Subject: [PATCH 05/26] minor --- backend/pkdb_app/interventions/serializers.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/backend/pkdb_app/interventions/serializers.py b/backend/pkdb_app/interventions/serializers.py index ecd889df..d861fe84 100644 --- a/backend/pkdb_app/interventions/serializers.py +++ b/backend/pkdb_app/interventions/serializers.py @@ -2,6 +2,7 @@ Serializers for interventions. """ import itertools +from abc import ABC from rest_framework import serializers @@ -320,7 +321,7 @@ class InterventionElasticSerializerAnalysis(serializers.Serializer): measurement_type_label = serializers.SerializerMethodField() choice = serializers.SerializerMethodField() - choice_label =serializers.SerializerMethodField() + choice_label = serializers.SerializerMethodField() substance = serializers.SerializerMethodField() substance_label = serializers.SerializerMethodField() From c7e988f4804a86493a3f3321e674380e01650c0d Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Thu, 26 Nov 2020 17:10:55 +0100 Subject: [PATCH 06/26] bugfix in characteristica counts --- .../components/detail/CharacteristicaCard.vue | 21 +++++++------------ .../detail/CharacteristicaCardDeck.vue | 15 +++++++------ .../src/components/tables/GroupsTable.vue | 2 +- nginx/pk-db.com | 2 +- 4 files changed, 19 insertions(+), 21 deletions(-) diff --git a/frontend/src/components/detail/CharacteristicaCard.vue b/frontend/src/components/detail/CharacteristicaCard.vue index 1ab351c8..efb3e97f 100644 --- a/frontend/src/components/detail/CharacteristicaCard.vue +++ b/frontend/src/components/detail/CharacteristicaCard.vue @@ -94,15 +94,17 @@ }, subject_count(){ if (this.data.group_count){ - return this.data.group_count.toString() + return this.data.group_count } - return this.count.toString() + return this.count }, count_label(){ - if (this.count == this.subject_count){ - return this.count.toString() + if (this.subject_count == this.count) { + return this.subject_count.toString() + } else if (this.subject_count < this.count){ + return ">" + this.subject_count.toString() } else { - return this.count.toString() + "/" + this.subject_count + return this.count.toString() + "/" + this.subject_count.toString() } }, error() { @@ -153,15 +155,8 @@ } return value; }, - card_class() { - if (this.value){ - return "characteristica_card" - } - else { - return "characteristica_card" - } - + return "characteristica_card" } }, methods: { diff --git a/frontend/src/components/detail/CharacteristicaCardDeck.vue b/frontend/src/components/detail/CharacteristicaCardDeck.vue index 4ddf2347..40ac987b 100644 --- a/frontend/src/components/detail/CharacteristicaCardDeck.vue +++ b/frontend/src/components/detail/CharacteristicaCardDeck.vue @@ -14,10 +14,8 @@ - - @@ -38,6 +36,10 @@ type: Array, required: true }, + group_count: { + type: Number, + required: true + }, layout: { type: Boolean, default: true @@ -71,10 +73,11 @@ sortedCharacteristica: function () { // split characteristica in choices and values and sort them - var choices = [] - var values = [] - for (var index in this.characteristica){ - var c = this.characteristica[index] + let choices = [] + let values = [] + for (let index in this.characteristica){ + let c = this.characteristica[index] + c.group_count = this.group_count; if (c.choice){ choices.push(c); } else { diff --git a/frontend/src/components/tables/GroupsTable.vue b/frontend/src/components/tables/GroupsTable.vue index 24560421..0041c077 100644 --- a/frontend/src/components/tables/GroupsTable.vue +++ b/frontend/src/components/tables/GroupsTable.vue @@ -41,7 +41,7 @@ --> diff --git a/nginx/pk-db.com b/nginx/pk-db.com index 3c759087..0df56de9 100644 --- a/nginx/pk-db.com +++ b/nginx/pk-db.com @@ -18,7 +18,7 @@ server { # https redirects location = / { return 301 https://pk-db.com$request_uri; - } + } } server { From 4a5012f27ea3cb881991751120897c6342410702 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Thu, 26 Nov 2020 17:40:22 +0100 Subject: [PATCH 07/26] working on info_node in pkdata --- backend/pkdb_app/studies/views.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/backend/pkdb_app/studies/views.py b/backend/pkdb_app/studies/views.py index 5b3fe3a0..8e4b0d05 100644 --- a/backend/pkdb_app/studies/views.py +++ b/backend/pkdb_app/studies/views.py @@ -30,6 +30,8 @@ from pkdb_app.data.serializers import TimecourseSerializer from pkdb_app.data.views import SubSetViewSet from pkdb_app.documents import UUID_PARAM +from pkdb_app.info_nodes.serializers import InfoNodeElasticSerializer +from pkdb_app.info_nodes.views import InfoNodeElasticViewSet from pkdb_app.interventions.serializers import InterventionElasticSerializerAnalysis from pkdb_app.outputs.serializers import OutputInterventionSerializer from pkdb_app.subjects.serializers import GroupCharacteristicaSerializer, IndividualCharacteristicaSerializer @@ -594,13 +596,13 @@ def _pks(self, view_class: DocumentViewSet, query_dict: Dict, pk_field: str = "p def data_by_query_dict(self, query_dict, viewset, serializer, boost): view = viewset(request=self.request) queryset = view.get_queryset() + if query_dict is not None: + queryset = queryset.filter("terms", **query_dict) if boost: - queryset = queryset.filter("terms", **query_dict).source(serializer.Meta.fields) + queryset = queryset.source(serializer.Meta.fields) return [hit.to_dict() for hit in queryset.params(size=5000).scan()] else: - queryset = queryset.filter("terms", **query_dict) - return serializer(queryset.params(size=5000).scan(), many=True).data @@ -761,7 +763,12 @@ def serialize_scatters(ids): "timecourses": Sheet("Timecourses", {"pk": pkdata.ids["timecourses"]}, SubSetViewSet, TimecourseSerializer, None, False), "scatters": Sheet("Scatter", {"subset_pk": pkdata.ids["scatters"]}, None, None, serialize_scatters, - None), + False), + "info_nodes": Sheet("InfoNodes", None, + InfoNodeElasticViewSet, + InfoNodeElasticSerializer, + None, + True), } # Create archive From c60e4a17a6ff715a8238607c21501b1e1b23c4ec Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Thu, 26 Nov 2020 17:58:43 +0100 Subject: [PATCH 08/26] info nodes in download --- backend/pkdb_app/info_nodes/serializers.py | 11 ++++++++++- backend/pkdb_app/studies/views.py | 6 +++--- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/backend/pkdb_app/info_nodes/serializers.py b/backend/pkdb_app/info_nodes/serializers.py index 3c288e84..5d6cf529 100644 --- a/backend/pkdb_app/info_nodes/serializers.py +++ b/backend/pkdb_app/info_nodes/serializers.py @@ -247,4 +247,13 @@ class Meta: fields = ["sid", "name", "label", "deprecated", "ntype", "dtype", "description", "synonyms", "parents", "annotations", "xrefs","measurement_type", "substance", ] def get_synonyms(self, obj): - return [synonym["name"] for synonym in obj.synonyms] \ No newline at end of file + return [synonym["name"] for synonym in obj.synonyms] + + +class IndoNodeFlatSerializer(serializers.Serializer): + sid = serializers.CharField() + label = serializers.CharField() + ntype = serializers.CharField() + + class Meta: + fields =["sid", "name", "label", "ntype", "dtype"] diff --git a/backend/pkdb_app/studies/views.py b/backend/pkdb_app/studies/views.py index 8e4b0d05..38aa8ec9 100644 --- a/backend/pkdb_app/studies/views.py +++ b/backend/pkdb_app/studies/views.py @@ -30,7 +30,7 @@ from pkdb_app.data.serializers import TimecourseSerializer from pkdb_app.data.views import SubSetViewSet from pkdb_app.documents import UUID_PARAM -from pkdb_app.info_nodes.serializers import InfoNodeElasticSerializer +from pkdb_app.info_nodes.serializers import InfoNodeElasticSerializer, IndoNodeFlatSerializer from pkdb_app.info_nodes.views import InfoNodeElasticViewSet from pkdb_app.interventions.serializers import InterventionElasticSerializerAnalysis from pkdb_app.outputs.serializers import OutputInterventionSerializer @@ -766,9 +766,9 @@ def serialize_scatters(ids): False), "info_nodes": Sheet("InfoNodes", None, InfoNodeElasticViewSet, - InfoNodeElasticSerializer, + IndoNodeFlatSerializer, None, - True), + False), } # Create archive From 9973c3db5e87dd2565b52bb7bdfaaf48904c46d1 Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Tue, 1 Dec 2020 20:06:21 +0100 Subject: [PATCH 09/26] Suekrue added to avatars and information --- .../assets/images/avatars/balcisue_128.png | Bin 0 -> 49918 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z)2ph;(uaR1vfTv-`-l6tkEE7#D%}<*3dQKY4eYDN@TF*Jjtl6jM6`d`?^6Qid_SI! zDrGL=5xhOIC<@4U3;4mXpr9zTeU?~Z%@yj`%;3IL#{qF69dHVbdl++!Byr)3rvW<| zs46R0;h-%w2aXzQjxS3w&ZeXs4xi%L)sk8ZbWX1;Rz>9)9;PR5DI7YmWXS>Oc^ zZqI#IyAM@NH|?Sh<&OkNm-qIK9 z$b%UPf1#V_Xv%D2OR+IqW@hZUuuW&gv4^YkWO_^a_bmFl2hn3HMg{-EnRWRTs2Cj| z9QLar>G=|J#6{I|dlN=W0_^#W+?gdPbK2D0NFF}NopdSuuZmpM_3Xu-PE*woWAJ_; zmg;kJ?-uNCxiWItB7!kTTjNVhBE^%m5?1Dut&NzVZZ4Ov&&(cwExg?rC=62IGH PK-DB: pharmacokinetics database for individualized and stratified computational modeling
- Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Barthorscht F, Köller A, Ke DYJ, De Angelis S, König M.
+ Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Bartsch F, Köller A, Ke DYJ, De Angelis S, König M.
Nucleic Acids Res. 2020 Nov 5:gkaa990. doi: 10.1093/nar/gkaa990. Epub ahead of print. PMID: 33151297 diff --git a/frontend/src/components/detail/CharacteristicaCard.vue b/frontend/src/components/detail/CharacteristicaCard.vue index efb3e97f..33fc3df0 100644 --- a/frontend/src/components/detail/CharacteristicaCard.vue +++ b/frontend/src/components/detail/CharacteristicaCard.vue @@ -89,7 +89,7 @@ if (!this.data.count){ return 1; // individual has no count ? FIXME bug } else { - return this.data.count + return this.data.countO } }, subject_count(){ diff --git a/frontend/src/components/home/About.vue b/frontend/src/components/home/About.vue index 676b4a8b..1726d727 100644 --- a/frontend/src/components/home/About.vue +++ b/frontend/src/components/home/About.vue @@ -17,6 +17,7 @@ +

If you have questions or feedback please contact @@ -34,10 +35,11 @@

How to cite

- PK-DB: pharmacokinetics database for individualized and stratified computational modeling
- Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Barthorscht F, Köller A, Ke DYJ, De Angelis S, König M.
- bioRxiv 760884; doi: https://doi.org/10.1101/760884 + + PK-DB: pharmacokinetics database for individualized and stratified computational modeling
+ Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Bartsch F, Köller A, Ke DYJ, De Angelis S, König M.
Nucleic Acids Res. 2020 Nov 5:gkaa990. doi: 10.1093/nar/gkaa990. Epub ahead of print. PMID: 33151297 +

Licensing

diff --git a/frontend/src/components/lib/UserAvatar.vue b/frontend/src/components/lib/UserAvatar.vue index 9dc63d2b..304bc025 100644 --- a/frontend/src/components/lib/UserAvatar.vue +++ b/frontend/src/components/lib/UserAvatar.vue @@ -62,6 +62,8 @@ image = 'danny_128.png'; } else if (this.initials === 'SD'){ image = 'sara_128.png'; + } else if (this.initials === 'SB'){ + image = 'balcisue_128.png'; } } else if (this.username) { image = 'user_128.png'; @@ -87,6 +89,8 @@ image = 'danny_128.png'; } else if (this.username === 'SaraD-hub'){ image = 'sara_128.png'; + } else if (this.username === 'balcisue'){ + image = 'balcisue_128.png'; } } return img_dir + image From 88fbf55157f0ac502bc625513c08d00036b521ca Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Tue, 1 Dec 2020 20:39:58 +0100 Subject: [PATCH 10/26] bugfix regression --- frontend/src/components/detail/CharacteristicaCard.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/src/components/detail/CharacteristicaCard.vue b/frontend/src/components/detail/CharacteristicaCard.vue index 33fc3df0..c4ec1d9b 100644 --- a/frontend/src/components/detail/CharacteristicaCard.vue +++ b/frontend/src/components/detail/CharacteristicaCard.vue @@ -89,7 +89,7 @@ if (!this.data.count){ return 1; // individual has no count ? FIXME bug } else { - return this.data.countO + return this.data.count; } }, subject_count(){ From 878940bac70e1f70deeaf8077e9e4659dc3737ea Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Tue, 1 Dec 2020 22:47:51 +0100 Subject: [PATCH 11/26] bugfix user search --- frontend/src/components/search/UserSearch.vue | 1 + 1 file changed, 1 insertion(+) diff --git a/frontend/src/components/search/UserSearch.vue b/frontend/src/components/search/UserSearch.vue index 82ed8cfe..26726b13 100644 --- a/frontend/src/components/search/UserSearch.vue +++ b/frontend/src/components/search/UserSearch.vue @@ -61,6 +61,7 @@ export default { {"username": "adriankl", "first_name": "Adrian", "last_name": "Koeller",}, {"username": "dannythekey", "first_name": "Danny", "last_name": "Ke",}, {"username": "SaraD-hub", "first_name": "Sara", "last_name": "De Angelis",}, + {"username": "balcisue", "first_name": "Sükrü", "last_name": "Balci",}, ], } }, From ff52774b4bec2826fa7dd5ddbd1190c498703d18 Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Wed, 2 Dec 2020 01:17:40 +0100 Subject: [PATCH 12/26] Fix #689, bump django version --- backend/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/requirements.txt b/backend/requirements.txt index 71c0caaa..0fe2054a 100644 --- a/backend/requirements.txt +++ b/backend/requirements.txt @@ -5,7 +5,7 @@ json-logging>=1.2.6 psycopg2-binary>=2.8.5 # django -Django == 3.1.3 +Django == 3.1.4 django-model-utils>=4.0.0 django-extra-fields>=3.0.0 django-storages>=1.9.1 From 5593f59dc0ff7db6dc2176fc14a970637f16219c Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Fri, 4 Dec 2020 15:54:04 +0100 Subject: [PATCH 13/26] closes 691, closes #192 --- backend/pkdb_app/data/serializers.py | 7 ++++++- backend/pkdb_app/error_measures.py | 28 ++++++++++++------------- backend/pkdb_app/outputs/serializers.py | 2 +- 3 files changed, 21 insertions(+), 16 deletions(-) diff --git a/backend/pkdb_app/data/serializers.py b/backend/pkdb_app/data/serializers.py index 345ad3a7..f95a8745 100644 --- a/backend/pkdb_app/data/serializers.py +++ b/backend/pkdb_app/data/serializers.py @@ -70,9 +70,14 @@ def create(self, validated_data): # subset_instance.save() return subset_instance + def validate_shared(self, shared): + if isinstance(shared,str): + raise serializers.ValidationError({"shared": "Shared field has to be a list not a string.", "detail": shared}) + + def _validate_time(self, time): if any(np.isnan(np.array(time))): - raise serializers.ValidationError({"time": "no time points are allowed to be nan", "detail": time}) + raise serializers.ValidationError({"time": "No time points are allowed to be nan", "detail": time}) def calculate_pks_from_timecourses(self, subset): # calculate pharmacokinetics outputs diff --git a/backend/pkdb_app/error_measures.py b/backend/pkdb_app/error_measures.py index b24cbbe9..77b73bf9 100644 --- a/backend/pkdb_app/error_measures.py +++ b/backend/pkdb_app/error_measures.py @@ -6,16 +6,16 @@ cv is coefficient of variation. sd/mean """ import numpy as np -import warnings - +def _is(value): + return value is not None and value is not np.nan def calculate_sd(se, count, cv, mean): """Calculates standard deviation from other error measurements.""" sd = None - is_se = sd is not None - is_count = count is not None - is_mean = mean is not None - is_cv = cv is not None + is_se = _is(se) + is_count = _is(count) + is_mean = _is(mean) + is_cv = _is(cv) if is_se and is_count: sd = np.multiply(se, np.sqrt(count)) @@ -28,10 +28,10 @@ def calculate_se(sd, count, cv, mean): """Calculates SE from given fields.""" se = None - is_sd = sd is not None - is_count = count is not None - is_mean = mean is not None - is_cv = cv is not None + is_sd = _is(sd) + is_count = _is(count) + is_mean = _is(mean) + is_cv = _is(cv) if is_sd and is_count: se = np.true_divide(sd, np.sqrt(count)) @@ -44,10 +44,10 @@ def calculate_cv(sd, count, se, mean): """Calculates CV from given fields""" cv = None - is_sd = sd is not None - is_count = count is not None - is_mean = mean is not None - is_se = se is not None + is_sd = _is(sd) + is_count = _is(count) + is_mean = _is(mean) + is_se = _is(se) # mean can be zero, CV not calculatable, resulting in -inf/inf # mean data must be cleaned before calculation diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index f1c0dbdc..7f4f8128 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -94,7 +94,7 @@ def to_internal_value(self, data): data = self.retransform_map_fields(data) data = self.to_internal_related_fields(data) - self.validate_wrong_keys(data, additional_fields=OutputExSerializer.Meta.fields) + self.validate_wrong_keys(data, additional_fields=OutputSerializer.Meta.fields) return super(serializers.ModelSerializer, self).to_internal_value(data) def validate(self, attrs): From e0bb6545218bebee1c4bc9f4981d39fe2a0bc02a Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Sun, 6 Dec 2020 17:01:17 +0100 Subject: [PATCH 14/26] error measures removed bug --- backend/pkdb_app/error_measures.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/backend/pkdb_app/error_measures.py b/backend/pkdb_app/error_measures.py index 77b73bf9..7d998478 100644 --- a/backend/pkdb_app/error_measures.py +++ b/backend/pkdb_app/error_measures.py @@ -7,8 +7,11 @@ """ import numpy as np + def _is(value): return value is not None and value is not np.nan + + def calculate_sd(se, count, cv, mean): """Calculates standard deviation from other error measurements.""" sd = None From 18f3a818cce05b04f250893923d6f338519b6aff Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Mon, 7 Dec 2020 12:23:51 +0100 Subject: [PATCH 15/26] introduced a bug --- backend/pkdb_app/outputs/serializers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index 7f4f8128..f1c0dbdc 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -94,7 +94,7 @@ def to_internal_value(self, data): data = self.retransform_map_fields(data) data = self.to_internal_related_fields(data) - self.validate_wrong_keys(data, additional_fields=OutputSerializer.Meta.fields) + self.validate_wrong_keys(data, additional_fields=OutputExSerializer.Meta.fields) return super(serializers.ModelSerializer, self).to_internal_value(data) def validate(self, attrs): From 19b830a42535a6914a7c6cb77ad9731025914f34 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Mon, 7 Dec 2020 13:45:40 +0100 Subject: [PATCH 16/26] closes #695 --- frontend/src/components/Data.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/src/components/Data.vue b/frontend/src/components/Data.vue index bfa4284d..0abd4450 100644 --- a/frontend/src/components/Data.vue +++ b/frontend/src/components/Data.vue @@ -29,7 +29,7 @@ export default { created() { if(this.sid){ this.getStudy(this.sid, true) - this.hide_search=false + this.hide_search=true }else{ this.loading = false } From 47164fb6cd597473a41a4ff2eae32a6c0d0f99f9 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Wed, 9 Dec 2020 23:23:36 +0100 Subject: [PATCH 17/26] better message on wrong field in outputs --- backend/pkdb_app/outputs/serializers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index f1c0dbdc..1866add7 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -195,7 +195,7 @@ def to_internal_value(self, data): [data.pop(field, None) for field in drop_fields] data["outputs"] = outputs data = self.transform_map_fields(data) - self.validate_wrong_keys(data) + self.validate_wrong_keys(data, OutputSerializer.Meta.fields) return super(serializers.ModelSerializer, self).to_internal_value(data) def validate_label_map(self, value) -> None: From 79e8ca26d62205d02c9938e7098298bb56c09af1 Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Sun, 13 Dec 2020 01:02:11 +0100 Subject: [PATCH 18/26] sorted options --- backend/pkdb_app/info_nodes/documents.py | 20 +++++++------------- backend/pkdb_app/info_nodes/models.py | 4 ++-- 2 files changed, 9 insertions(+), 15 deletions(-) diff --git a/backend/pkdb_app/info_nodes/documents.py b/backend/pkdb_app/info_nodes/documents.py index 61c8b3c0..8a782bec 100644 --- a/backend/pkdb_app/info_nodes/documents.py +++ b/backend/pkdb_app/info_nodes/documents.py @@ -41,16 +41,13 @@ class InfoNodeDocument(Document): ntype = string_field('ntype') dtype = string_field('dtype') xrefs = ObjectField( - properties= - { - "name": string_field("name"), - "accession":string_field("accession"), - "url":string_field("url") - - }, multi=True) - - - # measurement type + properties={ + "name": string_field("name"), + "accession": string_field("accession"), + "url": string_field("url") + }, + multi=True + ) measurement_type = ObjectField( properties={ "choices": ObjectField( @@ -61,15 +58,12 @@ class InfoNodeDocument(Document): "units": basic_object("units", multi=True) } ) - # substance substance = ObjectField( properties={ - "chebi": string_field('chebi'), "mass": string_field('mass'), "charge": string_field('charge'), "formula": string_field('formula'), - }) class Django: diff --git a/backend/pkdb_app/info_nodes/models.py b/backend/pkdb_app/info_nodes/models.py index 6f825bc9..5e9fb210 100644 --- a/backend/pkdb_app/info_nodes/models.py +++ b/backend/pkdb_app/info_nodes/models.py @@ -315,7 +315,7 @@ def validate_choice(self, choice): self.info_node.DTypes.NumericCategorical]: if not self.is_valid_choice(choice): msg = f"The choice `{choice}` is not a valid choice for measurement type `{self.info_node.name}`. " \ - f"Allowed choices are: `{list(self.choices_list())}`." + f"Allowed choices are: `{sorted(self.choices_list())}`." raise ValueError({"choice": msg}) return self.choices.get(info_node__name=choice) else: @@ -325,7 +325,7 @@ def validate_choice(self, choice): raise ValueError({"choice": msg}) elif self.choices.exists(): msg = f"{choice}. A choice is required for `{self.info_node.name}`." \ - f" Allowed choices are: `{list(self.choices_list())}`." + f" Allowed choices are: `{sorted(self.choices_list())}`." raise ValueError({"choice": msg}) @property From e22acb0d253f3086ba8c1ea0e210ba5f331bb8cf Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Mon, 14 Dec 2020 15:54:57 +0100 Subject: [PATCH 19/26] closes #698 --- backend/pkdb_app/info_nodes/models.py | 2 +- backend/pkdb_app/outputs/serializers.py | 2 +- backend/pkdb_app/studies/models.py | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/backend/pkdb_app/info_nodes/models.py b/backend/pkdb_app/info_nodes/models.py index 6f825bc9..6dd806e7 100644 --- a/backend/pkdb_app/info_nodes/models.py +++ b/backend/pkdb_app/info_nodes/models.py @@ -154,7 +154,7 @@ class MeasurementType(AbstractInfoNode): NO_UNIT = 'NO_UNIT' # todo: remove NO_UNIT and add extra keyword or add an extra measurement_type with optional no units. TIME_REQUIRED_MEASUREMENT_TYPES = ["cumulative amount", "cumulative metabolic ratio", "recovery", - "auc_end"] # todo: remove and add extra keyword. + "auc_end", "ptf"] # todo: remove and add extra keyword. CAN_NEGATIVE = [ "tmax" # tmax can be negative due to time offsets, i.e. pre-simulation with subsequent fall after intervention # this often happens in placebo simulations diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index 1866add7..1b3118f7 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -29,7 +29,7 @@ from ..utils import list_of_pk, _validate_required_key, create_multiple, _create, create_multiple_bulk_normalized, \ create_multiple_bulk -EXTRA_FIELDS = ["tissue", "method", "label","output_type"] +EXTRA_FIELDS = ["tissue", "method", "label", "output_type"] TIME_FIELDS = ["time", "time_unit"] OUTPUT_FIELDS = EXTRA_FIELDS + TIME_FIELDS diff --git a/backend/pkdb_app/studies/models.py b/backend/pkdb_app/studies/models.py index 7c8fa792..5eccb424 100644 --- a/backend/pkdb_app/studies/models.py +++ b/backend/pkdb_app/studies/models.py @@ -78,6 +78,7 @@ def study_name(self): return self.study.name return "" + class Author(models.Model): """ Author in reference. """ first_name = models.CharField(max_length=CHAR_MAX_LENGTH, blank=True) From 09e6a2289ad8e35453d988662baed1bfde2a7cfe Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Tue, 15 Dec 2020 11:34:01 +0100 Subject: [PATCH 20/26] closes #690 --- backend/pkdb_app/info_nodes/models.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/backend/pkdb_app/info_nodes/models.py b/backend/pkdb_app/info_nodes/models.py index 5253b229..fe1dd44c 100644 --- a/backend/pkdb_app/info_nodes/models.py +++ b/backend/pkdb_app/info_nodes/models.py @@ -153,8 +153,15 @@ class MeasurementType(AbstractInfoNode): ) NO_UNIT = 'NO_UNIT' # todo: remove NO_UNIT and add extra keyword or add an extra measurement_type with optional no units. - TIME_REQUIRED_MEASUREMENT_TYPES = ["cumulative amount", "cumulative metabolic ratio", "recovery", - "auc_end", "ptf"] # todo: remove and add extra keyword. + TIME_REQUIRED_MEASUREMENT_TYPES = [ + "concentration", + "cumulative amount", + "metabolic_ratio", + "cumulative metabolic ratio", + "recovery", + "auc_end", + "ptf", + ] # todo: remove and add extra keyword. CAN_NEGATIVE = [ "tmax" # tmax can be negative due to time offsets, i.e. pre-simulation with subsequent fall after intervention # this often happens in placebo simulations From 3d92ea449679c37a1051d0e67b9c2e8c113e8bd5 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Wed, 16 Dec 2020 21:57:04 +0100 Subject: [PATCH 21/26] closes #700 --- backend/pkdb_app/info_nodes/models.py | 19 ++++++++++++------- backend/pkdb_app/info_nodes/serializers.py | 6 ++++-- backend/pkdb_app/interventions/serializers.py | 4 ++-- backend/pkdb_app/outputs/serializers.py | 4 ---- backend/pkdb_app/serializers.py | 19 +++++++++++++++++++ backend/pkdb_app/utils.py | 12 +++++++++++- 6 files changed, 48 insertions(+), 16 deletions(-) diff --git a/backend/pkdb_app/info_nodes/models.py b/backend/pkdb_app/info_nodes/models.py index fe1dd44c..ca787533 100644 --- a/backend/pkdb_app/info_nodes/models.py +++ b/backend/pkdb_app/info_nodes/models.py @@ -11,8 +11,7 @@ from pkdb_app.behaviours import Sidable from pkdb_app.info_nodes.units import ureg -from pkdb_app.utils import CHAR_MAX_LENGTH, CHAR_MAX_LENGTH_LONG, \ - _validate_required_key_and_value +from pkdb_app.utils import CHAR_MAX_LENGTH, CHAR_MAX_LENGTH_LONG, _validate_required_key_and_value_or_nr from rest_framework import serializers @@ -156,12 +155,15 @@ class MeasurementType(AbstractInfoNode): TIME_REQUIRED_MEASUREMENT_TYPES = [ "concentration", "cumulative amount", - "metabolic_ratio", + "metabolic ratio", "cumulative metabolic ratio", "recovery", "auc_end", "ptf", ] # todo: remove and add extra keyword. + TIME_REQUIRED_MEASUREMENT_TYPES_NR_ALLOWED = [ + + ] CAN_NEGATIVE = [ "tmax" # tmax can be negative due to time offsets, i.e. pre-simulation with subsequent fall after intervention # this often happens in placebo simulations @@ -376,15 +378,18 @@ def validate_complete(self, data): d_choice = self.validate_choice(choice) time_unit = data.get("time_unit", None) - if time_unit: + time = data.get("time", None) + + if time_unit and time_unit != "NR": self.validate_time_unit(time_unit) if self.time_required: details = f"for measurement type `{self.info_node.name}`" - _validate_required_key_and_value(data, "time", details=details) - _validate_required_key_and_value(data, "time_unit", details=details) + if time != "NR": + _validate_required_key_and_value_or_nr(data, "time_unit", details=details) + _validate_required_key_and_value_or_nr(data, "time", details=details) - return {"choice":d_choice} + return {"choice": d_choice} class Choice(AbstractInfoNode): diff --git a/backend/pkdb_app/info_nodes/serializers.py b/backend/pkdb_app/info_nodes/serializers.py index 5d6cf529..868bc493 100644 --- a/backend/pkdb_app/info_nodes/serializers.py +++ b/backend/pkdb_app/info_nodes/serializers.py @@ -4,7 +4,7 @@ from pkdb_app.info_nodes.documents import InfoNodeDocument from pkdb_app.info_nodes.models import InfoNode, Synonym, Annotation, Unit, MeasurementType, Substance, Choice, Route, \ Form, Tissue, Application, Method, CrossReference -from pkdb_app.serializers import WrongKeyValidationSerializer, ExSerializer, SidNameLabelSerializer +from pkdb_app.serializers import WrongKeyValidationSerializer, ExSerializer, SidNameLabelSerializer, FloatNRField from pkdb_app.utils import update_or_create_multiple from rest_framework.fields import empty @@ -28,6 +28,8 @@ class MeasurementTypeableSerializer(EXMeasurementTypeableSerializer): ) choice = serializers.CharField(allow_null=True) + time = FloatNRField(allow_null=True) + def to_representation(self, instance): rep = super().to_representation(instance) @@ -38,7 +40,7 @@ class SynonymSerializer(WrongKeyValidationSerializer): pk = serializers.IntegerField(read_only=True) class Meta: model = Synonym - fields = ["name","pk"] + fields = ["name", "pk"] def to_internal_value(self, data): return {"name": data} diff --git a/backend/pkdb_app/interventions/serializers.py b/backend/pkdb_app/interventions/serializers.py index d861fe84..f85f34cb 100644 --- a/backend/pkdb_app/interventions/serializers.py +++ b/backend/pkdb_app/interventions/serializers.py @@ -109,7 +109,7 @@ def validate(self, attrs): for info_node in ['substance', 'measurement_type', 'form', 'application', 'route']: if info_node in attrs: if attrs[info_node] is not None: - attrs[info_node] = getattr(attrs[info_node],info_node) + attrs[info_node] = getattr(attrs[info_node], info_node) attrs["choice"] = attrs["measurement_type"].validate_complete(data=attrs)["choice"] @@ -166,7 +166,7 @@ def to_internal_value(self, data): interventions_from_file = self.entries_from_file(intervention) interventions.extend(interventions_from_file) - drop_fields = INTERVENTION_FIELDS + INTERVENTION_MAP_FIELDS + EX_MEASUREMENTTYPE_FIELDS + drop_fields = INTERVENTION_FIELDS + INTERVENTION_MAP_FIELDS + EX_MEASUREMENTTYPE_FIELDS [data.pop(field, None) for field in drop_fields] # ---------------------------------- # finished diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index 1b3118f7..215ae1d9 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -110,8 +110,6 @@ def validate(self, attrs): _validate_required_key(attrs, "output_type") self._validate_timecourse(attrs) - - try: attrs['measurement_type'] = attrs['measurement_type'].measurement_type @@ -119,8 +117,6 @@ def validate(self, attrs): if key in attrs: if attrs[key] is not None: attrs[key] = getattr(attrs[key], key) - - attrs["choice"] = attrs["measurement_type"].validate_complete(data=attrs)["choice"] except ValueError as err: diff --git a/backend/pkdb_app/serializers.py b/backend/pkdb_app/serializers.py index 4a758a01..b6d04251 100644 --- a/backend/pkdb_app/serializers.py +++ b/backend/pkdb_app/serializers.py @@ -740,21 +740,25 @@ class NameSerializer(serializers.Serializer): class Meta: fields = ["pk","name", "study_sid"] + class PkStringSerializer(serializers.Serializer): pk = serializers.CharField() class Meta: fields = ["pk"] + class SidNameSerializer(serializers.Serializer): sid = serializers.CharField(allow_null=True) name = serializers.CharField(allow_null=True) + class SidNameLabelSerializer(serializers.Serializer): sid = serializers.CharField(allow_null=True) name = serializers.CharField(allow_null=True) label = serializers.CharField(allow_null=True) + def validate_dict(dic): if not isinstance(dic, dict): raise serializers.ValidationError( @@ -762,7 +766,22 @@ def validate_dict(dic): "detail": dic} ) + class StudySmallElasticSerializer(serializers.ModelSerializer): class Meta: model = Study fields = ['pk', 'sid', 'name'] # ,'url'] + + +class FloatNRField(serializers.FloatField): + + def to_internal_value(self, data): + if data == "NR": + return data + if isinstance(data, str) and len(data) > self.MAX_STRING_LENGTH: + self.fail('max_string_length') + + try: + return float(data) + except (TypeError, ValueError): + self.fail('invalid') diff --git a/backend/pkdb_app/utils.py b/backend/pkdb_app/utils.py index 3eed0fe7..20699faf 100644 --- a/backend/pkdb_app/utils.py +++ b/backend/pkdb_app/utils.py @@ -196,13 +196,23 @@ def set_keys(d, value, *keys): d = d[key] d[keys[-1]] = value + def _validate_required_key_and_value(attrs, key, details=None, extra_message: str = ""): - if pd.isnull(attrs.get(key,None)) or pd.isna(attrs.get(key,None)): + if pd.isnull(attrs.get(key, None)) or pd.isna(attrs.get(key, None)): error_json = {key: f"The key <{key}> is required. {extra_message}"} if details: error_json["details"] = details raise serializers.ValidationError(error_json) + +def _validate_required_key_and_value_or_nr(attrs, key, details=None, extra_message: str = ""): + value = attrs.get(key, None) + if value != "NR": + _validate_required_key_and_value(attrs, key, details, extra_message) + else: + attrs[key] = None + + def _validate_required_key(attrs, key, details=None, extra_message: str = ""): if key not in attrs: error_json = {key: f"The key <{key}> is required. {extra_message}"} From 64c3ff9e8862dde898cfeb620d91dd00b23e7c2e Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Thu, 17 Dec 2020 00:44:53 +0100 Subject: [PATCH 22/26] minor updates to validation of time required --- backend/pkdb_app/info_nodes/models.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/backend/pkdb_app/info_nodes/models.py b/backend/pkdb_app/info_nodes/models.py index ca787533..e7362aa2 100644 --- a/backend/pkdb_app/info_nodes/models.py +++ b/backend/pkdb_app/info_nodes/models.py @@ -11,7 +11,8 @@ from pkdb_app.behaviours import Sidable from pkdb_app.info_nodes.units import ureg -from pkdb_app.utils import CHAR_MAX_LENGTH, CHAR_MAX_LENGTH_LONG, _validate_required_key_and_value_or_nr +from pkdb_app.utils import CHAR_MAX_LENGTH, CHAR_MAX_LENGTH_LONG, _validate_required_key_and_value_or_nr, \ + _validate_required_key_and_value from rest_framework import serializers @@ -385,9 +386,16 @@ def validate_complete(self, data): if self.time_required: details = f"for measurement type `{self.info_node.name}`" + if time != "NR": - _validate_required_key_and_value_or_nr(data, "time_unit", details=details) - _validate_required_key_and_value_or_nr(data, "time", details=details) + _validate_required_key_and_value(data, "time", details=details) + if time_unit != "NR": + _validate_required_key_and_value(data, "time_unit", details=details) + + if time == "NR": + data["time"] = None + if time_unit == "NR": + data["time_unit"] = None return {"choice": d_choice} From 65cc24489076c6677d44a64951923a464b0dc706 Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Sat, 19 Dec 2020 00:55:17 +0100 Subject: [PATCH 23/26] allow interventions to be none closes #701 --- backend/pkdb_app/info_nodes/models.py | 31 +++++++++++----------- backend/pkdb_app/info_nodes/serializers.py | 5 ---- backend/pkdb_app/outputs/models.py | 4 +-- backend/pkdb_app/outputs/serializers.py | 20 +++++++------- backend/pkdb_app/serializers.py | 9 ++++--- backend/pkdb_app/subjects/serializers.py | 2 +- backend/pkdb_app/utils.py | 10 +++---- 7 files changed, 38 insertions(+), 43 deletions(-) diff --git a/backend/pkdb_app/info_nodes/models.py b/backend/pkdb_app/info_nodes/models.py index e7362aa2..85ff53db 100644 --- a/backend/pkdb_app/info_nodes/models.py +++ b/backend/pkdb_app/info_nodes/models.py @@ -368,7 +368,7 @@ def validate_numeric(self, data): f"for all measurement types except " f"<{self.CAN_NEGATIVE}>.", "detail": data}) - def validate_complete(self, data): + def validate_complete(self, data, time_allowed: bool = True): """Complete validation.""" # check unit @@ -378,24 +378,25 @@ def validate_complete(self, data): choice = data.get("choice", None) d_choice = self.validate_choice(choice) - time_unit = data.get("time_unit", None) - time = data.get("time", None) + if time_allowed: + time_unit = data.get("time_unit", None) + time = data.get("time", None) - if time_unit and time_unit != "NR": - self.validate_time_unit(time_unit) + if time_unit and time_unit != "NR": + self.validate_time_unit(time_unit) - if self.time_required: - details = f"for measurement type `{self.info_node.name}`" + if self.time_required: + details = f"for measurement type `{self.info_node.name}`" - if time != "NR": - _validate_required_key_and_value(data, "time", details=details) - if time_unit != "NR": - _validate_required_key_and_value(data, "time_unit", details=details) + if time != "NR": + _validate_required_key_and_value(data, "time", details=details) + if time_unit != "NR": + _validate_required_key_and_value(data, "time_unit", details=details) - if time == "NR": - data["time"] = None - if time_unit == "NR": - data["time_unit"] = None + if time == "NR": + data["time"] = None + if time_unit == "NR": + data["time_unit"] = None return {"choice": d_choice} diff --git a/backend/pkdb_app/info_nodes/serializers.py b/backend/pkdb_app/info_nodes/serializers.py index 868bc493..0c96d975 100644 --- a/backend/pkdb_app/info_nodes/serializers.py +++ b/backend/pkdb_app/info_nodes/serializers.py @@ -31,11 +31,6 @@ class MeasurementTypeableSerializer(EXMeasurementTypeableSerializer): time = FloatNRField(allow_null=True) - def to_representation(self, instance): - rep = super().to_representation(instance) - return rep - - class SynonymSerializer(WrongKeyValidationSerializer): pk = serializers.IntegerField(read_only=True) class Meta: diff --git a/backend/pkdb_app/outputs/models.py b/backend/pkdb_app/outputs/models.py index 0dd85740..7f987412 100644 --- a/backend/pkdb_app/outputs/models.py +++ b/backend/pkdb_app/outputs/models.py @@ -109,7 +109,7 @@ class OutputTypes(models.TextChoices): group = models.ForeignKey(Group, null=True, blank=True, on_delete=models.CASCADE) individual = models.ForeignKey(Individual, null=True, blank=True, on_delete=models.CASCADE) - interventions = models.ManyToManyField(Intervention, through="OutputIntervention", related_name="outputs") + interventions = models.ManyToManyField(Intervention, through="OutputIntervention", related_name="outputs", null=True, blank=True) subset = models.ForeignKey('data.Subset', on_delete=models.CASCADE, null=True, blank=True, related_name="pks") tissue = models.ForeignKey(Tissue, related_name="outputs", null=True, blank=True, on_delete=models.CASCADE) @@ -130,7 +130,7 @@ def null_attr(self, attr): def is_timecourse(self): if self.timecourse: - if self.timecourse.data.data_type=="timecourse": + if self.timecourse.data.data_type == "timecourse": return True return False diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index 215ae1d9..76cc3cde 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -19,7 +19,7 @@ CommentElasticSerializer from ..interventions.models import Intervention from ..serializers import ( - ExSerializer, StudySmallElasticSerializer, SidNameLabelSerializer) + ExSerializer, StudySmallElasticSerializer, SidNameLabelSerializer, PKField) from ..subjects.models import Group, DataFile, Individual from ..subjects.serializers import ( EXTERN_FILE_FIELDS, GroupSmallElasticSerializer, IndividualSmallElasticSerializer) @@ -51,6 +51,7 @@ # Outputs # ---------------------------------- + class OutputSerializer(MeasurementTypeableSerializer): group = serializers.PrimaryKeyRelatedField( @@ -62,13 +63,10 @@ class OutputSerializer(MeasurementTypeableSerializer): required=False, allow_null=True, ) - interventions = serializers.PrimaryKeyRelatedField( + interventions = PKField( queryset=Intervention.objects.all(), - many=True, - read_only=False, - required=False, - allow_null=True, - ) + many=True, required=True, allow_null=True) + tissue = utils.SlugRelatedField( slug_field="name", queryset=InfoNode.objects.filter(ntype=InfoNode.NTypes.Tissue), @@ -91,10 +89,12 @@ class Meta: def to_internal_value(self, data): data.pop("comments", None) data.pop("descriptions", None) + data.pop("image", None) + data.pop("source", None) data = self.retransform_map_fields(data) data = self.to_internal_related_fields(data) - self.validate_wrong_keys(data, additional_fields=OutputExSerializer.Meta.fields) + self.validate_wrong_keys(data) return super(serializers.ModelSerializer, self).to_internal_value(data) def validate(self, attrs): @@ -103,7 +103,6 @@ def validate(self, attrs): self.validate_group_individual_output(attrs) _validate_required_key(attrs, "measurement_type") - _validate_required_key(attrs, "substance") _validate_required_key(attrs, "tissue") _validate_required_key(attrs, "interventions") @@ -173,7 +172,6 @@ def to_internal_value(self, data): for output in temp_outputs: outputs_from_file = self.entries_from_file(output) outputs.extend(outputs_from_file) - # ---------------------------------- # finished # ---------------------------------- @@ -191,7 +189,7 @@ def to_internal_value(self, data): [data.pop(field, None) for field in drop_fields] data["outputs"] = outputs data = self.transform_map_fields(data) - self.validate_wrong_keys(data, OutputSerializer.Meta.fields) + self.validate_wrong_keys(data) return super(serializers.ModelSerializer, self).to_internal_value(data) def validate_label_map(self, value) -> None: diff --git a/backend/pkdb_app/serializers.py b/backend/pkdb_app/serializers.py index b6d04251..dfda994b 100644 --- a/backend/pkdb_app/serializers.py +++ b/backend/pkdb_app/serializers.py @@ -8,6 +8,7 @@ from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned from django.db.models import Q from rest_framework import serializers +from rest_framework.fields import empty from rest_framework.settings import api_settings from pkdb_app.behaviours import map_field @@ -354,8 +355,6 @@ def make_entry(self, entry, template, data, source): try: entry_value = getattr(entry, values[1]) - - except AttributeError: raise serializers.ValidationError( @@ -464,7 +463,7 @@ def to_representation(self, instance): request = self.context.get('request') # url representation of file - for file in ["source","image"]: + for file in ["source", "image"]: if file in rep: if "||" not in str(rep[file]): rep[file] = request.build_absolute_uri(getattr(instance, file).file.url) @@ -530,6 +529,8 @@ def to_internal_related_fields(self, data): f"intervention <{intervention}> does not exist, check interventions." ) data["interventions"] = interventions + else: + data["interventions"] = [] return data @@ -784,4 +785,4 @@ def to_internal_value(self, data): try: return float(data) except (TypeError, ValueError): - self.fail('invalid') + self.fail('invalid') \ No newline at end of file diff --git a/backend/pkdb_app/subjects/serializers.py b/backend/pkdb_app/subjects/serializers.py index 657bb3db..2d12099e 100644 --- a/backend/pkdb_app/subjects/serializers.py +++ b/backend/pkdb_app/subjects/serializers.py @@ -102,7 +102,7 @@ def validate(self, attrs): if attrs[info_node] is not None: attrs[info_node] = getattr(attrs[info_node], info_node) - attrs["choice"] = attrs["measurement_type"].validate_complete(data=attrs)["choice"] + attrs["choice"] = attrs["measurement_type"].validate_complete(data=attrs, time_allowed=False)["choice"] except ValueError as err: raise serializers.ValidationError(err) diff --git a/backend/pkdb_app/utils.py b/backend/pkdb_app/utils.py index 20699faf..797b5f76 100644 --- a/backend/pkdb_app/utils.py +++ b/backend/pkdb_app/utils.py @@ -149,20 +149,20 @@ def _create(validated_data, model_manager=None, model_serializer=None, return instance, popped_data -def initialize_normed(notnorm_instance): - norm = copy.copy(notnorm_instance) +def initialize_normed(not_norm_instance): + norm = copy.copy(not_norm_instance) norm.pk = None norm.normed = True norm.normalize() - norm.raw_id = notnorm_instance.pk + norm.raw_id = not_norm_instance.pk try: - norm.individual_id = notnorm_instance.individual.pk + norm.individual_id = not_norm_instance.individual.pk except AttributeError: pass try: - norm.group_id = notnorm_instance.group.pk + norm.group_id = not_norm_instance.group.pk except AttributeError: pass From e8d5de7fe5bb2655a11dd7a977b67a9dad6a2c2d Mon Sep 17 00:00:00 2001 From: Jan Grzegorzewski Date: Sun, 20 Dec 2020 17:59:14 +0100 Subject: [PATCH 24/26] debug --- backend/pkdb_app/outputs/serializers.py | 4 ++-- backend/pkdb_app/subjects/serializers.py | 2 -- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/backend/pkdb_app/outputs/serializers.py b/backend/pkdb_app/outputs/serializers.py index 76cc3cde..6ae32488 100644 --- a/backend/pkdb_app/outputs/serializers.py +++ b/backend/pkdb_app/outputs/serializers.py @@ -19,7 +19,7 @@ CommentElasticSerializer from ..interventions.models import Intervention from ..serializers import ( - ExSerializer, StudySmallElasticSerializer, SidNameLabelSerializer, PKField) + ExSerializer, StudySmallElasticSerializer, SidNameLabelSerializer) from ..subjects.models import Group, DataFile, Individual from ..subjects.serializers import ( EXTERN_FILE_FIELDS, GroupSmallElasticSerializer, IndividualSmallElasticSerializer) @@ -63,7 +63,7 @@ class OutputSerializer(MeasurementTypeableSerializer): required=False, allow_null=True, ) - interventions = PKField( + interventions = serializers.PrimaryKeyRelatedField( queryset=Intervention.objects.all(), many=True, required=True, allow_null=True) diff --git a/backend/pkdb_app/subjects/serializers.py b/backend/pkdb_app/subjects/serializers.py index 2d12099e..30367aca 100644 --- a/backend/pkdb_app/subjects/serializers.py +++ b/backend/pkdb_app/subjects/serializers.py @@ -92,9 +92,7 @@ def validate_count(count): raise serializers.ValidationError(f"count <{count}> has to be greater or equal to 1. 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z?f>xOk3W6)&F@jDxAwpOZ~x1epTGN`|KorB{{XT{VBseEU_Jl<002ovPDHLkV1i2~ B7YqOZ literal 0 HcmV?d00001 diff --git a/frontend/src/components/home/About.vue b/frontend/src/components/home/About.vue index 1726d727..70f78cc5 100644 --- a/frontend/src/components/home/About.vue +++ b/frontend/src/components/home/About.vue @@ -18,6 +18,7 @@ +

If you have questions or feedback please contact diff --git a/frontend/src/components/lib/UserAvatar.vue b/frontend/src/components/lib/UserAvatar.vue index 304bc025..cc216a63 100644 --- a/frontend/src/components/lib/UserAvatar.vue +++ b/frontend/src/components/lib/UserAvatar.vue @@ -64,6 +64,8 @@ image = 'sara_128.png'; } else if (this.initials === 'SB'){ image = 'balcisue_128.png'; + } else if (this.initials === 'PO'){ + image = 'paula_128.png'; } } else if (this.username) { image = 'user_128.png'; @@ -91,6 +93,8 @@ image = 'sara_128.png'; } else if (this.username === 'balcisue'){ image = 'balcisue_128.png'; + } else if (this.username === 'paula-ogata'){ + image = 'paula_128.png'; } } return img_dir + image From 1d06b00b4fc90cdd83cf343fc112fdac67a9280d Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Tue, 19 Jan 2021 10:25:53 +0100 Subject: [PATCH 26/26] version bump for release --- backend/pkdb_app/_version.py | 2 +- frontend/package.json | 2 +- release-notes/0.9.5.md | 2 ++ 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/backend/pkdb_app/_version.py b/backend/pkdb_app/_version.py index 9f65c118..198533a2 100644 --- a/backend/pkdb_app/_version.py +++ b/backend/pkdb_app/_version.py @@ -1,4 +1,4 @@ """ Definition of version string. """ -__version__ = "0.9.4" +__version__ = "0.9.5" diff --git a/frontend/package.json b/frontend/package.json index 792b7f0c..c39f8c10 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -1,6 +1,6 @@ { "name": "pkdb", - "version": "0.9.2", + "version": "0.9.5", "private": true, "scripts": { "serve": "vue-cli-service serve", diff --git a/release-notes/0.9.5.md b/release-notes/0.9.5.md index e66cbe2f..1ce3ba95 100644 --- a/release-notes/0.9.5.md +++ b/release-notes/0.9.5.md @@ -4,5 +4,7 @@ ## Fixes - interventions were missing in download (#683) +- bugfixes and additional validation rules +- security updates