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AgeCommit message (Collapse)Author
2025-04-21Include dot file that can render scripts dependenciesLan Hui
2025-04-21To include Graphviz dot fileLan Hui
2025-04-21Update doc 3Lan Hui
2025-04-21Update doc 2Lan Hui
2025-04-21Update docLan Hui
2025-04-21Fix error: name path is not definedHui Lan
2025-04-20Save RNA_SEQ_INFO_DATABASE; do not need commland-line redirect now.Lan Hui
2025-04-20Remove test file for backup_fileLan Hui
2025-04-20Backup old RNA_SEQ_INFO_DATABASE_JSON and replace it with an updated oneLan Hui
2025-04-20Remove unused linesLan Hui
2025-04-16Describe the code updateLan Hui
2025-04-16Include sample id and study id in the JSON outputLan Hui
2025-04-16Remove unused codeLan Hui
2025-04-16Output some stats, beginning with %%Lan Hui
2025-04-16Fix key errorsLan Hui
2025-04-16Retrieve more tissue information from ena_study.xmlLan Hui
2025-04-16Retrieve more tissue information from read_experimentLan Hui
2025-04-15Retrieve more tissue informationLan Hui
2025-04-14Futher improve XML processing logicHui Lan
2025-04-13Parse ENA records XML files. It seems that XML structure for experiment, ↵Hui Lan
study and sample has changed.
2025-04-13Fix typo 'expriment' in 'read_expriment'Hui Lan
2025-04-12Show script name in the log line.Hui Lan
2025-04-12Save ENA records to XML files under Data/temp/Hui Lan
2025-04-09Run this file from time to time to get the most recent RNA-Seq records at ENAHui Lan
2025-04-09MaintenanceHui Lan
2025-04-06Show number of remaining RNA-Seq data to reflect remaining workHui Lan
2025-04-06Remove the line in configure.py that caused downloading not work for 4 daysHui Lan
2025-04-02Reverse download log lines and write them to a new file ↵Hui Lan
download_log_reversed.txt so that the most recent log line appears on the top. Purpose: easier to check log from the web browser.
2025-03-09Remove the experimental file killprocess.pyHui Lan
2025-03-09Kill wget if it takes too longHui Lan
2025-03-09Append DONE to the download log in case the downloading process cannot move ↵Hui Lan
on. Added two helper functions: age_of_file_in_hours() and append_done(). Ran dos2unix; that is why there are so many changes.
2025-03-09Sync changes made on my Ubuntu desktop machine i7-13700HHui Lan
2025-03-09configure.pyHui Lan
2024-08-28Pretty print JSONLan Hui
2024-08-26JSON file should look like '{key:value}' but not ['{key:value}']Lan Hui
2024-08-26Use R package jsonlite instead of rjson, to support the 'digits' option, ↵Lan Hui
which allows keeping fewer digits after decimal, thus saving disk storage space
2024-08-17[mergeTPM.py] correct grammar errorLan Hui
2024-08-17merge all TPM files and put the merged file in folder assembleLan Hui
2024-08-16Count all downloaded RUNsLan Hui
2024-08-11Required Python modulesLan Hui
2024-08-11Remove temporary fileLan Hui
2024-08-11dos2unixLan Hui
2024-08-10[create_edges0B.py] Correct Python script nameHui Lan
2024-08-10[create_edges0.py] Store edges in folder ../Data/history/edges/many_targetsHui Lan
2024-08-10[update_network.py] Do not generation json files for gene expression if not ↵Hui Lan
do webapp
2024-08-09[update_network.py] Simplify codeHui Lan
2024-08-08Remove index.htmlHui Lan
2024-08-08Improve memory efficency while building TPM.txtHui Lan
2024-08-07Use TPM_FILE instead of TPM_TABLEHui Lan
2024-08-07Fix error occurred while running update_network.pyHui Lan
generated by cgit v1.2.1 (git 2.18.0) at 2025-07-15 23:23:07 +0000