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How to use change_option method in tempest

Best Python code snippet using tempest_python

refrna_copy_delete.py

Source:refrna_copy_delete.py

1# -*- coding: utf-8 -*-2from biocluster.config import Config3from biocluster.api.database.base import Base4from pymongo import MongoClient5class RefrnaCopyDelete(Base):6    def __init__(self):7        super(RefrnaCopyDelete, self).__init__()8        self._project_type = 'ref_rna'9    def remove_collection(self, task_id, main_coll, detatil_coll=[], change_option=''):10        """11        å é¤ä¸»è¡¨åå¯¹åºçè¯¦ç»è¡¨12        task_id:task_idï¼detatil_coll:ä¸»è¡¨å¯¹åºçè¯¦ç»è¡¨, change_option:è¯¦ç»è¡¨ä¸ä¸»è¡¨åæ®µ13        """14        results = self.db[main_coll].find({"task_id": task_id})15        if results:16            for result in results:17                main_id = result["_id"]18                for coll in detatil_coll:19                    items = self.db[coll].remove({change_option: main_id})20                    print "æåå é¤task_idä¸º{}çç»èè¡¨{}".format(task_id, coll)21                self.db[main_coll].remove({"_id": result["_id"]})22                print "æåå é¤task_idä¸º{}çä¸»è¡¨{}".format(task_id, main_coll)23        else:24            print "æ²¡ææ¾å°task_idä¸º{}çä¸»è¡¨{}".format(task_id, main_coll)25    def remove(self, task_id):26        self.remove_collection(task_id=task_id, main_coll="sg_task", detatil_coll=[], change_option="")27        self.remove_collection(task_id=task_id, main_coll="sg_specimen", detatil_coll=[], change_option="")28        self.remove_collection(task_id=task_id, main_coll="sg_specimen_graphic", detatil_coll=[], change_option="")29        self.remove_collection(task_id=task_id, main_coll="sg_specimen_group", detatil_coll=[], change_option="")30        self.remove_collection(task_id=task_id, main_coll="sg_specimen_group_compare", detatil_coll=[], change_option="")31        self.remove_collection(task_id=task_id, main_coll="sg_specimen_info", detatil_coll=[], change_option="")32        self.remove_collection(task_id=task_id, main_coll="sg_specimen_mapping", detatil_coll=[], change_option="")33        self.remove_collection(task_id=task_id, main_coll="sg_annotation_stat", detatil_coll=["sg_annotation_stat_detail"], change_option="stat_id")34        self.remove_collection(task_id=task_id, main_coll="sg_express", detatil_coll=["sg_express_detail", "sg_express_gragh", "sg_express_box"], change_option="express_id")35        self.remove_collection(task_id=task_id, main_coll="sg_geneset", detatil_coll=["sg_geneset_detail"], change_option="geneset_id")36        self.remove_collection(task_id=task_id, main_coll="sg_software_para", detatil_coll=[], change_option="")37        self.remove_collection(task_id=task_id, main_coll="sg_annotation_blast", detatil_coll=["sg_annotation_blast_detail"], change_option="blast_id")38        self.remove_collection(task_id=task_id, main_coll="sg_annotation_nr", detatil_coll=["sg_annotation_nr_pie"], change_option="nr_id")39        self.remove_collection(task_id=task_id, main_coll="sg_annotation_swissprot", detatil_coll=["sg_annotation_swissprot_pie"], change_option="swissprot_id")40        self.remove_collection(task_id=task_id, main_coll="sg_annotation_pfam", detatil_coll=["sg_annotation_pfam_bar", "sg_annotation_pfam_detail"], change_option="pfam_id")41        self.remove_collection(task_id=task_id, main_coll="sg_annotation_cog", detatil_coll=["sg_annotation_cog_detail"], change_option="cog_id")42        self.remove_collection(task_id=task_id, main_coll="sg_annotation_go", detatil_coll=["sg_annotation_go_detail", "sg_annotation_go_graph", "sg_annotation_go_level", "sg_annotation_go_list"], change_option="go_id")43        self.remove_collection(task_id=task_id, main_coll="sg_annotation_kegg", detatil_coll=["sg_annotation_kegg_categories", "sg_annotation_kegg_level", "sg_annotation_kegg_table"], change_option="kegg_id")44        self.remove_collection(task_id=task_id, main_coll="sg_annotation_query", detatil_coll=["sg_annotation_query_detail"], change_option="query_id")45        self.remove_collection(task_id=task_id, main_coll="sg_assessment_chrom_distribution", detatil_coll=["sg_assessment_chrom_distribution_detail"], change_option="chrom_distribution_id")46        self.remove_collection(task_id=task_id, main_coll="sg_assessment_coverage", detatil_coll=["sg_assessment_coverage_detail"], change_option="coverage_id")47        self.remove_collection(task_id=task_id, main_coll="sg_assessment_distribution", detatil_coll=["sg_assessment_distribution_detail"], change_option="distribution_id")48        self.remove_collection(task_id=task_id, main_coll="sg_assessment_duplicate", detatil_coll=["sg_assessment_duplicate_detail"], change_option="dup_id")49        self.remove_collection(task_id=task_id, main_coll="sg_assessment_saturation", detatil_coll=["sg_assessment_saturation_curve"], change_option="saturation_id")50        self.remove_collection(task_id=task_id, main_coll="sg_express_diff", detatil_coll=["sg_express_diff_detail", "sg_express_diff_summary"], change_option="express_diff_id")51        self.remove_collection(task_id=task_id, main_coll="sg_express_correlation", detatil_coll=["sg_express_correlation_detail"], change_option="correlation_id")52        self.remove_collection(task_id=task_id, main_coll="sg_express_pca", detatil_coll=["sg_express_pca_rotation"], change_option="pca_id")53        self.remove_collection(task_id=task_id, main_coll="sg_express_venn", detatil_coll=["sg_express_venn_detail", "sg_express_venn_graph"], change_option="venn_id")54        self.remove_collection(task_id=task_id, main_coll="sg_express_class_code", detatil_coll=["sg_express_class_code_detail"], change_option="class_code_id")55        self.remove_collection(task_id=task_id, main_coll="sg_geneset_venn", detatil_coll=["sg_geneset_venn_detail", "sg_geneset_venn_graph"], change_option="venn_id")56        self.remove_collection(task_id=task_id, main_coll="sg_geneset_cluster", detatil_coll=["sg_geneset_cluster_detail"], change_option="cluster_id")57        self.remove_collection(task_id=task_id, main_coll="sg_geneset_cog_class", detatil_coll=["sg_geneset_cog_class_detail"], change_option="geneset_cog_id")58        self.remove_collection(task_id=task_id, main_coll="sg_geneset_go_class", detatil_coll=["sg_geneset_go_class_detail"], change_option="go_regulate_id")59        self.remove_collection(task_id=task_id, main_coll="sg_geneset_go_enrich", detatil_coll=["sg_geneset_go_enrich_detail"], change_option="go_enrich_id")60        self.remove_collection(task_id=task_id, main_coll="sg_geneset_kegg_class", detatil_coll=["sg_geneset_kegg_class_detail", "sg_geneset_kegg_class_pathway"], change_option="kegg_id")61        self.remove_collection(task_id=task_id, main_coll="sg_geneset_kegg_enrich", detatil_coll=["sg_geneset_kegg_enrich_detail"], change_option="kegg_enrich_id")62        self.remove_collection(task_id=task_id, main_coll="sg_ppinetwork", detatil_coll=["sg_ppinetwork_centrality_node", "sg_ppinetwork_distribution_node", "sg_ppinetwork_node_table", "sg_ppinetwork_structure_attributes", "sg_ppinetwork_structure_link", "sg_ppinetwork_structure_node"], change_option="ppi_id")63        self.remove_collection(task_id=task_id, main_coll="sg_snp", detatil_coll=["sg_snp_detail", "sg_snp_stat"], change_option="snp_id")64        self.remove_collection(task_id=task_id, main_coll="sg_species_information", detatil_coll=["sg_species_information_detail"], change_option="species_id")65        self.remove_collection(task_id=task_id, main_coll="sg_splicing_rmats", detatil_coll=["sg_splicing_rmats_detail", "sg_splicing_rmats_graph", "sg_splicing_rmats_psi", "sg_splicing_rmats_stats"], change_option="splicing_id")66        self.remove_collection(task_id=task_id, main_coll="sg_transcripts", detatil_coll=["sg_transcripts_seq_type", "sg_transcripts_step", "sg_transcripts_relations"], change_option="transcripts_id")67    def find_task_id(self, task_id):68        results = self.db["sg_task"].find({"task_id": {"$regex": task_id + "_.*_.*"}})69        if results:70            for result in results:71                target_task_id = result["task_id"]72                self.remove(target_task_id)73        else:74            print "æ²¡ææ¾å°ä»¥task_idä¸º{}å¤ä»½çdemo,è¯·æ£æ¥!".format(task_id)75if __name__ == "__main__":76    test = RefrnaCopyDelete()...

delete_demo.py

Source:delete_demo.py

1# -*- coding: utf-8 -*-2from biocluster.config import Config3from pymongo import MongoClient4from biocluster.api.database.base import Base5class DeleteDemo(Base):6    def __init__(self):7        super(DeleteDemo, self).__init__()8        self._project_type = 'metagenomic'9    def remove_collection(self, task_id, main_coll, detail_coll=[], change_option=''):10        """11        å é¤ä¸»è¡¨åå¯¹åºçè¯¦ç»è¡¨12        task_id:task_idï¼detail_coll:ä¸»è¡¨å¯¹åºçè¯¦ç»è¡¨, change_option:è¯¦ç»è¡¨ä¸ä¸»è¡¨åæ®µ13        """14        results = self.db[main_coll].find({"task_id": task_id})15        if results:16            for result in results:17                main_id = result["_id"]18                for coll in detail_coll:19                    try:20                        items = self.db[coll].remove({change_option: main_id})21                        print "æåå é¤task_idä¸º {} çç»èè¡¨ {}".format(task_id, coll)22                    except:23                        print "å é¤task_idä¸º {} çç»èè¡¨ {} å¤±è´¥".format(task_id, coll)24                self.db[main_coll].remove({"_id": result["_id"]})25                print "æåå é¤task_idä¸º {} çä¸»è¡¨ {}".format(task_id, main_coll)26        else:27            print "æ²¡ææ¾å°task_idä¸º {} çä¸»è¡¨ {}".format(task_id, main_coll)28    def remove(self, task_id):29        self.remove_collection(task_id=task_id, main_coll="sg_task", detail_coll=[], change_option="")30        self.remove_collection(task_id=task_id, main_coll="data_stat", detail_coll=["data_stat_detail"], change_option="data_stat_id")31        self.remove_collection(task_id=task_id, main_coll="specimen_group", detail_coll=[], change_option="")32        self.remove_collection(task_id=task_id, main_coll="specimen_graphic", detail_coll=[], change_option="")33        self.remove_collection(task_id=task_id, main_coll="env", detail_coll=["env_detail"], change_option="env_id")34        self.remove_collection(task_id=task_id, main_coll="assemble_stat", detail_coll=["assemble_stat_bar", "assemble_stat_detail"], change_option="assem_id")35        self.remove_collection(task_id=task_id, main_coll="predict_gene", detail_coll=["predict_gene_bar", "predict_gene_detail"], change_option="predict_gene_id")36        self.remove_collection(task_id=task_id, main_coll="predict_gene_total", detail_coll=[], change_option="")37        self.remove_collection(task_id=task_id, main_coll="geneset", detail_coll=["geneset_bar", "geneset_readsn", "geneset_readsr"], change_option="geneset_id")38        anno_list = ["ardb", "card", "cazy", "cog", "kegg", "nr", "vfdb", "overview"]39        anno_detail = {40            "ardb": ["ardb_arg", "ardb_class", "ardb_type"],41            "card": ["card_aro", "card_class"],42            "cazy": ["cazy_class", "cazy_family"],43            "cog": ["cog_category", "cog_function", "cog_nog"],44            "kegg": ["kegg_enzyme", "kegg_gene", "kegg_module", "kegg_orthology", "kegg_pathway"],45            "nr": ["nr_detail"],46            "vfdb": ["vfdb_pie", "vfdb_vfs"],47            "overview": [],48        }49        for anno in anno_list:50            collection = "anno_" + anno51            position = "" if anno == "overview" else anno + "_id"52            self.remove_collection(task_id=task_id, main_coll=collection, detail_coll=anno_detail[anno], change_option=position)53        self.remove_collection(task_id=task_id, main_coll="hcluster_tree", detail_coll=[], change_option="")54        self.remove_collection(task_id=task_id, main_coll="anosim", detail_coll=["anosim_detail"], change_option="anosim_id")55        self.remove_collection(task_id=task_id, main_coll="beta_diversity", detail_coll=["beta_diversity_detail"], change_option="beta_diversity_id")56        self.remove_collection(task_id=task_id, main_coll="composition", detail_coll=["composition_detail"], change_option="composition_id")57        self.remove_collection(task_id=task_id, main_coll="enterotype", detail_coll=['enterotype_detail','enterotype_detail_cluster'], change_option="enterotype_id")58        self.remove_collection(task_id=task_id, main_coll="env_vif", detail_coll=["env_vif_detail"], change_option="vif_id")59        self.remove_collection(task_id=task_id, main_coll="heatmap_cor", detail_coll=["heatmap_cor_detail"], change_option="heatmap_cor_id")60        self.remove_collection(task_id=task_id, main_coll="lefse", detail_coll=["lefse_detail"], change_option="species_lefse_id")61        self.remove_collection(task_id=task_id, main_coll="mantel_test", detail_coll=['mantel_test_detail'], change_option="mantel_id")62        self.remove_collection(task_id=task_id, main_coll="metastat", detail_coll=['metastat_detail', 'metastat_plot'], change_option="metastat_id")63        self.remove_collection(task_id=task_id, main_coll="network", detail_coll=['network_degree', 'network_link', 'network_node'], change_option="network_id")64        self.remove_collection(task_id=task_id, main_coll="network_cor", detail_coll=['network_cor_degree', 'network_cor_link', 'network_cor_node'], change_option="network_cor_id")65        self.remove_collection(task_id=task_id, main_coll="permanova", detail_coll=["permanova_detail"], change_option="permanova_id")66        self.remove_collection(task_id=task_id, main_coll="regression", detail_coll=["regression_curve", "regression_line"], change_option="regression_id")67        self.remove_collection(task_id=task_id, main_coll="specimen_distance", detail_coll=["specimen_distance_detail"], change_option="specimen_distance_id")68        self.remove_collection(task_id=task_id, main_coll="contribute", detail_coll=["contribute_detail"], change_option="contribute_id")69    def find_task_id(self, task_id):70        # results = self.db["sg_task"].find({"task_id": {"$regex": task_id + "_.*_.*"}})71        results = self.db["sg_task"].find({"task_id": task_id})72        if results or results.count() != 0:73            for result in results:74                target_task_id = result["task_id"]75                print "å¼å§å é¤"76                self.remove(target_task_id)77        else:78            print "æ²¡ææ¾å°ä»¥task_idä¸º{}å¤ä»½çdemo,è¯·æ£æ¥!".format(task_id)79if __name__ == "__main__":80    test = DeleteDemo()...

html_sql_client.py

Source:html_sql_client.py

1__author__ = 'Yossi'23import os4import socket5import webbrowser6import threading7from tcp_by_size import send_with_size, recv_by_size8910def sent_to_html(data):11    file_name = "iemp.html"12    with open(file_name, 'w') as file:13        file.write(f"<head> {data} <br> "14                   f"<button onclick='self.close()'>Close</button>"15                   f"</head>")16    print(os.path.realpath(file_name))17    os.system(f"start iemp.html")181920def recieve_full_spece():21    serial_num = input("Enter serial num > ")22    brand_name = input("Enter brand name > ")23    gpu = input("Enter gpu > ")24    ram = input("Enter ram > ")25    storage = input("Enter storage > ")26    is_mobile_bool = input("Enter if mobile (True/False) > ")27    if is_mobile_bool == "True":28        is_mobile = 129    else:30        is_mobile = 031    return [serial_num, brand_name, gpu, ram, storage, is_mobile]323334def update_computer_query():35    specs_dict = {"1": "gpu", "2": "ram", "3": "storage"}36    serial = input("[?] What is the serial num of the computer\n[?] you wish to modify? ")37    print("[?] What will you wish to modify?\n"38          "[1] gpu\n"39          "[2] ram\n"40          "[3] storage")41    change_option = input("[?] 1 / 2 / 3 >> ")42    while change_option != "1" and change_option != "2" and change_option != "3":43        print("[-] Mmmmm, WHAT?")44        change_option = input("[?] 1 / 2 / 3 >>")45    change_option = specs_dict[change_option]46    the_change = input("[?] what do you wish to change for? ")47    return change_option + "|" + the_change + "|" + serial484950def manu():51    print ("1. Update Computer\n" + \52          "2. Insert Computer\n" + \53          "3. Delete Computer\n" + \54          "4. Get All Computer\n>" +\55          "5. Get Computer\n>" +\56          "9. exit\n\n>")5758    data = input("Enter Num> ")5960    if data == "9":61        return "q"62    elif data == "1":63        specs = update_computer_query()64        return "UPDCOM|" + specs65    elif data == "2":66        specs = recieve_full_spece()67        return "INSCOM|" + "|".join(str(elem) for elem in specs)68    elif data == "3":69        pc_id = input("pc to delete serial num > ")70        return "DELCOM|" + str(pc_id)71    elif data == "4":72        pc_type = input("1. All Computers\n" + \73                        "2. laptops\n" + \74                        "3. station\n")75        return "GETALL|" + str(pc_type)76    elif data == "5":77        pc_id = input("pc to get serial num > ")78        return "GETCOM|" + str(pc_id)79    else:80        return "RULIVE"818283def handle_recieve(data):84    if data == "":85        print("seems server DC")86        return87    print("Got>>" + "\n".join(data.split("|")))88    sent_to_html("<br>".join(("\n".join(data.split("|"))).split("\n")))899091def main():9293    cli_s = socket.socket()94    cli_s.connect(("127.0.0.1", 33445))95    print("[+] Connected to server!")9697    while True:98        data = manu()99100        if data == "q":101            break102        send_with_size(cli_s, data)103        data = recv_by_size(cli_s)104        handle_recieve(data)105106107108if __name__ == '__main__':
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