20710d4500737f2022bed8e3935ee8428fd88702
kent
  Wed Sep 4 08:05:28 2019 -0700
Adding test files and script.  Test script isn't perfect yet, it's a little tricky working with stuff that modifies a database like this.

diff --git src/hg/sqlUpdateRelated/tests/hcat_project.tsv src/hg/sqlUpdateRelated/tests/hcat_project.tsv
new file mode 100644
index 0000000..25a6d2a
--- /dev/null
+++ src/hg/sqlUpdateRelated/tests/hcat_project.tsv
@@ -0,0 +1,2 @@
+#short_name	@state_reached_id@hcat_projectstate@state@id	title	stars	@@lab@id@hcat_project_labs@project_id@lab_id@hcat_lab@short_name@id	@consent_id@hcat_consent@short_name@id	@cur_state_id@hcat_projectstate@state@id	@effort_id@hcat_efforttype@short_name@id	origin_name	sheet_from_lab	description	@@publications@id@hcat_project_publications@project_id@publication_id@hcat_publication@short_name@id	@@species@id@hcat_project_species@project_id@species_id@hcat_species@common_name@id	@@contributors@id@hcat_project_contributors@project_id@contributor_id@hcat_contributor@name@id	@@organ@id@hcat_project_organ@project_id@organ_id@hcat_organ@short_name@id	@@organ_part@id@hcat_project_organ_part@project_id@organpart_id@hcat_organpart@short_name@id	@@assay_type@id@hcat_project_assay_type@project_id@assaytype_id@hcat_assaytype@short_name@id	@@disease@id@hcat_project_disease@project_id@disease_id@hcat_disease@short_name@id
+HumanLymphoMyeloidProgenitorCells	suitable	"Single Cell RNA sequencing analysis of human haemopoietic lympho-myeloid progenitor populations (LMPP, MLP and GMP)"	5	Gottgens University of Cambridge	already openly published	suitable	import GEO	GSE100618	/uploads/project/GSE100618.tsv	"We performed single cell RNA sequencing of human haemopoietic lympho-myeloid progenitors with the aim to separate functionally and transcriptionally distinct progenitors within the heterogeneous GMP, LMPP and MLP populations. We performed RNA sequencing in a total of 415 single cells. From donors 1 (CB369) and 2 (CB431), 163/166 and 157/249 cells passed quality control.We further analysed the 320 single cells that passed quality control from two  different donors (157 and 163 from each donor; 91 LMPP, 110 MLP and 119 GMP). We performed clustering using Seurat package, which identified 3 clusters of cells.  We identified genes that were differentially expressed among cells of the different clusters. The majority of the cells in cluster 1 were MLP, the majority of cluster 3 were GMP while cluster comprised of LMPP and GMP cells. Cluster 1 showed high expression of lymphoid-affiliated genes. Conversely, cluster 3 showed increased expression of myeloid genes, while cluster 2 showed a mixed transcriptional signature. PCA analysis revealed a transcriptional continuum of LMPP, MLP and GMP populations."	pmid: 29167569	human	"Evangelia,,Diamanti","Fiona,,Hamey","Dimitris,,Karamitros","Bilyana,,Stoilova"	umbilical cord	cord blood	RNA levels	healthy