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MPIIComputationalEpigenetics / DeepBlue-Web

DeepBlue Epigenomic Data Server - Web Interface
http://deepblue.mpi-inf.mpg.de
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Filter/List experiments by signal and peaks #3

Closed felipealbrecht closed 9 years ago

felipealbrecht commented 9 years ago

Show if the experiment is Peak or Signal in the Experiments Data Table

felipealbrecht commented 9 years ago

One more column, "Type".

felipealbrecht commented 9 years ago

From the info(experiment_id), the the "data_type" field. e.g.: server.info("e10002", userkey) ['okay', [{'description': '', **'datatype': 'signal'**, 'format': 'CHROMOSOME,START,END,VALUE', 'extra_metadata': {'SPECIMEN_STORAGE': 'NA', 'SPECIMEN_PROCESSING': 'fresh', 'CENTER_NAME': 'MPIMG', 'EST_FRAG_LENGTH': '-', 'SAMPLE_DESC_1': 'Venous blood', 'MOLECULE': 'total RNA', 'INSTRUMENT_MODEL': 'Illumina HiSeq 2000', 'FILE_MD5': '3074eb86f85c73a27e2aaec3079dd8e7', 'TISSUE_TYPE': 'Venous blood', 'DONOR_REGION_OF_RESIDENCE': 'East Anglia', 'FILE': 'blueprint/data/homo_sapiens/Venous_blood/S002EV/CD4-positive_alpha-beta_T_cell/RNA-Seq/MPIMG/S002EV11.plusStrand.gem_grape_crg.20141014.bw', 'FILE_SIZE': '286244221', 'CELL_LINE': '-', 'LIBRARY_STRATEGY': 'RNA-Seq', 'CELL_TYPE': 'CD4-positive, alpha-beta T cell', 'DONOR_ETHNICITY': 'NA', 'NSC': '-', 'POOL_ID': '-', 'FILE_TYPE': 'RNA_SIGNAL_CRG', 'TISSUE_DEPOT': '-', 'DONOR_ID': 'S002EV', 'EXPERIMENT_ID': 'ERX607015', 'DONOR_HEALTH_STATUS': 'NA', 'READ_STRAND': 'Mate2_Sense', 'SAMPLE_ONTOLOGY_URI': 'http://purl.obolibrary.org/obo/CL_0000624;http://purl.obolibrary.org/obo/UBERON_0013756', 'SEQ_RUNS_COUNT': '1', 'POOLED_DONOR_IDS': '-', 'READ_QUALITIES': 'phred', 'SAMPLE_NAME': 'S002EV11', 'DISEASE': 'None', 'STUDY_NAME': 'Blueprint RNA-seq data (common cell types)', 'GENETIC_CHARACTERISTICS': '-', 'SAMPLE_DESC_2': 'S002EV', 'LIBRARY_NAME': 'I_bc_pelib_2314', 'SAMPLE_ID': 'ERS487305', 'STUDY_ID': 'ERP001664', 'DONOR_SEX': 'Male', 'TWIN_PAIR_ID': '-', 'BIOMATERIAL_TYPE': 'Primary Cell', 'DISEASE_ONTOLOGY_URI': 'NA', 'RSC': '-', 'FIRST_SUBMISSION_DATE': '07-OCT-2014 09:32:54', 'EXPERIMENT_TYPE': 'mRNA-seq', 'INSTRUMENT_PLATFORM': 'ILLUMINA', 'BIOMATERIAL_PROVIDER': 'NIHR Cambridge BioResource', 'LIBRARY_LAYOUT': 'PAIRED', 'DONOR_AGE': '45 - 50', 'SAMPLE_DESC_3': 'CD4-positive, alpha-beta T cell', 'TREATMENT': '-'}, 'sample_info': {'SPECIMEN_PROCESSING': 'fresh', 'DONOR_ETHNICITY': 'NA', 'SAMPLE_NAME': 'S002EV11', 'source': 'BLUEPRINT Epigenomics', 'DONOR_SEX': 'Male', 'DONOR_HEALTH_STATUS': 'NA', 'SAMPLE_ID': 'ERS487305', 'BIOMATERIAL_TYPE': 'Primary Cell', 'DISEASE': 'None', 'SPECIMEN_STORAGE': 'NA', 'biosource_name': 'CD4-positive, alpha-beta T cell', 'DONOR_ID': 'S002EV', 'DONOR_REGION_OF_RESIDENCE': 'East Anglia', 'BIOMATERIAL_PROVIDER': 'NIHR Cambridge BioResource', 'DONOR_AGE': '45 - 50'}, 'technique': 'RNA-Seq', 'upload_info': {'total_size': '599841442', 'content_format': 'wig', 'done': 'true', 'user': 'Populator', 'upload_end': '22.01.2015 11:21:37', 'upload_start': '22.01.2015 11:21:15', 'client_address': '127.0.0.1'}, 'project': 'Blueprint Epigenetics', 'genome': 'hg19', 'sample_id': 's788', 'epigenetic_mark': 'mRNA-seq', '_id': 'e10002', 'type': 'experiment', 'columns': [{'name': 'CHROMOSOME', 'column_type': 'stri

felipealbrecht commented 9 years ago

The commit 2f2a1077eb87c83d04a095b13bcfa4feea5e4367 does it for the experiments data table view.

Now, you have to implement for the others experiments data tables (dashboards and others)

edeas123 commented 9 years ago

Implemented for dashboard, Experiment Download and for Experiment Search (the datatables part).