d7620abf791fd7d117a9c8b5a810a92274146c0a
kent
  Fri Aug 9 12:34:44 2019 -0700
Refactoring a bit to improve error reporting.  Going from higher level to lower level .ra file parsing functions on the spec file so can keep track of line numbers when we are checking for errors better.

diff --git src/tabFile/tabToTabDir/test/spec.txt src/tabFile/tabToTabDir/test/spec.txt
new file mode 100644
index 0000000..89d1ac7
--- /dev/null
+++ src/tabFile/tabToTabDir/test/spec.txt
@@ -0,0 +1,50 @@
+table a_strex_test id
+id "constant ID"
+array0 GEO_Series_summary[0]
+array1 GEO_Series_summary[1]
+array2 GEO_Series_summary[2]
+mm	separate(submission_date, '-', 1)
+dd	separate(submission_date, '-', 2)
+yyyy	separate(submission_date, '-', 0)
+usaDate separate(submission_date, '-', 1) + '/' + separate(submission_date, '-', 2) + '/' + separate(submission_date, '-', 0)
+company split(fluidics_chip, 0)
+md5.sum md5(GEO_Series_summary)
+organ trim(between('human', title, 'transcriptome'))
+untrimmed_organ "'" + between('human', title, 'transcriptome') + "'"
+
+table project id
+id data_set_id
+title	
+lab	lab
+submitter
+
+table donor biosample_source_id
+biosample_source_id
+species
+biosample_source_gender 
+biosample_source_age biosample_source_age_value
+biosample_source_age_unit
+# GEO_Sample_age looks like:  prenatal 16-18 W
+geo_age split(GEO_Sample_age, 1)
+geo_age_unit split(GEO_Sample_age, 2)
+geo_life_stage split(GEO_Sample_age, 0)
+project	@project
+
+table specimen id
+id 	biosample_source_id + ' ' + split(sample_label, 0) + ' ' + split(sample_label, 1) + ' ' + split(sample_label, 2)
+donor	@donor
+organ	"brain"
+tissue 	split(sample_label, 0) + ' ' + split(sample_label, 1) + ' ' + split(sample_label, 2)
+
+table fluidics_chip id
+id lab_quake_fluidics_chip
+specimen @specimen
+
+table sample id
+fluidics_chip @fluidics_chip
+specimen @specimen
+donor @donor
+id ncbi_bio_sample
+biosample_cell_type
+lab_quake_cell
+