GenomicsStandardsConsortium · cmungall · Apr 19, 2021 · Apr 19, 2021 · Apr 19, 2021 · Apr 19, 2021
diff --git a/Makefile b/Makefile
@@ -0,0 +1,92 @@
+SRC_DIR = src
+SCHEMA_DIR = $(SRC_DIR)/schema
+SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml')
+SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES))
+
+TARGETDIR = .
+
+SCHEMA_NAME = mixs
+SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml
+TGTS = graphql jsonschema docs shex owl csv graphql python
+
+#GEN_OPTS = --no-mergeimports
+GEN_OPTS = 
+
+all: gen-all
+gen: $(patsubst %,gen-%,$(TGTS))
+
+t:
+	echo $(SCHEMA_NAMES)
+
+echo:
+	echo $(patsubst %,gen-%,$(TGTS))
+
+test: all
+
+install:
+	. environment.sh
+	pip install -r requirements.txt
+
+tdir-%:
+	mkdir -p $(TARGETDIR)/$*
+docs:
+	mkdir $@
+
+stage: $(patsubst %,stage-%,$(TGTS))
+stage-%: gen-%
+	cp -pr $(TARGETDIR)/$* .
+
+
+###  -- MARKDOWN DOCS --
+# Generate documentation ready for mkdocs
+# TODO: modularize imports
+gen-docs: $(TARGETDIR)/mixs6/index.md 
+.PHONY: gen-docs
+$(TARGETDIR)/mixs6/%.md: $(SCHEMA_SRC)
+	gen-markdown $(GEN_OPTS) --dir $(TARGETDIR)/mixs6 $<
+
+###  -- MARKDOWN DOCS --
+# TODO: modularize imports. For now imports are merged.
+gen-graphql:$(TARGETDIR)/graphql/$(SCHEMA_NAME).graphql 
+$(TARGETDIR)/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql
+	gen-graphql $(GEN_OPTS) $< > $@
+
+###  -- JSON schema --
+# TODO: modularize imports. For now imports are merged.
+gen-jsonschema: $(TARGETDIR)/jsonschema/$(SCHEMA_NAME).schema.json
+$(TARGETDIR)/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema
+	gen-json-schema $(GEN_OPTS) -t transaction $< > $@
+
+###  -- Shex --
+# one file per module
+gen-shex: $(patsubst %, $(TARGETDIR)/shex/%.shex, $(SCHEMA_NAMES))
+$(TARGETDIR)/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex
+	gen-shex --no-mergeimports $(GEN_OPTS) $< > $@
+
+###  -- CSV --
+# one file per module
+gen-csv: $(patsubst %, $(TARGETDIR)/csv/%.csv, $(SCHEMA_NAMES))
+$(TARGETDIR)/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv
+	gen-csv $(GEN_OPTS) $< > $@
+
+###  -- OWL --
+# TODO: modularize imports. For now imports are merged.
+gen-owl: $(TARGETDIR)/owl/$(SCHEMA_NAME).owl.ttl
+.PHONY: gen-owl
+$(TARGETDIR)/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl
+	gen-owl $(GEN_OPTS) $< > $@
+
+###  -- RDF (direct mapping) --
+# TODO: modularize imports. For now imports are merged.
+gen-rdf: $(TARGETDIR)/rdf/$(SCHEMA_NAME).ttl
+$(TARGETDIR)/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml tdir-rdf
+	gen-rdf $(GEN_OPTS) $< > $@
+
+###  -- LinkML --
+# linkml (copy)
+# one file per module
+gen-linkml: $(TARGETDIR)/linkml/$(SCHEMA_NAME).yaml
+$(TARGETDIR)/linkml/%.yaml: $(SCHEMA_DIR)/%.yaml tdir-limkml
+	cp $< > $@
+
+
diff --git a/index.md b/index.md
@@ -1,7 +1,7 @@
 {% include header.html %}
 
 <br>
-<p style="font-size:30px; color:red" >THIS IS A DEVELOPMENT VERSION OF THE GSC Website<br><br>
+<p style="font-size:30px; color:red" >THIS IS A DEVELOPMENT VERSION OF THE GSC Website (cjm version)<br><br>
 For the live website, please visit <a href="https://gensc.org/">https://gensc.org/</a>.</p>
 <br>
 

diff --git a/mixs6/AddRecovMethodEnum.md b/mixs6/AddRecovMethodEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: add_recov_method_enum
+
+
+
+
+URI: [mixs.vocab:add_recov_method_enum](https://w3id.org/mixs/vocab/add_recov_method_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/Air.md b/mixs6/Air.md
diff --git a/mixs6/AirMIGSBacteria.md b/mixs6/AirMIGSBacteria.md
diff --git a/mixs6/AirMIGSEukaryote.md b/mixs6/AirMIGSEukaryote.md
diff --git a/mixs6/AirMIGSPlant.md b/mixs6/AirMIGSPlant.md
diff --git a/mixs6/AirMIGSVirus.md b/mixs6/AirMIGSVirus.md
diff --git a/mixs6/AirMIMARKSSpecimen.md b/mixs6/AirMIMARKSSpecimen.md
diff --git a/mixs6/AirMIMARKSSurvey.md b/mixs6/AirMIMARKSSurvey.md
diff --git a/mixs6/AirMe.md b/mixs6/AirMe.md
diff --git a/mixs6/AirMigsOrg.md b/mixs6/AirMigsOrg.md
diff --git a/mixs6/AirMimag.md b/mixs6/AirMimag.md
diff --git a/mixs6/AirMisag.md b/mixs6/AirMisag.md
diff --git a/mixs6/AirMiuvig.md b/mixs6/AirMiuvig.md
diff --git a/mixs6/ArchStrucEnum.md b/mixs6/ArchStrucEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: arch_struc_enum
+
+
+
+
+URI: [mixs.vocab:arch_struc_enum](https://w3id.org/mixs/vocab/arch_struc_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/AssemblyQualEnum.md b/mixs6/AssemblyQualEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: assembly_qual_enum
+
+
+
+
+URI: [mixs.vocab:assembly_qual_enum](https://w3id.org/mixs/vocab/assembly_qual_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BinParamEnum.md b/mixs6/BinParamEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: bin_param_enum
+
+
+
+
+URI: [mixs.vocab:bin_param_enum](https://w3id.org/mixs/vocab/bin_param_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BinSoftwareEnum.md b/mixs6/BinSoftwareEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: bin_software_enum
+
+
+
+
+URI: [mixs.vocab:bin_software_enum](https://w3id.org/mixs/vocab/bin_software_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BiolStatEnum.md b/mixs6/BiolStatEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: biol_stat_enum
+
+
+
+
+URI: [mixs.vocab:biol_stat_enum](https://w3id.org/mixs/vocab/biol_stat_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BioticRelationshipEnum.md b/mixs6/BioticRelationshipEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: biotic_relationship_enum
+
+
+
+
+URI: [mixs.vocab:biotic_relationship_enum](https://w3id.org/mixs/vocab/biotic_relationship_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BuildDocsEnum.md b/mixs6/BuildDocsEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: build_docs_enum
+
+
+
+
+URI: [mixs.vocab:build_docs_enum](https://w3id.org/mixs/vocab/build_docs_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BuildOccupTypeEnum.md b/mixs6/BuildOccupTypeEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: build_occup_type_enum
+
+
+
+
+URI: [mixs.vocab:build_occup_type_enum](https://w3id.org/mixs/vocab/build_occup_type_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+
diff --git a/mixs6/BuildingSettingEnum.md b/mixs6/BuildingSettingEnum.md
@@ -0,0 +1,19 @@
+
+# Enum: building_setting_enum
+
+
+
+
+URI: [mixs.vocab:building_setting_enum](https://w3id.org/mixs/vocab/building_setting_enum)
+
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+
+## Permissible Values
+
+| Text | Meaning |
+| :--- | --------: |
+