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IGVF-207-biosample-requirements (#103)
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‎src/igvfd/__init__.py

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@@ -229,6 +229,8 @@ def main(global_config, **local_config):
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config.include(static_resources)
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config.include(changelogs)
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config.include('.upgrade')
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if asbool(settings.get('testing', False)):
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config.include('.tests.testing_views')
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‎src/igvfd/schemas/biosample.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"additionalProperties": false,
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"mixinProperties": [

‎src/igvfd/schemas/cell_line.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"identifyingProperties": [
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"uuid",
@@ -52,7 +54,7 @@
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},
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"properties": {
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"schema_version": {
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"default": "1"
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"default": "2"
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},
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"passage_number": {
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"title": "Passage number",

‎src/igvfd/schemas/changelogs/biosample.md

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@@ -1,5 +1,9 @@
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## Changelog for *`biosample.json`*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.
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### Minor changes since schema version 1
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* Rename `organism` to `taxa`.

‎src/igvfd/schemas/changelogs/cell_line.md

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@@ -1,5 +1,9 @@
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## Changelog for *`cell_line.json`*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.
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### Minor changes since schema version 1
48

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* Rename `organism` to `taxa`.

‎src/igvfd/schemas/changelogs/differentiated_cell.md

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@@ -1,5 +1,9 @@
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## Changelog for *`differentiated_cell.json`*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.
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### Minor changes since schema version 1
48

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* Rename `organism` to `taxa`.

‎src/igvfd/schemas/changelogs/differentiated_tissue.md

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@@ -1,5 +1,9 @@
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## Changelog for *`differentiated_tissue.json`*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.
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### Minor changes since schema version 1
48

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* Rename `organism` to `taxa`.

‎src/igvfd/schemas/changelogs/primary_cell.md

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@@ -1,5 +1,9 @@
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## Changelog for *`primary_cell.json'*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.
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### Minor changes since schema version 1
48

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* Rename `organism` to `taxa`.

‎src/igvfd/schemas/changelogs/tissue.md

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@@ -1,5 +1,9 @@
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## Changelog for *`tissue.json`*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.
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### Minor changes since schema version 1
48

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* Rename `organism` to `taxa`.

‎src/igvfd/schemas/changelogs/whole_organism.md

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@@ -1 +1,5 @@
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## Changelog for *`whole_organism.json`*
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### Schema version 2
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* Add `donors` and `taxa` to requirements.

‎src/igvfd/schemas/differentiated_cell.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"identifyingProperties": [
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"uuid",
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},
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"properties": {
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"schema_version": {
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"default": "1"
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"default": "2"
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},
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"post_differentiation_time": {
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"title": "Post-differentiation time",

‎src/igvfd/schemas/differentiated_tissue.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"identifyingProperties": [
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"uuid",
@@ -64,7 +66,7 @@
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},
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"properties": {
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"schema_version": {
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"default": "1"
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"default": "2"
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},
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"post_differentiation_time": {
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"title": "Post-differentiation time",

‎src/igvfd/schemas/primary_cell.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"identifyingProperties": [
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"uuid",
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},
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"properties": {
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"schema_version": {
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"default": "1"
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"default": "2"
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},
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"passage_number": {
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"title": "Passage number",

‎src/igvfd/schemas/tissue.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"identifyingProperties": [
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"uuid",
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},
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"properties": {
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"schema_version": {
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"default": "1"
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"default": "2"
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},
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"pmi": {
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"title": "Post-mortem interval",

‎src/igvfd/schemas/whole_organism.json

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@@ -7,7 +7,9 @@
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"required": [
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"award",
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"lab",
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"source"
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"source",
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"donors",
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"taxa"
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],
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"identifyingProperties": [
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"uuid",
@@ -173,7 +175,7 @@
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},
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"properties": {
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"schema_version": {
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"default": "1"
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"default": "2"
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},
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"description": {
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"title": "Description",

‎src/igvfd/tests/data/inserts/cell_line.json

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@@ -7,6 +7,9 @@
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"aliases": [
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"igvf-dacc:cell_line"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor1"
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],
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"status": "released",
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"submitter_comment": "The submitter had very little to say.",
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"documents": [
@@ -72,6 +75,9 @@
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"aliases": [
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"ali-mortazavi:pooled_cell_line"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor1"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/ali-mortazavi/",

‎src/igvfd/tests/data/inserts/differentiated_cell.json

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@@ -7,6 +7,9 @@
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"aliases": [
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"j-michael-cherry:alias5"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor2"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/j-michael-cherry/",
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"aliases": [
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"gary-hon:cardiomyocytes"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor_child"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/gary-hon/",
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"aliases": [
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"gary-hon:pooled_cardiomyocytes"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor_child"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/gary-hon/",

‎src/igvfd/tests/data/inserts/differentiated_tissue.json

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@@ -7,6 +7,9 @@
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"aliases": [
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"igvf:organoid"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor2"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/j-michael-cherry/",
@@ -30,6 +33,9 @@
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"aliases": [
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"igvf:gastruloid"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor1"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/jay-shendure/",
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"aliases": [
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"igvf:pooled_gastruloid"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor_child"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/jay-shendure/",

‎src/igvfd/tests/data/inserts/primary_cell.json

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"documents": [
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"bcb5f3c8-d5e9-40d2-805f-4274f940c36d"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor2"
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],
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"notes": "This is a note.",
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"product_id": "CL000001",
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"lot_id": "R56701",
@@ -73,6 +76,9 @@
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"aliases": [
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"j-michael-cherry:pooled_primary_cell"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor_child"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/j-michael-cherry/",

‎src/igvfd/tests/data/inserts/tissue.json

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"aliases": [
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"j-michael-cherry:alias3"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor2"
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],
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"status": "in progress",
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"taxa": "Homo sapiens",
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"source": "/labs/j-michael-cherry/",
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"aliases": [
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"j-michael-cherry:pooled_tissue"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor_child"
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],
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"status": "released",
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"taxa": "Homo sapiens",
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"source": "/labs/j-michael-cherry/",

‎src/igvfd/tests/data/inserts/whole_organism.json

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"aliases": [
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"j-michael-cherry:yeastF"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor1"
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],
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"status": "released",
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"source": "/labs/j-michael-cherry/",
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"description": "frozen yeast sample",
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"aliases": [
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"j-michael-cherry:yeastF2"
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],
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"donors": [
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"j-michael-cherry:alias_human_donor_child"
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],
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"status": "released",
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"source": "/labs/j-michael-cherry/",
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"taxa": "Saccharomyces"

‎src/igvfd/tests/fixtures/schemas/cell_line.py

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33

44
@pytest.fixture
5-
def cell_line(testapp, other_lab, award):
5+
def cell_line(testapp, other_lab, award, rodent_donor):
66
item = {
77
'award': award['@id'],
88
'lab': other_lab['@id'],
9-
'source': other_lab['@id']
9+
'source': other_lab['@id'],
10+
'taxa': 'Mus musculus',
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'donors': [rodent_donor['@id']]
1012
}
1113
return testapp.post_json('/cell_line', item, status=201).json['@graph'][0]
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1315

1416
@pytest.fixture
15-
def cell_line_with_date_obtained(testapp, other_lab, award):
17+
def cell_line_with_date_obtained(testapp, other_lab, award, human_donor):
1618
item = {
1719
'award': award['@id'],
1820
'lab': other_lab['@id'],
1921
'source': other_lab['@id'],
20-
'date_obtained': '2022-04-02'
22+
'date_obtained': '2022-04-02',
23+
'taxa': 'Homo sapiens',
24+
'donors': [human_donor['@id']]
2125
}
2226
return testapp.post_json('/cell_line', item, status=201).json['@graph'][0]
27+
28+
29+
@pytest.fixture
30+
def cell_line_1(cell_line):
31+
item = cell_line.copy()
32+
item.update({
33+
'schema_version': '1'
34+
})
35+
return item

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