diff --git a/qiita_db/support_files/patches/test_db_sql/92.sql b/qiita_db/support_files/patches/test_db_sql/92.sql index f0449c275..d645aa84a 100644 --- a/qiita_db/support_files/patches/test_db_sql/92.sql +++ b/qiita_db/support_files/patches/test_db_sql/92.sql @@ -1,4 +1,928 @@ --- .. date .. --- tmp file for @Gossty +-- 05/07/24 +-- This file serves as a comprehensive testcase for resource allocation plots -SELECT 1; + +INSERT INTO qiita.processing_job(processing_job_id, email, command_id, command_parameters, processing_job_status_id) + VALUES ('ca27ddbc-a678-4b09-8a1d-b65f52f8eb49', 'admin@foo.bar', 1, '""'::json, 1), +('b0f36550-d97c-4dd5-ba1b-910470062801', 'admin@foo.bar', 1, '""'::json, 1), +('b13eefd1-12b7-4c3e-a380-94ec0a3f9f91', 'admin@foo.bar', 1, '""'::json, 1), +('469c27b7-81c4-4f41-b09d-149260961227', 'admin@foo.bar', 1, '""'::json, 1), +('6f198e33-b4ae-47e9-973b-bd5e0b06c353', 'admin@foo.bar', 1, '""'::json, 1), +('045eb36c-5144-4d54-a621-23eb5dc4d6ef', 'admin@foo.bar', 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+('9308c777-1c30-43ac-acf6-9454601601ba', 'admin@foo.bar', 1, '""'::json, 1), +('a1910b9b-2d93-4239-9bc1-1250fea56837', 'admin@foo.bar', 1, '""'::json, 1), +('1280dc5a-d797-42ca-a613-3fbce32f55a0', 'admin@foo.bar', 1, '""'::json, 1), +('0a329ce1-1b82-4faf-a1f7-0d17e4b25251', 'admin@foo.bar', 1, '""'::json, 1), +('3b212797-bb0b-422c-bba1-79921ce40c78', 'admin@foo.bar', 1, '""'::json, 1), +('c14e97a2-a083-4e49-a14b-0abd23483272', 'admin@foo.bar', 1, '""'::json, 1), +('7cd84e00-773a-4387-bcdb-37da819ce5f7', 'admin@foo.bar', 1, '""'::json, 1), +('8553c8e2-5bc9-41b6-9f5e-96a2abfb7055', 'admin@foo.bar', 1, '""'::json, 1), +('65212822-529e-4cf4-a427-78032b9e569b', 'admin@foo.bar', 1, '""'::json, 1), +('3a8d8b29-d408-45ab-8d63-043741de9679', 'admin@foo.bar', 1, '""'::json, 1), +('d68f1265-c669-4f2b-a3ab-ee0e547e0143', 'admin@foo.bar', 1, '""'::json, 1), +('f0b0c5aa-9f97-42e3-82e4-71968f28ad15', 'admin@foo.bar', 1, '""'::json, 1), +('1bf64e7e-4ab9-4dfa-9aeb-6402ad95c165', 'admin@foo.bar', 1, '""'::json, 1), +('605f6954-8697-42c4-97a4-7c3aa6b3cde9', 'admin@foo.bar', 1, '""'::json, 1), +('3688f502-6895-4041-b957-6487f6ba7c98', 'admin@foo.bar', 1, '""'::json, 1), +('013f8041-6f36-4dcb-8af9-67ac1fd78d9e', 'admin@foo.bar', 1, '""'::json, 1), +('58e69a18-ecef-4b61-a62f-7efc1f733731', 'admin@foo.bar', 1, '""'::json, 1), +('e7cb303d-ffe0-4a5e-8eb0-627dd0513f51', 'admin@foo.bar', 1, '""'::json, 1), +('7cc4a810-137c-468e-a249-60b0faf9a003', 'admin@foo.bar', 1, '""'::json, 1), +('056330e4-36eb-4c38-b87f-56484ac69623', 'admin@foo.bar', 1, '""'::json, 1), +('ea9e5c11-f7a7-4dcb-b8b5-20b499611b9f', 'admin@foo.bar', 1, '""'::json, 1), +('8df2b291-adbf-4def-a172-ece656410050', 'admin@foo.bar', 1, '""'::json, 1), +('ce47b98d-8a78-4e97-b20c-297f75394f28', 'admin@foo.bar', 1, '""'::json, 1), +('d8e90f5f-1b10-4f00-9c3b-6bc8daf2cc8a', 'admin@foo.bar', 1, '""'::json, 1), +('cec46141-0286-4430-ac41-ed830decb5e8', 'admin@foo.bar', 1, '""'::json, 1), +('fc9b54c3-0447-49db-a6d0-5b913d0e285a', 'admin@foo.bar', 1, '""'::json, 1), +('3e6d362e-3880-4b90-b693-868547ce0f5a', 'admin@foo.bar', 1, '""'::json, 1), +('d5891efa-0e7d-409b-9bb7-b6ecc081c836', 'admin@foo.bar', 1, '""'::json, 1), +('e4b960c8-33c6-4304-8355-9bafd70569ed', 'admin@foo.bar', 1, '""'::json, 1), +('35c4eb46-3560-4d17-a210-979ba3037c53', 'admin@foo.bar', 1, '""'::json, 1), +('2b85bd17-6d7e-48e0-8e02-477eb9ffe353', 'admin@foo.bar', 1, '""'::json, 1), +('8c7e4562-dcc2-4a31-ab20-b873182b334d', 'admin@foo.bar', 1, '""'::json, 1), +('49fda716-a469-4a6d-a3ef-3bcbd166e668', 'admin@foo.bar', 1, '""'::json, 1), +('f424b26a-840a-42d3-a61f-3bbffd8b194d', 'admin@foo.bar', 1, '""'::json, 1), +('7226d658-da67-4d7c-a898-e59cd77d977b', 'admin@foo.bar', 1, '""'::json, 1), +('50dc9288-e18c-41c2-a271-601289ff5685', 'admin@foo.bar', 1, '""'::json, 1), +('4883db35-3ca6-4b0c-9377-cf7d1d97245d', 'admin@foo.bar', 1, '""'::json, 1), +('3ff09f4e-ada5-45d6-b7e1-fa003e31bf77', 'admin@foo.bar', 1, '""'::json, 1), +('26c68022-6df2-4928-a4fb-220a156b86f7', 'admin@foo.bar', 1, '""'::json, 1), +('cdd878a9-e3f1-4478-b613-90f2b2e9ccbd', 'admin@foo.bar', 1, '""'::json, 1), +('d6e02749-45fb-4b92-8a8e-48b33b617f9c', 'admin@foo.bar', 1, '""'::json, 1), +('47900ec7-0fea-41db-a320-c78b9da36538', 'admin@foo.bar', 1, '""'::json, 1), +('1ef4d550-afaa-44b5-a06c-65286b9f3e00', 'admin@foo.bar', 1, '""'::json, 1), +('8533d2a8-1fcf-4842-8826-c5458c002332', 'admin@foo.bar', 1, '""'::json, 1), +('ab9095d1-af6d-49d5-9c87-bc2576f06135', 'admin@foo.bar', 1, '""'::json, 1), +('61da73ff-b4ff-49a1-b775-c6215cfbd291', 'admin@foo.bar', 1, '""'::json, 1), +('6c84dcf1-c5ea-4e69-b17f-d2d5b8d48bdf', 'admin@foo.bar', 1, '""'::json, 1), +('dcb12603-4142-44d1-9a52-3ca3511e380e', 'admin@foo.bar', 1, '""'::json, 1), +('a0dd0a4d-b73f-4e9d-87dd-d29efba25336', 'admin@foo.bar', 1, '""'::json, 1); +-- SPLIT + +INSERT INTO qiita.slurm_resource_allocations(processing_job_id, samples, columns, input_size, extra_info, memory_used, walltime_used) + VALUES ('ca27ddbc-a678-4b09-8a1d-b65f52f8eb49', 39, 81, 2, 'nan', 327036000, 91), +('b0f36550-d97c-4dd5-ba1b-910470062801', 160, 212, 2, 'nan', 342204000, 219), +('b13eefd1-12b7-4c3e-a380-94ec0a3f9f91', 62, 83, 2, 'nan', 328716000, 165), +('469c27b7-81c4-4f41-b09d-149260961227', 16, 83, 2, 'nan', 326344000, 154), +('6f198e33-b4ae-47e9-973b-bd5e0b06c353', 96, 152, 2, 'nan', 332492000, 185), +('045eb36c-5144-4d54-a621-23eb5dc4d6ef', 242, 43, 2, 'nan', 369988000, 137), +('041f3278-2752-44f9-8caa-ac6ae80c98e6', 231, 97, 2, 'nan', 375820000, 151), +('6325e683-b215-4c56-bf5a-cbbc92330067', 120, 83, 2, 'nan', 373536000, 234), +('03dcca05-0d4f-48c5-bc7a-7ef884be8efc', 92, 83, 2, 'nan', 372188000, 407), +('8d84685f-97f4-4ea7-8857-2dcec5a20775', 40, 83, 2, 'nan', 368816000, 296), +('8b714fe7-51d9-492c-9b49-4fe09b595067', 96, 87, 2, 'nan', 371972000, 138), +('490c0623-4ed7-4064-9ffe-ba5afc0f0aa0', 28, 50, 2, 'nan', 369696000, 185), +('c8301f3d-a4fe-407a-9aec-b9dfee0cc2fd', 12, 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+('ab9095d1-af6d-49d5-9c87-bc2576f06135', 68, 43, 2, 'nan', 326896000, 235), +('61da73ff-b4ff-49a1-b775-c6215cfbd291', 231, 107, 2, 'nan', 333544000, 200), +('6c84dcf1-c5ea-4e69-b17f-d2d5b8d48bdf', 123, 50, 2, 'nan', 327520000, 82), +('dcb12603-4142-44d1-9a52-3ca3511e380e', 320, 44, 2, 'nan', 329448000, 475), +('a0dd0a4d-b73f-4e9d-87dd-d29efba25336', 41, 50, 2, 'nan', 301108000, 144); \ No newline at end of file diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py index 1f8a30a23..8bfe05d9a 100644 --- a/qiita_db/test/test_meta_util.py +++ b/qiita_db/test/test_meta_util.py @@ -286,7 +286,7 @@ def _get_daily_stats(): ('num_studies_ebi', b'1', r_client.get), ('num_samples_ebi', b'27', r_client.get), ('number_samples_ebi_prep', b'54', r_client.get), - ('num_processing_jobs', b'14', r_client.get) + ('num_processing_jobs', b'474', r_client.get) # not testing img/time for simplicity # ('img', r_client.get), # ('time', r_client.get) diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py index 0b5094f27..f7e63ef39 100644 --- a/qiita_db/test/test_software.py +++ b/qiita_db/test/test_software.py @@ -494,13 +494,20 @@ def test_processing_jobs(self): '6ad4d590-4fa3-44d3-9a8f-ddbb472b1b5f', '063e553b-327c-4818-ab4a-adfe58e49860', 'ac653cb5-76a6-4a45-929e-eb9b2dee6b63'] - exp = [qdb.processing_job.ProcessingJob(j) for j in exp_jids] - self.assertCountEqual(qdb.software.Command(1).processing_jobs, exp) + + jobs = qdb.software.Command(1).processing_jobs + set_jobs = set(jobs) + + # comparing the length of jobs and set_jobs, since there could've been + # duplicates in the tests + self.assertEqual(len(jobs), len(set_jobs)) + + exp = set([qdb.processing_job.ProcessingJob(j) for j in exp_jids]) + self.assertEqual(len(set_jobs & exp), len(exp_jids)) exp_jids = ['bcc7ebcd-39c1-43e4-af2d-822e3589f14d'] exp = [qdb.processing_job.ProcessingJob(j) for j in exp_jids] self.assertCountEqual(qdb.software.Command(2).processing_jobs, exp) - self.assertCountEqual(qdb.software.Command(4).processing_jobs, []) diff --git a/qiita_db/test/test_user.py b/qiita_db/test/test_user.py index 6978e3dba..2dced88d9 100644 --- a/qiita_db/test/test_user.py +++ b/qiita_db/test/test_user.py @@ -491,17 +491,10 @@ def test_jobs(self): limit=1, ignore_status=ignore_status), [ PJ('b72369f9-a886-4193-8d3d-f7b504168e75')]) - # no jobs - self.assertEqual(qdb.user.User('admin@foo.bar').jobs( - ignore_status=ignore_status), []) - # generates expected jobs jobs = qdb.user.User('shared@foo.bar').jobs() self.assertEqual(jobs, []) - # no jobs - self.assertEqual(qdb.user.User('admin@foo.bar').jobs(), []) - def test_update_email(self): user = qdb.user.User('shared@foo.bar') with self.assertRaisesRegex(IncorrectEmailError, 'Bad email given:'): diff --git a/qiita_db/test/test_util.py b/qiita_db/test/test_util.py index a72918529..a8df7ed3c 100644 --- a/qiita_db/test/test_util.py +++ b/qiita_db/test/test_util.py @@ -1309,19 +1309,23 @@ def test_quick_mounts_purge(self): class ResourceAllocationPlotTests(TestCase): def setUp(self): - - self.PATH_TO_DATA = ('./qiita_db/test/test_data/' - 'jobs_2024-02-21.tsv.gz') - self.CNAME = "Validate" - self.SNAME = "Diversity types - alpha_vector" + self.CNAME = "Split libraries FASTQ" + self.SNAME = "QIIMEq2" self.col_name = 'samples * columns' - self.df = pd.read_csv(self.PATH_TO_DATA, sep='\t', - dtype={'extra_info': str}) + self.columns = [ + "sName", "sVersion", "cID", "cName", "processing_job_id", + "parameters", "samples", "columns", "input_size", "extra_info", + "MaxRSSRaw", "ElapsedRaw"] + + # df is a dataframe that represents a table with columns specified in + # self.columns + self.df = qdb.util._retrieve_resource_data( + self.CNAME, self.SNAME, self.columns) def test_plot_return(self): # check the plot returns correct objects fig1, axs1 = qdb.util.resource_allocation_plot( - self.PATH_TO_DATA, self.CNAME, self.SNAME, self.col_name) + self.df, self.CNAME, self.SNAME, self.col_name) self.assertIsInstance( fig1, Figure, "Returned object fig1 is not a Matplotlib Figure") @@ -1346,7 +1350,7 @@ def test_minimize_const(self): failures_df = qdb.util._resource_allocation_failures( self.df, k, a, b, bm, self.col_name, 'MaxRSSRaw') failures = failures_df.shape[0] - self.assertEqual(bm, qdb.util.mem_model4, msg="""Best memory model + self.assertEqual(bm, qdb.util.mem_model3, msg="""Best memory model doesn't match""") self.assertEqual(failures, 0, "Number of failures must be 0") diff --git a/qiita_db/util.py b/qiita_db/util.py index ebfe0ed11..402a03e87 100644 --- a/qiita_db/util.py +++ b/qiita_db/util.py @@ -73,10 +73,10 @@ from email.mime.multipart import MIMEMultipart from email.mime.text import MIMEText -import pandas as pd from datetime import timedelta import matplotlib.pyplot as plt import numpy as np +import pandas as pd from scipy.optimize import minimize # memory constant functions defined for @resource_allocation_plot @@ -2341,7 +2341,7 @@ def send_email(to, subject, body): smtp.close() -def resource_allocation_plot(file, cname, sname, col_name): +def resource_allocation_plot(df, cname, sname, col_name): """Builds resource allocation plot for given filename and jobs Parameters @@ -2361,9 +2361,6 @@ def resource_allocation_plot(file, cname, sname, col_name): Returns a matplotlib object with a plot """ - df = pd.read_csv(file, sep='\t', dtype={'extra_info': str}) - df['ElapsedRawTime'] = pd.to_timedelta(df.ElapsedRawTime) - df = df[(df.cName == cname) & (df.sName == sname)] df.dropna(subset=['samples', 'columns'], inplace=True) df[col_name] = df.samples * df['columns'] df[col_name] = df[col_name].astype(int) @@ -2383,6 +2380,41 @@ def resource_allocation_plot(file, cname, sname, col_name): return fig, axs +def _retrieve_resource_data(cname, sname, columns): + with qdb.sql_connection.TRN: + sql = """ + SELECT + s.name AS sName, + s.version AS sVersion, + sc.command_id AS cID, + sc.name AS cName, + pr.processing_job_id AS processing_job_id, + pr.command_parameters AS parameters, + sra.samples AS samples, + sra.columns AS columns, + sra.input_size AS input_size, + sra.extra_info AS extra_info, + sra.memory_used AS memory_used, + sra.walltime_used AS walltime_used + FROM + qiita.processing_job pr + JOIN + qiita.software_command sc ON pr.command_id = sc.command_id + JOIN + qiita.software s ON sc.software_id = s.software_id + JOIN + qiita.slurm_resource_allocations sra + ON pr.processing_job_id = sra.processing_job_id + WHERE + sc.name = %s + AND s.name = %s; + """ + qdb.sql_connection.TRN.add(sql, sql_args=[cname, sname]) + res = qdb.sql_connection.TRN.execute_fetchindex() + df = pd.DataFrame(res, columns=columns) + return df + + def _resource_allocation_plot_helper( df, ax, cname, sname, curr, models, col_name): """Helper function for resource allocation plot. Builds plot for MaxRSSRaw