Merge branch 'master' into gl-geo

data/mmcif-popular-field-names.csv → data/mmcif-field-names.csv

@@ -19,6 +19,7 @@ atom_site.auth_comp_id
 atom_site.auth_asym_id
 atom_site.auth_seq_id
 atom_site.pdbx_PDB_model_num
+atom_site.ihm_model_id
 
 chem_comp.id
 chem_comp.type
@@ -252,4 +253,338 @@ pdbx_struct_mod_residue.auth_seq_id
 pdbx_struct_mod_residue.auth_comp_id
 pdbx_struct_mod_residue.PDB_ins_code
 pdbx_struct_mod_residue.parent_comp_id
-pdbx_struct_mod_residue.details
+pdbx_struct_mod_residue.details
\ No newline at end of file
+
+ihm_struct_assembly.ordinal_id
+ihm_struct_assembly.assembly_id
+ihm_struct_assembly.parent_assembly_id
+ihm_struct_assembly.entity_description
+ihm_struct_assembly.entity_id
+ihm_struct_assembly.asym_id
+ihm_struct_assembly.seq_id_begin
+ihm_struct_assembly.seq_id_end
+
+ihm_struct_assembly_details.assembly_id
+ihm_struct_assembly_details.assembly_name
+ihm_struct_assembly_details.assembly_description
+
+ihm_model_representation.ordinal_id
+ihm_model_representation.representation_id
+ihm_model_representation.segment_id
+ihm_model_representation.entity_id
+ihm_model_representation.entity_description
+ihm_model_representation.entity_asym_id
+ihm_model_representation.seq_id_begin
+ihm_model_representation.seq_id_end
+ihm_model_representation.model_object_primitive
+ihm_model_representation.starting_model_id
+ihm_model_representation.model_mode
+ihm_model_representation.model_granularity
+ihm_model_representation.model_object_count
+
+ihm_external_reference_info.reference_id
+ihm_external_reference_info.reference_provider
+ihm_external_reference_info.reference_type
+ihm_external_reference_info.reference
+ihm_external_reference_info.refers_to
+ihm_external_reference_info.associated_url
+
+ihm_external_files.id
+ihm_external_files.reference_id
+ihm_external_files.file_path
+ihm_external_files.content_type
+ihm_external_files.file_size_bytes
+ihm_external_files.details
+
+ihm_dataset_list.id
+ihm_dataset_list.data_type
+ihm_dataset_list.database_hosted
+
+ihm_dataset_group.ordinal_id
+ihm_dataset_group.group_id
+ihm_dataset_group.dataset_list_id
+
+ihm_dataset_external_reference.id
+ihm_dataset_external_reference.dataset_list_id
+ihm_dataset_external_reference.file_id
+
+ihm_dataset_related_db_reference.id
+ihm_dataset_related_db_reference.dataset_list_id
+ihm_dataset_related_db_reference.db_name
+ihm_dataset_related_db_reference.accession_code
+ihm_dataset_related_db_reference.version
+ihm_dataset_related_db_reference.details
+
+ihm_related_datasets.ordinal_id
+ihm_related_datasets.dataset_list_id_derived
+ihm_related_datasets.dataset_list_id_primary
+
+ihm_poly_residue_feature.ordinal_id
+ihm_poly_residue_feature.feature_id
+ihm_poly_residue_feature.entity_id
+ihm_poly_residue_feature.asym_id
+ihm_poly_residue_feature.seq_id_begin
+ihm_poly_residue_feature.comp_id_begin
+ihm_poly_residue_feature.seq_id_end
+ihm_poly_residue_feature.comp_id_end
+
+ihm_feature_list.feature_id
+ihm_feature_list.feature_type
+ihm_feature_list.entity_type
+
+ihm_cross_link_list.id
+ihm_cross_link_list.group_id
+ihm_cross_link_list.entity_description_1
+ihm_cross_link_list.entity_id_1
+ihm_cross_link_list.seq_id_1
+ihm_cross_link_list.comp_id_1
+ihm_cross_link_list.entity_description_2
+ihm_cross_link_list.entity_id_2
+ihm_cross_link_list.seq_id_2
+ihm_cross_link_list.comp_id_2
+ihm_cross_link_list.linker_type
+ihm_cross_link_list.dataset_list_id
+
+ihm_cross_link_restraint.id
+ihm_cross_link_restraint.group_id
+ihm_cross_link_restraint.entity_id_1
+ihm_cross_link_restraint.asym_id_1
+ihm_cross_link_restraint.seq_id_1
+ihm_cross_link_restraint.comp_id_1
+ihm_cross_link_restraint.entity_id_2
+ihm_cross_link_restraint.asym_id_2
+ihm_cross_link_restraint.seq_id_2
+ihm_cross_link_restraint.comp_id_2
+ihm_cross_link_restraint.restraint_type
+ihm_cross_link_restraint.conditional_crosslink_flag
+ihm_cross_link_restraint.model_granularity
+ihm_cross_link_restraint.distance_threshold
+ihm_cross_link_restraint.psi
+ihm_cross_link_restraint.sigma_1
+ihm_cross_link_restraint.sigma_2
+
+ihm_cross_link_result_parameters.ordinal_id
+ihm_cross_link_result_parameters.restraint_id
+ihm_cross_link_result_parameters.model_id
+ihm_cross_link_result_parameters.psi
+ihm_cross_link_result_parameters.sigma_1
+ihm_cross_link_result_parameters.sigma_2
+
+ihm_sas_restraint.ordinal_id
+ihm_sas_restraint.dataset_list_id
+ihm_sas_restraint.model_id
+ihm_sas_restraint.struct_assembly_id
+ihm_sas_restraint.profile_segment_flag
+ihm_sas_restraint.fitting_atom_type
+ihm_sas_restraint.fitting_method
+ihm_sas_restraint.fitting_state
+ihm_sas_restraint.radius_of_gyration
+ihm_sas_restraint.chi_value
+ihm_sas_restraint.details
+
+ihm_derived_distance_restraint.id
+ihm_derived_distance_restraint.group_id
+ihm_derived_distance_restraint.feature_id_1
+ihm_derived_distance_restraint.feature_id_2
+ihm_derived_distance_restraint.group_conditionality
+ihm_derived_distance_restraint.restraint_type
+ihm_derived_distance_restraint.distance_upper_limit
+ihm_derived_distance_restraint.random_exclusion_fraction
+ihm_derived_distance_restraint.dataset_list_id
+
+ihm_2dem_class_average_restraint.id
+ihm_2dem_class_average_restraint.dataset_list_id
+ihm_2dem_class_average_restraint.number_raw_micrographs
+ihm_2dem_class_average_restraint.pixel_size_width
+ihm_2dem_class_average_restraint.pixel_size_height
+ihm_2dem_class_average_restraint.image_resolution
+ihm_2dem_class_average_restraint.image_segment_flag
+ihm_2dem_class_average_restraint.number_of_projections
+ihm_2dem_class_average_restraint.struct_assembly_id
+ihm_2dem_class_average_restraint.details
+
+ihm_2dem_class_average_fitting.ordinal_id
+ihm_2dem_class_average_fitting.restraint_id
+ihm_2dem_class_average_fitting.model_id
+ihm_2dem_class_average_fitting.cross_correlation_coefficient
+ihm_2dem_class_average_fitting.rot_matrix
+ihm_2dem_class_average_fitting.tr_vector
+
+ihm_3dem_restraint.ordinal_id
+ihm_3dem_restraint.dataset_list_id
+ihm_3dem_restraint.fitting_method
+ihm_3dem_restraint.struct_assembly_id
+ihm_3dem_restraint.number_of_gaussians
+ihm_3dem_restraint.model_id
+ihm_3dem_restraint.cross_correlation_coefficient
+
+ihm_predicted_contact_restraint.id
+ihm_predicted_contact_restraint.entity_id_1
+ihm_predicted_contact_restraint.asym_id_1
+ihm_predicted_contact_restraint.seq_id_1
+ihm_predicted_contact_restraint.comp_id_1
+ihm_predicted_contact_restraint.atom_id_1
+ihm_predicted_contact_restraint.entity_id_2
+ihm_predicted_contact_restraint.asym_id_2
+ihm_predicted_contact_restraint.seq_id_2
+ihm_predicted_contact_restraint.comp_id_2
+ihm_predicted_contact_restraint.atom_id_2
+ihm_predicted_contact_restraint.restraint_type
+ihm_predicted_contact_restraint.distance_upper_limit
+ihm_predicted_contact_restraint.probability
+ihm_predicted_contact_restraint.model_granularity
+ihm_predicted_contact_restraint.dataset_list_id
+ihm_predicted_contact_restraint.software_id
+
+ihm_starting_model_details.starting_model_id
+ihm_starting_model_details.entity_id
+ihm_starting_model_details.entity_description
+ihm_starting_model_details.asym_id
+ihm_starting_model_details.seq_id_begin
+ihm_starting_model_details.seq_id_end
+ihm_starting_model_details.starting_model_source
+ihm_starting_model_details.starting_model_auth_asym_id
+ihm_starting_model_details.starting_model_sequence_offset
+ihm_starting_model_details.dataset_list_id
+
+ihm_starting_comparative_models.ordinal_id
+ihm_starting_comparative_models.starting_model_id
+ihm_starting_comparative_models.starting_model_auth_asym_id
+ihm_starting_comparative_models.starting_model_seq_id_begin
+ihm_starting_comparative_models.starting_model_seq_id_end
+ihm_starting_comparative_models.template_auth_asym_id
+ihm_starting_comparative_models.template_seq_id_begin
+ihm_starting_comparative_models.template_seq_id_end
+ihm_starting_comparative_models.template_sequence_identity
+ihm_starting_comparative_models.template_sequence_identity_denominator
+ihm_starting_comparative_models.template_dataset_list_id
+ihm_starting_comparative_models.alignment_file_id
+
+ihm_starting_model_coord.starting_model_id
+ihm_starting_model_coord.group_PDB
+ihm_starting_model_coord.id
+ihm_starting_model_coord.type_symbol
+ihm_starting_model_coord.atom_id
+ihm_starting_model_coord.comp_id
+ihm_starting_model_coord.entity_id
+ihm_starting_model_coord.asym_id
+ihm_starting_model_coord.seq_id
+ihm_starting_model_coord.Cartn_x
+ihm_starting_model_coord.Cartn_y
+ihm_starting_model_coord.Cartn_z
+ihm_starting_model_coord.B_iso_or_equiv
+ihm_starting_model_coord.ordinal_id
+
+ihm_starting_model_seq_dif.ordinal_id
+ihm_starting_model_seq_dif.entity_id
+ihm_starting_model_seq_dif.asym_id
+ihm_starting_model_seq_dif.seq_id
+ihm_starting_model_seq_dif.comp_id
+ihm_starting_model_seq_dif.starting_model_id
+ihm_starting_model_seq_dif.db_asym_id
+ihm_starting_model_seq_dif.db_seq_id
+ihm_starting_model_seq_dif.db_comp_id
+ihm_starting_model_seq_dif.details
+
+ihm_modeling_protocol.ordinal_id
+ihm_modeling_protocol.protocol_id
+ihm_modeling_protocol.step_id
+ihm_modeling_protocol.struct_assembly_id
+ihm_modeling_protocol.dataset_group_id
+ihm_modeling_protocol.struct_assembly_description
+ihm_modeling_protocol.protocol_name
+ihm_modeling_protocol.step_name
+ihm_modeling_protocol.step_method
+ihm_modeling_protocol.num_models_begin
+ihm_modeling_protocol.num_models_end
+ihm_modeling_protocol.multi_scale_flag
+ihm_modeling_protocol.multi_state_flag
+ihm_modeling_protocol.ordered_flag
+
+ihm_modeling_post_process.id
+ihm_modeling_post_process.protocol_id
+ihm_modeling_post_process.analysis_id
+ihm_modeling_post_process.step_id
+ihm_modeling_post_process.type
+ihm_modeling_post_process.feature
+ihm_modeling_post_process.num_models_begin
+ihm_modeling_post_process.num_models_end
+
+ihm_ensemble_info.ensemble_id
+ihm_ensemble_info.ensemble_name
+ihm_ensemble_info.post_process_id
+ihm_ensemble_info.model_group_id
+ihm_ensemble_info.ensemble_clustering_method
+ihm_ensemble_info.ensemble_clustering_feature
+ihm_ensemble_info.num_ensemble_models
+ihm_ensemble_info.num_ensemble_models_deposited
+ihm_ensemble_info.ensemble_precision_value
+ihm_ensemble_info.ensemble_file_id
+
+ihm_localization_density_files.id
+ihm_localization_density_files.file_id
+ihm_localization_density_files.ensemble_id
+ihm_localization_density_files.entity_id
+ihm_localization_density_files.asym_id
+ihm_localization_density_files.seq_id_begin
+ihm_localization_density_files.seq_id_end
+
+ihm_model_list.ordinal_id
+ihm_model_list.model_id
+ihm_model_list.model_group_id
+ihm_model_list.model_name
+ihm_model_list.model_group_name
+ihm_model_list.assembly_id
+ihm_model_list.protocol_id
+ihm_model_list.representation_id
+
+ihm_model_representative.id
+ihm_model_representative.model_group_id
+ihm_model_representative.model_id
+ihm_model_representative.selection_criteria
+
+ihm_sphere_obj_site.ordinal_id
+ihm_sphere_obj_site.entity_id
+ihm_sphere_obj_site.seq_id_begin
+ihm_sphere_obj_site.seq_id_end
+ihm_sphere_obj_site.asym_id
+ihm_sphere_obj_site.Cartn_x
+ihm_sphere_obj_site.Cartn_y
+ihm_sphere_obj_site.Cartn_z
+ihm_sphere_obj_site.object_radius
+ihm_sphere_obj_site.rmsf
+ihm_sphere_obj_site.model_id
+
+ihm_gaussian_obj_site.ordinal_id
+ihm_gaussian_obj_site.entity_id
+ihm_gaussian_obj_site.seq_id_begin
+ihm_gaussian_obj_site.seq_id_end
+ihm_gaussian_obj_site.asym_id
+ihm_gaussian_obj_site.mean_Cartn_x
+ihm_gaussian_obj_site.mean_Cartn_y
+ihm_gaussian_obj_site.mean_Cartn_z
+ihm_gaussian_obj_site.weight
+ihm_gaussian_obj_site.covariance_matrix
+ihm_gaussian_obj_site.model_id
+
+ihm_gaussian_obj_ensemble.ordinal_id
+ihm_gaussian_obj_ensemble.entity_id
+ihm_gaussian_obj_ensemble.seq_id_begin
+ihm_gaussian_obj_ensemble.seq_id_end
+ihm_gaussian_obj_ensemble.asym_id
+ihm_gaussian_obj_ensemble.mean_Cartn_x
+ihm_gaussian_obj_ensemble.mean_Cartn_y
+ihm_gaussian_obj_ensemble.mean_Cartn_z
+ihm_gaussian_obj_ensemble.weight
+ihm_gaussian_obj_ensemble.covariance_matrix
+ihm_gaussian_obj_ensemble.ensemble_id
+
+ihm_multi_state_modeling.ordinal_id
+ihm_multi_state_modeling.state_id
+ihm_multi_state_modeling.state_group_id
+ihm_multi_state_modeling.population_fraction
+ihm_multi_state_modeling.state_type
+ihm_multi_state_modeling.state_name
+ihm_multi_state_modeling.model_group_id
+ihm_multi_state_modeling.experiment_type
+ihm_multi_state_modeling.details
\ No newline at end of file

src/apps/schema-generator/generate-typescript.ts

@@ -11,7 +11,7 @@ import { generate } from './util/generate'
 
 function generateSchema (name: string, path: string) {
     const str = fs.readFileSync(path, 'utf8')
-    return generate(name, JSON.parse(str))
+    return generate(name, '', JSON.parse(str))
 }
 
 const parser = new argparse.ArgumentParser({

src/apps/schema-generator/schema-from-mmcif-dic.ts

@@ -10,34 +10,30 @@ import * as fs from 'fs'
 import fetch from 'node-fetch'
 
 import Csv from 'mol-io/reader/csv/parser'
-import CIF from 'mol-io/reader/cif'
+import CIF, { Frame } from 'mol-io/reader/cif'
 import { generateSchema } from './util/cif-dic'
 import { generate } from './util/generate'
-import { Filter, mergeFilters } from './util/json-schema'
-import { Run } from 'mol-task';
+import { Filter } from './util/json-schema'
+import { Run } from 'mol-task'
 
-async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount = 0, typescript = false, out?: string) {
+async function runGenerateSchema(name: string, fieldNamesPath?: string, typescript = false, out?: string) {
     await ensureMmcifDicAvailable()
-    const comp = CIF.parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8'))
-    const parsed = await Run(comp);
-    if (parsed.isError) throw parsed
-
-    // console.log(fieldNamesPath, minCount)
-
-    let filter: Filter | undefined
-    if (minCount && fieldNamesPath) {
-        filter = mergeFilters(
-            await getUsageCountsFilter(minCount),
-            await getFieldNamesFilter(fieldNamesPath)
-        )
-    } else if (minCount) {
-        filter = await getUsageCountsFilter(minCount)
-    } else if (fieldNamesPath) {
-        filter = await getFieldNamesFilter(fieldNamesPath)
-    }
+    const mmcifDic = await Run(CIF.parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')));
+    if (mmcifDic.isError) throw mmcifDic
+
+    await ensureIhmDicAvailable()
+    const ihmDic = await Run(CIF.parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')));
+    if (ihmDic.isError) throw ihmDic
+
+    const mmcifDicVersion = CIF.schema.dic(mmcifDic.result.blocks[0]).dictionary.version.value(0)
+    const ihmDicVersion = CIF.schema.dic(ihmDic.result.blocks[0]).dictionary.version.value(0)
+    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}.`
 
-    const schema = generateSchema(parsed.result.blocks[0])
-    const output = typescript ? generate(name, schema, filter) : JSON.stringify(schema, undefined, 4)
+    const frames: Frame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames]
+    const schema = generateSchema(frames)
+
+    const filter = fieldNamesPath ? await getFieldNamesFilter(fieldNamesPath) : undefined
+    const output = typescript ? generate(name, version, schema, filter) : JSON.stringify(schema, undefined, 4)
 
     if (out) {
         fs.writeFileSync(out, output)
@@ -67,44 +63,31 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
     return filter
 }
 
-async function getUsageCountsFilter(minCount: number): Promise<Filter> {
-    const usageCountsStr = fs.readFileSync(MMCIF_USAGE_COUNTS_PATH, 'utf8')
-    const parsed = await Run(Csv(usageCountsStr, { delimiter: ' ' }));
-    if (parsed.isError) throw parser.error
-    const csvFile = parsed.result;
-
-    const fieldNamesCol = csvFile.table.getColumn('field_name')
-    const usageCountsCol = csvFile.table.getColumn('usage_count')
-    if (!fieldNamesCol || !usageCountsCol) throw 'error getting usage columns'
-    const fieldNames = fieldNamesCol.toStringArray()
-    const usageCounts = usageCountsCol.toIntArray()
+async function ensureMmcifDicAvailable() {
+    await ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL)
+}
 
-    const filter: Filter = {}
-    fieldNames.forEach((name, i) => {
-        if (usageCounts[i] < minCount) return
-        const [ category, field ] = name.substr(1).split('.')
-        if (!filter[ category ]) filter[ category ] = {}
-        filter[ category ][ field ] = true
-    })
-    return filter
+async function ensureIhmDicAvailable() {
+    await ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL)
 }
 
-async function ensureMmcifDicAvailable() {
-    if (FORCE_MMCIF_DOWNLOAD || !fs.existsSync(MMCIF_DIC_PATH)) {
+async function ensureDicAvailable(dicPath: string, dicUrl: string) {
+    if (FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath)) {
         console.log('downloading mmcif dic...')
-        const data = await fetch(MMCIF_DIC_URL)
-        if (!fs.existsSync(MMCIF_DIC_DIR)) {
-            fs.mkdirSync(MMCIF_DIC_DIR);
+        const data = await fetch(dicUrl)
+        if (!fs.existsSync(DIC_DIR)) {
+            fs.mkdirSync(DIC_DIR);
         }
-        fs.writeFileSync(MMCIF_DIC_PATH, await data.text())
+        fs.writeFileSync(dicPath, await data.text())
         console.log('done downloading mmcif dic')
     }
 }
 
-const MMCIF_USAGE_COUNTS_PATH = './data/mmcif-usage-counts.txt'
-const MMCIF_DIC_DIR = './build/dics'
-const MMCIF_DIC_PATH = `${MMCIF_DIC_DIR}/mmcif_pdbx_v50.dic`
+const DIC_DIR = './build/dics'
+const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`
 const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic'
+const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`
+const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic'
 
 const parser = new argparse.ArgumentParser({
   addHelp: true,
@@ -121,31 +104,25 @@ parser.addArgument([ '--typescript', '-ts' ], {
     action: 'storeTrue',
     help: 'Output schema as TypeScript instead of as JSON'
 });
-parser.addArgument([ '--minFieldUsageCount', '-mc' ], {
-    defaultValue: 0,
-    type: parseInt,
-    help: 'Minimum mmcif field usage counts'
-});
 parser.addArgument([ '--fieldNamesPath', '-fn' ], {
     defaultValue: '',
     help: 'Field names to include'
 });
-parser.addArgument([ '--forceMmcifDicDownload', '-f' ], {
+parser.addArgument([ '--forceDicDownload', '-f' ], {
     action: 'storeTrue',
-    help: 'Force download of mmcif dictionary'
+    help: 'Force download of dictionaries'
 });
 interface Args {
     name: string
-    forceMmcifDicDownload: boolean
+    forceDicDownload: boolean
     fieldNamesPath: string
-    minFieldUsageCount: number
     typescript: boolean
     out: string
 }
 const args: Args = parser.parseArgs();
 
-const FORCE_MMCIF_DOWNLOAD = args.forceMmcifDicDownload
+const FORCE_DIC_DOWNLOAD = args.forceDicDownload
 
 if (args.name) {
-    runGenerateSchema(args.name, args.fieldNamesPath, args.minFieldUsageCount, args.typescript, args.out)
+    runGenerateSchema(args.name, args.fieldNamesPath, args.typescript, args.out)
 }

src/apps/schema-generator/util/cif-dic.ts

@@ -6,6 +6,7 @@
 
 import { Database, ValueColumn, ListColumn } from './json-schema'
 import * as Data from 'mol-io/reader/cif/data-model'
+import { Frame } from 'mol-io/reader/cif/data-model';
 
 export function getFieldType (type: string, values?: string[]): ValueColumn|ListColumn {
     switch (type) {
@@ -92,7 +93,12 @@ function getField ( category: string, field: string, d: Data.Frame, ctx: FrameDa
         return cat.getField(field)
     } else {
         if (d.header in links) {
-            return getField(category, field, categories[links[d.header]], ctx)
+            const linkName = links[d.header]
+            if (linkName in categories) {
+                return getField(category, field, categories[linkName], ctx)
+            } else {
+                console.log(`link '${linkName}' not found`)
+            }
         } else {
             // console.log(`no links found for '${d.header}'`)
         }
@@ -172,14 +178,14 @@ const SPACE_SEPARATED_LIST_FIELDS = [
     '_pdbx_soln_scatter.data_analysis_software_list', // SCTPL5 GNOM
 ];
 
-export function generateSchema (dic: Data.Block) {
+export function generateSchema (frames: Frame[]) {
     const schema: Database = {}
 
     const categories: FrameCategories = {}
     const links: FrameLinks = {}
     const ctx = { categories, links }
 
-    dic.saveFrames.forEach(d => {
+    frames.forEach(d => {
         if (d.header[0] !== '_') return
         categories[d.header] = d
         const item_linked = d.categories['item_linked']
@@ -201,6 +207,10 @@ export function generateSchema (dic: Data.Block) {
 
     Object.keys(categories).forEach(fullName => {
         const d = categories[fullName]
+        if (!d) {
+            console.log('foo', fullName)
+            return
+        }
         const categoryName = d.header.substring(1, d.header.indexOf('.'))
         const itemName = d.header.substring(d.header.indexOf('.') + 1)
         let fields