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<TITLE>GXD High Throughput Loads</TITLE>
<H1>GXD High Throughput GEO Load</H1>
See <A HREF="http://mgiwiki/mediawiki/index.php/sw:GEO_GXD_HT_Load">GEO Load Wiki </A> for input file format, report descriptions, processing algorithms, etc.
<H3>Input</H3>
<UL>
<LI><A HREF="/data/downloads/eutils.ncbi.nlm.nih.gov.geo/">GEO Input Directory </A>
<UL>
<LI> geo.xml.* - files of 5000 experiments
<LI> GSExxxxx_family.xml - files of samples for a given experiment
</UL>
<LI><A HREF="/data/loads/mgi/geo_htload/input/">geo.uid.xml -- This is the file of GEO UIDs and meta data used to fetch the experiments </A>
</UL>
<H3>Output Files</H3>
<UL>
<LI><A HREF="/data/loads/mgi/geo_htload/output">BCP File directory</A>
<LI><A HREF="/data/loads/mgi/geo_htload/output/notevaluated.experiment.txt">List of experiments in the DB that are not evaluated; used by the classifier</A>
<LI><A HREF="/data/loads/mgi/geo_htload/output/predicted.experiment.txt">The classifier predictions; used to update the experiment predicted evaluation state and confidence </A>
</UL>
<H3>Logs</H3>
<UL>
<LI><A HREF="/data/loads/mgi/geo_htload/logs/mirror_geo.cur.log">Sample Mirror Curator Log</A>
<LI><A HREF="/data/loads/mgi/geo_htload/logs/mirror_geo.log"> Experiment Mirror Log</A>
<LI><A HREF="/data/loads/mgi/geo_htload/logs/mirror_geo.log.sample"> Sample Mirror Log</A>
<LI><A HREF="/data/loads/mgi/geo_htload/logs/geo_htload.proc.log">Process Log</A>
<LI><A HREF="/data/loads/mgi/geo_htload/logs/geo_htload.diag.log">Diagnostic Log</A>
<LI><A HREF="/data/loads/mgi/geo_htload/logs/predicted.log">Classifier Prediction Log</A>
</UL>
<H3>Reports</H3>
<UL>
<LI><A HREF="/data/loads/mgi/geo_htload/reports/">GEO QC Report - load stats: geo_htload_qc.[date].rpt</A>
<LI><A HREF="/data/loads/mgi/geo_htload/reports/">Curated Experiment with changed Samples Report: geo_htload_curated_qc.[date].rpt</A>
<LI>Parsing reports
<UL>
<LI> <A HREF="/data/loads/mgi/geo_htload/reports/geo_experiment_parsing.rpt">Experiment Parsing Report</A>
<LI><A HREF="/data/loads/mgi/geo_htload/reports/geo_sample_parsing.rpt">Sample Parsing Report</A>
<LI><A HREF="/data/loads/mgi/geo_htload/reports/geo_sample_in_db_parsing.rpt">Samples In Database Parsing Report</A>
</UL>
</UL>
<H1>GXD High Throughput ArrayExpress Load</H1>
See <A HREF="http://mgiwiki/mediawiki/index.php/sw:ArrayExpress_GXD_HT_Load"> ArrayExpress Load Wiki </A> for input file format, report descriptions, processing algorithms, etc.
<H3>Input</H3>
<UL>
<LI><A HREF="/data/loads/mgi/ae_htload/input/">ArrayExpress Input Directory </A>
<UL>
<LI> experiment.txt - Connie's list of experiment IDs she would like loaded
<LI> <exptID>.json - the BioStudies experiment file for "exptID"
<LI> <exptID>.sdrf.txt - the BioStudies sample file for "exptID"
</UL>
</UL>
<H3>Output Files</H3>
<UL>
<LI><A HREF="/data/loads/mgi/ae_htload/output">BCP File directory</A>
</UL>
<H3>Logs</H3>
<UL>
<LI><A HREF="/data/loads/mgi/ae_htload/logs/mirror_ae.cur.log">Mirror Curator Log - files that could not be downloaded</A>
<LI><A HREF="/data/loads/mgi/ae_htload/logs/mirror_ae.log"> Mirror Log - the wget commands for each file with the status of the download</A>
<LI><A HREF="/data/loads/mgi/ae_htload/logs/ae_htload.proc.log">Process Log</A>
<LI><A HREF="/data/loads/mgi/ae_htload/logs/ae_htload.diag.log">Diagnostic Log</A>
<LI><A HREF="/data/loads/mgi/ae_htload/logs/ae_htload.cur.log">Curator Log - stats and list of any experiments that could not be loaded</A>
</UL>
<H3>Reports</H3>
<UL>
<LI><A HREF="/data/loads/mgi/ae_htload/reports/ae_htload_qc.rpt">ArrayExpress Curator File QC Report</A>
<LI> <A HREF="/data/loads/mgi/ae_htload/reports/ae_experiment_parsing.rpt">Experiment Parsing Report</A>
</UL>