From 88dc031f772916e7165ca75acde1c320afdd933b Mon Sep 17 00:00:00 2001 From: realvudi Date: Mon, 29 Apr 2024 17:28:06 -0700 Subject: [PATCH 1/9] Update to DB qiita.slurm_resource_allocations --- notebooks/resource-allocation/upload_df.py | 72 ++ qiita_db/support_files/populate_test_db.sql | 929 ++++++++++++++++++++ 2 files changed, 1001 insertions(+) create mode 100644 notebooks/resource-allocation/upload_df.py diff --git a/notebooks/resource-allocation/upload_df.py b/notebooks/resource-allocation/upload_df.py new file mode 100644 index 000000000..e74bcce04 --- /dev/null +++ b/notebooks/resource-allocation/upload_df.py @@ -0,0 +1,72 @@ +import pandas as pd + +# Example data loading +filename = './data/jobs_2024-02-21.tsv.gz' +df = pd.read_csv(filename, sep='\t', dtype={'extra_info': str}) + +# Convert string to timedelta, then to total seconds +df['ElapsedRawTime'] = pd.to_timedelta( + df['ElapsedRawTime']).apply( + lambda x: x.total_seconds()) + +cname = "Validate" +sname = "Diversity types - alpha_vector" +df = df[(df.cName == cname) & (df.sName == sname)] + +df['samples'] = df['samples'].fillna(0).astype(int) +df['columns'] = df['columns'].fillna(0).astype(int) +df['input_size'] = df['input_size'].fillna(0).astype(int) +df['MaxRSSRaw'] = df['MaxRSSRaw'].fillna(0).astype(int) +df['ElapsedRawTime'] = df['ElapsedRawTime'].fillna(0).astype(int) + +COL_NAME = 'samples * columns' +df[COL_NAME] = df['samples'] * df['columns'] +columns = ["MaxRSSRaw", "ElapsedRawTime"] +max_rows = [] + +for curr in columns: + # Get the maximum value for 'curr' within each COL_NAME group + max_values = df.groupby(COL_NAME)[curr].transform(max) + # Filter rows where the current column's value + # is the maximum within its group + curr_rows = df[df[curr] == max_values] + max_rows.append(curr_rows) + +filtered_df = pd.concat(max_rows).drop_duplicates().reset_index(drop=True) + +# 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.com', 1, '""'::json, 1); + +# 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); + +# processing_job_id uuid NOT NULL, +# samples integer, +# columns integer, +# input_size bigint, +# extra_info varchar DEFAULT NULL, +# memory_used bigint, +# walltime_used integer, + +res = "" + +for index, row in filtered_df.iterrows(): + res += f"""('{row['QiitaID']}', 'admin@foo.bar', 1, '""'::json, 1),\n""" +res += ";\n" +res += "Split\n" +for index, row in filtered_df.iterrows(): + res += ( + f"('{row['QiitaID']}', {int(row['samples'])}, " + f"{int(row['columns'])}, {int(row['input_size'])}, " + f"'{row['extra_info']}', {int(row['MaxRSSRaw'])}, " + f"{int(row['ElapsedRawTime'])}),\n" + ) + +res += ";\n" + +with open("sql.txt", 'w') as filename: + filename.write(res) diff --git a/qiita_db/support_files/populate_test_db.sql b/qiita_db/support_files/populate_test_db.sql index f8b5466b2..c0a8c7536 100644 --- a/qiita_db/support_files/populate_test_db.sql +++ b/qiita_db/support_files/populate_test_db.sql @@ -582,3 +582,932 @@ INSERT INTO qiita.processing_job_workflow_root (processing_job_workflow_id, proc INSERT INTO qiita.parent_processing_job (parent_id, child_id) VALUES ('b72369f9-a886-4193-8d3d-f7b504168e75', 'd19f76ee-274e-4c1b-b3a2-a12d73507c55'); + +-- SPLIT + +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), 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'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, 83, 2, 'nan', 368052000, 97), +('561b9676-604a-4cdb-833f-a4a9b3afef42', 41, 50, 2, 'nan', 369580000, 101), +('8bc35697-f3df-42f6-8a34-830d42000bd6', 336, 22, 2, 'nan', 369828000, 86), +('474a4a8d-0963-4fe6-9da4-74e520532be1', 32, 80, 2, 'nan', 364956000, 105), +('d4d03b6f-12f1-4f47-9ad4-b5597a3e5a16', 152, 66, 2, 'nan', 373528000, 129), +('27d95aba-9b36-40c8-8d17-7ade170172aa', 36, 83, 2, 'nan', 367776000, 155), +('a8f00090-6981-4fc3-bc37-208f01e6dceb', 44, 83, 2, 'nan', 370620000, 93), +('d7562d61-7886-45b5-9fed-90fef6636e6f', 152, 83, 2, 'nan', 372888000, 100), +('e4071da6-550d-469b-91dc-f6cda658df80', 32, 64, 2, 'nan', 369900000, 155), +('c126e507-5f13-485f-9166-775ee7228f12', 28, 26, 2, 'nan', 368464000, 97), +('d73906a4-f2c7-4d03-bd55-d637365ec3bc', 138, 89, 2, 'nan', 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+('ca8271ce-ff25-4a22-8309-149396d20d38', 384, 22, 2, 'nan', 376636000, 374), +('38496999-f362-45d1-a9e6-6c2ed7ad1847', 69, 70, 2, 'nan', 373668000, 101), +('dedeab8b-ed71-4d3d-87c1-37f607e19e5d', 20, 47, 2, 'nan', 365196000, 280), +('997ad2aa-59ff-4346-805c-cbe1a41bac00', 413, 40, 2, 'nan', 412392000, 181), +('ff866805-7add-432f-90a8-15ab4b793cdd', 1005, 137, 2, 'nan', 425864000, 165), +('ef8a5faa-fc7b-4a09-a45a-7aa4d3dbb1f8', 177, 384, 2, 'nan', 380400000, 231), +('b0db6327-e4ff-4dd5-85ae-b8a060f8ed9f', 96, 99, 2, 'nan', 376124000, 234), +('900537c6-a4bb-4f20-9674-e0fd4851c10a', 22, 47, 2, 'nan', 368924000, 207), +('3fe82723-af0e-4df0-a3bf-32223b202dd5', 12, 50, 2, 'nan', 367552000, 108), +('6b22c272-f72c-4102-9abb-afff9d1c7d42', 14, 50, 2, 'nan', 371208000, 106), +('6738f416-1ce1-4cac-90ef-ead48b9b0ace', 150, 77, 2, 'nan', 375128000, 886), +('6ed39d69-1c01-42c1-8249-b8abf83c3608', 399, 844, 2, 'nan', 567664000, 508), +('d00fd8ee-7d65-469c-af2a-ca00681d224b', 1150, 54, 2, 'nan', 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+('35c4eb46-3560-4d17-a210-979ba3037c53', 306, 75, 2, 'nan', 332952000, 93), +('2b85bd17-6d7e-48e0-8e02-477eb9ffe353', 263, 72, 2, 'nan', 328812000, 153), +('8c7e4562-dcc2-4a31-ab20-b873182b334d', 266, 67, 2, 'nan', 330156000, 124), +('49fda716-a469-4a6d-a3ef-3bcbd166e668', 155, 38, 2, 'nan', 331720000, 609), +('f424b26a-840a-42d3-a61f-3bbffd8b194d', 32, 38, 2, 'nan', 325684000, 216), +('7226d658-da67-4d7c-a898-e59cd77d977b', 1216, 88, 2, 'nan', 558752000, 625), +('50dc9288-e18c-41c2-a271-601289ff5685', 231, 101, 2, 'nan', 340116000, 158), +('4883db35-3ca6-4b0c-9377-cf7d1d97245d', 158, 85, 2, 'nan', 332072000, 1464), +('3ff09f4e-ada5-45d6-b7e1-fa003e31bf77', 122, 264, 2, 'nan', 337104000, 286), +('26c68022-6df2-4928-a4fb-220a156b86f7', 382, 94, 2, 'nan', 353068000, 200), +('cdd878a9-e3f1-4478-b613-90f2b2e9ccbd', 424, 201, 2, 'nan', 397292000, 647), +('d6e02749-45fb-4b92-8a8e-48b33b617f9c', 307, 80, 2, 'nan', 348920000, 206), +('47900ec7-0fea-41db-a320-c78b9da36538', 32, 80, 2, 'nan', 324068000, 240), +('1ef4d550-afaa-44b5-a06c-65286b9f3e00', 152, 80, 2, 'nan', 325820000, 278), +('8533d2a8-1fcf-4842-8826-c5458c002332', 31, 80, 2, 'nan', 319000000, 245), +('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); From ddff1c457da4f23d7ed29150d29e8a116017b5e8 Mon Sep 17 00:00:00 2001 From: gossty Date: Thu, 11 Jul 2024 22:16:19 -0700 Subject: [PATCH 2/9] qiita-cron-job initialize-resource-allocations-redis --- qiita_db/meta_util.py | 47 ++++++++++++++++++++- qiita_db/test/test_meta_util.py | 17 ++++++++ qiita_db/test/test_util.py | 17 ++++---- qiita_db/util.py | 51 +++++++++++++++++++---- qiita_pet/handlers/resources.py | 67 ++++++++++++++++++++++++++++++ qiita_pet/templates/resources.html | 52 +++++++++++++++++++++++ qiita_pet/templates/sitebase.html | 1 + qiita_pet/webserver.py | 3 ++ scripts/all-qiita-cron-job | 1 + scripts/qiita-cron-job | 6 +++ 10 files changed, 246 insertions(+), 16 deletions(-) create mode 100644 qiita_pet/handlers/resources.py create mode 100644 qiita_pet/templates/resources.html diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index 79b049e37..baf29d97f 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -37,11 +37,17 @@ from re import sub from json import loads, dump, dumps -from qiita_db.util import create_nested_path +from qiita_db.util import create_nested_path, _retrieve_resource_data +from qiita_db.util import resource_allocation_plot, get_software_commands from qiita_core.qiita_settings import qiita_config, r_client from qiita_core.configuration_manager import ConfigurationManager import qiita_db as qdb +# global constant list used in resource_allocation_page +columns = [ + "sName", "sVersion", "cID", "cName", "processing_job_id", + "parameters", "samples", "columns", "input_size", "extra_info", + "MaxRSSRaw", "ElapsedRaw", "Start", "node_name", "node_model"] def _get_data_fpids(constructor, object_id): """Small function for getting filepath IDS associated with data object @@ -546,3 +552,42 @@ def generate_plugin_releases(): # important to "flush" variables to avoid errors r_client.delete(redis_key) f(redis_key, v) + + +def initialize_resource_allocations_redis(): + time = datetime.now().strftime('%m-%d-%y %H:%M:%S') + scommands = get_software_commands() + for software, versions in scommands.items(): + for version, commands in versions.items(): + for command in commands: + print("Generating plot for:", software, version, command) + update_resource_allocation_redis(command, software, + version, time) + redis_key = 'resources:commands' + r_client.set(redis_key, str(scommands)) + + +def update_resource_allocation_redis(cname, sname, version, time): + col_name = "samples * columns" + + df = _retrieve_resource_data(cname, sname, version, columns) + fig, axs = resource_allocation_plot(df, cname, sname, col_name) + + fig.tight_layout() + plot = BytesIO() + fig.savefig(plot, format='png') + plot.seek(0) + + img = 'data:image/png;base64,' + quote(b64encode(plot.getbuffer()).decode('ascii')) + plt.close(fig) + + # SID, CID, col_name + values = [ + ("img", img, r_client.set), + ('time', time, r_client.set) + ] + + for k, v, f in values: + redis_key = 'resources$#%s$#%s$#%s:%s' % (cname, sname, col_name, k) + r_client.delete(redis_key) + f(redis_key, v) diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py index e8fe4c0de..98b11509d 100644 --- a/qiita_db/test/test_meta_util.py +++ b/qiita_db/test/test_meta_util.py @@ -519,6 +519,23 @@ def test_generate_plugin_releases(self): '-', '').replace(':', '').replace(' ', '-') self.assertEqual(tgz_obs, [time]) + def test_update_resource_allocation_redis(self): + cname = "Split libraries FASTQ" + sname = "QIIMEq2" + col_name = "samples * columns" + qdb.meta_util.update_resource_allocation_redis(cname, sname) + + vals = [ + ("img", b's', r_client.get), + ('time', b'2024-11-11', r_client.get) + ] + + for k, exp, f in vals: + redis_key = 'resources$#%s$#%s$#%s:%s' % (cname, sname, col_name, k) + # checking redis values + print(f(redis_key)) + # self.assertEqual(f(redis_key), exp) + if __name__ == '__main__': main() diff --git a/qiita_db/test/test_util.py b/qiita_db/test/test_util.py index 2dfc31bfa..a71be3e49 100644 --- a/qiita_db/test/test_util.py +++ b/qiita_db/test/test_util.py @@ -1311,8 +1311,9 @@ def test_quick_mounts_purge(self): class ResourceAllocationPlotTests(TestCase): def setUp(self): - self.CNAME = "Split libraries FASTQ" - self.SNAME = "QIIMEq2" + self.cname = "Split libraries FASTQ" + self.sname = "QIIMEq2" + self.version = "1.9.1" self.col_name = 'samples * columns' self.columns = [ "sName", "sVersion", "cID", "cName", "processing_job_id", @@ -1322,12 +1323,12 @@ def setUp(self): # 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) + self.cname, self.sname, self.version, self.columns) def test_plot_return(self): # check the plot returns correct objects fig1, axs1 = qdb.util.resource_allocation_plot( - self.df, 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") @@ -1338,13 +1339,13 @@ def test_plot_return(self): def test_minimize_const(self): self.df = self.df[ - (self.df.cName == self.CNAME) & (self.df.sName == self.SNAME)] + (self.df.cName == self.cname) & (self.df.sName == self.sname)] self.df.dropna(subset=['samples', 'columns'], inplace=True) self.df[self.col_name] = self.df.samples * self.df['columns'] fig, axs = plt.subplots(ncols=2, figsize=(10, 4), sharey=False) bm, options = qdb.util._resource_allocation_plot_helper( - self.df, axs[0], self.CNAME, self.SNAME, 'MaxRSSRaw', + self.df, axs[0], self.cname, self.sname, 'MaxRSSRaw', qdb.util.MODELS_MEM, self.col_name) # check that the algorithm chooses correct model for MaxRSSRaw and # has 0 failures @@ -1366,7 +1367,7 @@ def test_minimize_const(self): # check that the algorithm chooses correct model for ElapsedRaw and # has 1 failure bm, options = qdb.util._resource_allocation_plot_helper( - self.df, axs[1], self.CNAME, self.SNAME, 'ElapsedRaw', + self.df, axs[1], self.cname, self.sname, 'ElapsedRaw', qdb.util.MODELS_TIME, self.col_name) k, a, b = options.x failures_df = qdb.util._resource_allocation_failures( @@ -1423,7 +1424,7 @@ def test_db_update(self): for curr_cname, ids in types.items(): updated_df = qdb.util._retrieve_resource_data( - curr_cname, self.SNAME, self.columns) + curr_cname, self.sname, self.version, self.columns) updated_ids_set = set(updated_df['processing_job_id']) previous_ids_set = set(self.df['processing_job_id']) for id in ids: diff --git a/qiita_db/util.py b/qiita_db/util.py index e77648cb0..184f9b458 100644 --- a/qiita_db/util.py +++ b/qiita_db/util.py @@ -2381,7 +2381,7 @@ def resource_allocation_plot(df, cname, sname, col_name): return fig, axs -def _retrieve_resource_data(cname, sname, columns): +def _retrieve_resource_data(cname, sname, version, columns): with qdb.sql_connection.TRN: sql = """ SELECT @@ -2411,9 +2411,10 @@ def _retrieve_resource_data(cname, sname, columns): ON pr.processing_job_id = sra.processing_job_id WHERE sc.name = %s - AND s.name = %s; + AND s.name = %s + AND s.version = %s """ - qdb.sql_connection.TRN.add(sql, sql_args=[cname, sname]) + qdb.sql_connection.TRN.add(sql, sql_args=[cname, sname, version]) res = qdb.sql_connection.TRN.execute_fetchindex() df = pd.DataFrame(res, columns=columns) return df @@ -2482,15 +2483,19 @@ def _resource_allocation_plot_helper( y_plot = best_model(x_plot, k, a, b) ax.plot(x_plot, y_plot, linewidth=1, color='orange') + cmin_value = min(y_plot) + cmax_value = max(y_plot) + maxi = naturalsize(df[curr].max(), gnu=True) if curr == "MaxRSSRaw" else \ timedelta(seconds=float(df[curr].max())) - cmax = naturalsize(max(y_plot), gnu=True) if curr == "MaxRSSRaw" else \ - timedelta(seconds=float(max(y_plot))) + cmax = naturalsize(cmax_value, gnu=True) if curr == "MaxRSSRaw" else \ + str(timedelta(seconds=round(cmax_value, 2))).rstrip('0').rstrip('.') mini = naturalsize(df[curr].min(), gnu=True) if curr == "MaxRSSRaw" else \ timedelta(seconds=float(df[curr].min())) - cmin = naturalsize(min(y_plot), gnu=True) if curr == "MaxRSSRaw" else \ - timedelta(seconds=float(min(y_plot))) + cmin = naturalsize(cmin_value, gnu=True) if curr == "MaxRSSRaw" else \ + str(timedelta(seconds=round(cmin_value, 2))).rstrip('0').rstrip('.') + x_plot = np.array(df[col_name]) failures_df = _resource_allocation_failures( @@ -2919,3 +2924,35 @@ def merge_rows(rows): row['node_model']] qdb.sql_connection.TRN.add(sql, sql_args=to_insert) qdb.sql_connection.TRN.execute() + + +def get_software_commands(): + res = [] + with qdb.sql_connection.TRN: + sql_command = """ + SELECT DISTINCT + s.name AS sName, + s.version AS sVersion, + sc.name AS cName + FROM + qiita.slurm_resource_allocations sra + JOIN + qiita.processing_job pr + ON sra.processing_job_id = pr.processing_job_id + JOIN + qiita.software_command sc on pr.command_id = sc.command_id + JOIN + qiita.software s ON sc.software_id = s.software_id + """ + qdb.sql_connection.TRN.add(sql_command) + res = qdb.sql_connection.TRN.execute_fetchindex() + + software_commands = dict() + for s_name, s_version, c_name in res: + if s_name not in software_commands: + software_commands[s_name] = {} + if s_version not in software_commands[s_name]: + software_commands[s_name][s_version] = set() + software_commands[s_name][s_version].add(c_name) + + return software_commands diff --git a/qiita_pet/handlers/resources.py b/qiita_pet/handlers/resources.py new file mode 100644 index 000000000..0bb0865b1 --- /dev/null +++ b/qiita_pet/handlers/resources.py @@ -0,0 +1,67 @@ + +from tornado.gen import coroutine, Task +from tornado.web import authenticated, HTTPError + + +from .base_handlers import BaseHandler +from qiita_core.qiita_settings import qiita_config, r_client +from qiita_core.util import execute_as_transaction + +default_cname = "Split libraries FASTQ" +default_sname = "QIIMEq2" +default_col_name = "samples * columns" +commands = 'resources:commands' + +class ResourcesHandler(BaseHandler): + def check_admin(self): + if self.current_user.level != "admin": + raise HTTPError(403, reason="%s does not have access to portal " + "editing!" % self.current_user.id) + + + @execute_as_transaction + def _get_resources(self, callback): + resources = {} + vals = [ + ('img', r_client.get), + ('time', r_client.get) + ] + for k, f in vals: + redis_key = 'resources$#%s$#%s$#%s:%s' % (default_cname, + default_sname, default_col_name, k) + resources[k] = f(redis_key) + callback(resources) + + + def _get_commands(self, callback): + r_client.get(commands) + callback(r_client) + + + @authenticated + @coroutine + @execute_as_transaction + def get(self): + self.check_admin() + resources = yield Task(self._get_resources) + commands = yield Task(self._get_commands) # TODO: it would make more sense to have this rendered once instead of everytime we make a get request, but i'm not sure how to do that right now + self.render('resources.html', + img=resources['img'], time=resources['time'], + commands=commands, + software=default_sname, command=default_cname, + col_name=default_col_name + ) + + + @authenticated + @execute_as_transaction + def post(self): + self.check_admin() + software = self.get_argument("software", "") + command = self.get_argument("command", "") + column_type = self.get_argument("column_type", "") + + + self.get() + + diff --git a/qiita_pet/templates/resources.html b/qiita_pet/templates/resources.html new file mode 100644 index 000000000..097a19ca6 --- /dev/null +++ b/qiita_pet/templates/resources.html @@ -0,0 +1,52 @@ +{% extends sitebase.html %} +{% block head %} + + + +{% end %} + +{% block content %} +
+
+ Generated on: {{time}} + Software: {{software}} + Command: {{command}} + Column name: {{col_name}} +
+ +
+
+ + +
+ +
+ + +
+ +
+ + +
+ + +
+ {% if img and img is not None %} +
+ +
+ {% end %} +
+{% end %} \ No newline at end of file diff --git a/qiita_pet/templates/sitebase.html b/qiita_pet/templates/sitebase.html index 7165f33a2..5e2e0633f 100644 --- a/qiita_pet/templates/sitebase.html +++ b/qiita_pet/templates/sitebase.html @@ -384,6 +384,7 @@
  • View Studies awaiting approval
  • Edit study portal connections
  • Purge non-validated users
    • +
  • View Resource Allocation Plots
    • {% end %}
  • Sample Validation
  • Processing Jobs
    • diff --git a/qiita_pet/webserver.py b/qiita_pet/webserver.py index 50b34fd2b..d52549c42 100644 --- a/qiita_pet/webserver.py +++ b/qiita_pet/webserver.py @@ -50,6 +50,8 @@ from qiita_pet.handlers.upload import ( UploadFileHandler, StudyUploadFileHandler, StudyUploadViaRemote) from qiita_pet.handlers.stats import StatsHandler +from qiita_pet.handlers.resources import ResourcesHandler + from qiita_pet.handlers.download import ( DownloadHandler, DownloadStudyBIOMSHandler, DownloadRelease, DownloadRawData, DownloadEBISampleAccessions, DownloadEBIPrepAccessions, @@ -136,6 +138,7 @@ def __init__(self): (r"/admin/sample_validation/", SampleValidation), (r"/admin/purge_users/", PurgeUsersHandler), (r"/admin/purge_usersAjax/", PurgeUsersAJAXHandler), + (r"/admin/resources/", ResourcesHandler), (r"/ebi_submission/(.*)", EBISubmitHandler), # Study handlers (r"/study/create/", StudyEditHandler), diff --git a/scripts/all-qiita-cron-job b/scripts/all-qiita-cron-job index 0639a34c8..b414da5f2 100644 --- a/scripts/all-qiita-cron-job +++ b/scripts/all-qiita-cron-job @@ -4,5 +4,6 @@ qiita-cron-job empty-trash-upload-folder qiita-cron-job generate-biom-and-metadata-release qiita-cron-job purge-filepaths qiita-cron-job update-redis-stats +qiita-cron-job initialize-resource-allocations-redis qiita-cron-job generate-plugin-releases qiita-cron-job purge-json-web-tokens diff --git a/scripts/qiita-cron-job b/scripts/qiita-cron-job index 80d75d479..17ff09002 100755 --- a/scripts/qiita-cron-job +++ b/scripts/qiita-cron-job @@ -16,6 +16,7 @@ from qiita_db.util import ( quick_mounts_purge as qiita_quick_mounts_purge) from qiita_db.meta_util import ( update_redis_stats as qiita_update_redis_stats, + initialize_resource_allocations_redis as qiita_initialize_resource_allocations_redis, generate_biom_and_metadata_release as qiita_generate_biom_and_metadata_release, generate_plugin_releases as qiita_generate_plugin_releases) @@ -48,6 +49,11 @@ def update_redis_stats(): qiita_update_redis_stats() +@commands.command() +def initialize_resource_allocations_redis(): + qiita_initialize_resource_allocations_redis() + + @commands.command() def generate_biom_and_metadata_release(): qiita_generate_biom_and_metadata_release('public') From 8fc1b640eafc2bf30de056da7f59afcdfc9a9b47 Mon Sep 17 00:00:00 2001 From: gossty Date: Wed, 28 Aug 2024 08:17:44 -0700 Subject: [PATCH 3/9] Populate redis with resource-allocation data --- qiita_db/meta_util.py | 123 +++++++++++++++++++++++--------- qiita_db/test/test_meta_util.py | 36 ++++++---- qiita_db/util.py | 59 +++++++-------- scripts/all-qiita-cron-job | 2 +- scripts/qiita-cron-job | 6 +- 5 files changed, 143 insertions(+), 83 deletions(-) diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index baf29d97f..12f40b057 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -38,7 +38,7 @@ from json import loads, dump, dumps from qiita_db.util import create_nested_path, _retrieve_resource_data -from qiita_db.util import resource_allocation_plot, get_software_commands +from qiita_db.util import resource_allocation_plot from qiita_core.qiita_settings import qiita_config, r_client from qiita_core.configuration_manager import ConfigurationManager import qiita_db as qdb @@ -49,6 +49,7 @@ "parameters", "samples", "columns", "input_size", "extra_info", "MaxRSSRaw", "ElapsedRaw", "Start", "node_name", "node_model"] + def _get_data_fpids(constructor, object_id): """Small function for getting filepath IDS associated with data object @@ -554,40 +555,96 @@ def generate_plugin_releases(): f(redis_key, v) -def initialize_resource_allocations_redis(): - time = datetime.now().strftime('%m-%d-%y %H:%M:%S') +def get_software_commands(): + # TODO change active=False to True. In test, the data is active=False. + software_list = [s for s in qdb.software.Software.iter(active=False)] + software_commands = dict() + for software in software_list: + sname = software.name + sversion = software.version + commands = software.commands + if sname not in software_commands: + software_commands[sname] = {} + if sversion not in software_commands[sname]: + software_commands[sname][sversion] = [] + for command in commands: + software_commands[sname][sversion].append(command.name) + return software_commands + + +def update_resource_allocation_redis(): + time = datetime.now().strftime('%m-%d-%y') scommands = get_software_commands() - for software, versions in scommands.items(): - for version, commands in versions.items(): - for command in commands: - print("Generating plot for:", software, version, command) - update_resource_allocation_redis(command, software, - version, time) redis_key = 'resources:commands' r_client.set(redis_key, str(scommands)) + for sname, versions in scommands.items(): + for version, commands in versions.items(): + for cname in commands: -def update_resource_allocation_redis(cname, sname, version, time): - col_name = "samples * columns" - - df = _retrieve_resource_data(cname, sname, version, columns) - fig, axs = resource_allocation_plot(df, cname, sname, col_name) - - fig.tight_layout() - plot = BytesIO() - fig.savefig(plot, format='png') - plot.seek(0) - - img = 'data:image/png;base64,' + quote(b64encode(plot.getbuffer()).decode('ascii')) - plt.close(fig) - - # SID, CID, col_name - values = [ - ("img", img, r_client.set), - ('time', time, r_client.set) - ] - - for k, v, f in values: - redis_key = 'resources$#%s$#%s$#%s:%s' % (cname, sname, col_name, k) - r_client.delete(redis_key) - f(redis_key, v) + print("Generating plot for:", sname, version, cname) + col_name = "samples * columns" + df = _retrieve_resource_data(cname, sname, version, columns) + if len(df) == 0: + print("No available data for", sname, version, cname) + continue + + fig, axs = resource_allocation_plot(df, cname, sname, col_name) + titles = [0, 0] + images = [0, 0] + + # Splitting 1 image plot into 2 separate for better layout. + for i, ax in enumerate(axs): + titles[i] = ax.get_title() + ax.set_title("") + # new_fig, new_ax – copy with either only memory plot or + # only time + new_fig = plt.figure() + new_ax = new_fig.add_subplot(111) + + scatter_data = ax.collections[0] + new_ax.scatter(scatter_data.get_offsets()[:, 0], + scatter_data.get_offsets()[:, 1], + s=scatter_data.get_sizes(), label="data") + + line = ax.lines[0] + new_ax.plot(line.get_xdata(), line.get_ydata(), + linewidth=1, color='orange') + + if len(ax.collections) > 1: + failure_data = ax.collections[1] + new_ax.scatter(failure_data.get_offsets()[:, 0], + failure_data.get_offsets()[:, 1], + color='red', s=3, label="failures") + + new_ax.set_xscale('log') + new_ax.set_yscale('log') + new_ax.set_xlabel(ax.get_xlabel()) + new_ax.set_ylabel(ax.get_ylabel()) + new_ax.legend(loc='upper left') + + new_fig.tight_layout() + plot = BytesIO() + new_fig.savefig(plot, format='png') + plot.seek(0) + img = 'data:image/png;base64,' + quote( + b64encode(plot.getvalue()).decode('ascii')) + images[i] = img + plt.close(new_fig) + plt.close(fig) + + # SID, CID, col_name + values = [ + ("img_mem", images[0], r_client.set), + ("img_time", images[1], r_client.set), + ('time', time, r_client.set), + ("title_mem", titles[0], r_client.set), + ("title_time", titles[1], r_client.set) + ] + print(time, titles[0], titles[1]) + + for k, v, f in values: + redis_key = 'resources$#%s$#%s$#%s$#%s:%s' % ( + cname, sname, version, col_name, k) + r_client.delete(redis_key) + f(redis_key, v) diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py index 98b11509d..f57109322 100644 --- a/qiita_db/test/test_meta_util.py +++ b/qiita_db/test/test_meta_util.py @@ -13,6 +13,7 @@ from os.path import exists, join import pandas as pd +from datetime import datetime from qiita_core.qiita_settings import qiita_config, r_client from qiita_core.util import qiita_test_checker @@ -523,18 +524,29 @@ def test_update_resource_allocation_redis(self): cname = "Split libraries FASTQ" sname = "QIIMEq2" col_name = "samples * columns" - qdb.meta_util.update_resource_allocation_redis(cname, sname) - - vals = [ - ("img", b's', r_client.get), - ('time', b'2024-11-11', r_client.get) - ] - - for k, exp, f in vals: - redis_key = 'resources$#%s$#%s$#%s:%s' % (cname, sname, col_name, k) - # checking redis values - print(f(redis_key)) - # self.assertEqual(f(redis_key), exp) + version = "1.9.1" + qdb.meta_util.update_resource_allocation_redis() + # since time is month, day, year, it should be equal unless test is ran + # at midnight. + time = datetime.now().strftime('%m-%d-%y') + title_mem_str = 'resources$#%s$#%s$#%s$#%s:%s' % ( + cname, sname, version, col_name, 'title_mem') + title_mem = str(r_client.get(title_mem_str)) + self.assertTrue( + "model_chosen: " + "k * log(x) + " + "b * log(x)^2 + " + "a * log(x)^2.5" in title_mem + ) + + title_time_str = 'resources$#%s$#%s$#%s$#%s:%s' % ( + cname, sname, version, col_name, 'title_time') + title_time = str(r_client.get(title_time_str)) + self.assertTrue("model_chosen: a + b + log(x) * k" in title_time) + time_create_str = 'resources$#%s$#%s$#%s$#%s:%s' % ( + cname, sname, version, col_name, 'time') + time_create = str(r_client.get(time_create_str)) + self.assertTrue(time in time_create) if __name__ == '__main__': diff --git a/qiita_db/util.py b/qiita_db/util.py index 184f9b458..1b4f232bf 100644 --- a/qiita_db/util.py +++ b/qiita_db/util.py @@ -99,6 +99,27 @@ MODELS_TIME = [time_model1, time_model2, time_model3, time_model4] +def get_model_name(model): + if model == mem_model1: + return "k * log(x) + x * a + b" + elif model == mem_model2: + return "k * log(x) + b * log(x)^2 + a" + elif model == mem_model3: + return "k * log(x) + b * log(x)^2 + a * log(x)^3" + elif model == mem_model4: + return "k * log(x) + b * log(x)^2 + a * log(x)^2.5" + elif model == time_model1: + return "a + b + log(x) * k" + elif model == time_model2: + return "a + b * x + log(x) * k" + elif model == time_model3: + return "a + b * log(x)^2 + log(x) * k" + elif model == time_model4: + return "a * log(x)^3 + b * log(x)^2 + log(x) * k" + else: + return "Unknown model" + + def scrub_data(s): r"""Scrubs data fields of characters not allowed by PostgreSQL @@ -2496,7 +2517,6 @@ def _resource_allocation_plot_helper( cmin = naturalsize(cmin_value, gnu=True) if curr == "MaxRSSRaw" else \ str(timedelta(seconds=round(cmin_value, 2))).rstrip('0').rstrip('.') - x_plot = np.array(df[col_name]) failures_df = _resource_allocation_failures( df, k, a, b, best_model, col_name, curr) @@ -2505,7 +2525,10 @@ def _resource_allocation_plot_helper( ax.scatter(failures_df[col_name], failures_df[curr], color='red', s=3, label="failures") - ax.set_title(f'{cname}: {sname}\n real: {mini} || {maxi}\n' + ax.set_title( + f'k||a||b: {k}||{a}||{b}\n' + f'model_chosen: {get_model_name(best_model)}\n' + f'real: {mini} || {maxi}\n' f'calculated: {cmin} || {cmax}\n' f'failures: {failures}') ax.legend(loc='upper left') @@ -2924,35 +2947,3 @@ def merge_rows(rows): row['node_model']] qdb.sql_connection.TRN.add(sql, sql_args=to_insert) qdb.sql_connection.TRN.execute() - - -def get_software_commands(): - res = [] - with qdb.sql_connection.TRN: - sql_command = """ - SELECT DISTINCT - s.name AS sName, - s.version AS sVersion, - sc.name AS cName - FROM - qiita.slurm_resource_allocations sra - JOIN - qiita.processing_job pr - ON sra.processing_job_id = pr.processing_job_id - JOIN - qiita.software_command sc on pr.command_id = sc.command_id - JOIN - qiita.software s ON sc.software_id = s.software_id - """ - qdb.sql_connection.TRN.add(sql_command) - res = qdb.sql_connection.TRN.execute_fetchindex() - - software_commands = dict() - for s_name, s_version, c_name in res: - if s_name not in software_commands: - software_commands[s_name] = {} - if s_version not in software_commands[s_name]: - software_commands[s_name][s_version] = set() - software_commands[s_name][s_version].add(c_name) - - return software_commands diff --git a/scripts/all-qiita-cron-job b/scripts/all-qiita-cron-job index b414da5f2..7534fda51 100644 --- a/scripts/all-qiita-cron-job +++ b/scripts/all-qiita-cron-job @@ -4,6 +4,6 @@ qiita-cron-job empty-trash-upload-folder qiita-cron-job generate-biom-and-metadata-release qiita-cron-job purge-filepaths qiita-cron-job update-redis-stats -qiita-cron-job initialize-resource-allocations-redis +qiita-cron-job update-resource-allocation-redis qiita-cron-job generate-plugin-releases qiita-cron-job purge-json-web-tokens diff --git a/scripts/qiita-cron-job b/scripts/qiita-cron-job index 17ff09002..252252a38 100755 --- a/scripts/qiita-cron-job +++ b/scripts/qiita-cron-job @@ -16,7 +16,7 @@ from qiita_db.util import ( quick_mounts_purge as qiita_quick_mounts_purge) from qiita_db.meta_util import ( update_redis_stats as qiita_update_redis_stats, - initialize_resource_allocations_redis as qiita_initialize_resource_allocations_redis, + update_resource_allocation_redis as qiita_update_resource_allocation_redis, generate_biom_and_metadata_release as qiita_generate_biom_and_metadata_release, generate_plugin_releases as qiita_generate_plugin_releases) @@ -50,8 +50,8 @@ def update_redis_stats(): @commands.command() -def initialize_resource_allocations_redis(): - qiita_initialize_resource_allocations_redis() +def update_resource_allocation_redis(): + qiita_update_resource_allocation_redis() @commands.command() From 7241754af42ec5f3287f96623eebefb5796e779f Mon Sep 17 00:00:00 2001 From: gossty Date: Wed, 28 Aug 2024 08:33:44 -0700 Subject: [PATCH 4/9] Removed changes to qiita_pet This pull request should only contain changes with uploading data to redis. I accidentally commited some changes to qiita_pet here. --- notebooks/resource-allocation/upload_df.py | 72 ---------------------- qiita_db/meta_util.py | 2 +- qiita_pet/handlers/resources.py | 67 -------------------- qiita_pet/templates/resources.html | 52 ---------------- qiita_pet/webserver.py | 3 - 5 files changed, 1 insertion(+), 195 deletions(-) delete mode 100644 notebooks/resource-allocation/upload_df.py delete mode 100644 qiita_pet/handlers/resources.py delete mode 100644 qiita_pet/templates/resources.html diff --git a/notebooks/resource-allocation/upload_df.py b/notebooks/resource-allocation/upload_df.py deleted file mode 100644 index e74bcce04..000000000 --- a/notebooks/resource-allocation/upload_df.py +++ /dev/null @@ -1,72 +0,0 @@ -import pandas as pd - -# Example data loading -filename = './data/jobs_2024-02-21.tsv.gz' -df = pd.read_csv(filename, sep='\t', dtype={'extra_info': str}) - -# Convert string to timedelta, then to total seconds -df['ElapsedRawTime'] = pd.to_timedelta( - df['ElapsedRawTime']).apply( - lambda x: x.total_seconds()) - -cname = "Validate" -sname = "Diversity types - alpha_vector" -df = df[(df.cName == cname) & (df.sName == sname)] - -df['samples'] = df['samples'].fillna(0).astype(int) -df['columns'] = df['columns'].fillna(0).astype(int) -df['input_size'] = df['input_size'].fillna(0).astype(int) -df['MaxRSSRaw'] = df['MaxRSSRaw'].fillna(0).astype(int) -df['ElapsedRawTime'] = df['ElapsedRawTime'].fillna(0).astype(int) - -COL_NAME = 'samples * columns' -df[COL_NAME] = df['samples'] * df['columns'] -columns = ["MaxRSSRaw", "ElapsedRawTime"] -max_rows = [] - -for curr in columns: - # Get the maximum value for 'curr' within each COL_NAME group - max_values = df.groupby(COL_NAME)[curr].transform(max) - # Filter rows where the current column's value - # is the maximum within its group - curr_rows = df[df[curr] == max_values] - max_rows.append(curr_rows) - -filtered_df = pd.concat(max_rows).drop_duplicates().reset_index(drop=True) - -# 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.com', 1, '""'::json, 1); - -# 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); - -# processing_job_id uuid NOT NULL, -# samples integer, -# columns integer, -# input_size bigint, -# extra_info varchar DEFAULT NULL, -# memory_used bigint, -# walltime_used integer, - -res = "" - -for index, row in filtered_df.iterrows(): - res += f"""('{row['QiitaID']}', 'admin@foo.bar', 1, '""'::json, 1),\n""" -res += ";\n" -res += "Split\n" -for index, row in filtered_df.iterrows(): - res += ( - f"('{row['QiitaID']}', {int(row['samples'])}, " - f"{int(row['columns'])}, {int(row['input_size'])}, " - f"'{row['extra_info']}', {int(row['MaxRSSRaw'])}, " - f"{int(row['ElapsedRawTime'])}),\n" - ) - -res += ";\n" - -with open("sql.txt", 'w') as filename: - filename.write(res) diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index 12f40b057..ea5614b06 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -588,7 +588,7 @@ def update_resource_allocation_redis(): if len(df) == 0: print("No available data for", sname, version, cname) continue - + fig, axs = resource_allocation_plot(df, cname, sname, col_name) titles = [0, 0] images = [0, 0] diff --git a/qiita_pet/handlers/resources.py b/qiita_pet/handlers/resources.py deleted file mode 100644 index 0bb0865b1..000000000 --- a/qiita_pet/handlers/resources.py +++ /dev/null @@ -1,67 +0,0 @@ - -from tornado.gen import coroutine, Task -from tornado.web import authenticated, HTTPError - - -from .base_handlers import BaseHandler -from qiita_core.qiita_settings import qiita_config, r_client -from qiita_core.util import execute_as_transaction - -default_cname = "Split libraries FASTQ" -default_sname = "QIIMEq2" -default_col_name = "samples * columns" -commands = 'resources:commands' - -class ResourcesHandler(BaseHandler): - def check_admin(self): - if self.current_user.level != "admin": - raise HTTPError(403, reason="%s does not have access to portal " - "editing!" % self.current_user.id) - - - @execute_as_transaction - def _get_resources(self, callback): - resources = {} - vals = [ - ('img', r_client.get), - ('time', r_client.get) - ] - for k, f in vals: - redis_key = 'resources$#%s$#%s$#%s:%s' % (default_cname, - default_sname, default_col_name, k) - resources[k] = f(redis_key) - callback(resources) - - - def _get_commands(self, callback): - r_client.get(commands) - callback(r_client) - - - @authenticated - @coroutine - @execute_as_transaction - def get(self): - self.check_admin() - resources = yield Task(self._get_resources) - commands = yield Task(self._get_commands) # TODO: it would make more sense to have this rendered once instead of everytime we make a get request, but i'm not sure how to do that right now - self.render('resources.html', - img=resources['img'], time=resources['time'], - commands=commands, - software=default_sname, command=default_cname, - col_name=default_col_name - ) - - - @authenticated - @execute_as_transaction - def post(self): - self.check_admin() - software = self.get_argument("software", "") - command = self.get_argument("command", "") - column_type = self.get_argument("column_type", "") - - - self.get() - - diff --git a/qiita_pet/templates/resources.html b/qiita_pet/templates/resources.html deleted file mode 100644 index 097a19ca6..000000000 --- a/qiita_pet/templates/resources.html +++ /dev/null @@ -1,52 +0,0 @@ -{% extends sitebase.html %} -{% block head %} - - - -{% end %} - -{% block content %} -
    -
    - Generated on: {{time}} - Software: {{software}} - Command: {{command}} - Column name: {{col_name}} -
    - -
    -
    - - -
    - -
    - - -
    - -
    - - -
    - - -
    - {% if img and img is not None %} -
    - -
    - {% end %} -
    -{% end %} \ No newline at end of file diff --git a/qiita_pet/webserver.py b/qiita_pet/webserver.py index d52549c42..50b34fd2b 100644 --- a/qiita_pet/webserver.py +++ b/qiita_pet/webserver.py @@ -50,8 +50,6 @@ from qiita_pet.handlers.upload import ( UploadFileHandler, StudyUploadFileHandler, StudyUploadViaRemote) from qiita_pet.handlers.stats import StatsHandler -from qiita_pet.handlers.resources import ResourcesHandler - from qiita_pet.handlers.download import ( DownloadHandler, DownloadStudyBIOMSHandler, DownloadRelease, DownloadRawData, DownloadEBISampleAccessions, DownloadEBIPrepAccessions, @@ -138,7 +136,6 @@ def __init__(self): (r"/admin/sample_validation/", SampleValidation), (r"/admin/purge_users/", PurgeUsersHandler), (r"/admin/purge_usersAjax/", PurgeUsersAJAXHandler), - (r"/admin/resources/", ResourcesHandler), (r"/ebi_submission/(.*)", EBISubmitHandler), # Study handlers (r"/study/create/", StudyEditHandler), From 437b8c840ed65b62ee657a7124ea5ec3d6cc0d94 Mon Sep 17 00:00:00 2001 From: gossty Date: Wed, 28 Aug 2024 10:58:52 -0700 Subject: [PATCH 5/9] Minor changes --- qiita_db/meta_util.py | 20 ++++++++++++-------- qiita_db/test/test_meta_util.py | 16 ++++------------ qiita_db/util.py | 2 +- qiita_pet/templates/sitebase.html | 1 - 4 files changed, 17 insertions(+), 22 deletions(-) diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index ea5614b06..71a8df353 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -555,9 +555,8 @@ def generate_plugin_releases(): f(redis_key, v) -def get_software_commands(): - # TODO change active=False to True. In test, the data is active=False. - software_list = [s for s in qdb.software.Software.iter(active=False)] +def get_software_commands(active): + software_list = [s for s in qdb.software.Software.iter(active=active)] software_commands = dict() for software in software_list: sname = software.name @@ -572,9 +571,17 @@ def get_software_commands(): return software_commands -def update_resource_allocation_redis(): +def update_resource_allocation_redis(active=True): + """Updates redis with plots and information about current software. + + Parameters + ---------- + active: boolean, optional + Defaults to True. Should only be False when testing. + + """ time = datetime.now().strftime('%m-%d-%y') - scommands = get_software_commands() + scommands = get_software_commands(active) redis_key = 'resources:commands' r_client.set(redis_key, str(scommands)) @@ -582,11 +589,9 @@ def update_resource_allocation_redis(): for version, commands in versions.items(): for cname in commands: - print("Generating plot for:", sname, version, cname) col_name = "samples * columns" df = _retrieve_resource_data(cname, sname, version, columns) if len(df) == 0: - print("No available data for", sname, version, cname) continue fig, axs = resource_allocation_plot(df, cname, sname, col_name) @@ -641,7 +646,6 @@ def update_resource_allocation_redis(): ("title_mem", titles[0], r_client.set), ("title_time", titles[1], r_client.set) ] - print(time, titles[0], titles[1]) for k, v, f in values: redis_key = 'resources$#%s$#%s$#%s$#%s:%s' % ( diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py index f57109322..d1e409a7d 100644 --- a/qiita_db/test/test_meta_util.py +++ b/qiita_db/test/test_meta_util.py @@ -13,7 +13,6 @@ from os.path import exists, join import pandas as pd -from datetime import datetime from qiita_core.qiita_settings import qiita_config, r_client from qiita_core.util import qiita_test_checker @@ -525,28 +524,21 @@ def test_update_resource_allocation_redis(self): sname = "QIIMEq2" col_name = "samples * columns" version = "1.9.1" - qdb.meta_util.update_resource_allocation_redis() - # since time is month, day, year, it should be equal unless test is ran - # at midnight. - time = datetime.now().strftime('%m-%d-%y') + qdb.meta_util.update_resource_allocation_redis(False) title_mem_str = 'resources$#%s$#%s$#%s$#%s:%s' % ( cname, sname, version, col_name, 'title_mem') title_mem = str(r_client.get(title_mem_str)) self.assertTrue( - "model_chosen: " + "model: " "k * log(x) + " "b * log(x)^2 + " - "a * log(x)^2.5" in title_mem + "a * log(x)^3" in title_mem ) title_time_str = 'resources$#%s$#%s$#%s$#%s:%s' % ( cname, sname, version, col_name, 'title_time') title_time = str(r_client.get(title_time_str)) - self.assertTrue("model_chosen: a + b + log(x) * k" in title_time) - time_create_str = 'resources$#%s$#%s$#%s$#%s:%s' % ( - cname, sname, version, col_name, 'time') - time_create = str(r_client.get(time_create_str)) - self.assertTrue(time in time_create) + self.assertTrue("model: a + b + log(x) * k" in title_time) if __name__ == '__main__': diff --git a/qiita_db/util.py b/qiita_db/util.py index 1b4f232bf..1007298e5 100644 --- a/qiita_db/util.py +++ b/qiita_db/util.py @@ -2527,7 +2527,7 @@ def _resource_allocation_plot_helper( ax.set_title( f'k||a||b: {k}||{a}||{b}\n' - f'model_chosen: {get_model_name(best_model)}\n' + f'model: {get_model_name(best_model)}\n' f'real: {mini} || {maxi}\n' f'calculated: {cmin} || {cmax}\n' f'failures: {failures}') diff --git a/qiita_pet/templates/sitebase.html b/qiita_pet/templates/sitebase.html index 5e2e0633f..7165f33a2 100644 --- a/qiita_pet/templates/sitebase.html +++ b/qiita_pet/templates/sitebase.html @@ -384,7 +384,6 @@
  • View Studies awaiting approval
  • Edit study portal connections
  • Purge non-validated users
    • -
  • View Resource Allocation Plots
    • {% end %}
  • Sample Validation
  • Processing Jobs
    • From 4fa0c706c00255053281b7fac28155962f5b80e3 Mon Sep 17 00:00:00 2001 From: gossty Date: Fri, 30 Aug 2024 12:34:00 -0700 Subject: [PATCH 6/9] =?UTF-8?q?Updates=20to=20Antonio=E2=80=99s=20coments?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- qiita_db/meta_util.py | 17 ++++++++--------- qiita_db/test/test_util.py | 4 ++-- qiita_db/util.py | 2 +- 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index 71a8df353..c36e8764a 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -37,14 +37,14 @@ from re import sub from json import loads, dump, dumps -from qiita_db.util import create_nested_path, _retrieve_resource_data +from qiita_db.util import create_nested_path, retrieve_resource_data from qiita_db.util import resource_allocation_plot from qiita_core.qiita_settings import qiita_config, r_client from qiita_core.configuration_manager import ConfigurationManager import qiita_db as qdb # global constant list used in resource_allocation_page -columns = [ +COLUMNS = [ "sName", "sVersion", "cID", "cName", "processing_job_id", "parameters", "samples", "columns", "input_size", "extra_info", "MaxRSSRaw", "ElapsedRaw", "Start", "node_name", "node_model"] @@ -557,18 +557,17 @@ def generate_plugin_releases(): def get_software_commands(active): software_list = [s for s in qdb.software.Software.iter(active=active)] - software_commands = dict() + software_commands = defaultdict(lambda: defaultdict(list)) + for software in software_list: sname = software.name sversion = software.version commands = software.commands - if sname not in software_commands: - software_commands[sname] = {} - if sversion not in software_commands[sname]: - software_commands[sname][sversion] = [] + for command in commands: software_commands[sname][sversion].append(command.name) - return software_commands + + return dict(software_commands) def update_resource_allocation_redis(active=True): @@ -590,7 +589,7 @@ def update_resource_allocation_redis(active=True): for cname in commands: col_name = "samples * columns" - df = _retrieve_resource_data(cname, sname, version, columns) + df = retrieve_resource_data(cname, sname, version, COLUMNS) if len(df) == 0: continue diff --git a/qiita_db/test/test_util.py b/qiita_db/test/test_util.py index a71be3e49..cad800752 100644 --- a/qiita_db/test/test_util.py +++ b/qiita_db/test/test_util.py @@ -1322,7 +1322,7 @@ def setUp(self): # df is a dataframe that represents a table with columns specified in # self.columns - self.df = qdb.util._retrieve_resource_data( + self.df = qdb.util.retrieve_resource_data( self.cname, self.sname, self.version, self.columns) def test_plot_return(self): @@ -1423,7 +1423,7 @@ def test_db_update(self): qdb.util.update_resource_allocation_table(test=test_data) for curr_cname, ids in types.items(): - updated_df = qdb.util._retrieve_resource_data( + updated_df = qdb.util.retrieve_resource_data( curr_cname, self.sname, self.version, self.columns) updated_ids_set = set(updated_df['processing_job_id']) previous_ids_set = set(self.df['processing_job_id']) diff --git a/qiita_db/util.py b/qiita_db/util.py index 1007298e5..35a25cee9 100644 --- a/qiita_db/util.py +++ b/qiita_db/util.py @@ -2402,7 +2402,7 @@ def resource_allocation_plot(df, cname, sname, col_name): return fig, axs -def _retrieve_resource_data(cname, sname, version, columns): +def retrieve_resource_data(cname, sname, version, columns): with qdb.sql_connection.TRN: sql = """ SELECT From f5ab03575bcfc9c253bc6d4d00bfdc3a02493ddf Mon Sep 17 00:00:00 2001 From: gossty Date: Fri, 30 Aug 2024 12:37:45 -0700 Subject: [PATCH 7/9] Update meta_util.py --- qiita_db/meta_util.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index c36e8764a..86ad7db75 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -558,15 +558,15 @@ def generate_plugin_releases(): def get_software_commands(active): software_list = [s for s in qdb.software.Software.iter(active=active)] software_commands = defaultdict(lambda: defaultdict(list)) - + for software in software_list: sname = software.name sversion = software.version commands = software.commands - + for command in commands: software_commands[sname][sversion].append(command.name) - + return dict(software_commands) From 3220b7f597adff7c5dd66a2a461c12993b259177 Mon Sep 17 00:00:00 2001 From: gossty Date: Wed, 11 Sep 2024 08:51:00 -0700 Subject: [PATCH 8/9] Added webpage for resource allocation plots --- qiita_db/meta_util.py | 2 +- qiita_pet/handlers/resources.py | 135 ++++++++++++++ qiita_pet/templates/resources.html | 272 +++++++++++++++++++++++++++++ qiita_pet/templates/sitebase.html | 1 + qiita_pet/webserver.py | 2 + 5 files changed, 411 insertions(+), 1 deletion(-) create mode 100644 qiita_pet/handlers/resources.py create mode 100644 qiita_pet/templates/resources.html diff --git a/qiita_db/meta_util.py b/qiita_db/meta_util.py index 86ad7db75..f4b9bf7ff 100644 --- a/qiita_db/meta_util.py +++ b/qiita_db/meta_util.py @@ -566,6 +566,7 @@ def get_software_commands(active): for command in commands: software_commands[sname][sversion].append(command.name) + software_commands[sname] = dict(software_commands[sname]) return dict(software_commands) @@ -587,7 +588,6 @@ def update_resource_allocation_redis(active=True): for sname, versions in scommands.items(): for version, commands in versions.items(): for cname in commands: - col_name = "samples * columns" df = retrieve_resource_data(cname, sname, version, COLUMNS) if len(df) == 0: diff --git a/qiita_pet/handlers/resources.py b/qiita_pet/handlers/resources.py new file mode 100644 index 000000000..c6c8804ac --- /dev/null +++ b/qiita_pet/handlers/resources.py @@ -0,0 +1,135 @@ + +from tornado.gen import coroutine, Task +from tornado.web import authenticated, HTTPError +import json +import ast +from .base_handlers import BaseHandler +from qiita_core.qiita_settings import r_client +from qiita_core.util import execute_as_transaction + +commands = 'resources:commands' +default_col_name = "samples * columns" + + +class ResourcesHandler(BaseHandler): + def check_admin(self): + if self.current_user.level != "admin": + raise HTTPError(403, reason="%s does not have access to portal " + "editing!" % self.current_user.id) + + @execute_as_transaction + def _get_resources(self, cname, sname, version, col_name, callback): + resources = {} + vals = [ + ('img_mem', r_client.get), + ('img_time', r_client.get), + ('time', r_client.get), + ('title_mem', r_client.get), + ('title_time', r_client.get) + ] + for k, f in vals: + redis_key = 'resources$#%s$#%s$#%s$#%s:%s' % (cname, sname, + version, col_name, k) + resources[k] = f(redis_key) + callback(resources) + + @execute_as_transaction + def _get_commands(self, callback): + res = r_client.get(commands) + callback(res) + + @authenticated + @coroutine + @execute_as_transaction + def get(self): + self.check_admin() + commands = yield Task(self._get_commands) + + commands_str = commands.decode('utf-8') + commands_dict = ast.literal_eval(commands_str) + commands_json = json.dumps(commands_dict) + + self.render('resources.html', + img_mem=None, img_time=None, + time=None, + mk=None, ma=None, mb=None, + mmodel=None, mreal=None, + mcalc=None, mfail=None, + tk=None, ta=None, tb=None, + tmodel=None, treal=None, + tcalc=None, tfail=None, + commands=commands_json, + initial_load=True) + + @authenticated + @coroutine + @execute_as_transaction + def post(self): + try: + data = json.loads(self.request.body) + software = data.get('software') + version = data.get('version') + command = data.get('command') + + resources = yield Task(self._get_resources, command, software, + version, default_col_name) + + mcof, mmodel, mreal, mcalc, mfail = list( + map(lambda x: x.split(b": ")[1].strip().decode('utf-8'), + resources['title_mem'].split(b"\n"))) + + tcof, tmodel, treal, tcalc, tfail = list( + map(lambda x: x.split(b": ")[1].strip().decode('utf-8'), + resources['title_time'].split(b"\n"))) + + mk, ma, mb = mcof.split("||") + tk, ta, tb = tcof.split("||") + + response_data = { + "status": "success", + "img_mem": resources[ + 'img_mem'].decode('utf-8') if isinstance( + resources['img_mem'], bytes) else resources['img_mem'], + "img_time": resources[ + 'img_time'].decode('utf-8') if isinstance( + resources['img_time'], bytes) else resources['img_time'], + "time": resources[ + 'time'].decode('utf-8') if isinstance( + resources['time'], bytes) else resources['time'], + "mk": mk, "ma": ma, "mb": mb, + "tk": tk, "ta": ta, "tb": tb, + "mmodel": mmodel, "mreal": mreal, + "mcalc": mcalc, "mfail": mfail, + "tcof": tcof, + "tmodel": tmodel, "treal": treal, + "tcalc": tcalc, "tfail": tfail, + "initial_load": False + } + self.write(json.dumps(response_data)) + + except json.JSONDecodeError: + self.set_status(400) + self.finish({"error": "Invalid JSON data"}) + except Exception as e: + import traceback + print(traceback.format_exc()) + if resources['title_mem'] is None: + response_data = { + "status": "no_data", + "img_mem": None, + "img_time": None, + "time": None, + "mk": None, "ma": None, "mb": None, + "tk": None, "ta": None, "tb": None, + "mmodel": None, "mreal": None, + "mcalc": None, "mfail": None, + "tcof": None, + "tmodel": None, "treal": None, + "tcalc": None, "tfail": None, + "initial_load": False + } + self.set_status(200) + self.write(json.dumps(response_data)) + else: + self.set_status(500) + self.finish({"error": str(e)}) diff --git a/qiita_pet/templates/resources.html b/qiita_pet/templates/resources.html new file mode 100644 index 000000000..d4b9e870c --- /dev/null +++ b/qiita_pet/templates/resources.html @@ -0,0 +1,272 @@ +{% extends sitebase.html %} +{% block head %} + + + +{% end %} + +{% block content %} +
    + +
    +

    Please choose software, version, and command to view the data.

    +
    + +
    +
    + + +
    + +
    + + +
    + +
    + + +
    +
    + +
    +
    +

    Generated on: {{time}}

    +
    + + + + + + + + + + + + + + +
    Memory AllocationTime Allocation
    + {% if img_mem and img_mem is not None %} + + {% else %} + No memory allocation image available + {% end %} + + {% if img_time and img_time is not None %} + + {% else %} + No time allocation image available + {% end %} +
    +
      +
    • k: {{ mk }}
      • +
    • a: {{ ma }}
      • +
    • b: {{ mb }}
      • +
    • model: {{ mmodel }}
      • +
    • real: {{ mreal }}
      • +
    • calc: {{ mcalc }}
      • +
    • fail: {{ mfail }}
      • +
    +     		+
      +
    • k: {{ tk }}
      • +
    • a: {{ ta }}
      • +
    • b: {{ tb }}
      • +
    • model: {{ tmodel }}
      • +
    • real: {{ treal }}
      • +
    • calc: {{ tcalc }}
      • +
    • fail: {{ tfail }}
      • +
    +
    +
    + +
    + + +{% end %} \ No newline at end of file diff --git a/qiita_pet/templates/sitebase.html b/qiita_pet/templates/sitebase.html index 7165f33a2..5e2e0633f 100644 --- a/qiita_pet/templates/sitebase.html +++ b/qiita_pet/templates/sitebase.html @@ -384,6 +384,7 @@
  • View Studies awaiting approval
  • Edit study portal connections
  • Purge non-validated users
    • +
  • View Resource Allocation Plots
    • {% end %}
  • Sample Validation
  • Processing Jobs
    • diff --git a/qiita_pet/webserver.py b/qiita_pet/webserver.py index 50b34fd2b..74367489b 100644 --- a/qiita_pet/webserver.py +++ b/qiita_pet/webserver.py @@ -50,6 +50,7 @@ from qiita_pet.handlers.upload import ( UploadFileHandler, StudyUploadFileHandler, StudyUploadViaRemote) from qiita_pet.handlers.stats import StatsHandler +from qiita_pet.handlers.resources import ResourcesHandler from qiita_pet.handlers.download import ( DownloadHandler, DownloadStudyBIOMSHandler, DownloadRelease, DownloadRawData, DownloadEBISampleAccessions, DownloadEBIPrepAccessions, @@ -136,6 +137,7 @@ def __init__(self): (r"/admin/sample_validation/", SampleValidation), (r"/admin/purge_users/", PurgeUsersHandler), (r"/admin/purge_usersAjax/", PurgeUsersAJAXHandler), + (r"/admin/resources/", ResourcesHandler), (r"/ebi_submission/(.*)", EBISubmitHandler), # Study handlers (r"/study/create/", StudyEditHandler), From 6b4a718c2d76d9e963300e8ca371b923ca0e7366 Mon Sep 17 00:00:00 2001 From: gossty Date: Fri, 13 Sep 2024 09:08:00 -0700 Subject: [PATCH 9/9] Update resources.py --- qiita_pet/handlers/resources.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/qiita_pet/handlers/resources.py b/qiita_pet/handlers/resources.py index c6c8804ac..0b5873997 100644 --- a/qiita_pet/handlers/resources.py +++ b/qiita_pet/handlers/resources.py @@ -1,4 +1,3 @@ - from tornado.gen import coroutine, Task from tornado.web import authenticated, HTTPError import json @@ -105,7 +104,7 @@ def post(self): "tcalc": tcalc, "tfail": tfail, "initial_load": False } - self.write(json.dumps(response_data)) + self.write(json.dumps(response_data) + "\n") except json.JSONDecodeError: self.set_status(400) @@ -129,7 +128,7 @@ def post(self): "initial_load": False } self.set_status(200) - self.write(json.dumps(response_data)) + self.write(json.dumps(response_data) + "\n") else: self.set_status(500) self.finish({"error": str(e)})