chore: make setup was run

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/linkml/linkml-project-cookiecutter",
-  "commit": "b2da87eb7835bfec748a76823d098cac85e8363a",
+  "commit": "21dc84dd378e7aade7affaa329956ce93d38202d",
   "checkout": null,
   "context": {
     "cookiecutter": {

Makefile

@@ -11,7 +11,7 @@ SHELL := bash
 ifdef LINKML_ENVIRONMENT_FILENAME
 include ${LINKML_ENVIRONMENT_FILENAME}
 else
-include .env.public
+include config.public.mk
 endif
 
 RUN = poetry run
@@ -110,7 +110,7 @@ deploy: all mkd-gh-deploy
 
 # In future this will be done by conversion
 gen-examples:
-	cp src/data/examples/* $(EXAMPLEDIR)
+	cp -r src/data/examples/* $(EXAMPLEDIR)
 
 # generates all project files
 
@@ -189,7 +189,7 @@ $(DOCDIR):
 	mkdir -p $@
 
 gendoc: $(DOCDIR)
-	cp -rf $(SRC)/docs/* $(DOCDIR) ; \
+	cp -rf $(SRC)/docs/files/* $(DOCDIR) ; \
 	$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
 
 testdoc: gendoc serve

Makefile.rej

@@ -0,0 +1,44 @@
+diff a/Makefile b/Makefile	(rejected hunks)
+@@ -22,35 +22,37 @@ SRC = src
+ DEST = project
+ PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
+ DOCDIR = docs
++DOCTEMPLATES = $(SRC)/docs/templates
+ EXAMPLEDIR = examples
+ SHEET_MODULE = personinfo_enums
+ SHEET_ID = $(LINKML_SCHEMA_GOOGLE_SHEET_ID)
+ SHEET_TABS = $(LINKML_SCHEMA_GOOGLE_SHEET_TABS)
+ SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
+
++# Use += to append variables from the variables file
+ CONFIG_YAML =
+ ifdef LINKML_GENERATORS_CONFIG_YAML
+-CONFIG_YAML = ${LINKML_GENERATORS_CONFIG_YAML}
++CONFIG_YAML += ${LINKML_GENERATORS_CONFIG_YAML}
+ endif
+
+ GEN_DOC_ARGS =
+ ifdef LINKML_GENERATORS_DOC_ARGS
+-GEN_DOC_ARGS = ${LINKML_GENERATORS_DOC_ARGS}
++GEN_DOC_ARGS += ${LINKML_GENERATORS_DOC_ARGS}
+ endif
+
+ GEN_OWL_ARGS =
+ ifdef LINKML_GENERATORS_OWL_ARGS
+-GEN_OWL_ARGS = ${LINKML_GENERATORS_OWL_ARGS}
++GEN_OWL_ARGS += ${LINKML_GENERATORS_OWL_ARGS}
+ endif
+
+ GEN_JAVA_ARGS =
+ ifdef LINKML_GENERATORS_JAVA_ARGS
+-GEN_JAVA_ARGS = ${LINKML_GENERATORS_JAVA_ARGS}
++GEN_JAVA_ARGS += ${LINKML_GENERATORS_JAVA_ARGS}
+ endif
+
+ GEN_TS_ARGS =
+ ifdef LINKML_GENERATORS_TYPESCRIPT_ARGS
+-GEN_TS_ARGS = ${LINKML_GENERATORS_TYPESCRIPT_ARGS}
++GEN_TS_ARGS += ${LINKML_GENERATORS_TYPESCRIPT_ARGS}
+ endif
+
+

config.public.mk

@@ -0,0 +1,32 @@
+# config.public.mk
+
+# This file is public in git. No sensitive info allowed.
+# These variables are sourced in Makefile, following make-file conventions.
+# Be aware that this file does not follow python or bash conventions, so may appear a little unfamiliar.
+
+###### schema definition variables, used by makefile
+
+# Note: makefile variables should not be quoted, as makefile handles quoting differently than bash
+LINKML_SCHEMA_NAME=oscem_schemas
+LINKML_SCHEMA_AUTHOR=Yves Tittes <[email protected]>
+LINKML_SCHEMA_DESCRIPTION=Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
+LINKML_SCHEMA_SOURCE_PATH=src/oscem_schemas/schema/oscem_schemas.yaml
+LINKML_SCHEMA_GOOGLE_SHEET_ID=1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ
+LINKML_SCHEMA_GOOGLE_SHEET_TABS=personinfo enums
+
+###### linkml generator variables, used by makefile
+
+## gen-project configuration file
+LINKML_GENERATORS_CONFIG_YAML= --config-file config.yaml
+
+## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports)
+LINKML_GENERATORS_DOC_ARGS=
+
+## pass args to workaround genowl rdfs config bug (linkml#1453)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+LINKML_GENERATORS_OWL_ARGS=
+
+## pass args to trigger experimental java/typescript generation
+LINKML_GENERATORS_JAVA_ARGS=
+LINKML_GENERATORS_TYPESCRIPT_ARGS=
+

examples/EMDataset-001.yaml

@@ -1,74 +1,100 @@
 # Example data object
 ---
 instrument:
-  microscope: Titan
-  illumination: FloodBeam
-  imaging: Brightfield
-  electron_source: FEG
-  acceleration_voltage: 300
-  c2_aperture: 70
-  cs: 2.7
+  microscope: "Titan"
+  illumination: "FloodBeam"
+  imaging: "Brightfield"
+  electron_source: "FEG"
+  acceleration_voltage:
+    value: 300
+    unit: "kV"
+  c2_aperture:
+    value: 70
+    unit: "µm"
+  cs:
+    value: 2.7
+    unit: "mm"
 acquisition:
-  holder: testitest
-  detector: Falcon 4i
-  detector_mode: counting
-  dose_per_movie: 0.5
+  holder: "testitest"
+  detector: "Falcon 4i"
+  detector_mode: "counting"
+  dose_per_movie:
+    value: 0.5
+    unit: "1/Å^2"
   date_time: "2024-01-01"
   binning_camera: 2
-  pixel_size: 1.2
+  pixel_size:
+    value: 1.2
+    unit: "Å"
 grants:
-  - project_id: SNF321
-    funder: SNF
-  - project_id: Fundingofsomekind
-    funder: SNF
+  - project_id: "SNF321"
+    funder: "SNF"
+  - project_id: "Fundingofsomekind"
+    funder: "SNF"
 authors:
-  - name: Doe
-    first_name: John
-    email: [email protected]
+  - name: "Doe"
+    first_name: "John"
+    email: "[email protected]"
     work_phone: "+4132112312"
-    orcid: ORCID_123124151231
-    name_org: University of Blub
-    type_org: Academic
-    country: Switzerland
-  - name: Doe
-    first_name: Jane
-    email: [email protected]
+    orcid: "ORCID_123124151231"
+    name_org: "University of Blub"
+    type_org: "Academic"
+    country: "Switzerland"
+  - name: "Doe"
+    first_name: "Jane"
+    email: "[email protected]"
     work_phone: "+4132112312"
-    orcid: ORCID_123124151221
-    name_org: University of Bla
-    type_org: Academic
-    country: Switzerland
+    orcid: "ORCID_123124151221"
+    name_org: "University of Blub"
+    type_org: "Academic"
+    country: "Switzerland"
 sample:
   overall_molecule:
-    molecular_type: Complex
-    name_sample: Ribosome
-    source: yeast
-    molecular_weight: 3000000
+    molecular_type: "Complex"
+    assembly: "PARTICLE"
+    name_sample: "Ribosome"
+    source: "yeast"
+    molecular_weight:
+      value: 3000000
+      unit: "Da"
   molecule:
-    - name_mol: Ribosome_
-      molecular_type: polypeptide
-      molecular_class: None of these
-      sequence: MMKNMMKYMMMYSYKEKSEKRRWMMKREMMKYLELLNMRMNKWVKRMMMSRKRLLSRMNRLEKKNHMNDYKLMSYNFNKNSMMMKSMLSKLMMNLLENVMNGVDLKSGKSKMSGGNMMMSKPVMKENLNTVNMLFYYFLPNNKSYKYFNRMNMYLNKHMKNYKKLVKLNKNYSKSSYLLQDKLMMSNMFNNMMFNRNNMKYMNNNVNNLMSSLNMNSNNKSLYLSLLNKTLNNNLSNLYSNNNINKSIINNTLVNMSMLNNNYNNNNTTFNINNNLFNLLNLLNNNYNNNNNYNNMMSNTNMLLNNYNNNNNNNNNNKCNMHSKMKLERKNMMLNYLLKNEMMNKNQMWMSKMENNKMNNINNNNNMLKMNKENDKTNMFGYMMSYMDMLLGNMMNKSKKSNDMKMMMSKYFGLKEVNMTGMNLKYEFNNTEMLLKLMRKGMSKRKRTLSRMFRFRLKNRMPLLNDKGMLKNKMSNNLLKNLALNNNILNVEYNIKNVLFNSINNNNINNNNNNNMYNDMKDYYNNMSLENKKDLSLNNELLYKNMVGWSLLLKGKVGARKGKNRSNRMLMTKGSFKNNNLYIYNIFDDNSNNNGYTKDRLRLNYMKNSNFISYMDKSTNNGKLGMTLKVNIL
-      natural_source: yeast
-      taxonomy_id_source: GCA_003054445.1
-      expression_system: Pichia kudriavzevii
-      taxonomy_id_expression: GCA_003054445.1
-      gene_name: Rib
+    - name_mol: "Ribosome_"
+      molecular_type: "polypeptide"
+      molecular_class: "None of these"
+      sequence: "MMKNMMKYMMMYSYKEKSEKRRWMMKREMMKYLELLNMRMNKWVKRMMMSRKRLLSRMNRLEKKNHMNDYKLMSYNFNKNSMMMKSMLSKLMMNLLENVMNGVDLKSGKSKMSGGNMMMSKPVMKENLNTVNMLFYYFLPNNKSYKYFNRMNMYLNKHMKNYKKLVKLNKNYSKSSYLLQDKLMMSNMFNNMMFNRNNMKYMNNNVNNLMSSLNMNSNNKSLYLSLLNKTLNNNLSNLYSNNNINKSIINNTLVNMSMLNNNYNNNNTTFNINNNLFNLLNLLNNNYNNNNNYNNMMSNTNMLLNNYNNNNNNNNNNKCNMHSKMKLERKNMMLNYLLKNEMMNKNQMWMSKMENNKMNNINNNNNMLKMNKENDKTNMFGYMMSYMDMLLGNMMNKSKKSNDMKMMMSKYFGLKEVNMTGMNLKYEFNNTEMLLKLMRKGMSKRKRTLSRMFRFRLKNRMPLLNDKGMLKNKMSNNLLKNLALNNNILNVEYNIKNVLFNSINNNNINNNNNNNMYNDMKDYYNNMSLENKKDLSLNNELLYKNMVGWSLLLKGKVGARKGKNRSNRMLMTKGSFKNNNLYIYNIFDDNSNNNGYTKDRLRLNYMKNSNFISYMDKSTNNGKLGMTLKVNIL"
+      natural_source: "yeast"
+      taxonomy_id_source: "GCA_003054445.1"
+      expression_system: "Pichia kudriavzevii"
+      taxonomy_id_expression: "GCA_003054445.1"
+      gene_name: "Rib"
+  ligands:
+    - present: true
+      smiles: "OCC"
   specimen:
-    concentration: 0.3
+    concentration:
+      value: 0.3
+      unit: "M"
     ph: 7
     vitrification: false
-    vitrification_cryogen: None
-    humidity: 90
-    temperature: 300
+    vitrification_cryogen: "None"
+    humidity:
+      value: 90
+      unit: "%"
+    temperature:
+      value: 300
+      unit: "K"
     staining: false
     embedding: false
     shadowing: false
   grid:
-    manufacturer: Quantifoil
-    material: Au
+    manufacturer: "Quantifoil"
+    material: "Au"
     mesh: 300
     film_support: false
-    pretreatment_type: Glow discharge
-    pretreatment_time: 30
-    pretreatment_pressure: 0.000001
+    pretreatment_type: "Glow discharge"
+    pretreatment_time:
+      value: 30
+      unit: "s"
+    pretreatment_pressure:
+      value: 0.000001
+      unit: "Pa"

examples/invalid/EMDataset-invalid-001.yaml

@@ -0,0 +1,98 @@
+# Example data object
+---
+instrument:
+  microscope: "Titan"
+  illumination: "FloodBeam"
+  imaging: "Brightfield"
+  electron_source: "FEG"
+  acceleration_voltage: 
+    value: 300
+    unit: "kV"
+  c2_aperture: 
+    value: 70
+    unit: "µm"
+  cs: 
+    value: 2.7
+acquisition:
+  holder: "testitest"
+  detector: "Falcon 4i"
+  detector_mode: "counting"
+  dose_per_movie: 
+    value: 0.5
+    unit: "1/Å^2"
+  date_time: "2024-01-01"
+  binning_camera: 2
+  pixel_size: 
+    value: 1.2
+    unit: "Å"
+grants:
+  - project_id: "SNF321"
+    funder: "SNF"
+  - project_id: "Fundingofsomekind"
+    funder: "SNF"
+authors:
+  - name: "Doe"
+    first_name: "John"
+    email: "[email protected]"
+    work_phone: "+4132112312"
+    orcid: "ORCID_123124151231"
+    name_org: "University of Blub"
+    type_org: "Academic"
+    country: "Switzerland"
+  - name: "Doe"
+    first_name: "Jane"
+    email: "[email protected]"
+    work_phone: "+4132112312"
+    orcid: "ORCID_123124151221"
+    name_org: "University of Blub"
+    type_org: "Academic"
+    country: "Switzerland"
+sample:
+  overall_molecule:
+    molecular_type: "Complex"
+    name_sample: "Ribosome"
+    source: "yeast"
+    molecular_weight: 
+      value: 3000000
+      unit: "Da"
+  molecule:
+    - name_mol: "Ribosome_"
+      molecular_type: "polypeptide"
+      molecular_class: "None of these"
+      sequence: "MMKNMMKYMMMYSYKEKSEKRRWMMKREMMKYLELLNMRMNKWVKRMMMSRKRLLSRMNRLEKKNHMNDYKLMSYNFNKNSMMMKSMLSKLMMNLLENVMNGVDLKSGKSKMSGGNMMMSKPVMKENLNTVNMLFYYFLPNNKSYKYFNRMNMYLNKHMKNYKKLVKLNKNYSKSSYLLQDKLMMSNMFNNMMFNRNNMKYMNNNVNNLMSSLNMNSNNKSLYLSLLNKTLNNNLSNLYSNNNINKSIINNTLVNMSMLNNNYNNNNTTFNINNNLFNLLNLLNNNYNNNNNYNNMMSNTNMLLNNYNNNNNNNNNNKCNMHSKMKLERKNMMLNYLLKNEMMNKNQMWMSKMENNKMNNINNNNNMLKMNKENDKTNMFGYMMSYMDMLLGNMMNKSKKSNDMKMMMSKYFGLKEVNMTGMNLKYEFNNTEMLLKLMRKGMSKRKRTLSRMFRFRLKNRMPLLNDKGMLKNKMSNNLLKNLALNNNILNVEYNIKNVLFNSINNNNINNNNNNNMYNDMKDYYNNMSLENKKDLSLNNELLYKNMVGWSLLLKGKVGARKGKNRSNRMLMTKGSFKNNNLYIYNIFDDNSNNNGYTKDRLRLNYMKNSNFISYMDKSTNNGKLGMTLKVNIL"
+      natural_source: "yeast"
+      taxonomy_id_source: "GCA_003054445.1"
+      expression_system: "Pichia kudriavzevii"
+      taxonomy_id_expression: "GCA_003054445.1"
+      gene_name: "Rib"
+  ligands:
+    - present: true
+      smiles: "OC"
+  specimen:
+    concentration: 
+      value: 0.3
+      unit: "M"
+    ph: 7
+    vitrification: false
+    vitrification_cryogen: "None"
+    humidity: 
+      value: 90
+      unit: "%"
+    temperature: 
+      value: 300
+      unit: "K"
+    staining: false
+    embedding: false
+    shadowing: false
+  grid:
+    manufacturer: "Quantifoil"
+    material: "Au"
+    mesh: 300
+    film_support: false
+    pretreatment_type: "Glow discharge"
+    pretreatment_time: 
+      value: 30
+      unit: "s"
+    pretreatment_pressure: 
+      value: 0.000001
+      unit: "Pa"

project/graphql/oscem_schemas.graphql

@@ -220,10 +220,3 @@ type SphericalAberrationCorrector
     instrumentType: String!
   }
 
-type TiltAngle
-  {
-    minimal: QuantityValue
-    maximal: QuantityValue
-    increment: QuantityValue
-  }
-